Biology Flashcards:

Chapter 1:
Levels of biological organization - Biosphere
Ecosystems
Communities
Populations
Organisms
Organs and Organisms
Tissues
Cells
Macromolecules
Molecules

Biosphere - all life on Earth

Ecosystem - all living and nonliving components living or interacting with a given area

Community - all organisms living in a given area, a set of populations living in a given
area

Populations - all individuals in a species living in the given area

Organisms - individual living things

Organs and Organ Systems - major parts, consisting of multiple tissues, which help
comprise an organism, e.g. leaves, roots

Tissues - groups of cells, work together to carry out specialized function, e.g. epidermis

Cells - life's fundamental unit of structure and function, the smallest unit of organization
which can perform all activities needed for life

Organelles - functional components found inside of cells

Molecules - chemical structures made of two or more units (atoms), which are inside the
organelles of cells

How are structure and function related? - structure often indicates the function, e.g. leaf
is flat to maximize sunlight absorption

Gene expression - process through which a gene in DNA directs the manufacture of a
cellular product

Reductionism - zooming in on complex systems to break them into simpler components

Downsides to reductionism - looking at the individual parts might make you lose
perspective on the emergent properties which occur once you zoom out

Reductionism is often paired with what? - systems biology

Systems biology - studying interactions among the parts of the organism, ecosystem, or
even biosphere

Emergent propterties - properties which emerge while zooming out from a reductionist
viewpoint

Genome - the entire set of genetic instructions an organism inherits

Genomics - systems biology applied at a cellular and molecular level

Proteomics - systems biology applied to sets of proteins and their properties

Proteome - all proteins expressed by a cell or group of cells

High-Throughput - technology tools which have the ability to analyze numerous

biological samples very quickly, helps make the genomic and proteomic approach
possible

Bioinformatics - a method by which computational tools are used to store, organize and
analyze the data which comes from high-throughput methods

Energy transfer flow is... - one-way (through an ecosystem)

Chemical cycle flows are normally... - conserved, passed on from animal to animal

Energy cycle - 1. plants absorb sunlight and use photosynthesis to convert it to energy
2. consumers eat the plant and absorb the energy
3. consumers release that energy in the form of heat as they work

Chemical cycle - 1. plants absorb chemical from the air, soil, etc.

2. consumers eat the plant and absorb those chemicals

3. the chemicals are returned back to the ecosystem by decomposers

Feedback regulation - the output, or product, or a process regulates that process

Negative feedback - a loop where the response reduces the stimulus

Positive feedback - less common, a loop where the response increases the stimulus

Prokaryotic cells are... - * always unicellular

* Bacteria
* Archaea
* no nucleus
* no membrane enclosed organelles
* smaller than eukaryotic cells

Eukaryotic cells are... - * plants, animals

* have a nucleus
* have membrane enclosed organelles
* bigger than prokaryotic cells
* cells may have organelles specific to cell type
* Eukarya

Scientists often classify life... - into species and then into broader groupings based on
their similarities between other organisms

Hierarchical taxonomic system - Species

Genus
Family
Order

Class
Phylum
Kingdom
Domain

Three domains - Bacteria

Archaea
Eukarya

Bacteria - prokaryotic, most divers and widespread prokaryotes, classified in multiple

kingdoms

Archaea - prokaryotic, some live in extreme environments, multiple kingdoms

Eukarya - eukaryotic kingdoms are divided partially on how/what they eat

Eukarya domain, Plantae kingdom - convert light to chemical energy

Eukarya domain, Fungi kingdom - absorb nutrients from the outside environment

Eukarya domain, Animalia kingdom - ingest other organisms

Eukarya domain, Protist kingdom - unicellular eukaryotes

Examples of unity in the diversity of life - * similar skeletons

* universal genetic language of DNA
* features of cell structure
* vestigial organs/bones

Descent with modificaton - contemporary species came from ancestors who were
different that them

Natural selection - individuals with inherited traits that are better adapted to the local
environment are more likely to survive and reproduce than less advantageous
individuals

How is a mailing address analogous to biology's hierarchical taxonomic system? - It is

written going from broader to narrower.

How is editing similar to natural selection? - Natural selection edits out the traits which
are not suited for the given environment.

Taxonomy - branch of biology which names and classifies species

Natural selection - nature selecting certain traits amongst naturally occurring variant
traits in a populations

Scientific inquiry - making observations, forming logical and testable explanations, and
testing them

Deductive reasoning - extrapolate from general ideas, specific results we should expect
if the ideas are true, "if...then" logic

Falsifiable - the possibility that something can be proven false

Falsiability in a hypothesis means... - we can never prove a hypothesis is true beyond a

shadow of doubt, there could always be a source of error, or fallacy

A controlled experiment means... - because it is impossible to control every variable,

scientists cancel out the effects of the uncontrollable variables by using control groups

Scientific method - Observation

Question
Hypothesis
Experiment
Analysis
Conclusion

Scientific theories vs. Hypothesis - Scientific theory is:

* broader in scope
* general enough to result in many hypotheses which can be tested to support or
disprove it
* supported by a much greater body of evidence, non of which so far has contradicted it

Example of Scientific Theory - Evolutionary adaptations arise by natural selection

Example of Hypothesis - Fur coloration well-matched to their habitat is an adaptation

which protects mice from predators

Inquiry - search for information and explanations of natural phenomena

Data - recorded observations

Quantitative data - data in the form of numbers

Qualitative data - data in the form of descriptions

Hypothesis - tentative answer to a well-framed question, a rational account for a set of

observations, based on available data and guided by inductive reasoning

Experiment - scientific test, carried out under controlled conditions

Inductive reasoning - a process by which we derive generalizations from a large number

of specific observations

Deductive reasoning - a process which uses logic in the opposing direction, from
general to specific

Controlled experiment - one designed to compare an experimental group with a control

group

Independent variable - the factor manipulated in an experiment

Dependent variable - a factor which is measured in the experiment, the effect on this
variable should correlate with how the independent variable was manipulated

Variables - factors which vary in an experiment

Differences between science and technology - science works to understand natural

phenomena, technology applies that knowledge

Data - recorded observation

Science - starts with observation

Control group - group we are not changing the independent variable on, the group we
would expect to have a familiar and expected response

Treatment group - group we change the independent variable on

Replication - repeating an experiment to increase its reliability

More replication --> More data --> More statistical analysis

A hypothesis has to be - falsifiable, has to be testable so we can prove whether or not its
tru

Cells only come from... - pre-existing cells

Descent with modification - living things change over time through natural selection

Sexual reproduction... - increases variety because of differential inheritance

Mutations - mistakes in DNA replication

Mutation affects descent with modification how? - living things change via DNA
mutations

DNA is... - the instructions to make proteins

All species produce... - more than the envrironment can provide for so each variation will
have a greater advantage or greater disadvantage due to their genetic inheritance, and
mutations

An organism is fit if... - it contains can adaptation

Adaptation - a change which gives advantage

Four processes of natural selection - 1. Genetic variations

2. Over-reproduction of species
3. Struggle for existence
4. Differential survival and reproruction

What is science? - science is a process by which we discover information, and the

framework through which we establish it

What is biology? - biology is the study of life

How are science and biology related? - science is the process through which we study
life and the frame work through which we establish the discovered information. Science
is the process through which we study life

Chapter 22:

Evolution can be seen as a... - pattern and a process

Evolutionary pattern - recurring observations about evolutionary change from multiple

scientific disciplines

Evolutionary process - the mechanisms which cause the observations of evolutionary

change

Adaptation - inherited characteristic which enhances an organism's ability to survive and

reproduce

Darwin's two observations - 1. members of a population often vary in their inherited

traits
2. all species can produce more offspring than the environment can support

Darwin's two inferences - 1. organisms with adaptations have a higher likelihood of

surviving and reproducing
2. the unequal ability of some organisms to survive and reproduce than other will cause
accumulation of the favorable traits in the generation do

Which evolve? Individuals or populations? - Populations

Natural selection can increase which: heritable traits, traits every member of the
population has - heritable traits

Natural selection is dependent on... - time and place

How does natural selection vary? - Environmental factors vary from one place to
another, and over time, so a trait favorable for one ecosystem might not be for another,
or if something changes in X ecosystem, that trait might not be favorable anymore

Four types of data which document the pattern of evolution: - 1. direct observations drug resistant pathogens, beak structures based on types of food
2. homology - forelimbs of all mammals have the same bone structure
3. fossil records
4. biogeography

Biogeography - geographic distribution of species

Biogeography relates to... - Pangea, where species fossil record estimates where and
how long ago they could be found, and then we can compare that to the timeline of
Pangea and see if any other continents were connected to the continent where we think
X species first originated

Analogous features - The features have similar function, but do not have a common
ancestry
This is because the species have adapted to similar environments in similar ways

Homologous features - the species share a common ancestor, so their homologous

features share common ancestry, but not necessarily similar function

Homology - similarity because of common ancestry

Homologous structures - similar structures due to common ancestry

Vestigial structures - structures which played a role in an organisms ancestor, but not
anymore

Pseudogenes - like vestigial structures but for genes

Evolutionary tree - diagram which shows the evolutionary relationships between groups
of organisms

Digits - bones which in a number more than one, like the human forearm has two digits

Hatch mark - a mark on tree diagrams which represents a homologous characteristic

which is shared by all groups to the right of the mark

Aristotle and Scala Naturae - viewed species as fixed and unchanged

The Old Testament - Species were individually designed by God, and therefore perfect

Carolus Linnaeus - developed taxonomy, which would classify the diversity of God

Georges Cuvier - believed in catastrophism, not evolution

Explain the role of fossils in rock strata as a window to life in earlier times - fossils are
remains or traces of organisms from the past
because rocks are in layers, time periods can be divided into such layers, and thus the
gradual changes in creature over time periods can be observed

How would Georges Cuvier have explained the appearance of the record of life shown
in rock strata? - Catastrophism: each boundary represents a catastrophe that destroyed
many of the species at a time

James Hutton - Gradualism: Earth's geologic features could be explained by gradual

mechanisms currently operating in the world

Charles Lyell - Uniformitarianism: same geologic processes are operating today as in

the past at the same rate

What is the importance of uniformitarianism - It implied that the world is much older than
was believed at the time

Use and disuse - parts of the body that are used become bigger and stronger; those not
used would deteriorate

Inheritance of acquired characteristics - organisms could pass on modifications (from

use and disuse) to their offspring

What is considered to be the great importance of Lamarck's ideas? - The importance

was that variation was introduced through inheritance

What is indicated by branch points? - common ancestor of the lineage

Convergent evolution - independent evolution of similar characteristics in different

lineages

Biogeography definiton - geographic distribution of species

Endemic - found nowhere else in the world

Theory - an explanation which accounts for multiple observations, as well as both

explains and combines a variance of phenomena

How does speciation occur? - One species becomes isolated in two or more places.
Each experiences different natural pressures, and so different traits are selected for.
This causes different modifications to occur between the isolated species, and ultimately
causes them to become entirely separate species

Linnean taxonomic system: - Dear Katie, Please Come Out For Goodness Sake.
d-Domain
k-kingdom
p-Phylum
c-Class
o-Order
f-Family
g-Genus
s-Species

How is an organism named? - Genus + species

Ex: homo sapien

How does a species become endemic? - A few member of a species migrate from A->B and then evolved

Artificial selection - when humans play the role of nature in selection

Describe unity and diversity of life - no matter how diverse organisms are, they will have
structures which are the same

Are we (Eukarya) more closely related to Bacteria or Archaea? - Archaea

Domain - the most general classification of life

When writing classifications: - *Underline or italicize the names

*Species is always lowercase
*Genus is always capitalized

Atom - lowest level of biological organization

Emergent properties - properties which emerge at higher levels of organization which

are not apparent at a lower level

Example of emergent property: - Life is a property exhibited at the cellular level but not
at the atomic level, carbon and oxygen might make up a cell, but they don't individually
exhibit life like a cell does.

Chapter 2:
Emergent properties in compounds - A compound exhibits qualities/features which
aren't in their parent elements
Ex:
pure sodium --> metal
pure chlorine --> poisonous gas
salt --> edible compound

4 major elements of living matter - Oxygen, Nitrogen, Carbon, Hydrogen, they make up
96%

Other elements which compose living matter - Calcium, Phosphorous, Potassium, Sulfur

Atom - smalles unit of matter which still keeps the properties of an element

Matter - anything that takes up space and has mass

Element - substance which can't be broken down into other substances via chemical
reaction

Compound - substance composed of two or more elements combined in a fixed ratio

Essential elements - elements which an organism needs to live and reproduce

Trace elements - elements which an organism only needs very small amounts of

In periodic table terms, C could stand for - the element Carbon as well as an atom of
Carbon

Atoms are made of what three subatomic particles? - Protons, Neutrons Electron

Charge of proton - +1

Charge of neutron - none

Charge of electron - -1

Which subatomic particles are in the nucleus of an atom? - Protons and neutrons

Electrons are attracted to what? - The nucleus, because of the positive charge of the
proton(s)

Mass of neutron and proton - 1.7 * 10^-24, 1 dalton, 1 amu

Mass of electron - 1/2000 amu

All atoms of the same element have the same number of what? - Protons

When an atom is assumed to have a neutral charge, what can we assume? - The
number of protons equals the number of electrons

Atomic number - number of protons

Atomic mass - number of protons + neutrons

Atomic mass - atomic number - number of neutrons

Atomic number is written where - subscript to the left of the elemental symbol

Atomic mass is written where - superscript to the left of the elemental symbol

Isotopes behave... - in the same manner as the pure element

Radioactivity - tendency for a substance to gain or lose protons

An atom's uniqueness comes from - its number of protons

Radiometric dating is used - to discover how old something is through half lives

Half lives are - constant, not affected by temperature, pressure, or other environmental
factors

Which subatomic particle is directly involved with chemical reactions? - electrons

With regards to potential energy, what does matter want to do? - Move to the lowest
possible potential energy state

Electrons have potential energy because of what? - Their proximity to the nucleus

Changes in electron potential energy only occur in ___. - steps of fixed amounts
Ex: ball on staircase, electron can be on specific steps (closer or farther from the
nucleus), but if it moves from one step to another, it doesn't spend much time inbetween

___ is needed to move an electron from a lower state to a higher state - energy

_____ is released in the form of ___ when an electron moves from a higher state to a
lower state - energy, heat
Ex: car heating up

Going from left to right and top to bottom in the periodic table, the number of ____ and
_____ increase by one. - protons, electrons

How many electrons does the first electron shell hold - 2

How many electrons does the second shell hold? - 8

When is an atom un-reactive? - When its valence is full

Atom reactivity is dependent on what? - the presence of unpaired electrons in the

valence

Isotopes - atoms of X element with an abnormal number of neutrons in its nucleus,

however, all isotopes of X element must have the same number of protons

Half-life - the time it takes for one half of the parent isotope to decay into its daughter
isotope

Energy - the capacity to cause change

Potential energy - energy matter possesses due to its location or structure

Valence electrons - electrons in the outermost electron shell

Valence shell - outermost electron shell

Inert - chemically un-reactive

Strongest chemical bonds - covalent and ionic

Covalent bonds - sharing a pair(s) of electron(s)

We represent covalent bonds with - dashes, H-H

Each molecule has a bonding capacity equal to ___________. - the number of missing
electrons in their valence

Valence - the number of bonds an atom has the capacity to make due to the number of
unpaired electrons in its valence

Non-polar covalent bond - covalent bond where the atoms involved have equal
electronegativities and so share electrons equally and so don't have partial charges

Polar covalent bond - covalent bond where the atoms involved have unequal
electronegativities and so share electrons unequally and so have partial charges

Electronegativity of four main elements in living things - O>N>C>H

Sometimes an atom is so ___, it strips the ____ completely away from the other. This
results in two __. - electronegative, electron, ions

Cation - positively charged ion

Anion - negatively charged ion

Ionic bond - attraction between cations and anions

Two types of weak bonds: - hydrogen bonds, Van der Waals interactions

Hydrogen bonds - when an atom is covalently bonded to a more electronegative atom,

the less-electronegative atom has a partial positive charge which can then attract a
bond to a partial positive atom

Van der Waals Interactions - lectrons aren't always evenly distributed throughout an
atom, and so they may randomly end up in one part or another of an atom and this
causes ever-changing regions of positive and negative charges which let all atoms and
molecules stick to one another

Structure vs. function - shapes of molecules determine how biological molecules

recognize and respond to on another
ex; opiates vs. endorphins binding to endorphin receptors in the brain

Molecule - two or more atoms held together by covalent bonds

Compound - combination of two or more different elements in a fixed ratio

Ionic compound/salt - compound formed by ionic bonds

What isn't matter? - some forms of energy, sound waves

Simplest atom - 1 proton, H+

The number of ___ in an atom determines the element type. - proton

Trace elements represent... - .01% of the elements in an organism

Electronegativity - relative attractiveness of electrons to atoms

Oxygen electronegativity - 3.5

Nitrogen electronegativity - 3.1

Carbon electronegativity - 2.5

Hydrogen electronegativity - 2.1

Oxygen and hydrogen share ___. - unequally

Nitrogen and hydrogen share __. - unequally

Carbon and hydrogen share ____. - equally

Polar molecules have ______ _____ as a result of differential ____. - partial charges,
electronegativity

Decay - when an element has a change in its number of protons (could mean gain or
lost)

Carbon 14 dating - when X stops taking in carbon, all of the carbon inside X starts
decaying into nitrogen
we know carbon 14's half life so we can tell how long its been since X died by
measuring the ratio of carbon 14 to nitrogen.

Energy levels - where you can find an electron

Energy shells - where there are electrons

Energy can be split into two categories: - Potential energy

Kinetic energy

Kinetic energy - energy in motion

3rd energy shell can hold how many electrons? - 8

When an atom is electrically neutral, what can atomic number also tell us? - the number
of electrons

How to approach electronegativity: - 1. Determine the different atom electronegativities

2. Determine if the atoms are sharing equally
3. Determine if there are partial charges
4. If there are, determine where the partial positives and partial negatives are
5. If so, say its polar (covalent)

An ion has a full ___. - charge

Hydrogen bonds are indicated with a _____. - dashed or dotted line going from one
molecule's partial negative, to the other's partial positive

Bonds which occur because of non-fixed partial charges are ____. - Van der Waals
interaction - happen between two non polar molecules due to the random nonsymmetrical electron distribution

Chapter 3:
Cohesion - when water sticks to itself as a result of hydrogen bonding

Adhesion - water sticking to other substances as a result of hydrogen bonding

Surface tension - the measure of how difficult it is to stretch or break the surface of a
liquid

Water has a high surface tension because... - where water meets air, the water
molecules form hydrogen bonds with molecules beside and below them

Water bonds with the molecules beside and below it instead of the water vapor above it
because... - the water vapor is moving quicker than the liquid water, so it can't form
bonds with it

Specific heat - the amount of energy needed to raise one gram of a substance one
degree celsius

Specific heat can be though of... - as a measure of how well a substance resists a
change in its temperature

Water's high specific heat is due to... - hydrogen bonding

heat must be absorbed to break existing hydrogen bonds, and at the same time, heat is
released when hydrogen bonds are formed
so much of the heat absorbed is used to break the hydrogen bonds first before the water
molecules can even start moving faster

Heat of vaporization - heat needed to convert the liquid state of water into a gas state

Water's high heat vaporization - In the same way as the specific heat, it takes a log of
energy to heat up water, and even more to make it evaporate

Expansion upon freezing - when water cools down, it begins to lose the energy it needs
to escape the attraction which forms hydrogen bonds. When the molecules cool off
considerably, it allows for each one to form four hydrogen bonding partners, making a
crystal shape which is less dense than liquid water

Versatility as a solvent - water dissolves substances by bonding to charged or partially

charged molecules/compounds with their partial charges

What substances don't react with water? - nonionic and non-polar

Colloid - Large molecule which often has polar parts, but because of all of their strong
internal bonding, water only sticks to it, but can't pull it apart
molecule that, even though it contains partial charges, it does not dissolve in water
because of its large size, and incredible internal bonding

Example of a colloid: - Cotton is made of giant molecules of cellulose, compound with

numerous regions of partial charges which form hydrogen bonds with the water
molecules, which is why cotton towels stick to water and dry you off, but don't dissolve in
the washer. Cellulose is also in the walls of trees, so water sticks to it and resists gravity.

Thermal energy - kinetic energy associated with the random movement of atoms or
molecules

Temperature - measure of the average kinetic energy of a substance regardless of

volume
Measure of ambient KE

What scale do scientists use exclusively to measure temperature? - Celsius

Total thermal energy - measure of the thermal energy present in a substance,

dependent on volume of substance (temp in pot of coffee is much higher than in a
swimming pool, but there is a greater amount of thermal energy in the large mass of
water in the pool)

Heat - thermal energy in transfer from one body of matter to another

Calorie (cal) - the amount of heat needed to raise the temp of 1 gram of water by 1
degree celsius (.4184 J)

Kilocalorie - the amount of heat needed to raise 1,000 g of water by 1 degree celsius

Joule - .239 cal

Evaporative cooling - the quickest and most energetic molecules are going to leave X
and cause the rest of the substance to cool down

Solution - liquid which is a completely homogenous solution of two or more substances

Solvent - the dissolving agent

Solute - the substance that is being dissolved

Aqueous - solution where water is the solvent

Hydration shell - the sphere of water molecules around a dissolved ion

Hydrophilic - any substance which has an affinity for water

Hydrophobic - substances that do not have an affinity for water (nonionic and nonpolar), tend to repel water

Molecular mass - sum of the mass of all the atoms in a molecule

Avogadro's number (1 mol) - 6.023 * 10^ 23 atoms

Molarity - the number of moles of solute per liter of solution

H+ - hydrogen ion

OH- - hydroxide ion

H+ is used to represent what - H3O+ because the H+ normally bonds to another water
molecule

Acid - a substance which increases the H+ ion concentration, (it donates them)

Base - a substance which decrease the H+ ion concentration by directly taking them in
to form something else, or they disassociate and produce more OH- ions

A solution is neutral if... - the H+ ion concentration is equal to the OH- ion concentration

Brackets indicate - molar concentration

The exponents of molarity in scientific notation with a base 1 always add to what? - 14

pH - negative logarithm (base 10) of the hydrogen ion concentration

-log [H+]

1 pH unit represents a _____ difference in H+ and OH- concentrations. - tenfold

Buffers - solutions which contain a weak acid and its corresponding base in order to
minimize changes in the concentrations of H+ and H- in a solution by accepting H+ ions
when they are in excess and donating H+ ions when they have been depleted

Example of a buffer: - carbonic acid (H2CO3)

Carbonic acid reaction - H2CO3 (acid) <--> HCO3- (base) + H+

Which way does the reaction go if your blood becomes too basic (H+ count decreases)?
- To the right

Which way does the reaction go if your blood becomes to acidic (H+ count increases)? To the left

Ocean acidification - A process through which CO2 reacts with ocean water to produce
H2CO3 (carbonic acid).
The extra hydrogen ions in water bond with carbonate ions (CO3^2-) to form carbonic
acid.
This decreases the carbonate ion concentration in the water. This is not good because
carbonate ions are necessary for corals to build their shells through calcification.

