Enriched Biology Notes pay back daddy lunch money

Levels of Knowledge

Fact An observation that is repeatedly confirmed.

Hypothesis A testable statement about the natural world.
Law A generalization about how something works in the natural world
(describes behaviors).
Theory (in science) A well substantiated explanation of an aspect of the
natural world (the best possible explanation).

Scientific Method

Purpose or Problem statement

Hypothesis
o Ifthenbecause
Methods and Materials
Results
Conclusions
o Mention hypothesis (accepted or rejected), errors that have occurred in
the lab (scientific errors), analyze results (this is what we got, this is
why I think we got this).

Lab write-up

Analyze:
o The quality of your experimental design.
o The quality of your write-up.
Make notes or comments in a different colored writing utensil.
Dont panic. You will have the opportunity to re-do.
What are the elements of a good Purpose?
o Detailed yet brief.
o Includes variables (What are you changing? What are you measuring?)
Independent variable: The variable that doesnt depend on other
variables and the one that you change during the experiment.
Dependent variable: What youre measuring. Its dependent on
the independent variable.
What are the elements of a good Hypothesis?
o Independent and dependent variables.
o Prediction of results.
o Justification for prediction (background information)
o Ifthenbecause format for hypothesis.
What are the elements of a good methods section?
o Detailed!
Step by step instructions
List all materials needed for the experiment to succeed
o Multiple trials

o
o
o
What
o
What
o
What
o

What
o
o
o

Control
Single variable being tested
Constants
is a control group?
The absence of the independent variable.
is an experimental group?
The group with the independent variable.
is a constant?
All the details that should stay the same throughout the entire
experiment in both the experimental and the control group.
Example: amount of soil, amount of water, etc.
makes a good conclusion?
Was your hypothesis supported or rejected?
Dont use the word prove
Explain your data.
Sources of Error vs. Whoopsies

Unit 1: Biochemistry
Chemistry Review

Matter anything that takes up space

o Atoms:
Most common atoms in living things are: C, H, O, N and P, S
Nucleus contains:
Protons (positive charge)
Neutrons (no charge)
Electrons (negative charge)
o Energy levels: Energy of electrons, based on
distance from nucleus.
Octet Rule:
Atoms want to fill outer energy level
Share, donate, or accept electrons
Example: Carbon
6 total electrons
4 valence electrons:
o Electrons in outermost energy
level
o Involved in chemical bonds
Molecule: 2+ atoms bonded together
o Examples: H2O, C6H12O6 (Glucose), DNA

Chemical Bonds

Strong Bonds:
o Covalent Bonds share electrons
Polar Bonds share electrons unevenly

Ionic

Example: H2O
Non-Polar Bonds Share electrons evenly.
Example: Methane (CH4)
Bonds attraction between opposite ions
Example: Sodium Ion, Chloride Ion, Positive Sodium Ion,
Negative Sodium Ion.

Weak Bond:
o Hydrogen Bonds strong attraction, but a weak bond!
Hydrogen Bonds are the strongest kindergartners.

Properties of Water

Cohesion water is attracted to itself.

Adhesion water is attracted to other substances.
Temperature moderation takes a lot of energy to heat up.
Solvent Used to dissolve many substances.

Biochemistry

Biochemistry is a discipline which focuses on the chemicals of living

organisms.
o Bio- means life.
All biological molecules are organic.
All organic molecules have carbon in them.
The Carbon atom: 4 valence electrons means it has a lot of bonding
possibilities.
Most biological molecules are Polymers (chains) of smaller Monomers
(subunits).

Macromolecules

Polymers: Train-like (or chain-like) molecule made of repeating monomers.

o Poly- means many.
Monomers: The building blocks or subunits of polymers.
o Mono- means one.
Polymers are made through a process called Condensation Reactions.

Condensation Reactions

Similar to linking box cars together, these reactions:

o Link monomers together.
o Form relatively strong bonds where energy is stored.
o Form water as a by-product (hence the name condensation reactions).
OH + OH = H2O
o If Condensation reaction builds a polymer, what breaks it down?