Atomic mass is equal to the mass in ___ for one ____ of that substance. - grams, mole
Ex: 1 mol O = 16 g
whereas 1 mol H = 1 g

Same amount of atoms but diff weights:

12 bowling balls vs. 12 golf balls

Finding the molar mass of a compound - Add up all of the molar masses for the
elements in a compound:
CH4
1 mol C = 12 g
1 mol H = 1 g * 4
12 + 4 = 16 g/mol

Unit for molar mass - g/mol

How to calculate molarity - Ex: we need a 1 M solution of glucose

Find ? grams 1 mol of C6H12O6 = 180 g
Put 180 g of C6H12O6 in a beaker
Fill up the rest of the beaker w/water up to the 1 L mark

pH is - the measurement of the # of free hydrogen ions in an aqueous solution

Chapter 4:
Carbon is - tetravalent

Carbon fixation turns ______ ____ to _____ _____. - inorganic carbon, organic carbon

Carbon fixation occurs in _____ ______. - primary producers

Major elements of life - ONCHSP

Organic chemistry - the study of carbon

Carbon most often forms bonds with ____, _____, and _____. - hydrogen, oxygen, and
nitrogen

Carbon chains form the ____ of most organic molecules - skeletons

Are hydrocarbons normally polar or non polar? - non polar

Hydrocarbons - organic molecules composed of only carbon and hydrogen

Isomers - compounds which have the same numbers of atoms but different structures
and therefore different properties

Structural isomers - differ in the covalent arrangements of their atoms

Cis-trans isomers - differ in the spatial arrangements as a result of the inflexibility of

double bonds contained within them

Enantiomers - isomers which are mirror images of one another, and differ in shape
because of the presence of an asymmetric carbon (one that is attached to four different
atoms or groups of atoms)

Enantiomers can't be ____ upon one another. - superimposed

Example of enantiomer: - Methamphetamine occurs in two enantiomers, one which is

the addictive stimulant drug and the other is an ingredient in an over the counter vapor
inhaler for treating nasal congestion.

Seven functional groups - *Hydroxyl*

*Carbonyl*
*Carboxyl*
*Amino*
*Sulfhydryl*
*Phosphate*
*Methyl*

Which functional group is not reactive, but instead serves as a recognizable tag on
biological molecules? - Methyl

Which functional group hydrophobic? - Sulfhydryl

Functional groups - chemical groups which are directly involved in chemical reactions

Tetravalent - has to gain or lose four electrons to fill or empty its outer shell

Is CO2 organic or inorganic? - inorganic

Carbon fixation is when plants convert ____ to _____. - carbon to sugar

When drawing a hydrocarbon, at the end of each diagonal line is 1 __. - Carbon (unless
indicated otherwise)

Wherever a double bond is present.... - the diagram is bent at that point

When the drawing is just a straight zig-zag, it is said to to be ____. - saturated because
it has the max # of bonds it can with hydrogen

Unsaturated means - there a(re) double bond(s) present, so the carbon has not made
the max number of bonds with hydrogens

Molecular formula - type and number of atoms

Isomer - two different molecules with the same molecular formula but different physical
and chemical properties

Cis & Trans isomers are aka ____ ____. - geometric isomers

Cis isomers - Same side

Trans isomers - opposite sides

Chiral - can't be superimposed upon one another (enantiomers)

Functional groups are small organic molecules bonded to larger one but which have
great _____ _____. - biochemical effects

Hydroxyl - when OH is bonded to R

Ex: alcohol

Carbonyl - Carbon double bonded to an oxygen and has single bonds with two other Rs
Ex: acetone, propaol

Ketone - when the carbonyl is in the middle of a molecule

Aldehyde - when the carbonyl is at the end of a molecule

Carboxyl - when carbon is double bonded to an oxygen and single bonded with one OH
and one R
Note: O- often denotes what used to be an OH, but it has since given up its H+, in other
words the hydrogen left its electron behind
Ex: Acetic acid

Are carboxyls acids, bases, or neutral? - acids, they give up their H+ ions

Amino - nitrogen bonded to two hydrogen and one R, or nitrogen bonded to two
hydrogen, one R, and then because it has two paired electrons left, it is partially
negative in that portion of the atom, so it can hydrogen bond with an H+ ion
Ex: Glycine

Is an amino group an acid, base, or neither? - Acts as a weak base because it pulls H+
out of a solution

Sulfhydryl - Sulfur single bonded to hydrogen and single bonded to R

Ex: Cysteine

Sulfhydryl is acidic, basic, or neither? - Acidic

Phosphate group - phosphate double bonded to an oxygen, single bonded to two O-,
and single bonded to one oxygen which is then bonded to an r
Ex: glycerol phosphate

W/o the R attached to that last single bonded regular oxygen in a phosphate group, it
would be ____ ___. - phosphoric acid

Is a phosphate group acidic, basic, or neither? - acidic

Methyl - Carbon bonded to three hydrogens and on R

Ex: 5-Methy cytosine

If the R in the Methyl group was another hydrogen, what would it make that molecule? methane: CH4

Chapter 5:
What are the 4 major macromolecules? - Proteins
Nucleic acids
Carbohydrates
Lipids

What are covalent bonds in proteins called? - peptide bonds

What are covalent bonds in nucleic acids called? - phosphodiester bond

What are covalent bonds in carbohydrates called? - glycosidic linkage

glyco- always refers to what? - carbohydrate

What are the covalent bonds in fats called? - ester linkages

Dehydration synthesis - when a water is taken out of two monomers in order for them to
bond and make a polymer

Hydrolysis - adding water to break apart a polymer

Enzymes - proteins which speed up chemical reactions by speeding up dehydration

synthesis or hydrolysis

Functions of proteins - * Enzymatic

* Structural
* Storage
* Transport
* Hormonal
* Receptor
* Contractile
* Immune response

What are the monomers which make up proteins called? - amino acids

Examples of proteins: - meat, fish

Basic protein structure: -

What main functional groups are in a protein? - amino and carboxyl

Enzymes all have ___ at the end of their name? - -ase

Proteins all end in ___. - -ine

What are the three categories of R groups proteins can be bonded to? - 1. Non polar
2. Polar
3. Electrically charged
Thought process for non polar:
a. same electronegativities
b. share equally
c. no partial charges
d. non polar
Thought process for polar and electrically charged:
a. diff electronegativities
b. share unequally
c. partial charges
d. polar

How many types of amino acids are there? - 20, called protogenic amino acids

Peptide - short chain of amino acids, minimum of two

Polypeptide - long polymers of amino acids

If a protein doesn't function - called peptide or polypeptide

If a protein does function - called polypeptide and protein or peptide and protein

2 main shapes of proteins: - Globular - spherical, normally very active (transport,

speeding up reaction, etc.)
Structural - long linear structures, protect you, but don't move around and do things
(hair, nails)

Four levels of protein structure: - Primary

Secondary
Tertiary
Quaternary

What does primary structure of proteins indicate? - what type of amino acids are present
and what order they are in
At this point, the protein only looks like a long chain

What does secondary structure of proteins indicate? - hydrogen bonding

This results in the proteins taking shapes:
alpha helix
beta-pleated sheet

What does tertiary structure of proteins indicate? - all of the bonds, weak and strong
Strength of bonds scale:
Covalent>Ionic>Hydrogen>Van der Waals

What does quaternary structure of proteins indicate - How many polypeptide strands are
in the protein
A protein must have two or more polypeptide strands in order to have quaternary
structure
Once two or more polypeptides meet, they have function

What can happen if amino acid is transposed in a protein? - Ex: sickle cell anemia

Proteins denature if they are not in the right _____ and ____ range. - temperature, pH

Chaperonins - Already existing proteins which help the new protein fold
They do this by not letting them interact with other proteins which would influence the
way it folds

DNA - Instructions for making proteins, larger molecule which fits into smaller
classification of nucleic acids, units of inheritance, genetic inheritable information

How are proteins made? - DNA is protected in the nucleus, so we copy a RNA structure
which will travel outside the nucleus and then make the proteins

Molecular chain of command for making proteins: - Information-->DNA-->RNA-->Protein

What are the monomers which make up the polymer which make up DNA called? nucleic acids

Basic structure of a nucleic acid: -

What are the main components and functional groups which make up a nucleic acid? Phosphate, Nitrogenous base, and a Sugar

How are nucleic acids named? - Based on their sugar

What gives a nucleotide its identity? - nitrogenous base

What are the four main DNA base pairs? - Adenoside

Guanine
Cytosine
Thymine

Which bases are paired? - As with Ts

Cs with Gs
If you line them up in alphabetical order, the inner ones are paired and the outer ones
are paired:
ACGT

Cytosine and Thymine are _____. - pyrimidines, have one ring

(the one with the longer name are the smaller molecules)
AGatha ChrisTie (Christie is longer than Agatha so it is the pyrimidine pair)

Adenosine and Guanine are _____. - purines, have two rings (the ones with the shorter
name are the larger molecules) AGatha ChrisTie (Agatha is shorter than Christie so it is
the Purine pair)

In RNA which base pair is substituted? What is it substituted with? - T, U

So A is paired with U and C is paired with G in RNA

What is a nucleoside? - nucleotide without the phosphate functional group

What sugar is found in DNA? - deoxyribose

What sugar is found in RNA? - ribose

What is the difference between ribose and deoxyribose? - Ribose - 2 hydroxyl functional
groups
Deoxyribose - 1 hydroxyl functional group

Covalent bond specific to DNA? - phosphodiester

Antiparallel arrangement in DNA - the polynucleotide on the right side goes up, the lift
side goes down

Carbohydrates - hydrated carbon

What does -ose indicate? - sugar carbohydrate

If the sugar carbohydrate has a carbonyl group at the end, what is it called? - aldose

If a sugar carbohydrate has a carbonyl group in the middle, what is it called? - ketose

How many carbons are in the backbones of a carbohydrate? - 3-7

Monosaccharide - monomers for carbohydrates

A carbohydrate is like a ___ ____ where monosaccharides are the ____. - beaded
necklace, beads

General molecular formula for carbohydrate: - (CH2O) sub n

n = number of carbons (3-7)

Functions for Carbohydrates: - structural, energy, communicational

Glucose - monosaccharide, only one ring

Sucrose - disaccharide, two rings, one glucose + one fructose

Basic structure for a carbohydrate: -

All sugars have a ____ functional group. - carbonyl

Disaccharides - two monosaccharides bound to each other

Covalent bond for disaccharide? - glycosidic linkage - formed by dehydration synthesis

Starch is a ____. - polysaccharide

Starch is like a beaded necklace with ____ ____ ____ ____. - all the same beads

Starch is composed of a ... - repeating polymer of glucose

Amylose - type of unbranched starch

Amylopectin - type of branched starch

Glycogen - very branched, found in animals, types of carbohydrate

Cellulose - repeating unit og glucose, straight (not helical), de of different isomer of

glucose: beta glucose, arrange up and down, which allows for lots of hydrogen bonding
which makes it very strong
most organisms only have the enzymes to break alpha bonds, but not the beta bonds

Sugars are always either a ___ or _____. - monosaccharide, disaccharide

Lipids - always have one non-polar region, has logs of carbons and hydrogens

Lipids are diverse because... - there are many types

Proteins are diverse because... - they serve many functions

Lipids don't form... - polymers

Three main types of lipids: - 1. Fats

2. Phospholipids

3. Steroids

Covalent bonds for fats - Ester linkages

Main structure for fat: - H

|
H - C - OH O
| \\
H - C - OH C /\/\/\/\
|/
H - C - (OH H)O
|^
H where dehydration synthesis occurs so the fatty acid can attach, this bond is called
an ester linkage
abbreviation: vertical line with three horizontal lines, each horizontal line is where a fatty
acid could bond

When 1 fatty acid is bonded to a glycerol, its called a ______. - monoglyceride

2 - diglyceride
3 - triglyceride

S alliteration for saturated fats: - Saturated-Solid-Single-Straight

Animal fats are __ at room temp - Solid (saturated)

Plant fats are ____ at room temp - Liquid, oils (unsaturated

Hydrogenation - when food companies, to preserve food, take plant oils (unsaturated
fats) and take the double bond out so they stay solid at room temp

Trans fats - unsaturated fatty acid where they have attempted to take the double bond
out, but instead what happened was the double bond stayed, but it also absorbed the
extra hydrogens
Tras fats have a double bond that is unkinked, and is completely saturated

Phospholipid - has both polar and non polar properties, amphopathic

Phospholipids are made of - phosphate, choline, and diglyceride

The phosphate and choline are polar, and the diglyceride is non polar.

The head of a phospholipid is made of what? Is it polar or non polar? Hydrophilic or

hydrophobic? - phosphate and choline, polar, hydrophilic

The tail of a phospholipid is made of what? Is it polar or non polar? Hydrophilic or

hydrophobic? - diglyceride (fatty acid tails), non polar, hydrophobic

What is the basic building block for steroids? - Cholesterol

What are steroids characterized by? - A carbon skeleton of four fused rings

What category do steroids fall into? - lipids, because they are partially hydrophobic

Functions of steroids? - cell to cell communication, gene regulation, structure, storage,

energy, insulation

Chapter 6:
Cells are... - the basic unit of life

A dissection scope looks at... - the outer surface of a cell

How do light microscopes work? - They transmit light through the sample

What characteristic must a specimen for a light microscope have? - Must be transparent

What magnification can a light microscope go up to? - 1000x

Scanning electron microscope (SEM) - looks at the outer surface of a very small
specimen by bouncing electrons off its surface

What magnification can a SEM go up to? - 500,000x

Transmission electron microscope (TEM) - looks at the inside of a cell by passing

electrons through the small specimen

What magnification can a TEM go up to? - 50,000,000x

What is one biochemical technique used to analyze cells? - Cell fractionation

Cell fractionation - dividing up a cell

How does cell fractionation work? - You put a tissue in a test tube and then break up the
cells with a homogenizer. You then use a centrifuge to separate the different parts of the
cell

Homogenate - The solution you are left with after the solution goes through the
homogenizer

What is the part at the bottom part of the tube after the homogenate has been spun? Pellet, the densest or next densest material in the cell

What is the liquid above the pellet called? - supernatant

Cytoplasm = ___ + _____ - cytosol, all cellular structures

Cytosol - the liquid in the cell (mostly water)

What is the cell/plasma membrane mainly composed of? - phospholipid bilayer

Membrane bound organelles are... - compartments in a cell which have their own
phospholipid bilayer

Ribosomes - structures which coordinate the building of proteins

What structures do prokaryotes and eukaryotes have in common? - cell membrane,

cytoplasm, cytosol, DNA, ribosomes

Where is the DNA in eukaryotic cells housed? - nucleus

Where is the DNA in prokaryotic cells housed? - nucleoid region

Do prokaryotes have membrane bound organelles? - No, only eukaryotes

What are the main types of eukaryotic cells? - animal, plant, protist

Chloroplast is in a ___ ____ but not a ____ ___. - plant cell, animal cell

Cell wall is made of __. In ___ __ but not ____ ___. - cellulose, plant cell, animal cell

Centriole - helps coordinate cell division, it is in an animal cell, but not plant cell

What is the relationship between volume and surface area of a cell? - As a cell gets
larger, the surface area relative to volume decreases, so there is an advantage to being
smaller because otherwise diffusion can't occur at a fast enough rate to reach all parts
of the cell

Cells require a high _____ t0 ___ ratio. - surface, volume

What part of the phospholipid bilayer sticks out, what part in? - Tails are inside, heads
are out because both inside and outside the cell is water

Nuclear envelope - two phospholipid bilayers which prtect DNA

If DNA is not protected, it is called ____ ___. - naked DNA

What is our DNA combined with? - proteins, so it is more protected

Chromatin - all of the proteins + DNA

Chromosomes - separate structures of chromatin

Nucleous - inside the nucleus (nucleus of the nucleus) where we sort ribosomal RNA
(rRNA) and proteins (the building blocks to make a ribosome)

Ribosomes are made of ____ and ____. - rRNA, proteins

Where are ribosomes assembled? - in the nucleolus

Are ribosomes membrane bound? - no

Endoplasmic reticulum (ER) - sacs protruding from the nucleus, surrounded by 1

phospholipid bilayer

What are the two parts of the ER? - rough and smooth

What is the purpose of the rough ER? - this is where proteins are synthesized, the site
of fixed ribosomes, where phospholipid bilayer will pinch off and hold a protein inside or
one the membrane of it (called vesicle)
Think bubbles

Two places where proteins are made: - free ribosome, fixed ribosome on ER

What is the purpose of the smooth ER? - synthesized lipids, steroids, metabolized
carbohydrates and steroids, stores ions, detoxification
The sarcoplasmic reticulum releases and reaccepts ions which lt your muscles contract
In the liver, the smooth ER detoxifies

What is the endomembrane made up of? - In eukaryotes the organelles of the

endomembrane system include: the nuclear envelope, the endoplasmic reticulum, the
Golgi apparatus, lysosomes, vacuoles, vesicles, endosomes and the cell membrane.

Glycoprotein - carbohydrate and protein

Lipoprotein - lipid and protein

Golgi apparatus looks like - several flattened membranous sacs

What are the flattened membranous sacs called? - cisternae

What does the Golgi do? - The golgi is a structure which takes a protein that comes
from the ER in the form of a vesicle and changes it to form a final product which is then
sent off again

What is a vesicle called when it is let off? - A secretion

Lysosome - bag of enzymes, helps with the digestion of nutrients

Autophagy - when we have an old organelle or something else in the cell and we digest
is using a lysosome
Ex: amoeba eating a paramecium

Vacuole - phospholipid bilayer which stores things

Plants have a large central ___. - vacuole

Animal cells normally have small ____. - vacuoles

What two organelles are not part of the endomembrane system? - mitochondria and
chloroplasts (as well as ribosomes)

Mitochondria and chloroplasts have their own ____ ___. Their general functions are
to ... - 2 phospholipid bilayers, change energy from one form to another

Mitochondria - sites of cellular respiration

Chloroplasts - sites of photosynthesis, found only in photosynthetic organisms

Which phospholipid bilayer of the mitochondria is folded? What are those folds called?
Which is smooth? - Inner membrane, christae, outer layer

Where are mitochondria found? - in all eukaryotic cells

What is the fluid within the inner membrane of the mitochondria called? - matrix

Chloroplast is a type of... - plastid (plastid - phosotynthetic organism)

What give chloroplasts their green pigment? - chlorophyll

How many membranes can a chloroplast have? - Many, as many as seven outer ones

What are the stacks of green coins called? - granums

What is one individual green coin called? - thylakoid

What is the fluid that the geraniums "bathe" in? - stroma

What are the main parts of the cytoskeleton? - microfilaments, intermediate

filaments,and microtubules

Cytoskeleton - network of fibers which organize structures and activities in the cell,
filaments and microtubules which maintain the location of organelles and the stability of
the cell

Microfilaments are composed of what? - the protein actin

Relative to the three parts of the cytoskeleton, how does the diameter of microfilaments
compare? - the smallest intimater, 7nm in diameter

What is the purpose of microfilaments? - coordinate muscular contractions, help

coordinate cell division

Cytoplasmic streaming - where the microfilaments on an organism wave around and

cause a whirlpool effect to distribute nutrients to all parts of the cell

What type of organism utilizes cytoplasmic streaming? - ameobas

How else can amoebas move? - false feet, squeezing cytoplasm out and then pulling
back to move

Relative to the three parts of the cytoskeleton, how does the diameter of intermediate
filaments compare? - middle in diameter, 8-12 nm

What are intermediate filaments made of? - keratin

What is the purpose of intermediate filaments? - they anchor the nucleus and
organelles, they compose the nuclear lamina, help maintain the nucleus shape

Relative to the three parts of the cytoskeleton, how does the diameter of microtubules
compare? - largest of the three, 25 nm

What are microtubules composed of? - tubulin

What is the purpose of microtubules? - the railroad which guides and coordinated
movement in the cell, like vesicles moving from ER to the golgi and fro the golgi to
outside the cell
It also helps separate the chromosome copies in dividing cells

It also can move an entire cell

What is a good comparison to microtubules? - scaffolding, you can break it down and
put it up at the next job

Centrosome - part of an animal cell which coordinates cell division by coordinating the
building of microtubules

What are no the inside of centrosomes? - a pair of centrioles (in animals only)

Flagella - like a tail, normally less than a dozen on a cell (except cilia), like an outboard
motor or helicopter, can push you or drag you along

Cilia movement - flagella move like an oar

power stroke and recovery stroke, they beat in one continuous motion

What are the purposes of a cell wall? - protection

to maintain the shape of the cell
prevent excessive water uptake

Plasmodesmata - channels through which plants can share nutrients

SEM vs. TEM - SEM - used for detailed study of the topography of a specimen which is
normally coated with a thin film of gold
TEM - used to study the internal structure of cells, which is normally stained with heavy
metals so density can be determined

Light microscope vs. electron microscopes - Light microscopes can be used for live
specimens, electron microscopes involve killing the cells

Cell fractionation overall - Centrifuge holds a mix of homogenized cells (cells which have
been in a blender to break them up). Then it is spun, and the densest cellular structures
land at the bottom in a pellet. The pellet is then taken out and the homogenized mix is
spun again.

Cell def. - organism's basic unit of structure and function, the simplest collection of
matter that can be alive

Light microscope (LM) def. - light is passed through a specimen and then through glass
lenses which refract the light which magnifies the specimen

Organelles - membrane enclosed structures within eukaryotic cells

Electron microscope (EM) def. - focuses a beam of electrons through the specimen or
onto its surface

Cytology - the study of cell structure

Cell fractionation def. - cell studying technique which takes the cells apart and separates
major organelles and other sub cellular structures from one another

How many membranes does a eukaryotic nucleus have? - 2

Nucleoid region - DNA concentrated in a non membrane enclosed area (prokaryotic)

Where are organelles located in organelles? - in the cytoplasm and suspended in the
cytosol

Which cells are normally larger: Eukaryotic or Prokaryotic? - Eukaryotic

Ex:
Bacteria: 1 to 5 um
Eukaryotic cells: 10 to 100 um

Why is there a "metabolic limit" on the size of cells? - The plasma membrane is a
selective barrier that allows enough oxygen, nutrients, and wants in and out to service
the cell. Only a fixed amount of a particular substance can cross per second, so the
ratio of surface area to volume is especially important.

Microvilli - long hair like structures which increase the surface area in a cell w/o adding
too much volume to it

How do plasma and organelle membranes participate directly in a cell's metabolism? They have enzymes which are built right into the membranes

What is the basic structure of a membrane? - two phospholipid layers which other lipids
and proteins

Plasma membrane - selective barrier which binds all cells

Cytosol def - semifluid, jellylike substance inside all cell where sub cellular components
are suspended

Chromosomes - carry genes in the form of DNA

Cytoplasm - the region between the nucleus and the plasma membrane

Where is the major of a cell's DNA found? - nucleus

Where else can DNA be found? - in mitocondria and chloroplasts

Describe what is going on at at the lip of pores found on the two membranes of the
nuclear envelope. - At the lip of each pore the inner and outer membranes of the nuclear
envelope are continuous and there is an intricate protein structure called pore complex
which regulates the entry and exit of proteins and RNAs.

Nuclear lamina - netlike structure of protein filamens which keeps the shape of the
nucleus by mechanically supporting the nuclear envelope from the outside(except at the
pores)
There is evidence for a nuclear matrix as well which functions like the lamina but works
from the inside, perhaps separating and organizing the DNA

Chromosomes - DNA organized into small units

Where are chromosomes found? - in the nucleus

What are chromosome made of? - one long DNA molecule with many proteins
Some of the proteins help to cold the DNA so it can fit inside the nucleus

Chromatin - complex of DNA and proteins which make up chromosomes

Nucleolus - promient structure in the nondividing nucleus, where ribosomal RNA is

synthesized (rRNA) from instructions in DNA (sometimes there are 2 or more nucleoli)

Why are ribosomes not organelles? - they aren't membrane bound

What are ribosomes made out of? - ribosomal RNA and proteins

What two cytoplasmic locales do ribosomes operate in? - Free ribosomes - suspended
in cytosol, make proteins which normally function in the cytosol, ex: enzymes that
catalyze the first steps of sugar breakdown
Bound ribosomes - attached to the outside of the ER or nuclear envelope, make
proteins which are usually for insertion into membranes for packaging within certain
organelles, ex: lysosome

Nuclear envelope - enclosure which houses the nucleus, separating its contents from
the cytoplasm

Functions of the endomembrane system: - * Synthesis of proteins

* Transport of proteins to membranes and organelles, or out of the cell
* Metabolism and movement of lipids
* Detoxification of poisons

How are the parts of the endomembrane system related? - The membranes in the
endomembrane system are related via physical continuity or the transfer of membrane
segments via vesicles

What can the ER be thought of as? - a biosynthetic factory

What is the ER made of? - a network of membraneous tubules and sacs

What are the network of membraneous tubules and sacs in the ER called? - cisternae

The ER separates the __ ___ from the ____. - ER lumen, cytosol

What is the main difference between the smooth and rough ER? - Smooth ER - smooth
outer surface because no ribosomes
Rough ER - studded with ribosomes on outer surface

What part of the ER is continuous with the nuclear envelope? - the rough ER

Is the nuclear envelope studded with ribosomes or not? - yes

Main functions of the smooth ER: - Different in each cell type

Synthesis of lipids (including steroids, hormones)
Metabolism of carbohydrates
Detoxification of drugs and poisons (typically adding OH-R groups), more alcohol
causes more smooth ER to be made, so more tolerance
Storage of calcium ions (pumps calcium ions from the cytosol into the ER lumen, when
stimulated, the muscle cell's calcium ions rush back across the ER membrane into the
cytosol to trigger contraction of muscle cell

Main functions of the rough ER: - Polypeptide chains grow from bound ribosomes and i
is then threaded into the ER lumen via a pore made by the protein complex in the ER
membrane. In the ER lumen, the polypeptides fold into their functional shape

After secretory proteins are made, the ER membrane isolates them from proteins which
are produced via free ribosomes which remain in the cytosol. Instead the proteins leave
in vesicles.

Transport vesicles - vesicles in motion from one part of the cell to the other

How does the rough ER grow in place - Via adding membrane proteins and
phospholipids to its own membrane. As these types of proteins and phospholipids are
made, they are inserted into the ER membrane and anchored there by hydrophobic
portions.
When polypeptides which are going to be membrane proteins grow from the ribosomes,
they are inserted into the ER and anchored with their hydrophobic portions.
Rough ER makes membrane phospholipids.
Enzymes in the ER membrane assemble phospholipids from previous one in the
cytosol.
The ER membrane expands, and some of it is moved to other components of the
endomembrane system via transport vesicles

Golgi apparatus - Many transport vesicles leaving the ER go to the Golgi which
receives, sorts, ships, and even manufactures products.
Products from the ER, like proteins, are modified and stored, then sent to other
destinations

What do the membranes of each cistern separate? - the internal space from the cytosol

Describe the golgi stack's structural directionality: - Golgi stacks have structural
directionality with the cisternae on opposite side of the stack differing in thickness and
molecular composition. They are referred to as the cis face and the trans face which are
the receiving and shipping areas of the golgi, The cis face is normally near the ER. The
trans face is where the vesicles pinch off from. In between the two faces is where
alerations of the molecules are made to make a wide variety of carbohydrates and
varied phospholipids

Cisternal maturation model - the cisternae of the Golgi progress forward from the cis
face to the trans face, carrying and modifying cargo along the way
It sorts the molecules, often with phosphate id tags which act like zip codes on mailing
labels

Lysosomes can be though of as - digestive compartments

What are lysosomes, what do they do? - membraneous sac of hydrolytic enzymes that
many eukaryotic cells use to digest (hydrolyze) macromolecules

What environment do lysosomal enzymes work best in? - acidic environments

Where are the hydrolytic enzymes and lysosomal membranes made? - the rough ER,
they are then transferred to the golgi

How are the proteins on the inner surface of the lysosomal membrane protected from
the digestive enzymes? - the 3-D shape of the lysosome

What is the main function of lysosomes? - intracellular digestion

Phagocytosis - eating a vessel or cell

Ex: macrophages

What is autophagy? - When hydrolytic enzymes are used to recycle a cell's own organic
material

What can vacuoles be though of as? What are they actually? - diverse maintenance
compartments, large vesicles

Where are vacuoles made? - from the ER and golgi

How are food vacuoles made? - phagocytosis

What do many unicellular eukaryotes which live in fresh water have? - contractile
vacuoles to pump excess water out of the cell

What can small vacuoles do? - hold reserves of important organic compounds
ex: could hold a poison which can be released when attacked to protect the animal

How are the large central vacuoles formed in plant cells? - fusing of smaller vacuoles

What is the main purpose of a plant cell's large central vacuole? - To hold the main
repository of inorganic ions like potassium and chloride

Vesicles - sacs made out of membrane

In eukaryotic cells, what are the organelles which convert energy in forms which can be
used for cellular work? - mitochondria

Chloroplasts do what? - convert solar energy into chemical energy

Mitochondria do what? - extract energy from sugars, fats, and other fuels to replenish
the supply of ATP

Peroxisome - oxidative organelle

What lead to the formation of the endosymbiont theory? - Mitochondria and chloroplasts
show similarities to bacteria

Endosymbiont theory - an early ancestor of eukaryotic cells engulfed an oxygen using

non photosynthetic prokaryotic cell. Eventually, the engulfed cell formed a relationship
with the host cell , becoming an endosymbiont (a cell living within another cell) and the
merged into one organism

Evidence of evolution for mitochondria and chloroplasts: - mitochondria and chloroplasts

have double membranes, like prokaryotes, mitochondria and chloroplasts have
ribosomes and multiple curcular DNA molecules associated with their inner membranes
which programs the synthesis of some organelle proteins, lastly, these organelles are
somewhat autonomous or independent

What does the number of mitochondria in a cell correlate to? - the cell's level of
metabolic activity

Where is the inter membrane space found in a mitochondria/chloroplast? - It is the

narrow region between the inner and outer membranes

What do three compartments do the membranes of the chloroplast divide it into? - the
inter membrane space, the stoma, and the thylakoid space

How many membranes does a peroxisome have? - 1

What is a peroxisome? - a specialized metabolic compartment which has enzymes that

take hydrogen atoms from various substrates and transfer them to oxygen making
hydrogen peroxide (H2O2)

What do peroxisomes do to make a form of fuel for cellular respiration - They can use
oxygen to break down fatty acids

How can peroxisomes help detoxify alcohol and other harmful compounds? - By
transferring a hydrogen from the poisons to the oxygen. The hydrogen peroxide is toxic
as well though so it is compartmentalized from the cellular components which could be
damaged

How can peroxisomes grow larger? - via incorporating proteins made in the cytosol and
ER, as well as lipids in the ER and within the peroxisome itself

What can peroxisomes do which sparks the suggestion of an endosymbiotic

evolutionary origin? - once they reach a certain size, they can split into two

Functions of microtubules - * Maintenance of a cell shape (compression resisting

"girders")
* Cell motility (cilia or flagella)
* Chromosome movement in cell division
* Organelle movement

Functions of microfilaments: - * Maintenance of cell shape (tension bearing elements)

* Changes in cell shape
* Muscle contraction
* Cytoplasmic streaming
* Cell motility (as in pseudopodia - false feet (amoeba))
* Cell division

Functions of Intermediate filaments: - * Maintenance of cell shape (tension bearing

elements)
* Anchoring nucleus and certain organelles
* Formation of nuclear lamina

What are microtubules made of? - globular protein tubulin

What composes one microtubule? What is it called? - Two subunits: alpha tubulin, beta
tubulin
It is called a timer

Centrosomes and microtubules: - microtubules grow out from it in an anima cell, round
in an area often near the nucleus. and act as compression reisting girders of the
cityskeleton

What composes a centriole? - Nine sets of triplet microtubules arranged in a ring

What can cilia or flagella which texted from fixed tissue cell do? - move fluid over the
surface of the tissue

What do both cilia and flagella both contain? - microtubules

Flagella vs cilia? - Flagella has an undulating motion like the tail of a fish
Cilia work like oars with alternating power and recovery strokes
They can also be signal receiving antenna, cells with this type of cilia are normally nonmotile and there is only one per cell. Most all cells in a vertebrate animal have this type
of cilia and it is called the primary cilium

What motor protein makes the microtubules in flagella and cilia bend? - dynein

Myosin - thousands of actin and thicker filaments make up this protein which interacts to
cause the contraction of muscle cells

Pseudopodia - cellular extentions through which the actin myosin interactions can move
them, this contributes to cytoplasm streaming(a circular flow of cytoplasm within cells
speeds the distribution of materials within the cell

Intermediate filaments are... - only found in some eukaryotic organisms , they are very
diverse and are constructed with subunits which belong to a family of proteins of which
keratin is in
They are more permanent, the nucleus normally sits within a cage made of intermediate
filaments, they can help anchor microfilaments and play a very important role in
structure and overall sturdiness of a cell

What organisms beside plant cells have cell walls? - prokaryotes, fungi, and some
unicellular eukaryotes

What enzyme synthesizes the production of cellulose which is used to compose a cell
wall? - cellulose synthase

Describe how a plant forms a cell wall - A young plant cell first secretes a somewhat thin
and flexible wall called the primary cell wall, and between the primary walls of adjacent
cells is the middle lamella, a thin layer rich in sticky polysaccharides called pectins
This glues the adjacent cells together. When the cell stops growing its wall is
strengthened either by secreting hardening substances into the primaryy wall or adding
a secondary cell wall between the plasma membrane and the primary wall

In what way can plant cells connect themselves to one another? - plasmodesmata
(channels between adjacent cells with perforate both cell walls)

In compensation for not having a cell walls, animal cells also have a ____. Extracellular matris (ECM)

What are the main ingredients of the ECM? - glycoproteins and other carbohydrate
containing molecules

What is the most abundant molecule in the ECM? - collagen

Proteoglycan - small core protein with many carbohydrate chains covalently attached to
it

What are the three main types of cell junctions for animal cells? - Tight junctions,
desmosomes, and gap junctions

Which junction is most like a plant's plasmodesmata? - gap junctions, except their pores
are not lined with a membrane

Tight junctions - the plasma membranes of neighboring cells are pressed tightly agains
one another, bound together by specify proteins
This prevents leakage of extracellular fluid across a layer of epithelial cells

Desmosomes - fasten cells together into strong sheets, intermediate filaments anchor
desmosomes in the cytoplasm

Gap junctions - provide cytoplasmic channels from one cell to an adjacent cell

they are made of membrane proteins which surround a pore that ions, sugars, amino
acids, and other small molecules pass through
this allows for communication between cells in many types of tissues

Chapter 7:
Cellular membranes can be thought of as fluid mosaics of ______, _____, and _____. lipids, carbohydrates, proteins

Cellular membranes import: - water, energy sources, ions, building blocks, signals

Cellular membranes export: - water, products from cellular work, signals, waste, ions

The heads of phospholipids in a cell membrane face ___, and are ____ and ____. outward, hydrophilic, polar

The tails of phospholipids in a cell membrane face __, and are ___ and ______. inward, hydrophobic, non polar

Describe the fluidity of plasma membranes: - Phospholipids maintain their structure but
flow around. Most movement is vertical, but to replace, it happens horizontally

Buffering - maintaining a certain condition

Fluidity - movement

Enhanced fluidity - more movement

Depressed fluidity - less movement

With an increase in temperature, there is ___ ___ in the plasma membrane. - enhanced
fluidity

With a decrease in temperature, there is ___ ___ in the plasma membrane. - depressed
fluidity

Cholesterol acts as what in a plasma membrane? - a buffer, it prevents the

phospholipids from solidifying in cold temps and moving too fast in warm temps

Which enhance a plasma membrane's fluidity: saturated or unsaturated fatty acid tails? unsaturated because they can't squeeze together as much
ex: arctic fish, breast milk

Which depress a plasma membrane's fluidity: saturated or unsaturated fatty acid tails? saturated because they can squeeze tightly together
ex: warm temp fish

What molecules do phospholipids easily let through? - small non polar things because
of the hydrophobic tails which are on the inside of the membrane

Aquaporin protein - belongs to channel proteins - proteins on membranes which create

highways) - protein with hole in middle so water can effectively move through
phospholipid bilayer
They aren't in place, they can move around in the membrane

Integral proteins - inside the membrane - non polar (amino acids in non polar group)

Transmembrane integral proteins - ones that go completely through the bilayer

Describe domains with regard to membrane proteins. - based on where the protein or
protein part is, hydrophilic domains near the head, by the tail - hydrophobic

Peripheral proteins - attached to the outside (made of amino acids that are in polar
group)

Describe protein functions on a membrane for the following:

ATP synthase
Receptor protein
Anchor protein
ECM - ATP synthase - enzyme
Receptor proteins - look for signal in form of molecule so when that molecule binds to it,
it will kick off a chain of events
Anchor proteins - ex: connect to the cytoskeleton so it can maintain shape of cell
Extracellular matrix connection and communication

In regard to the ECM, and the filaments which compose it, which part of the name is the
primary part.
Ex: glycoprotein - The second part, in the example: protein

Passive transport - does not use energy to move substances across the membrane

What is another name for passive transport? - facilitated diffusion

Diffusion - the tendency of matter to spread out, and occurs as a result of a

concentration gradient

Equilibrium - where there is no longer a concentration gradient

Osmosis - the diffusion of water from a place of high water concentration to low water
concentration through a semi-permeable membrane

Aquaporins allow ___ to occur. - Osmosis

Water always goes to a place with more ___ because that is where there is a lower
water concentration. - solute

Cell in isotonic environment: - when concentration in solution of outside is equal in the

cell and outside

Cell is in hypertonic environment: - more solute outside than inside so cell shrinks
because cell will have its water move outside

Cell is in hypotonic environment: - more solute inside the cell than outside, so water
comes in and the cell expands, swell, maybe even burst

Osmoregulation - Ex:
Paramecium - unicellular eukaryotic organism - has pump to push water out called
contractile vacuole
Every fresh water organism lives in a hypotonic organism, so water is going to
constantly go in him

Plasmolysis - when plant cell is in a hypertonic environment so membrane shrinks in

Plant cells prefer which environment? - hypotonic

What happens to a plant cell in an isotonic environment? - it is limp

Active transport - Use energy to move substances across the membrane, go against
tendency of matter to spread out, need to move matter to where it doesn't want to go
Active transport is using energy to move matter in direction where matter does not want
to go

Why does ATP have so much potential energy? - ATP - adenoside triphosphate nucleotide w/two extra phosphate groups, the phosphate groups are all negative so they
repel each other so they have lots of potential energy
When you use ATP - we end up ADP, one less phosphate group, we break off the third
phosphate group

Membrane potential - gradient in charge on inside compared to outside of membrane,

separation of charge, hydrogen ions pumped to the outside on the membrane, and on
the inside, negative ions are lined up, always negative on inside, positive on outside, this
is called an electrochemical gradient

What are the upsides and uses of membrane potential, downsides? - Uses - enhanced
permeability, ATP production, action potential (neurons)
Like an escalator, cell spends lots of energy to set up an environment which the stuff
they need can come in, instead of each individually. This enhances permeability.

What are the two types of bulk transport, and why are they needed? - Endocytosis
Exocytosis
They are used when a cell needs to transport larger materials

Endocytosis - when you bring something large in, takes some of the outer membrane to
make a vesicle

Exocytosis - secretory vesicle, pushing something out

Two types of endocytosis: - Pinocytosis - cellular drinking - bringing in small molecules

Phagocytosis - cellular eating - bringing in larger molecules?

Describe how ligands mediate endocytosis with receptors. - Ligand - molecule that
bonds to receptor, key that fits into the lock (receptor), and initiates endocytosis

What can the extracellular matrix communicate to other cells. - The ECM is like a
communication layer, on outside of cell, which tell other cells what type of cell it is, or
even used to connect two cells

Gap junction - protein which runs all the way through the phospholipid bilayer of two
cells so you can share stuff between the cells

Where do membrane components come from? - ER, Golgi

What primarily holds together membranes? - hydrophobic interactions

When would membrane proteins be immobile in the plasma membrane? - when they are
anchored to the cytoskeleton or ECM

How does cholesterol act as a buffer in plasma membranes? - In animal cells,

cholesterol (steroid) is packed in-between phospholipid molecules, and can be though of
as a fluidity buffer because at human body temps cholesterol makes the membrane less

fluid by restraining phospholipid movement, but cholesterol also hinders the close
packing of phospholipids and lowers the temp needed for the membrane to solidify
Membranes must be fluid to work properly

What two things are influenced by the state of fluidity of a membrane? - Permeability,
ability of membrane proteins to move to where their function is needed, also enzymatic
proteins in the membrane may become inactive if the membrane solidifies

What determines the function of a membrane? - the proteins embedded in it

What are the two main types of membrane proteins: - integral proteins and peripheral
proteins

Integral proteins are... - can go all the way through the membrane, or only partially
through the hydrophobic interior, most are transmembrane

Peripheral proteins are... - loosely bound to the surface of the membrane, not
embedded in it, they are often bound to exposed parts of integral proteins

How can cells recognize other cells? - by finding to molecules on the ECM

Selective permeability - allowing some substances to cross more easily than others

Amphipathic - having both a hydrophilic region and a hydrophobic region

Fluid mosaic model - mosaic of protein molecules bobbing in a fluid bilayer of

phospholipids

What has a hard time passing through a plasma membrane? - Hydrophilic ions and
polar molecules, as well as large molecules

What type of protein can help specific ions and a variety of polar molecules move
through the membrane? - Transport proteins which span the membrane

Carrier proteins - hold onto their passengers and change shape in a way which shuttles
them across the membrane

An aquaporin protein is what type of protein? - channel

Channel protein - a type of transport protein which has hydrophilic channels so certain
molecules or ions can pass through

Supramolecular structure - many molecules ordered into a higher level of organization

with emergent properties beyond those of the individual molecules (ex: plasma
membrane)

Simple rule of diffusion - n the absence of other forces, a substance will diffuse from
where it is more concentrated to where it is less concentrated
aka the substance will diffuse down its concentration gradient

A concentration gradient represents ____ ___ and drives ____. - PE, diffusion

If there is a higher concentration of non-permeable solutes in the environment surround

a cell, water will... - leave the cell

If there is a higher concentration of non-permeable solutes in the cell, water will... come into the cell

Lyse - burst

What is one evolutionary adaptation which helps paramecium in hypotonic

environments? - contractile vacuole

Turgor pressure - back pressure on a cell which opposes water uptake when the cell is
in a hypotonic solution

Hypertonic - more solute outside the cell

Hypotonic - less solute outside the cell

Isotonic - same amount of solute inside the cell as outside

Turgid - very firm (plant cells are kept turgid by a surrounding hypotonic environment)

Flaccid - when plant cells become limp because they are in an isotonic environment and
so there will be no net movement of water whereas plant cells like to be turgid, have lots
of water

Ion channels - channel proteins which transport ions

Gated channels - channels which open or close in response to stimulus

What is the only type of transport protein which moves solutes against their
concentration gradients? - carrier proteins

What does active transport allow a cell to do? - maintain internal concentrations of small
solutes which differ from concentrations in its environment, ATP is used to fuel this

How can ATP provide the energy for active transport to occur? - by transferring its third
phosphate group right onto the transport protein which can cause it to change chape in
a way which translocates a solute bound to the protein across the membrane

Example of a carrier protein that participates in active transport: - odium-potassium

pump which exchanges Na+ for K across the plasma membrane of animal cells

Voltage - electrical potential energy

Electrogenic pump - a transport protein which generates voltage across a membrane

What is the main electrogenic pump in animals? Plants, fungi, and bacteria? - The main
one in animal cells is the sodium potassum pump which pumps three sodium ions out of
the cell for every two potassium ions it pumps into the cell
The main electrogenic pump of plants, fungi, and bacteria is the proton pump which
actively transports protons (H+) ions to the outside of the cell

By generating voltage across a membrane, electrogenic pumps help... - store energy

which can be tapped into for cellular work

Co-transport - a transport protein can couple the "downhill" diffusion of the solute to the
"uphill" transport of a second substance against its own concentration gradient

Active transport - to pump a solute across a membrane against its gradient (requires:
cell must expend energy)

Membrane potential - the cytoplasmic side of the membrane is negative in charge and
the extracellular side is positive, because of unequial distribution of anions and cations
on the two sides which causes voltage across a membrane

Electrochemical gradient - membrane potential acts like a batter which affects the traffic
of all charges substances across the membrane, this traffic favors passive transport of
cations into the cell and anions out of the cell as a result of the charges on either side of
the membrane. As a result, the two forces which fuel diffusion of ions across a
membrane are chemical (the ion's concentration gradient), and electrical (the effect of
the membrane potential on the ions movement

What molecules generally cross the membrane in bulk? - large molecules like proteins,
polysaccharides, they are packaged in vesicles which required energy

Exocytosis description - Cell secretes certain molecules via the fusion of vesicles with
the plasma membrane
A transport vesicle which buds from the Golgi moves to the membrane, and when the
vesicle membrane and plasma membrane fuse, proteins rearrange the lipid molecules
of the two bilyers so the two membranes fuse
The contents of the vesicle are pushed out the the cell and the membrane of the vesicle
become part of the plasma membrane

Endocytosis description - - the cell takes in molecules via forming new vesicles from the
plasma membrane, the proteins are different from the exocytosis
Looks like the reversal of exocytosis
Small part of the plasma membrane sinks in to form a pocket and then it pinches off
inward making a vesicle

Do endocytosis and exocytosis increase or decrease the plasma membrane in a

dangerous amount? - Endocytosis and exocytosis occur all the time in eukaryotic cells
but the amount of plasma membrane remains constant, the addition of membrane from
one process counteracts the loss of membrane from the other process

Ligand - any molecule which binds to a receptor site on another molecule

Phagocytosis - cell engulfs a particle by extending pseudopodia around it and

packaging it within a membranous sac called a food vacuole, the particle is then
digested after the food vacuole fuses with a lysosome

Pinocytosis - cell continuously "gulps; droplets of extracellular fluid into vesicles formed
by infolding of the plasma membrane, it is nonspecific about the substances it
transports

Receptor-mediated endocytosis - Specialized type of pinocytosis which enables the ell

to acquire bulk quantities of specific substances, even though this substances might not
be very concentrated in the extracellular fluid. This occurs by receptor proteins
embedded in the plasma membrane have specific solutes bind to their sites, the
receptor proteins then cluster in coated pits and form a vesicle containing the bound
molecules
After the ingested material is let free from the vesicle, the emptied receptors are cycled
to the plasma membrane via the same vesicle

Chapter 8:
Metabolism - cellular respiration and photosynthesis, all chemical reactions which occur
in a living thing

What is metabolism coordinated by? - enzymes

Thermodynamics - how energy moves through a system

Bioenergetics - how living things use energy, a discipline within thermodynamics

Metabolic pathway - series of chemical reactions coordinated by enzymes, collections of

enzymes which coordinate a reaction

Why are enzymes necessary? - reactions don't often occur fast enough to support life

Catabolic pathway - decomposition, something that has organization and breaks apart,
releasing energy

Anabolic pathway - synthesis, something that doesn't have organization and combines,
requiring energy

Energy - the capacity to do work

KE - result of random movement of molecules

Dephosphorylation - taking a phosphate group off of a molecule

PE - energy because of location, could at any moment turn into KE

ex: bomb, sugar cube

Another name for PE is? - chemical energy

Which molecules have more potential energy: polar or non polar? Why? - Nonpolar
molecules have lots of PE because they share their electrons equally, whereas polar
molecules have less KE because not sharing equally so they don't have as much PE

1st law of thermodynamics - energy can never be created or destroyed, only change
forms or be transferred (KE or PE)

2nd law of thermodynamics - energy conversion results in energy loss in the form of
heat, energy transformation increases the entropy of the universe

Entropy - increasing randomness, ex: diffusion, matter wants to spread out, living things
don't organize, occurs spontaneously

Enthalpy - how much energy is in a system

Catabolic reactions occur ___. - spontaneously

Anabolic reactions ____ spontaneously. - do not

Free energy equation - tells us whether a reaction is decomposition or synthesis

H - TS = G

Energy coupling - living things perform energy coupling to fuel endergonic reactions
Fueling endergonic reactions by use of exergonic reactions
Using the energy given off from a decomposition reaction to drive a synthesis reaction

What is an example of energy coupling? - ATP breaking down to fuel other reactions

Enzyme - type of protein which speeds up a specific metabolic reaction by lowering the
energy barrier

Why must a little energy be invested to start an exergonic reaction? - when particles are
going to break up they go through a transition stage where they are unstable and have
more energy than normal

Activation energy - the amount of energy needed to break the energy barrier

Energy barrier - the amount of energy needed to be overcome

Substrate - reactants in chemical reaction which bind to enzyme to get changed into
products

Active site - location on enzyme where reaction takes place, where the substrates bind
to

What reacts when the two substrates are pushed together while in an enzyme? - the R
groups of the reactants are pushed together so they interact

Describe induced fit and its relevance to enzymes. - enzyme claps down on reactants,
and changes shape a bit to do so as the reaction takes place, because the products are
different shapes than the reactants

Enzyme substrate complex - enzyme+substrate

Enzymes are specific to ___ conditions - pH, else they denature

Cofactors
Give examples - nonprotein enzyme helpers which can be permanent or temporary
Ex: minerals zinc iron, copper

Coenzymes - Organic cofactors, most are vitamins

Enzyme inhibitors - molecules which can turn off enzymes

Two types of enzyme inhibition: - competitive and noncompetitive

Competitive inhibition - will bond with enzyme but not react with it, to turn it off, called
competitive because it competes for the active site with the reactant that is trying to
bond to the enzyme

Noncompetitive (alosteric enzyme) - does the same thing but doesn't bond to the active
site, bonds to a different site (alosteric site), and turns it off by changing the shape of the
enzyme

Regulation of enzyme activity in regards to ATP - If ATP accumulates, ATP will bond to
enzymes to change their shape and turn them off to stop them from making ATP
However, if you are using that ATP, there is an accumulation of ADP, then they will bind
to the enzyme and keep it going
That enzyme is called an allosteric enzyme, has quaternary structure, multiple active
sites, activity dependent on substrates

Feedback inhibition - when the product of a metabolic pathway accumulates and turns
that pathway off
ex: AC

Energy is in a constant swing between what and what? - KE and PE

When talking about thermodynamics, the word systems is used to denote what? - the
matter under study

When talking about thermodynamics, what do scientists used to denote everything

except the matter under study? - the surroundings

What can an isolated system exchange with the environment? - neither matter or energy

What can an open system exchange with its surroundings? - both matter and energy

Are organisms open or isolated systems? - ...