Hydrolysis

Polymers are broken down through a process called Hydrolysis.

o Think of this like dismantling the train.
o The bonds holding monomers together are broken, releasing energy.
Hydrolysis Reactions Use water to help break polymers apart into their
smaller monomers.
o Hydro- means water.
o lys means to break.
All Biological molecules are synthesized and hydrolyzed in the same way.

4 Main Macromolecules

Carbohydrates: The main fuel which run most living organisms.

o Structure:
Ring-shaped molecules.
Three main types of carbohydrates:
o Monosaccharides (Simple Carbohydrates)
Primary monomer of carbohydrate polymers.
General formula for all monosaccharides is C6H12O6.
All monosaccharides have the same chemical formula.
Examples: Glucose (C6H12O6), Galactose, Fructose.
o Disaccharides
2 monosaccharide monomers bonded/linked together.
General formula for all disaccharides is C12H22O11.
When 2 monosaccharides are bonded together, water is created
as a by-product; therefore, the formula will be missing 2 H and 1
O molecule.
Examples: Maltose, Sucrose, Lactose.
o Polysaccharides (Complex Carbohydrates)
Complex carbohydrates.
Long chains of monosaccharides bonded together.
No general formula because there are so many different
forms of monosaccharides.
Examples:
o Glycogen (stores energy in animals).
o Cellulose (found in plant cell walls).
High fiber carbohydrate.
Human body cannot break down cellulose;
therefore, it is not digested.
o Starch (stores energy in plants).
Lipids:
o Fats, oils, waxes, phospholipids, etc.
o Structure:
All lipids have fatty acid tails.
Saturated fats:
Long, straight chains of Hydro-carbon atoms.
Saturated with Hydrogen atoms.

o Solid at room temperature.

o Animal products
Unsaturated fats:
Long, kinked chains of carbons due to one or more double
bonds.
o Unsaturated with Hydrogen atoms.
o Liquid at room temperature.
o Plant products
o Functions:
Long term energy storage molecule.
Insulation (blubber)
Cell membranes (Phospholipids)
Protective coating
Steroids (Cholesterol)
o Extra information about lipids:
Low Density Lipoproteins (LDL):
Bad kind of lipid. Causes blockages in blood vessels.
High Density Lipoproteins (HDL):
Good kind of lipid. Removes cholesterol from blood.
Trans Fats
Use a chemical catalyst to add hydrogen atoms to an
unsaturated fat to make it a Saturated Fat.
By hydrogenating, you make them more attractive for
cooking and extend shelf life.
Problems with Trans Fat:
o Body cannot metabolize or remove Trans fats, so
they stay in the blood stream longer.
o Contribute to coronary heart disease by raising
levels of (LDL) and lowering levels of HDL
o Suspected as contributing to other conditions such
as certain types of cancer, diabetes, and obesity.
Nucleic Acids
o DNA (Deoxyribonucleic Acid), RNA
o Structure:
Large Polymer
Monomers are called nucleotides.
Each nucleotide contains:
o One 5 Carbon sugar
Called Deoxyribose in DNA
o One phosphate group
o One nitrogen base
Adenine
Thymine
Cytosine
Guanine
Uracil

o
o

Phosphate Pentose Sugar

Nitrogenous Base
The order of the nucleotides determines how
people/animals look.
Functions:
DNA stores genetic information.
RNA used as codes or templates for making
proteins.