What is the principle of the conservation of energy aka? - the first law of
thermodynamics

What happens as energy performs work? - some is released as heat and can no longer
do work

When can a system put thermal energy to work? - A system can only put thermal energy
to work when there is a temp diff which results in thermal energy flowing as heat from a
warmer location to a cooler one

What is the consequence of the loss of usable energy as heat is released during each
reaction? - The consequence of the loss of usable energy as heat to the surroundings is
that each energy transfer or transformation makes the universe more disordered, the
measurement of this is entropy

When is a process energetically favorable? - process is energetically favorable or

spontaneous if it leads to an increase in entropy, or can proceed without requiring an
input of energy

When is a process not energetically favorable? - A process which leds to a decrease in

entropy is said to be non spontaneous and will only happen if energy is supplied

Describe entropy in relation to:

The universe
Organisms
Reactions - The universe tends toward disorder, but organisms are local spots of low
entropy, whenever we complete our catabolic processes, like breaking down glucose, or
moving which breaks apart ATP, we release energy in the form of heat making the
universe more disorderly.

Metabolism - the totality of an organism's chemical reactions

Metabolic pathway - begins with specific molecule which is then altered in a series of
defined steps resulting in a certain product

Catabolic pathway - the digressive processes, pathways

Anabolic pathway - they consume energy to build complicated molecules from simpler
ones, aka biosynthetic pathways

Bioenergetics - the study of how energy flows through living organisms

Energy - the capacity to cause change

KE - energy in motion

Thermal energy - KE associated with the random movement of atoms or molecules

Heat - thermal energy in transfer from one substance to another

PE - energy associated with location or structure

Chemical energy - PE available for release in a chemical reaction

Thermodynamics - the study of the energy transformations that occur in a collection of

matter

1st law of thermodynamics - energy of the universe is constant:energy can be

transferred and transformed, but it can't be created or destroyed

2nd law of thermodynamics - every energy transfer or transformation increases the

entropy of the universe

Spontaneous process - if a given process leads to an increase in entropy it can process

without an input of energy, doesn't have to occur quickly, but instead it is energetically
favorable

Entropy - a measure of disorder

What is free energy in relation to usefulness? - Free energy is usable energy, energy
that has not been let off or transformed into thermal energy

What is the free energy equation? Identify variables. - change in free energy = change
in enthalpy - temperature(K(C+273)) times change in entropy
delta G = delta H-T(delta S)

What is the delta G for processes that are spontaneous? - negative

What is the delta G for processes that are not spontaneous? - positive

What is another way to think of delta G? - Another way to think of it is that delta G = G
final state - G initial state
So delta G can only be negative when the process involves a loss of free energy during
the change from initial state to final state
We can also think of free energy as a measure of a system's instability - its tendency to
change to a more stable state

Equilibrium - a state of maximum stability

What are unstable systems (high G) likely to do? - change in a way which makes them
more stable (low G)

As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants
and products what? - decreases

When is delta G at its lowest in a system? - when the system is at equilibrium

When can a process be spontaneous and perform work? - when it is moving toward
equilibrium

Describe a cell at equilibrium. - Because systems at equilibrium are at a minimum of G

and can do no work, a cell that has reached equilibrium is dead. One of the defining
features of life is that metabolism as a whole is never at equilibrium

What is the key to keeping a cell out of equilibrium? - The key to keeping the cell at
equilibrium is not letting the product of a reaction accumulate, but instead making it the
reactant in the next step of the system, this and the constant flow of materials in and out
of the cell from reaching equilibrium.

Free energy - the portion of a system's energy that can perform work when temperature
and pressure are uniform throughout the system (ex: living cell)

Enthalpy - total energy

Exergonic reaction - proceeds with a net release of free energy because the chemical
mixture loses free energy G decreases negative delta G

Endergonic reaction - one that absorbs free energy from its surroundings because
essentially stores free energy in molecules, G increases, positive delta G

What are the three main kinds of work that a cell completes? - chemical, transport,
mechanical

Chemical work in a cell - completing endergonic reactions

Transport work in a cell - pumping substances across membranes against the direction
of spontaneous movement

Mechanical work in a cell - ex: beating of cilia

How can the bonds between the phosphate groups of ATP be broken down? - through
hydrolysis

What does hydrolysis involve in the breakdown of ATP? - Water being added to the last
phosphate, which breaks it off and releases energy

What the the release of energy from the hydrolysis of ATP come from? Why is it so
powerful? - The release of energy during the hydrolysis of ATP comes from the chemical
change of the system to a state of lower energy because the reactants ATP and water
have much more energy than the products ADP and P
This change in energy is so strong because all three of the phosphate groups are
negatively charged, so the energy is equivalent to a coiled spring.

What does energy coupling normally involve? Why? What type of work is this that ATP
is helping complete for the cell? - The coupling of the ATP>ADP reaction's exergonic
nature with an endergonic one is a phosphorylated intermediate because that molecule
than becomes less stable than the original unphosphorylated molecule
This is the chemical work that ATP can help complete.

How does ATP help with transport work in the cell? - For transport and mechanical, ATP
hydrolysis can lead to a change in the protein's shape and, many times, its ability to
bond to another molecule, sometimes via phosphorylated intermediate

How does ATP help with mechanical work in a cell? Describe in detail. - Most of the
time, mechanical work involves motor proteins "walking" along cytoskweletal elements
This occurs first by an ATP being bonded noncovalently to the motor protein, the ATP is
then hydrolyzed, releasing ADP and P. Another ATP molecule can then bind, at each
step, the protein changes shape and ability to bind to the cytoskeleton, causing
movement of the protein along the cytoskeleton
Phosphorylation and dephospho rylation promote crucial protein shape changes during
many other important cellular processes as well

How is ATP recharged? - ATP is renewable, just add the phosphate back onto the used
ADP, the free energy needed to phosphorylate the ADP comes from the exergonic
reactions (catabolism)

What is the shuttling of inorganic phosphate and energy called in relation to the ATP
regeneration? - the ATP cycle
This happes at a veryfast fate, for a muscle cell, it is about 10 million molecules of ATP
consumed and regretted per second per cell

Energy coupling - the use of an exergonic process to drive an endergonic one, ATP is
responsible for mediating most energy coupling, acts as immediate source of energy for
cellular work

ATP - contains sugar ribose with nitrogenous base adenine and a chain of three
phosphate functional groups

Phosphorylation - the transfer of a phosphate group from ATP some other molecule
such as the reactant

Phosphorylated intermediate - the molecules that receives the phosphate group

(covalently bonded to it) from the ATP

What is an enzyme? What are the two main types? - An enzyme is a macromolecule
which acts as a catalyst, a chemic againt which speeds up a reaction without being
consumed by the reaction.
Enzymes can be proteins or ribozymes. For now, we will talk about the protein ones

What does every chemical reaction involve in relation to bonds? - bond breaking and
bond forming

When you change one molecule into another what does it normally involve? How does
this occur? - When you change one molecule into another it normally involves contorting
the starting molecule into a very unstable state prior to the reaction proceeding To reach
this state where bonds can change, reactant molecule absorb energy from their
surroundings, and when the new bonds of the product molecules form, energy is
released as heat, and the molecules return to stable shapes with lower energy than the
contorted state.

What is the initial investment of energy for starting a reaction called? - The initial
investment of energy for starting a reaction, the energy needed to cconort the reactant
molecules so the bonds can break is called the free energy of activation or the activation
energy

How is the initial investment of energy needed to start a reaction often supplied? Where
does it come from? - This energy is often supplied by heat in the form of thermal energy
and the reactant molecules absorb that from the surroundings

When molecules have absorbed enough energy for their bonds to break and new ones
to form, they are in an unstable condition referred to as what? - the transition state

Why are enzymes needed to speed up reactions? Why can't we use heat instead? - In
most cases the activation energy is so high that the reaction will hardly proceed at all
How Enzymes Speed Up Reactions
If we were to just us heat to speed up the reacion, proteins would denature, cells would
die, etc. Instead an enzyme catalyzed a areaction by lowering the activation energy
barrier, letting the reactant molecules absorb enough energy to reach the transition state
even at moderate temperatures
Enzymes are very specific for the reactions they catalyze, so they can help determine
which chemical processes will be going on in the cell at any given time

What do most enzyme names end in? - ase

Describe the specificity of enzymes, and the why? - The specificity of an enzyme is a
result of the three dimensional shape of proteins the active site provides a place where
the specific shape of the substrate/s can fit into and nothing elseThe enzyme nor its
active site are rigid in shape, but change slightly between different forms throughout a
reaction

Describe induced fit. - when the substrate first binds to the enzyme, the enzyme
changes shape slightly because of te reactions between the R groups on the substrate
and on the active site reacting to make the enzyme fit a little snugger around that
specific molecule
This is called induced fit and brings the chemical groups of the active site into positions
which enhance their ability to catalyze the chemical reaction

How are substrates held to the active site of most enzymes? - In most enzymatic
reactions, the substrate is held to the active site by weak interactions like hydrogen and
ionic bonds,

The process is so quick that an enzyme can process about a thousand (sometimes
more) substrate molecules per secondEnzymes act in the direction of equilibrium of a
reaction catalyzing both forward and reverse reactions

What are the four main ways that enzymes lower activation energy and speed up a
reaction? - When there are two or more reactants, the active site provides a template on
which the substrates can come together in the proper orientation for a reaction to occur
between them
As the active site of an enzyme clutches the bound substrates, the enzyme may
stretchh the substrate molecules toward their transition state form, stressing and
bending critical bonds which must be broken during the reaction, and because the
activation energy is proportional to the difficult of breaking the bonds, distorting the
substrate helps it approach the transition state and thus reduces the amount of free
energy which must be absorbed to achieve that state
The active site may also provide a microenvironment which is more conducive to a
particular type of reaction than the solution itself would be without the enzyme. For
example, it the active siee has amino acids with acidic R groups, the active site may be
a pocket of low pH in an otherwise neutral cell. In such cases, an acidic amino acid may
facilitate H{ transfer to the substrate as a key step in catalyzing the reaction
Amino acids in the active site directly participate in the chemical reaction. Sometimes
this process even involves rief covalent bonding between the substrate and the chain of
tamino acid of the enzyme. Subsequent steps of the reaction restore the side chains to
their original states, so that the active site is the same after the reaction as it was before.

At what point can a reaction not be sped up any more by adding substrate to an area
with enzymes? How can this be overcome? - There is a point at which a reaction can
not be sped up any more by adding substrate to an area with enzymes because the
active site ofevery enzyme is booked up, and cells make more enzymes to keep the
reaction going ata a faster rate
Enzymes are also sensitive to temperature, pH, and chemicals so the rate of an
enzymatic reaction increases with temperature only until a certain temp and then the
enzyme won't work properly

Describe the general idea of enzyme inhibitors. Include both reversible and
nonreversible inhibitors, as well as an example of each. - Some enzyme inhibitors bond
covalently to the enzyme and stops its ability to react and the damage is normally
irreversible, but there are ones which bind to enzymes via weak interactions which are
reversible: competitive and noncompetitive inhibitors.
Ex of irreversible:
Most toxins and poisons
ex: sarin gas which bonds to the R groups on the amino acidterase covalently which is a
major factor in the nervous system
Penicillin blocks the active site of an enzyme which many bacteria use to make their cell
walls

Describe evolution of enzymes in terms of mutations. - mutation - permanent change in

a gene, which can occur by a change in the number or order of amino acids in proteins,
if this change occurred in the active site of an enzyme it would change the enzyme
Natural selection would tend to favor the mutated form of the enzyme if it better suited
an organism

Enzyme - macromolecule which acts as a catalyst

Catalyst - chemical agent which speeds up without being consumed by the reaction

Activation energy - the initial investment of energy for starting a reaction, the energy
required to contort the reactant molecules so the bonds can break, EA, the amount of
energy needed to push the reactants to the top of an energy barrier

Substrate - the reactant of an enzyme

Enzyme substrate complex - when the enzyme bonds to its substrate or substrates

Active Site - the region on the enzyme where the substrate can bond to where catalysis
occurs, formed by only a few of the enzyme's amino acids, the rest of the proteins
determine the shape of the enzyme

Induced fit - binding between enzyme and substrate becoming tighter after initial
contact, brings chemical groups on active sites into positions which enhance their ability
to catalyze the chemical reaction

Cofactors - nonprotein helpers for the catalytic activity of enzymes, may be bound to the
enzyme as a permanent resident, or may bind loosely and reversibly like the substrate,
some are inorganic like zinc iron, copper, in ionic form

Coenzyme - if the cofactor is an organic molecule it is more specifically referred to as a

coenzyme

Competitive inhibitors - some reversible inhibits resemble the substrate molecule and
compete for the active site, they reduce the productivity of enzymes by blocking
substrates from entering active sites, can be over come though by increasing the
concentration of substrate because then more active sites become open than there are
inhibitors to block

Noncompetitive inhibitors - don't directly compete with the substrate to bed to the active
site, instead the bond to another part of the enzyme which causes the enzyme molecule
to change its shape

Allosteric regulation of enzymes involves a molecule binding to what type of site on an

enzyme? - an allosteric site

How do activators of regulatory sites (allosteric) on enzymes affect the enzymes?

Inhibitors? - The activator of a regulatory site stabilizes the shape of the enzyme which

encourages the shape which has functional active sites, whereas the binding of an
inhibitor stabilizes the inactive form of the enzyme
The subunits of an allosteric enzyme fit together in such a way that a shape change in
one subunit is transmitted to all others
Ex: ATP and ADP regulating enzymes

What is another kind of allosteric regulation which involves a substrate molecule binding
to n active site of a multisubunit enzyme? How does this effect the shape of the subunits
in the enzymes? What is this type of allosteric regulation also known as?Why is it still
considered allosteric regulation? - In a different kind of allsteric activation, a asustrate
molecule binding to one active site a multisubunit enzyme triggers a shape change in all
the other subunits, thereby increasing the catalytic activity at the other sites
This is called cooperatively, this amplifies the response of enzymes to substrates
This is considered allosteric regulation because binding of the substrate to one active
site affects catalysis in another active site

Describe a multi enzyme complex and its relation to a metabolic pathway. - Cell is
compartmentalized and cellular structures help bring order to metabolic pathways, in
some cases, a team of enzymes for several steps of a metabolic pathway are
assembled into a multi enzyme complex which facilitates the sequence of reactions with
the product of one enzyme coming the reactant for the next

Cellular respiration - the major catabolic pathway which breaks down organic molecules,
releasing energy that an be used for the crucial processes of life

Allosteric regulation - any case in which a protein's function at one site is affected by the
binding of a regulatory molecule to a separate site, may result in inhabitation or
stimulation of an enzyme's activities

Cooperativity - amplifies the response of enzymes to substrates: one substrate primes

an enzyme to act on additional substrate molecules more readily, also considered
allosteric regulation - the affinity for oxygen of the remaining binding sites

Feedback inhibition - a metabolic pathway is inhibited by its end product by binding to

an enzyme which comes into play early in the metabolic pathway

Chapter 9:
How does energy enter the food chain? - through photosynthesis

Catabolic pathways yield... - energy

Catabolism+Anabolism = - metabolism

Equation for cellular respiration: - C6H12O6 + O2 --> CO2 +H2O + En

Example of a reduction oxidation reaction (redox): - Na + Cl > Na+ + Cl-

Redox reactions focus on... - where electrons are going

Reduction - when you gain an electron

Oxidation - when you lose an electron

OIL RIG - oxidation is losing, reduction is gaining

How is energy released at controlled intervals during cellular respiration? - via enzymes

What are the three stages of cellular respiration? - 1. Glycolysis

2. CAC
3. Oxidative phosphorylation

Two parts to glycolysis: - Investment phase

Payoff phase

What does enzyme one do in glycolysis? - takes a phosphate from ann ATP and tacks it
onto the glucose

What does the second enzyme do in glycolysis? - Rearranges the inner ring structure of
glucose

What does the third enzyme do in glycolysis? - takes another phosphate from ATP and
tacks it onto the changed glucose

What do the fourth and fifth enzymes do in glycolysis? - They break the glucose
molecule in half

What is the gist of the investment phase of glycolysis? How many ATP were used per
glucose molecule? - Took one glucose and two ATPs, took 1 phosphate from each ATP,
you added them to the glucose, and then we broke it in half
We used two ATP per one glucose molecule

Payoff phase occurs how many times per one investment phase? - twice

NAD - electron shuttle

NADH indicates what? - harvest of electrons

Substrate level phosphorylation - when an enzyme within glycolysis or CAC makes ATP
on their own

What does enzyme 6 in the payoff phase of glycolysis do? - takes NAD+ and makes
NADH

What do enzymes 7 and 10 do in the payoff phase of glycolysis? - They take the
substrate ADP and phosphorylate it to produce ATP (substrate level phosphorylation)

How does glycolysis harvest chemical energy? - By oxidizing glucose to pyruvate

Where does glycolysis occur? - In the cytoplasm, outside the mitochondria

Is glycolysis aerobic or anaerobic? - anaerobic, does not need oxygen gas

The CAC completes the energy yielding of the organic molecule which comes out of
____. - glycolysis

What is the first step of the CAC? - Coenzyme a is tacked onto pyruvate to get it
"through the door"

The CAC can be thought of as what? Why? - Pyruvate gets on the ferris wheel ride, and
gets completely dismembered afterward. Gory ferris wheel.

What is the second step in the CAC? - pyruvate is attached to oxaloacetate to make
citrate

What is the third step in the CAC? - enxyme 3 breaks off CO2 and harvests electrons

What is the fourth step in the CAC? - the fourth enzyme harvests more electrons and
breaks off more CO2

What is the fifth step in the CAC? - the fifth enzyme makes ATP via substrate level
phosphorylation

What is the sixth step in the CAC? - enzyme 6 harvests more electrons: FAD goes to
FADH3

What is the seventh step in the CAC? - water is taken in

What is the eight step in the CAC? - enzyme 8 harvests electrons and there is nothing
left of pyruvate

What is the gist of the CAC? - Essentially you are starting out with pyruvate, then you
are pulling off CO2 which has no potential energy and keeping the hydrogens with
electrons that do.

Where does the CAC occur? - In the interior of the mitochondria, the matrix

Is the CAC aerobic or anaerobic? - CAC is indirectly aerobic. It itself doesn't use oxygen
gas, but if the mitochondria it is in does not get the oxygen gas, it is shut down.

What two processes comprise oxidative phosphorylation? - chemiosmosis and the ETC

ATP synthase is an ___ not a ______ in the ETC. - enzyme, protein

Chemiosmosis - the diffusion of hydrogen from a high concentration to low

concentration through a semi-permeable membrane

Where does the ETC in oxidative phosphorylation take the electrons? - They start on the
inner of the innermembrane, then move to the outer of the inner membrane

What makes up the ETC? - the cytochrome proteins

Where does cellular respiration occur in a prokaryote? - in accessory membranes,

membranes which accompany the outer membrane, respiratory membrane

In the context of metabolism, what does respiration refer to? - the use of an ETC

What do fermentation and anaerobic respiration enable cells to do? - produce ATP w/o
oxygen

What is the gist of fermentation? - glycolysis with a few extra steps to make ATP, but it
only produces 10% of the ATP

Yeast - unicellular fungi

How is ATP produced in fermentation? - substrate level phosphorylation, the electrons

are harvested but then not used

What happens to electrons after fermentation - pyruvate is used as an electron dumping

ground because NAD+ is needed for glycolysis to occur

Why does fermentation occur? - Where there is no oxygen, the mitochondria shuts
down, so the only ATP producing process which can operate is glycolysis

What are the two types of fermentation? - Ethanol fermentation

Lactic acid fermentation

When does fermentation occur? - When an ETC is not present or available

Equation for anaerobic respiration: - CH4 +SO4^2- --> HCO3- + HS- + H2O

What is used in anaerobic respiration to attract electrons in the ETC? - SO4

What is used as the fuel in anaerobic respiration? - CH4

What is used in aerobic respiration to attract electrons in the ETC? - O2 H2O

Describe how methane crystals can fuel anaerobic respiration in organisms living near
the sea floor. - bubble of methane over top of oil, can seep up through sea bed make
methane ice crystals, methane hydrates, and sulfate reducing marine bacteria use that
and sulfate to fuel cellular respiration

What two organisms don't need oxygen to fuel their respiration? - Obligate anaerobes
Facultative anaerobes

Obligate anaerobes - need to be in a place absent of oxygen, respire anaerobically or

ferment, because the oxygen is more electronegative than the sulfate so disrupt their
ETC

Facultative anaerobes - aerobically respires in the presence of oxygen, ferments in the

absence of oxygen, bacteria, fungi/yeasts, polychaete worms, can live on fermentation
alone, can burrow deep in sand where decomposition occurring and taking up all
oxygen to escape predators

Chapter 10:
What indicates a chloroplast as opposed to a mitochondria? - PS proteins

Equation for photosynthesis: - CO2 + H2O + En --> C6H12O6 + O2

Autotrophs - can fix their own food

Heterotrophs - organisms which are dependent on autotroph energy

Photosynthesis converts... - light energy to chemical energy of food

Photoautotrophs - organisms which can get their energy from an inorganic source of
energy

Examples of photoautotrophs: - algae, unicellular protist, cyanobateria, most

photosynthetic organisms are found in the ocean

In the example of a tree, identify the photosynthetic organ, and zoom in, providing
description along the way. - Photosynthesis organ: leaf
Epidermis cells, little breaks in the skin cells for a guard cell, which makes a stomata,
inside the skin are mesophyll tissue which are jam-packed with chloroplasts (the
photosynthetic organelle), inside the chloroplasts are thylakoids, the stacks of green
coins, a stack of them is the granum, the fluid the coins are in is the stoma, on the
surface of the thylakoid coins is the chlorophyll which gives it the green color

Where does photosynthesis occur in algae, unicellular photosynthetic eukaryotes, and

prokaryotes? - accessory membranes which contain chloroplasts, but there is no
organelle

What are the two parts of photosynthesis? - The light reaction and the calvin cycle

What is the electron carrier in photosynthesis? How does it compare to the electron
carrier in cellular respiration? - NADP, there is an extra phosphate group

In photosynthesis, what type of phosphorylation occurs? - photosynthesis

What is the wavelength range for visible light? - 400 nm to 750 nm

What colors have the highest energy, lowest? - ROYGBIV is an an acronym going from
right to left in the visible light wavelength spectrum from lowest energy to highest based
on the length of the waves

What is the link between the sun's energy and cellular energy? - Chlorophyll

Pigments - indicate what color a substance does not absorb

Chlorophyll reflects and transmits ___ and absorbs ____. - green, everything else

Photosynthesis uses pigments to capture electromagnetic radiation. What are the

pigments? - Chlorophyll (a,b)
Carotenoids

What waves does chlorophyll a allow plants to take advantage of? - the BIV waves,
because it has a R-CH3 (methane) group

What waves does chlorophyll b allow plants to take advantage of? - light blues and
greens because it has CHO

What waves do carotenoids allow plants to take advantage of? - blue, indigo, dark green

Why don't plants normally absorb yellow or light green wavelengthed light? - The sun
produces more yellow and green visible light than any others, so it does not absorb
these really as a means of protection

Chlorophyll excitation
What color is chlorophyll in the light and outside of the light? - electron on chlorophyll
molecule gets excited and moves to a higher energy state, the difference in energy is
released as red light, because it is the weakest light that is released
red under light, green outside of light

The ETC in photosynthesis takes electrons from where to where? - the outface of the
membrane to the interface of the membrane (the thylakoid membrane)

Where does the calvin cycle occur? - in the stroma

Cyclic electron flow - when we pass electrons in a cycle instead of linear electron flow
(like the ETC)
Cyclic electron glow instead uses the same electrons over and over again

How does cyclic electron flow work? - instead of passing the electrons from the NADP+
reductase to the calvin cycle, it is put back into the beginning of the chain with PS II, this
produces ATP, but does not use lots of H2O, and so doesn't release lots of O2

What is the gist of cyclic electron flow? - For cyclic electron flow you're just using light
reactions to produce ATP through photophosphorylation

What part of photosynthesis fixed carbon? - the calvin cycle

What are the three phases of the calvin cycle? - Fixation

Reduction
Regeneration

Every time 3 CO2s go around the calvin cycle, we get __ glucose. What is this molecule
called? - 1/2, G3P

Photorespiration - When the calvin cycle uses oxygen in place of CO2

When the CO2 is used up, the oxygen waste product builds up, and rubisco has an
affinity for oxygen, so it will keep the cycle running, using ATP, and electrons but not
producing the sugar

What are the main plants which have developed photosynthetic/metabolic adaptations
which protect them against photorespiration? - C3 plants
C4 plants
CAM plants

Where do C3 plants grow best - in temperate region

What happens to a C3 plant if it gets too dry? - the plant can't get electrons

What happens to a C3 plant if it gets too hot? - Its stomata closes to conserve water so
oxygen and CO2 can't come in to fuel the calvin cycle

What is in C3 plants? - mesophyll tissue

Where do C4 plants get their name? - their first wast product is a four carbon sugar

What are the two types of cells in C4 plants? - there are mesophyll cells on the outside,
and bundle sheath cells surrounding the vascular tissue

Explain how mesophyll tissues help the C4 plants. - Mesophyll tissues don't have
rubisco so there is no calvin cycle so photorespiration can't occur
instead you have PEP which will take CO2 and combine it to Oxaloacetate (4 carbon
product) and reduce it to Malate which is then transported into the bundle sheath cells,
but they are protected from the atmosphere so no oxygen gas can get in so no
photorespiration

How do C4 plants work? - C4 plants separate the atmospheric uptake gases from the
calvin cycle by performing each in different cell types

C4 plants use two different cells in order to separate the atmospheric uptake of gases,
uptake of gasses in mesophyll and calvin in the bundle sheath, protecting the calvin
cycle from oxygen

How do CAM plants work? - separate the atmospheric uptake of gases from the Calvin
cycle by performing each at different times of the day
By separating gas uptake in one part of the day and the calvin cycle in another part of
the day, as apposed to two different types of cells
Close stomata during the day - otherwise lose water, uses CO2 stored from night to fuel
light reactions, malate stores the CO2, all energy of plant stored in form of starch, then
the plant taps into its starch to use that energy to fuel reactions to store the CO2
At night you have the atmospheric uptake of CO2 and storage, and during the day there
is no atmospheric uptake of gases and you convert that storage in CO2

Contrast C4 plants and CAM plants. - C4 plants protect themselves from

photorespiration by place, (having two different types of cells)
CAM plants protect themselves by time:
Open stomata at night - pulls CO2 all night long
Convert CO2 into organic acids in the mesophyll cells
Organic acids are stored in vacuoles which are later pulled out to be used

Chapter 16:
Gregor Mendel - Heritable factors

What did Mendel show? What did he not know? - organisms pass traits and information
along from one generation to another, did not know this was because of chromosomes
or DNA though

Thomas Hunt Morgan - genes on chromosomes

Mendel's genetic units were found on chromosomes in the nucleus of the cell

What did Morgan not know? - that the chromosomes were made of DNA

What is a nucleotide composed of? - nucleoside + phosphate

Phosphodiester bonds - covalent bonds which connect nucleic acids

Cells arise from... - pre-existing cells

What is each individual side of a DNA strand called? - polynucleotide

How are polynucleotides arranged in a DNA strand? (hint: think direction) - antiparallel
arrangement

In science terms, the arrangement is either 5' > 3' or 3' > 5', read 5 prime to three
prime or three prime to five prime

Chromosome - individual DNA molecule

depending on what species you are, you have a diff number in each cell

What are chromosomes made of? - Chromatin

What is chromatin made of? - DNA and protein

DNA + protein - chromatin

What is each individual strand consisting of DNA and protein called? - chromosome

How is the protein in chromatin made? - DNA

Pathogenic - causes illness or disease

What did Griffith show? - Griffith in 1920s was med student, and found that are diff
strains of pneumonia bacteria
The form that makes people sick was called the smooth form which has a capsule
around it
Whereas the rough form of pneumonia did not kill the mouse because does not have
capsule
when he put the smooth above a flame, and injected it into a mouse, it did not kill the
mouse
If is mixed the dead deadly with the like rough, it still killed the mouse because the cells
were able to pass on information
So he showed that dead bacteria was able to pass on DNA to live bacteria
Griffiths experiment showed that some sort of genetic information was being passed
from one bacteria to another bacteria

What are viruses capable of producing, what must they gain from others? - Only
capable of synthesizing proteins and nucleic acids, it might have carbohydrates and
lipids but can't make it themselves

Bacteriophage - virus that uses a bacteria cell as a host

Describe how a virus takes over a host cell. - In the example of a bacteriophage:
The virus lands on the bacteria, injects it with DNA, and makes the bacteria cell use that
DNA to make more viruses, and then when many are made, the cell explodes and the
viruses are let off to go attack some other cell
What are the two types of isotopes? - radioactive and stable
What does a radioactive isotope tend to do? - decay into another element

Describe the Hershey and Chase experiment. - These guys cultured two isotopes of
bacteria phage, one in radioactive sulfur, and others in radioactive phosphorous
DNA became radioactive in the radioactive phosphorous, and the proteins became
radioactive in the sulfur
This showed which molecule (DNA or protein) was the genetic information
Because the radioactive phosphorous in the DNA was injected into the bacteria by the
viruses, and we already knew that viruses inject DNA into the host cell, but the DNA is
reactive in the ones which were bathed in the radioactive phosphorous, whereas if DNA
was made of proteins were would have found radioactive sulfur in the cell (proteins)
This was the first link, but scientists didn't know that much so they thought that maybe
there was exception for viruses

Chargoff's Rule - the amount of A is going to equal the amount of T and the amount of G
is going to equal the amount of C
A = T, C = G

Why is Chargoff's Rule so? - complementary base pairing

Explain the historical timeline of DNA studies. - Mendel showed us that organisms pass
on traits through "heritable units." In the 50s we knew that genetics existed, Mogan
showed it was on chromosomes, Hershey and Chase showed that DNA was the genetic
code, and Chargoff showed complementary base pairing
Watson and Crick, Wilkens and Franklin showed us the composition and pairing of DNA
How did Rosland Franklin derive the shape of DNA? - X-ray chrystallography
How does the width of a DNA double helix remain constant? - Helices have a uniform
diameter
Every complementary base pair is a connection between a purine and a pyridine so the
width of the double helix is consistent
What is DNA replication analogous to? (hint: think recipes) - DNA Replication: taking a
recipe and making a photocopy, not taking a recipe and cooking the food
What were the two main models for DNA replication? - conservative and semiconservative

Describe the conservative DNA replication model. - we pull a strand apart and then
replicate the split parts
then connect the replicated parts, and the other parent strands back together
Describe the semi-conservative DNA replication model. - pull a strand apart and then
replicate the split parts
Describe the Mendelson and Stahl experiment. - They took E.Coli and:
The first generation had heavy nitrogen, then the second generation put in lighter
nitrogen had lighter DNA, this showed that instead of the conservative model where
there would be a new strand with light and the parent would stay heavy
However, there was a mix of heavy and light nitrogen inside it because in the tsest tube
that they centrifuged the bacteria in, and if it were the conservative model, there would
be the heay nitrogen DNA strand (parent) at the bottom and the lighter nitrogen at the
top, but instead it was somwhere in the middle
What does semi-conservative replication mean? Is there such a thing as conservative
replication? - Semi conservative replication means that all replication is going to make
have new and keep half old
No
What shape is bacteria's DNA in? - ring
What shape is eukaryote DNA in? - linear form
How do bacteria replicate? How is that different from us? - When bacteria replicate, an
area opens up in the ring where the two sides are separate, called replication forks ( 1
origin of replication)
In our replication, we open up many different replication forks, which fom bubbles
(multiple origins of replication
What hold base pairs together? - hydrogen bonds
What holds nucleotides together? - phosphodiester bonds
What does helicase do in DNA replication? - unzips the double helix
What bonds does helicase break? - the hydrogen bonds between complementary base
pairs
What do three prime and five prime refer to? - which carbon the base pairs are attached
to
What are the two functions that topoisomerase completes in DNA replication? - 1.
Topoisomerase cuts the double helix, lets it unwind, then connects it back to the double
helix, like the twisted rope

2. prevents binding
What do single stranded binding proteins do in DNA replication? - The single stranded
binding proteins keep the bubble open, they negate the weak binding proerties the base
pairs experience
Primase - lays down primers of RNA 3' nucleotides for DNA polymerase III to connect to
to form the lagging strand
What does DNA polymerase III need to start laying down base pairs? - an exposed
three prime carbon
DNA polymerase III - synthesizes the leading and lagging strands
DNA polymerase I - replaces RNA primers with DNA nucleotides in the lagging strand
Ligase - Then ligase connects the strands that the DNA polymerase I and the DNA
polymerase III synthesized
Okazaki fragment - one primer + one new piece of DNA
How are lagging strands laid down (direction wise)? - Each piece is laid down in the
opposite direction to the overall strand, whereas the leading strand is made in the
direction of the overall construction of the strand
What are the steps of DNA replication? - Helicase unzips
Topoisomerase prevents binding
primase lays the primers at top and bottom
DNA polymerase III lays leading strands
Primase lays down primers for lagging strands
DNA polymerase III lays down strands to connect the primers in lagging strand
DNA polymerase I removes the primers and replaces with DNA strands
Ligase binds the strands between the DNA polymerase I and III strands to form the
lagging strands
All of the replication bubble strands run into eachother, or the DNA ring for bacteria
Telomere - sacrificial sequence at both ends of the sequence : TTAGGG, because at the
ends are 5' so none of the DNA polymerases can lay down more nucleotides
Every time a DNA strand is replicated we lose the ends, we have telomere there instead
Telomerase - enzymes to lengthen telomere
Nuclease - enzyme that goes through to see that we have the complementary base
pairing, no mistakes
We make a mistake about 1 in every 100,000 base pairs laid
What is the protein in a chromosome called? - histone
Nucleosome - eight histones together

Histone proteins do what? - Help organize and loop and pack DNA into organized
structures which are called condensed chromatin
After Morgan's group showed that genes exist as parts of chromosomes, what were the
two proposals that chromosomes were composed of? - protein and dna
Why were proteins considered for the composition of DNA? - they were known to have
great variety, and specificity of function
Why were nucleic acids not highly considered for the composition of DNA? - not well
known, their chemical properties seemed too uniform to account for the multitude of
specific inherited traits that genes express
What two findings became known as Chargaff's Rules? - - The base composition of
DNA varies between species
- But, in any species the number of A and T bases are equal and the number of G and
C bases are equal
The bass for these rules was not understood until the discover of the double helix.
What extends at the 5' end of DNA? - phosphate group
What extends at the 3' end of DNA - -OH hydroxyl group
Transformation - a change in genotype and phenotype due to the assimilation of
external DNA by a cell
Virus - DNA (or sometimes RNA) enclosed by a protective coat, which is often just
protein
What part(s) of the DNA are on the outside of the double helix? - sugar and phosphate
backbones
What part(s) are on the inside of the DNA double helix? - the nitrogenous base
How did the Watson-Crick model explain Chargaff's rules? - They determined that
adenine paired only with thymine and guanine paired only with cytosine.
Who came up with the semi-conservative model for replication? - Watson and Crick
Describe the dispersive model of replication. - Each strand is a mix of old and new
Where does DNA begin replicating? - at the origins of replication where the two DNA
strands are separated, opening up a replication bubble
How many origins of replication can a bacterial chromosome have? - 1
How many origins of replication can a eukaryotic chromosome have? - hundreds or
thousands
Replication fork - Y-shaped region where new DNA strands are elongating
Helicases - enzymes that untwist the double helix at the replication fork
Single-strand binding proteins - bind to and stabilize single stranded DNA
Topoisomerase - corrects overwinding ahead of replication forks by breaking, swiveling,
and rejoining DNA strands

What is each nucleotide being added to a growing DNA strand called? - nucleoside
triphosphate
Mismatch repair of DNA - repair enzymes correct errors in base pairing
Nucleotide excision repair - Nuclease cuts out and replaces damaged stretches of DNA
Mutations - mistakes in dna replication, the basis for evolution
Telomeres don't prevent the ____ of DNA molecules, but they do postpone the __ of
genes near the ends of DNA molecules. - shortening, erosion
Most chromatin is ____ packed in the nucleus during ___ and condenses prior to ____.
- loosely, interphase, mitosis
Loosely packed chromatin is called... - euchromatin
Densely packed chromatin is called... - heterochromatin
Dense packing of heterochromatin makes it difficult for a cell to what? - express the
genetic information coded in these regions
What can cause changes in chromatin organization? - chemical modifications of
histones

Chapter 12:
Why does a unicellular organism divide? Give examples. - to reproduce
Ameoba
Yeast
Paramecium
E.Coli bacteria
Deuteromycetes - organisms that reproduce exclusively by mitotic cell division which
leads to identical types of cells
Ex: Athlete's foot
Yeast infecions
Penecillium notatum
Brie
Why do multicullular organisms divide? - - Development
- Growth
- Renewal: tissues
- Repair: broken bone
- Asexual reproduction
- Sexual reproduction
- Production of gametes
Genome - all genetic information in an organism

Haploid set: - all chromosomes got from one parent

Haploid+haploid = - diploid
n + n = 2n
Diploid abb - 2n
Homologous chromosomes - two separate chromosomes that have the same genes but
may have variations of those genes, diff alleys for the genes
Individual variations on a chromosome are called.. - alleles
Alleles aka - variation
Somatic cells - divide through mitosis, not for sexual reproduction
Gametocytes - produce gametes (meiosis) only sperm or egg in us
What does an X indicate? - that there are two copies of the chromosome, replicated, like
two documents stapled together
What is each side of the X called? - a sister chromatid
How many sister chromatids are there in a replicated chromosome? - 2
What holds the sister chromatids together at the center - centromere - (the indentation in
the X) where are the most cohesins
What holds the sister chromatids together not in the center? - cohesins
Is a replicated chromosome one or two chromosomes? - one
When the sister chromatids are separated, are there one or two chromosomes? - two
1 replicated chromosome --> 2 unreplicated chromosomes
Mitosis - the replication of the nucleus which occurs before the completion of mitotic
cells so when we say mitosis we are really talking about one event that occurs within
mitotic cell division
What happens after mitosis? - cytokinesis (cell break) splitting the cells apart
Where does a cell spend most of its time? - In interphase
What composes interphase? - G1 phase
S phase
G2 phase
What goes on in the G1 phase? - growth (you need to grow to accommodate splitting
into two)
What goes on in the S phase? - DNA replication
What goes on in the G2 phase? - checking itself to make sure it is ready to divide
Where does a cell spend the least time? - in the M phase - mitotic cell division
What composes the M phase? - cytokinesis and mitosis
Resting phase is also known as...
What goes on in the resting phase? - G0 phase
The cell is just performing its daily duties, not preparing to grow or divide

If 2n = 6
How many diploid chromosomes
How many homologous chromosome pairs?
How many haploid sets? - 6 diploid chromosomes
3 homologous chromosome pairs
2 haploid sets (each with 3)
How does DNA appear when we are using and replicating it? When we aren't? - Loose
and relaxed
Condensed
Centrosome - collection of proteins which coordinate cell division
MTO - microtubule organization center
What are microtubules made out of? - tubulin
How is a cell, MTO, and centrosome analogous to a pupped - Much like marionette, cell
is puppet, microtubules are string, and the centrosome is the person controlling it
The microtubules bind to things and then move them around.
What happens in prophase of mitosis? - Chromosomes condense
Nucleoli become undetectable
Mitotic spindle forms
Microtubules attach to the chromosomes and more them around so half the replicated
go to one side, and the other half to the other side
Nucleus fragments
What allows microtubules to bind to the replicated chromosomes in prophase of
mitosis? - A kinetichore, a protein
Analogous to the place where string would be tied onto the puppet
Metaphase plate - an imaginary sheet that runs across the middle of the cell with the
chromosomes lined up along that dimension
What goes on in metaphase of mitosis? - the chromosomes line up at the metaphase,
and the centrosomes complete their migration to the poles of the cell
What goes on in anaphase of mitosis? - Cohesions are cleaved
Each sister chromatid of a replicated chromosome becomes an independent
chromosome
Chromosomes migrate
Cell elongates
The two sisters get pulled apart
What are the two ways that microtubules pull apart sister chromatids in anaphase of
mitosis? - The microtubules are what pull the sister chromatids apart, the centrosome is
pulling the microtubules to either end either like a fishing rod reeling in, and others act

like a pac man (kinetochore protein) which eats the microtubules. pulling the chromatids
to either side
What goes on in telophase? - Mitosis occurs, two nuclei form
Cytokinesis - Microfilaments are in a circle and constrict like a hoodie with a drawstring
Where does cytokinesis occur? - at the cleavage furrow
Cytokinesis in plant cells - Cell plate (like a juvenile cell wall) formed through vesicular
transport with cellulose in the middle
What is cell division called in prokaryotes? - Don't use mitotic cell division because they
don't have a nucleus, instead they have binary cell division
Evidence suggests that _ mitosis originated from ____ mechanisms. - eukaryotic,
prokaryotic
Explain how the lineages of some organisms may exemplify intermediate states
between eukaryotic mitosis and prokaryotic mechanisms. - bacteria > dinoflagellates
> diatoms and yeasts > most eukaryotes
Cell division has evolved from simple binary fission to complex version in animals and
that we have some organisms today that show us the intermediate steps and how cell
division must have evolved through time
How do cells control their cell division? - molecular control system
What signals make up the molecular control system? - cytoplasmic: kinase and cyclin
What was the experiment that indicated there was a molecular control system that
regulates the cell cycle? - Evidence - if expose two cells to certain chemicals they will
fuse, so scientists put two cells that were in different phases, and the cell that was in the
earlier phase immediately went into the later phase
Kinase - phosphorylating enzyme, stays good over time
Cyclin - cofactor to kinase, goes bad in a very short amount of time
What forms when kinase and cyclin combine? - maturation promotion factor (MPF) growth increase factor
What increases as a cell is getting ready to divide? - When MPF increases in
concentration, it is an indication that you are ready to divide, and sends your cell into
mitotic division.
What happens to the MPF after cell division? Will your cell keep dividing? - The cyclin
degrades, and the mitotic division is over and so the cell doesn't keep dividing
When does the mitotic phase occur in relation to the cytoplasmic signal network? Mitotic phase occurs in the window when cyclin connection and MPF activity is high
What happens when we can't regulate cell division? How can this occur? - cancer, a
mutation in the gene that produces the proteins which are involved in cell division

Describe internal signals for mitosis. - M - checkpoint

Anaphase - Attachement of kinetochores to spindles/cohesin cleavage
Describe external signals for mitosis. - Nutrient limitation
Growth factor - epidermal cells
Anchorage dependence
Density dependence
What triggers bacteria cell division? - Food and nutrients so that that bacteria can cover
and encase the food so that other bacteria can't get ahold of the food and kill the
bacteria
Describe how mutations can affect cell division. - Mutations
abnormal signaling pathways
A result of a Deranged cell cycle
immortal cells
Benign tumor
What is a benign tumor and how is it caused? When does it metastasize? - A benign
tumor is a pocket of cells that are replicating uncontrollably, as a result of a mutation),
but are contained
The cancer cells are really bad, and metals if the uncontrollably replicating cells get into
the blood stream or get in a position where they can access your resources
Transformation (in cancer cells) - when the cancer cells get in a place where they can
escape the immune system
Are gametes haploid or diploid? What does this mean? - haploid, they have half the
genetic information that a diploid cell does
1/2 of a sister chromosome is an ___. - arm
Cytokinesis is the division of what? - the cytoplams
Mitosis is the division of _____ in the ___. - genetic material (chromosomes), nucleus
Mitotic (M) phase - mitosis and cytokinesis
Interphase - cell growth and copying of chromosomes in preparation for cell division
What four phases make up mitosis? - Prophase (prometaphase - late prophase)
Metaphase
Anaphase
Telophase
What phase overlaps the latter stages of mitosis? - cytokinesis
Mitotic spindle - structure made of microtubules that controls chromosome movement
during mitosis

In animal cells, where are spindle microtubules synthesized? What is this place known
as? - The centrosome, the microtubule organization center
What happens to the centrosome in interphase? Prophase? - The centrosome
replicates during interphase, forming two centrosomes that migrate to opposite ends of
the cell during prophase and prometaphase (late prophase)
Aster - radial array of short microtubules that extend from each centrosome
What composes the mitotic spindle? - centrosomes, spindle microtubules, the asters
Kinetochores - protein complexes associated with centromeres
Late in prophase, what happens to the microtubules? - Some spindle microtubules
attach to the kinetochores of chromosomes and begin to move the chromosomes
What process does cytokinesis occur through in animal cells? - cleavage
Where does cytokinesis occur in animal cells? - cleavage furrow
What forms during cytokinesis in plant cells? - cell plate
How do prokaryotes reproduce? What composes the domain prokaryote? - Binary
fisssion
Bacteria and archaea
Describe the three steps in binary fission. - In binary fission, the chromosome replicates
(beginning at the origin of replication)
The daughter chromosomes actively move apart
The plasma membrane pinches inward, dividing the cell into two
Mitosis probably evolved from what? - binary fission
Cell cycle control system - regulated by both internal and external controls and has
specific checkpoints where the cell cycle stops until a go-ahead signal is received
What are the three cell division checkpoints? - G1, G2, and M
For many cells, what seems to be the most important checkpoint? - G1, because if it
receives the go-ahead then, it will usually complete the S, G2, and M phases, and divide
If the cell doesn't receive the go-ahead signal there, it will exit the cycle, switching into a
non dividing state called the G0 phase.
MPF moves cells from what phase to what phase? - G2 to M
What is an example of an internal signal that regulates the cell division process? - When
kinetochores are not attached to spindle microtubules, they send a molecular signal that
delays anaphase
What is an example of an external signal that regulates the cell division process? Growth factor proteins released by certain cells stimulate other cells to divide.
Ex: Platelet-derived growth factor (PDGF) stimulates the division of human fibroblast
cells in culture
External signal: Density-dependent inhibition - crowded cells stop dividing

Anchorage dependence - most animal cells exhibit this signal, where they must be
attached to a substratum (a foundation, or layer beneath it) to divide
Do cancer cells exhibit density dependent inhibition or anchorage dependence? - no
Why do cancer cells often not need growth factors to divide? - * They may make their
own growth factor
* They may convey a growth factor's signal without the presence of the growth factor
* They may have an abnormal cell cycle control system
What is the process called in which a non-cancerous cell is converted to a cancerous
one? - transformation
What happens to cancer cells that are not eliminated by the immune system? - They
form tumors, masses of abnormal cells within otherwise normal tissue
If abnormal cells remain at their original site, the lump is called... - benign tumor
Malignant tumor - Tumor that invade surrounding tissues and can metastasize,
exporting cancer cells to other parts of the body, where they may form additional tumors

Chapter 13:
Budding and fragmenting - reproducing through mitosis, the new organism buds out
from the organism, then fragments off, a complete clone of the original organism, just
younger
Ex: hydra
Meiosis - modified form of cell division, two rounds of division, parents each contribute
1/2 of their DNA to offspring
Genetics - the study of heredity and hereditary variation
Genetic recombination - unique individuals that have new traits that could have an
advantage in a given environment
Where does meiosis occur? - gonads:
ladies - ovaries
men - testicles
Gemetogenesis - another name for meiosis, the production of sex cells
What is the product of meiosis? - gametes:
sperm or egg
Are gametes diploid or haploid? - haploid
Germ cell - stem cell for gametogenesis
Is a germ cell diploid or haploid? - diploid
Describe how germ cell --> gamete - Germ cell divides into two gametocytes, then the
two gametocytes undergo 2 rounds of meiosis

A diploid organism has two ___ sets of chromosomes. - haploid

Somatic cells - any cells that are not sperm or egg, any that diploid
Alleles - variation
Locus - the location of a gene, its address on a chromosome
What does meiosis do with the genome of an organism? - Divides it in half and gives
that half to the gamete
Homologous chromosomes - chromosomes that have the same genes in the same
places
Karyotype - checks for chromosomal mistakes in the infant DNA that would otherwise
kill or defect the infant, by harvesting a few cells from the infant, then lets them grow,
then freezes them in metaphase and then checks the DNA
Sex chromosomes determine what in organism? - the gender
female will always contribute an X, male will give X or Y, so male determines the gender
of offspring
How many autosomes are in somatic cells in humans? How many sex chromosomes? 44 autosomes
2 sex cells
How many autosomes are in a sex cell in humans? How many sex chromosomes? - 22
autosomes
1 sex chromosome
How many sex chromosomes are in every reproducing organism, what are the rest of
the chromosomes called? - 2, autosomes
Synapsis - Synapsis (also called syndesis) is the pairing of two homologous
chromosomes that occurs during meiosis. It allows matching-up of homologous pairs
prior to their segregation, and possible chromosomal crossover between them. Synapsis
takes place during prophase I of meiosis.
Crossing over - sister chromatids swap genes so that the genes recombine between
homologous chromosomes
Which to sisters cross over? - the inner ones of the tetrad
Chiasma - the point at which the chromosomes exchange genetic material in
chromosomal crossover
What part of meiosis contributes to genetic recombination? - crossing over in prophase I
and metaphase I, and independent asst. in metaphase I
What is independent assortment? - Whether the paternal or maternal chromatids are on
top of the tetrad or not, it is random and leads to genetic recombination.
At what point in meiosis does the cell become haploid? - anaphase and telophase I

What are the two things that contribute to genetic recombination? - crossing over,
independent assortment
What is the purpose of meiosis II? - to separate replicated chromosomes
Bisexual organism - has both male and female reproductive parts and so can reproduce
with them-self
How do living things change? - genetic recombination (crossing over & independent
asst.), and mutations
Why might deuteromycetes not have as much of an evolutionary advantage? - because
they only reproduce through mitosis
Heredity - the transmission of traits from one generation to the next
Variation is demonstrated by... - demonstrated by the differences in appearance that
offspring show from parents and siblings
Genes - units of heredity made up of segments of DNA
How are genes passed from one generation to the next? - gametes
Asexual reproduction - a single individual passes genes to its offspring without the
fusion of gametes
Sexual reproduction - two parents give rise to offspring that have unique combinations of
genes inherited from the two parents
Life cycle - the generation-to-generation sequence of stages in the reproductive history
of an organism
A karyotype is ... - an ordered display of the pairs of chromosomes from a cell
What is the diploid number for humans? - 2n = 46
Each replicated chromosome consists of two what? - identical sister chromatids
Fertilization - union of gametes (sperm and egg)
Zygote - fertilized egg - -has one set of chromosomes fro each parent (diploid)
Explain alternation of generations in plants and algae. - Life cycle includdes a diploid
and haploid multicellular stage
The diploid organism is called a sporophyte and makes haploid spores via meiosis
Each spore grows by mitosis into a haploid organism called gametophyte
The gametophyte makes haploid gametes via mitosis
Fertilization of gametes results in a diploid sporophyte
In fungi and some protists the only __ stage is the single-celled zygote. Explain what
happens after this. - diploid
The zygote produces haploid cells via meiosis
Each haploid cell grows via mitosis into a haploid multicellular organism
The haploid adult produces gametes by mitosis
How many daughter cells are produced after meiosis? - four

After the chromosomes duplicate before meiosis (in interphase), what are the two
divisions that follow? - * Meiosis I (reductional division): homologs pair up and separate,
resulting in two haploid daughter cells with replicated chromosomes
* Meiosis II ( equational division): sister chromatids separate
What are the four phases that meiosis I occurs in? - - Prophase I
- Metaphae I
- Anaphase I
- Telophase I and cytokinesis
Prophase I - * Typically occupies more that ninety percent of the time required for
meiosis
* Chromosomes begin to condense
* In synapsis, homologous chromosomes loosely pair up, aligned gene by gene
Each pair of chromosomes form what? - tetrad
How many chromatids are in a tetrad? - four
Chiasmata - X-shaped regions where crossing over occurred (each tetrad normally has
one or more of these)
Metaphase I - * Tetrads line up at the metaphase plate, with one chromosome facing
each pole
* Microtubules from one pole are attached to the kinetochore of one chromosome of
each tetrad
* Microtubules from the other pole are attached to the kinetochore of the other
chromosome
Anaphase I - * Pairs of homologous chromosomes separate, (the tetrads separate)
* One chromosome moves toward each pole, guided by the spindle apparatus
* Sister chromatids remain attached at the centromere and move as one unit toward the
pole
Telophase I and Cytokinesis - * In the beginning of telophase I, each half of the cell has
a haploid set of chromosomes; each chromosome still consists of two sister chromatids
* Cytokinesis usually occurs simultaneously, forming two haploid daughter cells
What four phases does meiosis II occur in? - - Prophase II
- Metaphase II
- Anaphase II
- Telophase II and cytokinesis
Meiosis II is very similar to what? - mitosis
Prophase II - * A spindle apparatus forms
* In late prophase II, chromosomes (each still composed of two sister chromatids) move
toward the metaphase plate

Metaphae II - * The sister chromatids are arranged at the metaphase plate

* Because of crossing over in meiosis I, the two sister chromatids of each chromosome
are no longer genetically identical
* The kinetochores of sister chromatids attach to microtubules extending from opposite
poles
Anaphase II - * Sister chromatids separate
* The sister chromatids of each chromosome now move as two newly individual
chromosomes toward opposite poles
Telophase II and Cytokinesis - * The chromosomes arrive at opposite poles in telophase
II
* Nuclei form and the chromosomes begin de-condensing
* Cytokinesis separates the cytoplasm
* At the end of meiosis, there are four daughter cells, each with a haploid set of
unreplicated chromosomes
* Each daughter cell is genetically distinct from the other and from the parent cell
Mitosis vs. Meiosis
* Chromosomes number and sameness - * Mitosis conserves the number of
chromosome sets, producing cells that are genetically identical to the parent cell
* Meiosis reduces the number of chromosomes sets from two (diploids) to one (haploid),
producing cells that differ genetically from each other and from the parent cell
What three events are unique to meiosis? Do they occur in meiosis I or II? - They all
occur in meiosis I:
- Synapsis and crossing over in prophase I: Homologous chromosomes physically
connect and exchange genetic information
- At the metaphase plate, there are paired homologous chromosomes (tetrads) instead
of individual replicated chromosomes
- At anaphase I, it is homologous chromosomes, instead of sister chromatids, that
separate
Mutations - changes in an organism's DNA are the original source of genetic diversity
Mutations create different versions of genes called... - alleles
Recombinant chromosomes - chromosomes that have undergone independent asst.
and crossing over, which combine DNA inherited from each parent
How does random fertilization add to genetic variation? - Any sperm can fuse with any
ovum (unfertilized egg) so diff genes combining
Describe the evolutionary significance of genetic variation within populations. - * Natural
selection results in the accumulation of genetic variations favored by the environment

* Sexual reproduction contributes to the genetic variation in a population, which

originates from mutations

Chapter 14:
Describe a bit of the life of Gregor Mendel (1822-1884). - - Raised on a farm in Austria,
now Czech Rep.
- Entered a Catholic monastery at the age of 21
- Failed an examination to become a teacher
- Attended the university of vienna
- Studied physics, chemistry, and botany
- Returned to the monastery to teach
- Began his scientific research
How did Mendel employ the "observe" part of the scientific method? - Observe - Mendel
worked on a farm and observed peaplants
Saw that there were two strains of pea plants, one with purple plants, and one with white
flowers
Offspring may or may not feature certain properties exhibited by the parents
Blending hypothesis - overtime, when two individuals reproduced, the offspring was a
mix of the genes of which the individual ones couldn't be pulled back out, like mixing
paint
Ex: red snap dragon + white snap dragon = pink snap dragon
Character/Gene - a heritable feature that can vary among individuals
Traits/Alleles - variants of a character
Locus - location of a gene on a chromosome
How did Mendel employ the "hypothesis" part of the scientific method? - An alternative
to the blending hypothesis. Genes are passed on undiluted in discrete units, like a deck
of cards: shuffling and then passing back out
What are Mendel's laws? - * The law of segregation
* The law of independent assortment

The law of segregation - - A. Alleles for a heritable character segregate during gamete
formation and end up in different gametes. For each character, an organism inherits one
allele from each parent
- B. Alternative versions of genes account for variations in inherited characters (alleles)
- C. If the two alleles at a locus differ, then the dominant allele, determines the
organism's phenotype and the single recessive allelee has no noticeble effect on the
phenotype
(the splitting of homologous pairs of chromosomes)
In relation to Mendel's experiment what was the:
Independent variable - - Changing factor of experiment
- Producing hybridization offspring vs. true breed offspring
In relation to Mendel's experiment what was the:
Dependent variable - - Factor influenced in the experiment
- Observable traits of offspring
In relation to Mendel's experiment what were the:
Controlled variables - - Factors that influence the dependent variable if they are not
controlled
- Light, water, temp, soil, pH, soil nutrient, composition, etc.
In relation to Mendel's experiment what was the:
Control group - group that's kept the same
Ex: continued true-breeding of pea plants
In relation to Mendel's experiment what was the:
Treatment group - group that the independent variable is used on
Ex: breeding between two different true breed varieties - hybridization
In relation to Mendel's experiment what was the:
Replication - Repetition
Mendel repeated his experiments hundreds of times

Test cross - when you have an individual with an unknown genotype and you cross it
with a homozygous recessive
Mendel hypothesized that the plants in the P generation were homozygous. What were
his actual results when he completed the test cross? - heterozygous
Describe the evidence that proved Mendel's three hypotheses. - - A. Alleles for a
heritable character segregate during gamete formation and end up in different gametes.
For each character, an organism inherits one allele from each parent
- Law of segregation
- Evidence: test cross data
- B. Alternative versions of genes account for variations in inherited characteristics
- Evidence: F2 generation data
- C. If the two alleles at a locus differ, the dominant allele determines the organism's
phenotype and the recessive allele has no noticeable effect on the phenotype
- Evidence: F1 generation data
The Law of Independent Assortment - refers to how the chromosomes line up
Monohybrids - - One gene hybrids, breed two true breeds of one gene, (flower color)
- Resulting heterozygous F1 progeny from true breed parents, both parents
homozygous, one dominant and one recessive
Dihybrid crosses helped support what? - the law of independent assortment
Independent mutually exclusive event - where the roll of one die doesn't impact the roll
of the second, can only get one outcome
What is the key word for using the multiplication rule? - and
What do we use the multiplication rule for? - to calculate the probability that two mutually
exclusive events will occur in a specific combination
Ex: the probability of rolling a three and then a four

What is the key word for using the addition rule? - or

What do we use the addition rule for? - to calculate the probability that one of two or
more mutually exclusive events will occur
Ex: the probability of rolling a 3 and then a 4, or a 4 and then a 3
Complete dominance - phenotype of heterozygote and dominant homozygote are the
same
Incomplete dominance - phenotype of heterozygote and homozygous dominant are
different, when the phenotype of a heterozygote is a mixture of the two alleles
Codominance - when you have two different alleles for the same gene and they affect
the phenotype in separate distinguishable ways
Consider an individual that is heterozygous for Tay-Sachs.
What would dominance for the alleles involving Tay-Sachs look like at their organismal
level? - - Complete dominance
- Do not exhibit symptoms, similar to homozygous dominant
Consider an individual that is heterozygous for Tay-Sachs.
What would dominance for the alleles involving Tay-Sachs look like at their biochemical
level? - - Incomplete dominance
- Enzyme activity is lower than dominant homozygotes
- But effective enough to prevent lipid accumulation
Consider an individual that is heterozygous for Tay-Sachs.
What would dominance for the alleles involving Tay-Sachs look like at their molecular
level? - - Codominance
- If we were able to count the functional and dysfunctional enzymes, T = t, we would
recognize the alleles in separate distinguishable alleles
- Heterozygotes produce equal numbrs of functional and dysfunctional enzymes
Pleitropy/Pleitropic effects - When one gene influences multiple, seemingly unrelated
phenotypic traits
When you get many different phenotypes (observable traits) as a result of one gene

Epistasis - When one gene affects whether or not another gene is expressed in the
phenotype
* A gene at one locus alters the phenotypic expression of a gene at a second locus
Give an example of epistasis. - There are two genes which affect hair color: one which
determines the pigment you will produce, and a second which determines whether or
not that pigment is deposited in the hair
Polygenic inheritance - when you have several different genes that all contribute to one
common particular) phenotype
Melanocytes - produce pigment melanin which determines skin color
Multifactorial - when the genotype and environment have an effect on the phenotype,
these characters are referred to as quantitative characters
Give an example of multifactorial expression. - Genotype affects what melanin is
produced, UV rays can cause melanocytes to become more active and produce more
melanin
Tay Sachs - an autosomal recessive disorder
Carrier - where an organism has a bad allele but has one other allele that is dominant
so the organism doesn't have the given disorder
What genotype would a carrier have? - heterozygous
Tt
If a disorder is recessive, does a homozygous dominant carry or express the disorder? no
What are two ways that recessively inherited disorders can increase in possibility? - Consanguineous relationship increases the possibilities of having children with
recessive disorders
- Isolated populations increase the possibilities of having children with recessive
disorder, the bad allele will stay within the population

Are dominantly disorders more or less likely to be inherited than recessive ones? - more
Give an example of a dominant disorder. - - Achondroplasia - dwarf
- DD - kills embryo, Dd - dwarf, dd - not a dwarf
- 50/50 chance of being a dwarf if dd x Dd, instead of recessive 25%
How do we determine whether an allele is dominant or recessive in humans? - - Truebreeding humans is unethical
- Have to examine a family history for a certain trait and record it on a pedigree trait and
then we can trace whether it is dominant or recessive over generations
What do squares indicate on pedigree charts? - men
What do circles indicate on pedigree charts? - women
What does shading indicate on a pedigree chart? - that a person expresses a certain
trait (could be dominant or recessive)
Describe the purpose for genetic testing and counseling. - - Simple Mendelian disorders
can be avoided
- Test for identifying carriers
- Genetic counselors can provide the probability of producing an offspring with a life
threatening disorder
Blending hypothesis - * The blending hypothesis is the idea that genetic material from
the two parents blends together (like blue and yellow paint blent to make green)
Particulate hypothesis - * The particulate hypothesis is the idea that parents pass on
discrete heritable units (genes)
What does the particulate hypothesis help explain? - The reappearance of traits after
several generations
Hybridization - mating two contrasting true-breeding varieties
P generation - true breeding parents in Mendel's experiment

F1 generation - the hybrid offspring of the P generation

F2 generation - when F1 individuals self or cross-pollinate with other F1 hybrids
When Mendel crossed contrasting, true breeding white- and purple-flowered pea plants,
what color(s) were the F1 hybrids? - all purple
When Mendel crossed the F1 hybrids, what color(s) were the F2 hybrids? - some
purple, and some white
What was the ratio Mendel got of purple to white flowers in the F2 generation - three to
one
What Mendel called a heritable factor, we call what? - gene
Homozygous - when an organism has two identical alleles for a character
Heterozygous - when an organism ha two different alleles for a gene
Are heterozygotes true breeds? - No
Phenotype - physical appearance
Genotype - genetic makeup
Why do we distinguish between an organism's genotype and phenotype? - Because of
the different effects of dominant and recessive alleles, an organism's traits do not always
reveal its genetic composition
Why does completing a test cross reveal whether an organism is heterozygous or
homozygous dominant (in other words, how does a test cross help us determine the
genotype of an individual with the dominant phenotype? - If any offspring display the
recessive phenotype, the mystery parent must be heterozygous. If none of the offspring
display the recessive phenotype, then the organism must have a homozygous dominant
genotype.
Monohybrid - when individuals are heterozygous for one character

Monohybrid cross - a cross between two monohybrids (heterozygotes)

Dihybrids - individuals that are heterozygous for two characters
Genes located near each other on the same chromosome tend to... - be inherited
together
In what instances would the simple Mendelian patterns of inheritance not apply? - When alleles are not completely dominant or recessive
When a gene has more than two alleles
- When a gene produces multiple phenotypes
- When the phenotype for a character depends on the environment as well as the
genotype
Do dominant alleles subdue recessive ones? - no
Describe quantitativ characters and their relation to polygenic inheritance. - Quantitative
characters are those that vary in the population along a continuum
Quantitative variation usually indicates polygenic inheritance, an additive effect of two or
more genes on a single phenotype
Ex: human skin color
Norm of reaction - the phenotypic range of a genotype influenced by the environment
When are norms of reaction generally the broadest? - for polygenic characters
these are called multifactorial because genetic and environmental factors collectively
influence phenotype
Pedigree - family tree that describes the interrelationships of parents and children
across generations
inheritance patterns of particular traits can be traced and described using pedigrees
Recessively inherited disorders show up only in individuals ____ for the allele. homozygous (recessive)

Chapter 15:
On what type of chromosome is a sex linked gene found? - sex chromosome
Who was the first person to provide evidence that showed that Mendel's genetic units of
inheritance were located on chromosomes? - Morgan
What did Morgan use as a test organism? - fruit flies
Why did Morgan use fruit flies as test subjects? - * Produce many offspring at one time
* Eight chromosomes that are large
* Short generation time
* Easy to feed
What did W^t represent? - dominant normal red eye color allele, wild type
What did W represent? - white recessive (mutant type)
Describe the historical timeline of people who discovered patterns and laws of
inheritance. - Mendel > Morgan > Hershey & Chase > Watson & Crick
Chromosome theory of inheritance - - Mendelian genes have specific loci (positions) on
chromosomes
- Chromosomes undergo segregation and independent assortment
What can account for mender's laws of segregation and independent assortment? - the
behavior of chromosomes during meiosis
What are genes found on the Y chromosome called? - Y-Linked genes
What are genes found on the X chromosome called? - X-linked genes
Describe X-linked gene inheritance.
For a recessive X-linked trait to be expressed, what must happen for male to inherit it, a
female? - - A female needs two copies of the allele (homozygous)
- A male needs only one copy of the allele (hemizygous)

Are X-linked recessive disorders more common in males or females? - males

What are some disorders caused by recessive alleles on the X chromosome in
humans? - - Color blindless
- Duchenne muscular dystrophy
- Hemophilia
What happens to one of the two X chromosomes in each cell during embryonic
development in mammalian females? - one is randomly inactivated
What happens to the deactivated X chromosome in women? - it condenses in a Barr
body
If a female is heterozygous for a particular gene located on the X chromosome, what will
happen to that character? - she will be mosaic for that character
Linked genes - genes located on the same chromosome that tend to be inherited
together
Morgan did experiments with fruit flies to see how linkage affects the inheritance of two
characters by crossing flies that differed in traits of body color and wing size. What were
his results? - * Morgan found that body color and wing size are inherited together in
specific combinations (parental phenotypes)
* He noted that these genes do not assort independently , and reasoned that they were
on the same chromosome
* Non-parental phenotypes were also produced
Genetic recombination - the production of offspring with combinations of traits differing
from either parent
Parental types - offspring with a phenotype matching one of the parental phenotypes
Recombinant types/Recombinants - Offspring with non parental phenotypes (new
combinations of traits)

Mendel observed that combinations of traits in some offspring differ from either parent.
What is the frequency of recombination for any two genes on different chromosomes? 50%
Morgan discovered that genes can be linked, but often the linkage was incomplete
because some recombinant phenotypes were observed. What mechanism drives this
phenomenon? - crossing over, it breaks the physical connection between genes on the
same chromosome
Who came up with the genetic map? - Alfred Sturtevant, one of Morgan's students
Genetic map - an ordered list of the genetic loci along a particular chromosome
What was Sturtevant's prediction? - That the farther apart two genes are, the higher the
probability that a crossover will occur between them and therefore the higher the
recombination frequency.
Linkage map - genetic map of a chromosome based on recombinaion frequencies
Map units - distances between genes can be expressed as map units: one map unit, or
centimorgan represents 1% recombination frequency
What do map units indicate? - relative distance and order, not precise locations of genes
Genes that are far apart on the same chromosome can have a recombination frequency
near 50%. How do these genes behave? - These genes are physically linked, but
genetically unlinked, and behave as if found on different chromosomes.
What do large-scale chromosomal alterations in humans and other mammals often lead
to? How do plants tolerate this? - Spontaneous abortions (miscarriages) or a variety of
developmental disorders
Plants tolerate such genetic changes better than animals do
Nondisjunction - * Pairs of homologous chromosomes do not separate normally during
meiosis

* As a result, one gamete receives two of the same type of chromosome, and another
gamete receives no copy
Aneuploidy - Results from the fertilization of gametes in which nondisjunction occurred
* Offspring with this condition have an abnormal number of a particular chromosome
Monosomic zygote - This kind of zygote has only one copy of a particular chromosome
Trisomic zygote - This kind of zygote has three copies of particular chromosome
Polyploidy - A condition in which an organism has more than two complete sets of
chromosomes
Triploidy - (3n) Three sets of chromosomes
Tetraploidy - (4n) Four sets of chromosomes
Is polyploidy common in plant s or animals? - plants
Are polyploids more normal in appearance or aneuploids? - polyploids
What four types of changes in chromosome structure can be caused by breakage of a
chromosome? - - Deletion: removes a chromosomal segment
- Duplication: repeats a segment
- Inversion: reverses orientation of a segment within a chromosome
- Translocation: moves a segment from one chromosome to another
What is a type of syndrome that is associated with aneuploidy? - Down syndrome (three
copies of chromosome 21)
Nondisjunction of sex chromosomes produces a variety of ... - aneuploid conditions
Klinefelter syndrome is a result of what? - the result of an extra chromosome in a male,
producing XXY individuals

Monosomy X - Turner syndrom, produces X0 females who are sterile; it is the only
known viable monosomy in humans
Genomic imprinting - the silencing of certain genes that are "stamped" with an imprint
during gamete production, the phenotype is dependent on which parent passed along
the alleles for the traits
Extranuclear genes - cytoplasmic genes, found in organelles in the cytoplasm
* Mitochondria, chloroplasts, and other plant plastids carry small circular DNA molecules
How are extranuclear genes inherited? - maternally, because the zygote's cytoplasm
comes from the egg
Some defects in mitochondrial genes can cause what? - Can cause the cells to not
make enough ATP and result in diseases that affect the muscular and nervous systems
Ex: mitochondrial myopathy, Leber's hereditary optic neuropathy
Hemizygous - X and Y homologous pair, they behave like their homologous, but
technically they aren't: instead we call them hemizygous
In the X chromosome are the genes to become both male or female. What happens
when a Y chromosome is paired with the X? - the Y activates the male genes in the X
chromosome, and the Y chromosome also expresses the instructions to make male
body parts
Sex linked genes - We traditionally refer to sex linked genes s genes on the X
chromosome, but they could technically be on the X or Y.
To which gender(s) do father's pass their sex-linked genes onto? - to females, not males
To which gender(s) do mother's pass their sex-linked genes onto? - both males and
females
From which parent(s) do males receive their sex-linked genes from? - mother

X inactivation in female mammals - femaes shut down the second X chromosome into a
barr body
It condenses and lies inactive along the nuclear envelope
How are female cells like a mosaic? - Every female is a mosaic of cells, featuring one of
the two X chromosomes, randomly shutting one of the two down
Ex: calico cat: half orange allele X chromosome use, half black allele X chromosome
use because it is random which X chromosome is inactivated
In what type of organisms does X0 reproduction occur? - only in some insects
Describe X0 reproduction. - Male only has X chromosome
Female has XX
In what type of organisms does Z-W reproduction occur? - some birds, fish, and insects
Describe Z-W reproduction. - Females determine gender of offspring. Females are ZW,
males are ZZ
In what type of organisms does Haplo-diploid reproduction occur? - most bees and ants
Describe the Haplo-Diploid system. - Males produce gametes through mitosis
Females produce gametes through meiosis
An unfertilized haploid egg will grow to a haploid male through mitosis
Females are diploid, and males are haploid
Females develop from fertilized eggs, males develop from unfertilized eggs
Which reproductive system does not have any sex chromosomes? - the halo-diploid
system
What type of genes will often not follow the same patterns of inheritance as Mendel
predicted? - linked genes

Why do linked genes often defy mendelian genetic inheritance patterns/ - because they
are on the same chromosome they can be un paired because crossing over can occur
between them in meiosis I
How to determine genetic recombination crossing over percentage? - number of
recombinants/total number of offspring
What is the relationship between distance linked genes and the recombination
frequency between them? - Recombination frequency is a relative indication of how
close two linked genes are...
Because the more space between two genes, the more places a crossover could occur
in-between them (higher recombination frequency)
The less the space, the less places a crossover could occur in-between them (lower
recombination frequency)
Aneuploidy - when you have one less or one extra chromosome as a result of
nondisjunction
Describe nondisjunction in a cell with a diploid number of 4. How would the outcome be
different if nondisjunction occurred in meiosis II as opposed to meiosis I? Nondisjunction: for 2n = 4, 2 chromosomes go to one cell, and one goes to the other:
Iff this occurs in meiosis I, half of the gameses are aneuploidy monosomic half trisomic,
if in meiosis II, one is monosomic and one is trisomic (2 gametes are aneuploidy)
Trisomic - one extra chromosome for one of the pairs because the sperm gave one extra
chromosome while the egg gave the normal amount
Monosomic - one less chromosome for one of the pairs because the sperm gave one
less chromosome while the egg gave the normal amount
What happens when chromosome 21 is trisomic? - Trisomy 21
Susceptible to:
- Mental retardation
- Leukemia
- Alzheimer's disease

Sex chromosome aneuploidy;: Kleinfelter syndrome - Trisomic males have an extra X

(XXY)
- Even though one X is in activated, men with this disorder:
are sterile, have abnormally small testes, exhibit brea enlargements
may have sub normal intellenence
Syndrome - when you have a set of traits as a result of a chromosome alteration
Turner syndrome - - Monosomic females (one X-sex chromosome)
- Sterile, ex organs do not mature
- Requre estrogen horomone to develop secondary sex characteristics
Are there any monosomic males (tuner syndrome)? - No.
There are no men with this because you can't live w/o and x,take away the x in a man
and you'd jest have y
Trisomic males - XYY
- Do not exhibit a well defined syndrome
- Are taller than average
Trisomic females - XXX
- No distinguisable differences
Polyploidy - when an organism has more than two complete sets of chromosomes
Triploidy - 3n
Fertilization of an abnormal diploid egg (meiosis)
Tetraploidy - 4n
Failure of a 2n zygote to divide after replicating chromosomes (mitosis) all
chromosomes go to one egg, none go to the other
In what species is polyploidy common and often beneficial? - plants, strawberries are
octaploids
Some frogs and fish are polyploids,and one known mammal is a polyploid, a chilean
burrowing rodent

Why are plants able to overcome and thrive with polyploidy? - they are much simpler
Translocation - when two non homologous chromosomes cross over
Inversion - when a piece if a chromosome breaks off, spins around, and then hooks
back on
Deletion - deletes one or more genes
Duplication - extra copy, not always bad
Genomic imprinting - - when one sex always silences their version of the gene, the sex
is still passing off their genes but they tacked on something that makes the chromosome
"inactive" or unable to be used
Whether it is the mom or dad that does the imprinting, the male genes are always
silenced

Chapter 16:
Gregor Mendel - Heritable factors
What did Mendel show? What did he not know? - organisms pass traits and information
along from one generation to another, did not know this was because of chromosomes
or DNA though
Thomas Hunt Morgan - genes on chromosomes
Mendel's genetic units were found on chromosomes in the nucleus of the cell
What did Morgan not know? - that the chromosomes were made of DNA
What is a nucleotide composed of? - nucleoside + phosphate
Phosphodiester bonds - covalent bonds which connect nucleic acids
Cells arise from... - pre-existing cells

What is each individual side of a DNA strand called? - polynucleotide

How are polynucleotides arranged in a DNA strand? (hint: think direction) - antiparallel
arrangement
In science terms, the arrangement is either 5' > 3' or 3' > 5', read 5 prime to three
prime or three prime to five prime
Chromosome - individual DNA molecule
depending on what species you are, you have a diff number in each cell
What are chromosomes made of? - Chromatin
What is chromatin made of? - DNA and protein
DNA + protein - chromatin
What is each individual strand consisting of DNA and protein called? - chromosome
How is the protein in chromatin made? - DNA
Pathogenic - causes illness or disease
What did Griffith show? - Griffith in 1920s was med student, and found that are diff
strains of pneumonia bacteria
The form that makes people sick was called the smooth form which has a capsule
around it
Whereas the rough form of pneumonia did not kill the mouse because does not have
capsule
when he put the smooth above a flame, and injected it into a mouse, it did not kill the
mouse
If is mixed the dead deadly with the like rough, it still killed the mouse because the cells
were able to pass on information
So he showed that dead bacteria was able to pass on DNA to live bacteria
Griffiths experiment showed that some sort of genetic information was being passed
from one bacteria to another bacteria

What are viruses capable of producing, what must they gain from others? - Only
capable of synthesizing proteins and nucleic acids, it might have carbohydrates and
lipids but can't make it themselves
Bacteriophage - virus that uses a bacteria cell as a host
Describe how a virus takes over a host cell. - In the example of a bacteriophage:
The virus lands on the bacteria, injects it with DNA, and makes the bacteria cell use that
DNA to make more viruses, and then when many are made, the cell explodes and the
viruses are let off to go attack some other cell
What are the two types of isotopes? - radioactive and stable
What does a radioactive isotope tend to do? - decay into another element
Describe the Hershey and Chase experiment. - These guys cultured two isotopes of
bacteria phage, one in radioactive sulfur, and others in radioactive phosphorous
DNA became radioactive in the radioactive phosphorous, and the proteins became
radioactive in the sulfur
This showed which molecule (DNA or protein) was the genetic information
Because the radioactive phosphorous in the DNA was injected into the bacteria by the
viruses, and we already knew that viruses inject DNA into the host cell, but the DNA is
reactive in the ones which were bathed in the radioactive phosphorous, whereas if DNA
was made of proteins were would have found radioactive sulfur in the cell (proteins)
This was the first link, but scientists didn't know that much so they thought that maybe
there was exception for viruses
Chargoff's Rule - the amount of A is going to equal the amount of T and the amount of G
is going to equal the amount of C
A = T, C = G
Why is Chargoff's Rule so? - complementary base pairing
Explain the historical timeline of DNA studies. - Mendel showed us that organisms pass
on traits through "heritable units." In the 50s we knew that genetics existed, Mogan

showed it was on chromosomes, Hershey and Chase showed that DNA was the genetic
code, and Chargoff showed complementary base pairing
Watson and Crick, Wilkens and Franklin showed us the composition and pairing of DNA
How did Rosland Franklin derive the shape of DNA? - X-ray chrystallography
How does the width of a DNA double helix remain constant? - Helices have a uniform
diameter
Every complementary base pair is a connection between a purine and a pyridine so the
width of the double helix is consistent
What is DNA replication analogous to? (hint: think recipes) - DNA Replication: taking a
recipe and making a photocopy, not taking a recipe and cooking the food
What were the two main models for DNA replication? - conservative and semiconservative
Describe the conservative DNA replication model. - we pull a strand apart and then
replicate the split parts
then connect the replicated parts, and the other parent strands back together
Describe the semi-conservative DNA replication model. - pull a strand apart and then
replicate the split parts
Describe the Mendelson and Stahl experiment. - They took E.Coli and:
The first generation had heavy nitrogen, then the second generation put in lighter
nitrogen had lighter DNA, this showed that instead of the conservative model where
there would be a new strand with light and the parent would stay heavy
However, there was a mix of heavy and light nitrogen inside it because in the tsest tube
that they centrifuged the bacteria in, and if it were the conservative model, there would
be the heay nitrogen DNA strand (parent) at the bottom and the lighter nitrogen at the
top, but instead it was somwhere in the middle

What does semi-conservative replication mean? Is there such a thing as conservative

replication? - Semi conservative replication means that all replication is going to make
have new and keep half old
No
What shape is bacteria's DNA in? - ring
What shape is eukaryote DNA in? - linear form
How do bacteria replicate? How is that different from us? - When bacteria replicate, an
area opens up in the ring where the two sides are separate, called replication forks ( 1
origin of replication)
In our replication, we open up many different replication forks, which fom bubbles
(multiple origins of replication
What hold base pairs together? - hydrogen bonds
What holds nucleotides together? - phosphodiester bonds
What does helicase do in DNA replication? - unzips the double helix
What bonds does helicase break? - the hydrogen bonds between complementary base
pairs
What do three prime and five prime refer to? - which carbon the base pairs are attached
to
What are the two functions that topoisomerase completes in DNA replication? - 1.
Topoisomerase cuts the double helix, lets it unwind, then connects it back to the double
helix, like the twisted rope
2. prevents binding

What do single stranded binding proteins do in DNA replication? - The single stranded
binding proteins keep the bubble open, they negate the weak binding proerties the base
pairs experience
Primase - lays down primers of RNA 3' nucleotides for DNA polymerase III to connect to
to form the lagging strand
What does DNA polymerase III need to start laying down base pairs? - an exposed
three prime carbon
DNA polymerase III - synthesizes the leading and lagging strands
DNA polymerase I - replaces RNA primers with DNA nucleotides in the lagging strand
Ligase - Then ligase connects the strands that the DNA polymerase I and the DNA
polymerase III synthesized
Okazaki fragment - one primer + one new piece of DNA
How are lagging strands laid down (direction wise)? - Each piece is laid down in the
opposite direction to the overall strand, whereas the leading strand is made in the
direction of the overall construction of the strand
What are the steps of DNA replication? - Helicase unzips
Topoisomerase prevents binding
primase lays the primers at top and bottom
DNA polymerase III lays leading strands
Primase lays down primers for lagging strands
DNA polymerase III lays down strands to connect the primers in lagging strand
DNA polymerase I removes the primers and replaces with DNA strands
Ligase binds the strands between the DNA polymerase I and III strands to form the
lagging strands
All of the replication bubble strands run into eachother, or the DNA ring for bacteria
Telomere - sacrificial sequence at both ends of the sequence : TTAGGG, because at the
ends are 5' so none of the DNA polymerases can lay down more nucleotides
Every time a DNA strand is replicated we lose the ends, we have telomere there instead

Telomerase - enzymes to lengthen telomere

Nuclease - enzyme that goes through to see that we have the complementary base
pairing, no mistakes
We make a mistake about 1 in every 100,000 base pairs laid
What is the protein in a chromosome called? - histone
Nucleosome - eight histones together
Histone proteins do what? - Help organize and loop and pack DNA into organized
structures which are called condensed chromatin
After Morgan's group showed that genes exist as parts of chromosomes, what were the
two proposals that chromosomes were composed of? - protein and dna
Why were proteins considered for the composition of DNA? - they were known to have
great variety, and specificity of function
Why were nucleic acids not highly considered for the composition of DNA? - not well
known, their chemical properties seemed too uniform to account for the multitude of
specific inherited traits that genes express
What two findings became known as Chargaff's Rules? - - The base composition of
DNA varies between species
- But, in any species the number of A and T bases are equal and the number of G and
C bases are equal
The bass for these rules was not understood until the discover of the double helix.
What extends at the 5' end of DNA? - phosphate group
What extends at the 3' end of DNA - -OH hydroxyl group
Transformation - a change in genotype and phenotype due to the assimilation of
external DNA by a cell

Virus - DNA (or sometimes RNA) enclosed by a protective coat, which is often just
protein
What part(s) of the DNA are on the outside of the double helix? - sugar and phosphate
backbones
What part(s) are on the inside of the DNA double helix? - the nitrogenous base
How did the Watson-Crick model explain Chargaff's rules? - They determined that
adenine paired only with thymine and guanine paired only with cytosine.
Who came up with the semi-conservative model for replication? - Watson and Crick
Describe the dispersive model of replication. - Each strand is a mix of old and new
Where does DNA begin replicating? - at the origins of replication where the two DNA
strands are separated, opening up a replication bubble
How many origins of replication can a bacterial chromosome have? - 1
How many origins of replication can a eukaryotic chromosome have? - hundreds or
thousands
Replication fork - Y-shaped region where new DNA strands are elongating
Helicases - enzymes that untwist the double helix at the replication fork
Single-strand binding proteins - bind to and stabilize single stranded DNA
Topoisomerase - corrects overwinding ahead of replication forks by breaking, swiveling,
and rejoining DNA strands
What is each nucleotide being added to a growing DNA strand called? - nucleoside
triphosphate
Mismatch repair of DNA - repair enzymes correct errors in base pairing

Nucleotide excision repair - Nuclease cuts out and replaces damaged stretches of DNA
Mutations - mistakes in dna replication, the basis for evolution
Telomeres don't prevent the ____ of DNA molecules, but they do postpone the __ of
genes near the ends of DNA molecules. - shortening, erosion
Most chromatin is ____ packed in the nucleus during ___ and condenses prior to ____.
- loosely, interphase, mitosis
Loosely packed chromatin is called... - euchromatin
Densely packed chromatin is called... - heterochromatin
Dense packing of heterochromatin makes it difficult for a cell to what? - express the
genetic information coded in these regions
What can cause changes in chromatin organization? - chemical modifications of
histones

Chapter 17:
What are the two parts to protein synthesis? - transcription and translation
What is a protein? - a chain of amino acids which perform a variety of metabolic
functions
What did Beadle and Tatum show? - Showed that genes make protein, took a mold, and
added vitamins, and the mold was able to make all of the amino acids that they needed
to make their proteins
They did not want to wait for the mold to form mutations, and so they irradiated it with xrays, making 3 classes of mutants
The significance of this was that they were able to relate the mutation in a specific gene
that caused the transcription of a specific protein. So they are credited with the one
gene-one enzyme hypothesis. They were the first people provide evidence to support
the hypothesis that genes are used as instructions to make proteins.

Proteinogenic amino acids - one of the 20 base amino acids

What is Crick's central dogma? - There is a molecular chain of command or flow of
information that you must know before studying anything else in genetics:
DNA --> RNA --> Protein
DNA --> RNA - Transcription
Transcription - the synthesis of an RNA copy of a segment of DNA, making messenger
RNA by using a template strand in DNA
RNA --> Protein - Translation
RNA polymerase - makes a complementary strand to one of the sections of DNA
How many sides of the double helix are used for transcription? - Only one side of the
double helix is used to for replication, this side is called the template strand, the other
side just there to protect the template strand, called the nontemplate strand
What base pair is missing in RNA, which is substituted in? - Thymine, Uracil
Primary transcript - the first mRNA strand transcribed from DNA (for both prokaryotes
and eukaryotes)
How do prokaryotes DNA --> Protein? - For prokaryotes, just translate the primary
transcript, because the prokaryote doesn't have a nucleus, the RNA is assembled in the
cytoplasm, and that is where the translation occurs as well
They happen simultaneously
Translation - the process of using messenger RNA to make proteins, when the mRNA
goes from the nucleus to the cytoplasm and is used as instructions to assemble a
protein
What two places can ribosomes be found? - rough ER, free in cytoplasm

Transfer RNA - tRNA reads the RNA nucleotides at a time and goes and gets one amino
acid per three to translate the RNA into proteins
Triplet code - codon, three nucleotides that code for one specific amino acid
Is mRNA single or double stranded? - single
At what point on the RNA strand does the ribosome actually start translating? - the AUG
starting sequence
What does the AUG starting sequence set for the ribosome? - the reading frame
Is our genetic code repetitive or ambiguous - Repetitive, there can be multiple codons
which correspond to one amino acid, not ambiguous, everthing is clear
Is there a universal genetic code? - Yes, every organism abides by the same translation
code, called the genetic code, and it corresponds to how the mRNA translates into
proteins
What does a universal genetic code provide evidence for? - evolution
Frame shift - a shift in the reading frame, the protein will not turn out the same
Point mutation - when you have one base pair or nucleotide change which can fall into
one of two categories
What two categories can a point mutation fall into? - subtitution and insertion/deletion
What three mutations are in the substitution category? - Missense
Silent
Nonsense
Describe Substitution: Missense. - When you get one wrong amino acid
Describe Substitution: Silent. - doesn't result in a change in the animo acid coded for
because the genetic code is redundant and so there can be multiple codons for one
amino acid

Describe Substitution: Nonsense - when you get an early stop codon, result in making
the protein either not fully or not at all
What are the three mutations which fall under the insertion/deletion category? Nonsense
Extensive missense
3-base pair
What is often the result of an insertion/deletion mutation? - frame shift - a change in the
reading frame
What is the only insertion/deletion mutation that does not cause a frame shift? - 3 base
pair deletion/addition
Describe Insertion/Deletion: Nonsense - frame shift which causes an early stop codon
Describe Insertion/Deletion: Extensive Missense. - a protein is still made, but we have
shifted the reading frame so different amino acids are being laid down
Describe Insertion/Deletion: 3 base pair deletion/addition. - when add or subtract three
nucleotides at a time, this does not change the reading frame
What is a mutation that we can get from substitution or insertion/deletion? - nonsense
What three regions can every gene be divided into? - the promoter, the transcription
unit, and the termination sequence
Promoter - region that helps you determine whether or not you are going to make a
protein
Transcription factors - regulatory proteins for RNA transcription
they mediate the binding of RNA polymerase the the initiation of transcription
Transcription initiation complex - polymerase, transcription factors, and promoter
Transcription unit - the part we transcribe

Where on the promoters do transcription factors, and then RNA polymerase ultimately
bind to? - the TATA box (nucleotide sequence)
Termination sequence - signals polymerase to jump off
What does the termination sequence signal eukaryotes to do? - tack on a poly strand to
the tail of the mRNA, signaled by the sequence AUAAA
Before mRNA leaves the nucleus, what does a eukaryote do? - processes it
tacks on a cap (guanosine triphosphate), and a poly A tail
What is the purpose of the processing? - These two things (cap and tail) direct the
mRNA out of the nucleus
In the cytoplasm, there are enzymes which depolymerize the RNA to break it down
because we don't want the ran hanging around, so we tack onto the end the AAAAA tail,
the enzyme always starts eating at the tail. the longer the AAA tail, the more protein we
want of that protein
Also introns are cut out and the exons are spliced together
Eons are what are actually used to make the proteins in translation, alternative RNA
splicing
Introns - RNA not used to code for proteins
Exons - RNA used to code for protein
Spliceosome - type of enzyme that has nucleic acids as well (categorized as a
ribonucleoprotein), does the splicing of introns out and eons together
What process associated with RNA splicing provides an evolutionary advantage? alternative RNA splicing
Describe alternative RNA splicing. - Alternative RNA splicing is using different
combinations of eons to make different versions of a protein from one gene.

Each exon give us one domain of a protein, we can use different protein splicing to code
for different parts of the protein to be coded for at different times, allowing us to make a
diffrent version of it by using different combinations of exons from a gene
Start and stop of transcription - TATA and termination sequence
Start and stop of translation - start (AUG) and stop codons (UAA, UAG, UGA)
What is tRNA made of? - Transfer RNA is made of RNA nucleotides - it has an
anticodon which is complementeray with a codon on the mRNA strand
Show the flow of information, and include the processes of transcription and translation.
- DNA > transcription > RNA > translation > Protein
The role that tRNA plays in translation is binding to amino acids and then bringing them
to the ribosome to be tacked onto a growing polypeptide chain. How do the amino acids
bind to the tRNA? - Aminoacetyl - tRNA synthases bind to tRNA and the free amino acid
and force them to bind
(tRNA is really amino acetyl - tRNA)
What are the steps in translation? - First, the tRNA with the MET lands on the P site,
then the rest land in the arrival site
Then the two amino acids bind, shifting to the right, then the lefthand MET tRNA shifts
to the E place, and the Phe will shift to the P site, then the next tRNA will come in, then
Shift to the right, then everuting shift to left\, then EF t-RNA binds to the A site,
hydrolyzes the GTP and that causes the ribosome to shift to original position, then EF tRNA leaves
vidon slide 33
What is the difference between transcription and translation in prokaryotes vs.
eukaryotes? - Prokaryotes have transcription and translation occurring at the same time.
Eukaryotes separate transcription and translation with the nucleus and processing.
What are the links between genotype and phenotype? - proteins

Gene expression - the process by which DNA directs protein synthesis, includes two
stages: transcription and translation
What is the bridge betweenness and the proteins they code for? - RNA
Transcription - the synthesis of RNA under the direction of DNA
What does transcription produce? - mRNA messenger RNA
Translation - the synthesis of a polypeptide using information in the mRNA
Ribosomes - the sites of translation
Primary transcript - the initial RNA transcript from any gene prior to processing
During translation, in which direction are the mRNA base triplets read? - 5' to 3' direction
Codons must be read in the correct ____ ____ (correct groupings) in order for the
specified _____ to be produced. - reading frame, polypeptide
RNA synthesis is catalyzed by what? - RNA polymerase which pries the DNA strands
apart and hooks together the RNA nucleotides, the RNA is complementary to the DNA
template strand
What is the DNA sequence where RNA polymerase attaches? - the promoter, they
signal the transcriptional start point, in eukaryotes, it is called the TATA box
What are the three steps in transcription? - initiation, elongation, termination
Elongation of the RNA Strand. - * As RNA polymerase moves along the DNA, it untwists
the double helix, 10 to 20 bases at a time
* Transcription progresses at a rate of 40 nucleotides per second in eukaryotes
* A gene can be transcribed simultaneously by several RNA polymerases
* Nucleotides are added to the 3' end of the growing RNA molecule
Termination of Transcription

Bacteria vs. Eukaryotes - * In bacteria, the polymerase stops transcription at the end of
the terminator, and the mRNA can be translated without further modification
* In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence
that codes for a polyadenylation signal (AAUAAA); the RNA transcript is cut free by
proteins about 10-35 nucleotides past the polyadenylation signal
What molecule undergoes processing in the nucleus after transcription? - pre-mRNA
What is attached to the 5' end of the pre-mRNA molecule in processing? - the cap
What is attached to the 3' end of the pre-mRNA molecule in processing? - poly-A tail
How do the tail and cap help the mRNA? - - They seem to facilitate the export of mRNA
- They protect mRNA from hydrolytic enzymes
- They help ribosomes attach to the 5' end
Ribozymes - catalytic RNA molecules that function as enzymes and can splice RNA,
rendering obsolete the belief that all biological catalysts were proteins
What three properties of RNA enable it to functions an enzyme? - - It can form a threedimensional structure because of is ability to base-pair with itself
- Some bases in RNA contain functional groups that may participate in catalysis
- RNA may hydrogen-bond with other nucleic acid molecules
Domain of a protein. - discrete region of a protein
in many cases different exons code for different domains in a protein
exon shuffling may result in the evolution of new proteins
Anticodon - Each tRNA molecule carries a specific amino aid on one end, and an
anticodon on the other end; the anticodon base pairs with a complementary codon on
mRNA
Accurate translation requires what two steps? - - First: a correct match between a tRNA
and an amino acid, done by the enzyme aminoacyl-tRNA synthetase
- Second: a correct match between the tRNA anticodon and an mRNA codon

What are the three binding sites for tRNA on a ribosome? - - The P site holds the tRNA
that carries the growing polypeptide chain
- The A site holds the tRNA that carries the next amino acid to be added to the chain
- the E site is the exit site, where discharged tRNAs leave the ribosome
What are three steps in translation? - Initiation, Elongation, Termination
Describe the initiation phase of translation. - - The initiation stage of translation brings
together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits
- First, a small ribosomal subunit binds with mRNA and a special initiator tRNA
- Then the small subunit moves along the mRNA until it reaches the start codon (AUG)
- Proteins called initiation factors bring in the large subunit that completes the
translation initiation complex
Describe the elongation phase of translation. - - During the elongation stage, amino
acids are added one by one to the preceding amino acid at the C-terminus of the
growing chain
- Each addition involves proteins called elongation factors and occurs in three steps:
codon recognition, peptide bond formation, and translocation
- Translocation proceeds along the mRNA in a 5' to 3' direction
Describe the termination phase of translation. - - Termination occurs when a stop codon
in the mRNA reaches the A site of the ribosome
- The A site accepts a protein called a release factor
- The release factor causes the addition of a water molecule instead of an amino acid
- This reaction releases the polypeptide, and the translation assembly then comes apart
Polyribosome (polysome) - A number or ribosomes can translate a single mRNA
simultaneously, forming a polyribosome.
Polyribosomes enable a cell to make many copies of a polypeptide very quickly
What type of proteins do free ribosomes usually make? - ones that function in the
cytosol
What type of proteins do bound ribosomes usually make? - ones of the endomembrane
system and proteins that are secreted from the cell

Ribosomes are identical and can switch from free to bound. Where does polypeptide
synthesis always begin? When does it finish there, and when does it finish at the ER? * Polypeptide synthesis always begins in the cytosol
* Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach
to the ER
* Polypeptides destined for the ER or for secretion are marked by a signal peptide
* s signal-recognition particle (SRP) binds to the signal peptide
* The SRP brings the signal peptide and its ribosome to the ER
Substitution point mutations: - * Nucleotide pair substitution - replaces one nucleotide
and its partner with another pair of nucleotides
* Silent mutations - no effect on the amino acid produced by a codon because of the
redundancy in the genetic code
* Missense mutations - still code for an amino acid, but not the correct amino acid
* Nonsense mutations - change an amino acid codon into a stop codon, nearly always
leading to a nonfunctional protein
Mutagens - physical or chemical agents that can cause mutations
What is a gene? - A gene is a region of DNA that can be expressed to produce a final
functional product, either a polypeptide or an RNA molecule.
We have considered it as:
- A discrete unit of inheritance
- A region of specific nucleotide sequence in a chromosome
- A DNA sequence that codes for a specific polypeptide chain

Chapter 18:
Through what mechanisms can a cell regulate the production of enzymes? - Feedback
inhibition and gene regulation
How is gene expresion in bacteria controlled? - by the operon model
What is an operon composed of? - the entire stretch of DNA that includes the operator
the promoter, and the genes that they control

What is the operator? - A cluster of functionally related genes can be under coordinated
control by a single "on-off switch." The operator is the regulatory "switch," and is usually
positioned within the promoter.
How can the operon be switched off? - by a protein *repressor*
How does a protein repressor work? - The repressor prevents gene transcription by
binding to the operator and blocking RNA polymerase
The repressor can be in an active or inactive form, depending on the presence of other
molecules
What is a corepressor? - a molecule that cooperates with a repressor protein to switch
an operon off
Ex: E.coli can synthesize the amino acid tryptophan
* By default, the trp operon is on and the genes for tryptophan synthesis are transcribed
* When tryptophan is present,it bind to the trp repressor protein, which turns the operon
off
* The repressor is active only in the presence of its corepressor tryptophan, thus the trp
operon is turned off (repressed) if tryptophan levels are high
What is the repressor a product of? - a separate regulatory gene
What are the two types of negative gene regulation? - repressive and inducible operon
Describe repressible operon gene regulation. - A repressible operon is one that is
usually on; binding of a repressor to the operator shuts off transcription
* The trp operon is a repressible operon
In what type of pathway do repressible operons usually operate? - Repressible enzymes
usually function in anabolic pathways; their synthesis is repressed by high levels of the
end product
Inducer - a molecule that inactivates an inducible operon to turn on transcription
Describe inducible operon gene regulation. - An inducible operon is one that is usually
off; a molecule called an inducer inactivates the repressor and turns on transcription

In what type of pathway do inducible enzymes normally function? - in catabolic

pathways; their synthesis is induced by a chemical signal
Catabolite activator protein (CAP) - An activator or transcription, a stimulatory protein for
some operons.
If we say we express a gene, what does that mean? - we are going to make a protein
out of it
If we say we silence or regulate a gene, what does that mean? - that we won't make a
protein out of it
Operon aka - gene
What is an operon? - operons are bacterial genes regulated at the transcriptional level
(eukaryotes don't use operons for regulation (just bacteria)
What is a repressible operon analogous to? - a furnace in a house in the winter, heats
house constantly, then kicks off for a short time, but is normally on
Operons are examples of gene regulation at what level? - the transcriptional level
What is an inducible operon analogous to? - like an oven
you leave it off unless you need it, most of the time it is not being used
What are the building blocks of protein? - amino acids
What is the source of those building blocks (amino acids)? - food
Essential amino acids - ones you can't make yourself
Non-Essential amino acids - ones you can make yourself, they are essential to your
body though
What type of bacteria lives in our colon? - E.coli

Is nutrient availability to this bacteria steady or variable? Give an example. - variable

E.coli typically synthesizes enzymes that synthesize tryptophan because it is not always
present in what you eat.
Describe what a bacteria does when there is tryptophan in its environment, and when it
is not. - - If tryptophan is available:
- E.coli does not wast energy producing tryptophan synthesizing enzymes
- If tryptophan is not available, E.coli will synthesize the enzyme
- trp operon: if tryptophan isn't present in E.coli's environment then it will use it to make
trp, if there is tryptophan present, the trp operon is turned off
trp operon - a gene that makes an enzyme to make tryptophan
- In the trp operon example, if there is tryptophan, it will bind to the repressor protein and
change its shape so that it can bind to the operator. If there is no tryptophan, the
tryptophan is taken off of the repressor protein to be used, the repressor protein
changes to its inactive form and unbinds from the operator, leaving RNA polymerase to
transcribe the gene
Corepressor - indicates either the presence or non presence of a substance (ex:
tryptophan), anything that binds to the repressor protein
Lactose - milk sugar, combination of galactose and one glucose
Lac operon - a gene that makes an enzyme that breaks lactose, freeing up glucose to
be used in cellular respiration
What happens when your diet is high on lactose, but low on glucose? - E.coli wants to
break apart the lactose to get the glucose so they can fuel their cellular respiration
Describe how E.coli uses a lac operon to coordinate the use or non-use of lactose? (this is like the oven example)
- If glucose is present, there is no need to catabolize lactose, so the lac operon is
inactivated
- If glucose is scarce, lactose hydrolysis provides glucose, so the lac operon is active

Compare and contrast the trp and lac operon. - Repressible operon: With the trp
operon, the corepressor turns it off
Inducible operon: With the lac operon, the corepresor turns it on
- The trp operon is a repressible operon
- Gene is normally expressed but can be turned off (repressed)
- The lac operon is an inducible operon
- Gene is normally not expressed but can be turned on when needed (induced)
Cell differentiation - the process of producing different types of cells
Morphogenesis - the beginning of an organism's shape, an organism must decide which
end is going to be top and which point to be bottom
Stem cell - a cell whose job is to produce other cells
Totipotent stem cell - stem cell that is capable of becoming every type of cell that will be
in the organism, and extra embryonic cells like the placenta
* capable of constructing a complete organism
Pluripotent - capable of becoming endo, meso, or ectoderm (cannot become extra
embryonic tissues)
Multipotent - capable of becoming several cell types (ex: stem cells capable of
becoming any type of blood cell)
Oligopotent - capable of becoming one of a few cell types (ex: osteoprogenitor produces a few bone cells)
Unipotent - capable of producing one cell type (ex: liver cell)
Transcription factors - allow for transcription occur
Cytoplasmic determinants - some of the first active transcription factors and are going to
lead the cells in the first round of division down different paths of development

Explain how cytoplasmic determinants help to bring divided cells down different
developmental paths. - There are different groups of cytoplasmic determinants in an egg
and they are not homogeneously mixed.
When this cell is fertilized and divides, some cytoplasmic determinants go in one cell,
and some go in another.
These determinants bind to the genes in the divided cell and determine what type of cell
they will become.
Induction leads to the coordinated production of transcription factors
Maternal effect gene aka - egg polarity gene
Cytoplasmic determinants aka - morphogens
Describe Nusslein-Volhard and Wieshcaus' experiment. (1980s) - - They fed their fruit
flies mutagenic food in hopes that they would cause mutations to maternal effect genes,
and they could identify that by looking at the larvae and seeing if they have two head or
two tails, and then they would look at the parents who produced that offspring
- They ended up with a larvae that had two tails, and called it a bicoid, and they went to
the parent to try and find the bicoid gene via linkage mapping
- To do this they had to cross a bunch of different flies with a bunch of different genes to
find where this bicoid gene was located in the fruit fly genome
The normal bicoid gene produces a head and a tail, but the mutated form gave two
tailed offspring
They transcribed mRNA from the normal bicoid maternal effect gene and then injected it
into a normal larvae, and injected it into the tail end, making another head, showing that
the greater the concentration of cytoplasmic determinants is where the head is going to
be.
Homeotic genes - determine late embryo development (ex: where legs, eyes, and arms
are going to grow

Maternal effect genes determine what? - early embryonic development

Describe Lewis's experiment (1940s) - causes mutations to homeotic genes in fruit flies
by shooting x rays at them
Does every cell have the organism's entire genome? - yes
At what stages can eukaryotes regulate their gene expression? - At any stage
Regulation of gene expression is ultimately determined by what? - the amount of
functional protein that is synthesized
(if one of the dominoes doesn't fall - gene won't be expressed)
What are the two ways to describe regions on a chromosome? - Euchromatin
Heterochromatin
Euchromatin - Accessible - relaxed and extended, available to the RNA polymerases
Heterochromatin - Inaccessible - condensed, not available to the RNA polymerases
What are the proteins that DNA is packaged with called? - histones
Why do DNA and histones bind? - Histones are slightly positive, and DNA is slightly
negative, they have an affinity for one another
What happens when we acetylate histones in a specific part of a DNA strand? - If we
acetylate the histone proteins, we open the chromosome up for use because it causes
the histones to lose their positive charge, so it is no longer attracted to the DNA:
relaxation (COCH3)
What happens when we methylate histones in a specific part of a DNA strand? - If we
methylate the histones, it condenses the chromatin: condensation (CH3/Me)
DNA methylation - DNA methylation - cytosine (c) is methylated, genes that are not
expressed in a cell type are usually heavily methylated
DNA and histones that are _____ are silenced. - methylated

Master regulatory genes (MRG) - some of the first genes that are influenced by
cytoplasmic determinants
What is a form of gene regulation at the general transcription level? - control elements
help determine which genes are going to be silenced and which expressed
Cytoplasmic determinants are transcription factors for what type of gene? - master
regulatory gene
Describe gene regulation at the transcriptional level as a sequence. Begin with activator
proteins. - express MRG > activator proteins (type of TF) > APs bind to enhancer
sequence of a control element > General transcription factors bind to activator
proteins on the enhancer sequence
START HERE FOR FLASHCARDS ON GENE REGULATION. - ...
What is the reason that cyclin in mitosis has a short "shelf-life?" - Because ubiquitin is
attached to the end when it is made
Ubiquitin is the "mark for death"
Proteasome - molecule that comes along and destroys proteins with ubiquitin attached
to the end into peptide fragments to be recycled
Proto-oncogene - no mutation causing the gene to be cancerous
Oncogene - when mutation causes the gene to become cancerous
What are two ways that a proto-oncogene can be transformed into an oncogene? - We
can get a mutation *within* the *gene* for *cyclin*, causing it to not be marked with
ubiquitin
We can get a mutation *within* the *control element* which causes too much attraction
of for the activation proteins causing a gene to become more active.
Coding mRNA - mRNA that you are going to use to translate a protein

Noncoding mRNA - mRNA that is transcribed, but has some other purpose, such as
gene regulation
What are three types of noncoding mRNAs? - - MicroRNAs, miRNAs
- Small interfering RNAs, siRNAs
- Piwi-RNAs, piRNAs
At what levels do noncoding mRNAs regulate gene expression? - These small pieces of
RNA can regulate genes at almost every level: chromatin, transcription, and
translational levels
How can noncoding mRNAs regulate gene expression? - How this works:
Enzyme opens up a part of the DNA double helix
The RNA piece then binds to part of the DNA helix, causes a sort of lock so no
pool,erase cam attach
They can also bind where the ribosome is supposed to go, and it can't be translated

Chapter 19:

What is a virus? - collection of nucleic acids and proteins

a strand of single/double stranded DNA/RNA encapsulated in protein structures
Are viruses living? - Most scientists agree that viruses are not living things
Can viruses reproduce themselves? - no, they must hijack a host cell's organelles
What do viruses have in common with living things? - they evolve
What are two differences between viruses and other organisms? - 1. Viruses don't have
a mitochondria or chloroplast
2. They don't have cells, they are not a cell
What was the first virus discovered? - 1st one: Tobacco mosaic virus (1930s): it gave
the tobacco plant muddled leaves, and stunted its growth
How did scientists discover and identify the tobacco mosaic virus? - At this point in time,
scientists thought that all disease came from bacteria

They couldn't find bacteria on the tobacco plant though, so they took sap from an
infected plant, and put it through a filter: they couldn't find bacteria, but when they took
the same sap and put it on a healthy plant, it became sick
They were able to dry the viruses up and crystallize them, and they were able to analyze
identify the first virus
What are the two main types of viruses? - Bacteriophages and animal viruses
Bacteriophages affect what organisms? - bacteria only, not animals
What encapsulates the genome of a virus? - capsid, (protein shell)
Describe the general structure of a bacteriophage. - there is an icosahedral shaped
head (which holds the genome), atop a cylindrical neck and v shaped pins attached to
the end of it (which help it land on the bacteria cell)
Describe the general structure of an animal virus - a capsid (which holds the genome)
encased in a lipid envelope with keys that fit into certain locks on animal cells
Does a virus ever change its genome? - no
Viral envelope - virus phospholipid bilayer
What are the "keys" on the viral envelope that let animal viruses into cells made out of? glycoproteins
These proteins bind with a corresponding protein receptor on the cell membrane. The
organism's cell recognizes this as something we need
What does the H stand for in H1N1 (swine flu)? What type of protein is this, and what is
its function? - hemagglutinin
This is an antigenic (communication) glycoprotein that gets the virus into the host cell
What does the N stand for in H1N1 (swine flu)? What type of protein is this, and what is
its function? - neuraminidase
This is a glycoside hydrolase enzyme that gets the new generation of viruses out of the
cell.

What is the size range for viruses? - from a bacteria, to a small ribosome
What is a virus' purpose? - obligate intracellular parasite
Host range - Different viruses have different host ranges - the type of species they can
infect, and the type of cells in those species they can affect
How do mutations change the host range of a virus? - they can change the proteins they
make: like the ones that let the virus in and out of the cell
What are the two goals of every virus? - To make copies of its genome
To make virus specific proteins
What are the basic general steps of virus interaction with a host cell? - 1. Entry into cell
2. Capsid fragments, exposing its genome
3. Virus replicates its genome & Virus produces mRNA (through transcription or
translation
4. mRNA is translated into capsid proteins, and some enzymes it needs, (ex: reverse
transcriptase which turns RNA > DNA)
(All the while, the virus is using the host cell's ribosomes, RNA polymerases etc.)
5. Packaging into new viruses (self-assembly)
6. Exit
Why is a virus an obligate parasite? - obligate because it has to use a host cell's
functions, parasite because it causes harm to the organism it infects
Lytic cycle - every generation of virus that gets into a host cell destroys the host cell,
then goes off and does it again
Prophage - insertion of DNA into bacterial chromosome
Lytic - when the virus enters a host cell, makes viruses and destroys the host cell
Lysogenic - when the virus DNA just lays dormant in the host cell's DNA, but doesn't
affect it, it could go back to the lytic cycle though in another generation
Temperate phage - generations alternate between lysogenic cycle and lytic cycle

If you have several generations of bacteria, that would mean some of those generations
will be in the lytic cycle, and some of the generations would just exist as a sequence in
the bacterial chromosome in the lysogenic cycle
Phage therapy - some countries use bacteriophages as a form of medicine
it is a capsule you take ad has phages inside of it, which then kills your bad bacteria, ex:
salmonella
Biocontrol - some countries use bacteriophages as a form of pesticide
they spray food with bacteriophages so it kills the bacteria that would be harmful to
humans
How do bacteria protect themselves from bacteriophages? - Restriction enzymes
Mutations
Restriction enzymes in bacteria. - they are enzymes that seek out and destroy viral
(bacteriophage) DNA/RNA sequences by cutting it out
Mutations in bacteria with regards to their role with viruses. - can change the proteins on
the membrane of the bacteria (viruses need a receptor to recognize a bacteria to know
whether or not they can infect it), so the virus might not be able to recognize that
bacteria anymore
Does a bacteria initiate mutations? If a mutation occurs in a bacteria what generation(s)
can it help? - A bacteria doesn't initiate a mutation, it is random and can only help future
generations
What parts of a cell is a virus with RNA using? - RNA polymerase, transcription factors,
ribosomes, some of the phospholipid bilayer to make viral envelope
What parts of a cell is a virus with DNA using? - - DNA polymerase I, III
- Helicase and topoisomerase (if double stranded)
- ligase
- Primase
- Ribosomes
- Transcription factors

- RNA polymerase,
- Some of the phospholipid bilayer to make viral envelope
What enzyme does a retrovirus use that no other virus uses? - reverse transcriptase
Reverse transcriptase - RNA --> DNA
General steps of interaction between retrovirus and host cell? - It comes into the cell
with its genome and reverse transcriptase.
In the midst of replicating its genome, and making virus-specific proteins, it uses reverse
transcriptase to integrate new DNA into cell's genome
Helper T Cells - human immune cells which help coordinate the body's immune
response
What is an example of a retrovirus? - HIV
Describe HIV. - and not coordinating the immune system, which causes AIDS and that is
what people actually die from, because their immune system can't fight off the other
diseases.
We've come up with a cocktail of drugs that fight the virus on all sides, destroying the
reverse transcriptionase, integrase, etc.
Integrase - the enzyme that integrates the retroviral DNA into the organism's DNA
How do viruses make us sick? - They take the function away from our cells
We can get secondary bacterial infections because some viruses are lytic and the
bacteria then feed on the cellular debris released
Inflammatory reponse all over causes fluid build up, hemmoraging: like swelling from a
bump, but all over your body
What are the two hypothesis for virus evolution? - Viruses evolved from cells
Cells evolved from viruses

What evidence supports the hypothesis that cells evolved from viruses? - They have
found genes in mimi viruses that haven't been found in any other virus:
- Translation proteins
- DNA repair proteins
- Protein folding proteins
What idea supports the hypothesis that viruses evolved from cells? - first virus arose as
an accessory chromosome leaving a bacteria cell
Which of the two hypothesis for virus evolution has enough evidence to prove its true? neither, no fossil evidence to act as a window through time, alternate methods have not
yet provided enough evidence
How are viruses classified? - by the properties of their genome (how they make mRNA)
How many classes of viruses are thee? - 6
What does the baltimore classification system depend on? - 1. The viral genome
2. The pathway to make mRNA
Class I virus. - - Double stranded DNA virus
+/- DNA --> +mRNA
ex: herpes virus
Class II virus. - - Single stranded DNA
+DNA --> +/- DNA --> +mRNA
ex: parvovirus, in humans: parvovirus
Class III virus. - - Double stranded RNA
+/- RNA --> +mRNA
ex: retrovirus, colorado tick fever
Class IV virus. - - Single stranded RNA
+RNA --> -RNA --> +mRNA
ex: Picornavirus, Rhinovirus
Class V virus. - - Single stranded RNA

-RNA --> +mRNA

ex: influenza
Class VI virus. - - Single stranded RNA
- Retrovirus
ex: HIV
+ RNA --> -DNA --> +/- DNA --> +mRNA
How does flu get so deadly? - When one person gets infected with flu from several
different animals or places at the same time in the same cell, they recombine their DNA
to produce a new recombined virus that we don't have a vaccine for.
Reservoir - the human and the one cell in that human where all of the viruses are
reproducing at the same time, resulting in a new form of the virus
Epidemic - if a new recombined deadly flu virus spreads
Pandemic - if a new recombined deadly flu virus spreads all over the world
Virus Vaccine - takes a virus and kills it, rendering it inoperable, making you a little sick,
but not much, so your immune system can recognize it when the real "live" virus comes
in
Prions - misfolded protein which cause surrounding proteins to unfold, they are
"infectious" proteins
What is an example of a prion? - Mad Cow Disease - in brain aka bovine spongiform
encephalopathy
How humans got it: used any part of cow to make burger (including bone (the part of the
cow that had the misfiled protein))
How animals got it: the cos were being fed bone meal of infected organisms
What causes a prion? - a mutation to a gene that makes proteins

Can prions be passed from one species to another? One organism to another? - Yes,
yes
What are other examples of a prion? - Kuru disease - eating family's brains
Fatal familial insomnia - mutation in gene that causes prions to be made which are then
deposited in the thalamus, preventing the person from sleeping
Chronic wasting disease - a transmissible spongiform encephalophy condition passed
on from deer and elk
Scrapie - a transmissible spongiform encephalopathy condition which affects the
nervous systems of some sheep and goats
Creutzfeldt - Jakob disease - transmissible spongiform encephalopathy condition which
affects some human brains