Proteins
o Grouped according to their function.
o Skin, hair, muscle, blood, enzymes are made of proteins.
Structure:
o Tons of different types and shapes of proteins.
o Monomers are called amino acids.
Amino group NH2
Every single amino acid has NH2
All amino acids also have a Carboxylic acid group (C(O)OH)
The R group (side group) changes depending on what amino
acid it is.
There are 20 types of amino acids.
Arranging these in different combinations allows for a
huge diversity of proteins.
Analogy: Our 26 letter alphabet can be used to create millions of
different words.
o Peptide bonds:
Formed between 2 amino acids following a condensation
reaction (rxn) between the acidic group and the amino group.
Amino acids form H-bonds with each other to produce different
3D shapes.
Proteins: Energy and Enzymes
o Energy The ability to do work or cause change.
Potential Energy Energy of position.
Kinetic Energy Energy of movement.
Exothermic Energy Diagram (Energy that is released from the reaction)

Endothermic Energy Diagram (Energy is needed/gained)

Enzymes
o Proteins that speed up chemical reactions (AKA organic catalysts).

Enzyme Structure
Very specific 3-D shape.
Active Site Pocket of the enzyme that binds to the substrate
(reactant).
Each enzyme can only work with certain reactants
because of the specific shape.
Enzyme Function
1. Substrate binds to active site of the enzyme.
2. Enzyme lowers activation energy and reaction occurs faster.
3. Products are released.
Activation Energy
o The energy needed to start a chemical reaction.
Example
Salivary amylase
Enzyme in spit that breaks polysaccharide (starch) down
to the monosaccharide (glucose).
o If it ends with -ase, its most likely an enzyme.
Coenzymes
(AKA Cofactor) assist in enzyme action by being part of the
active site.
Example:

o Vitamins
Competitive Inhibitors
Bind to the active site but dont react; slow the reaction by
getting in the way.
Factors Affecting Enzymatic Speed
o Enzyme Concentration
Increase enzymes, increase enzyme activity.
Due to more collisions between substrate molecules and
the enzymes.
Will eventually level out.
o Substrate Concentration
Increase substrates, increase enzyme activity.
Due to more collisions between substrate molecules and
the enzymes.
Will eventually level out when the number of enzymes
and substrates even out.
o Temperature
Increase in temperature increases enzyme activity. (Up to a
certain point)
If the temperature is too high, enzyme activity levels out and
then declines rapidly because the enzyme gets denatured.
Denatured: A change in the shape of the enzyme where
its no longer functional.
The same thing happens if the temperature gets too cold.
o pH
Each enzyme has an optimal pH at which the rate of reaction is
highest.
Too drastic of a change in pH will also lead to denatured
enzymes.
o

Unit 2: Cells
Types of Microscopes

Compound Microscope
o Allows humans to see things so small that it cannot be seen with the
naked eye.
o Allows us to see individual cells.
Stereomicroscope
o Sees things in greater detail.
o Sometimes called a Dissecting scope.

Microscope Terms

Magnification: How much large an object appears.

For our scopes:
o Eyepiece

 10x magnification
Objective lenses
Scanning: 4x magnification
Low: 10x magnification
High: 40x magnification
o Total magnification
Scanning: 40x magnification
Low: 100x magnification
High: 400x magnification
Resolution: The ability of a microscope to distinguish two objects as
separate.
Field of View: Everything that can be seen through a microscope.
Depth of Field: Portion of field that appears sharp.
o Determined by adjusting the fine adjustment knob.
o

Microscope Lab Skills

Carrying: 2 hands, 1 hand on arm, and 1 hand on base.

Preparing a wet mount:
o Obtain a clean slide.
o Put a drop of water on the slide and put your object on top of it.
o Obtain a clean cover slip and put it over your object at a 45 o angle and
slowly push it down into place.
Focusing:
o Always begin with the scanning objective lens.
o Use the course adjustment knob to adjust focus only when the
scanning objective lens is in use.
o Never use the course adjustment knob when using the high power
objective lens.
o Use the fine adjustment knob when using high and low power lenses.

Cells

Discovery of the cell

o Robert Hooke (1635 1703): First identified cells using a microscope.
o Anton von Leeuwenhoek (1632 1723): First person to identify living
cells.
o Cell Theory: (Schleiden, Schwann & Virchow, 1839)
All living things are made up of cells.
Cells are the basic unit of structure and function in all living
things.
Cells come only from the reproduction of living cells.
Cells are limited in size.
The only cell that is visible to the naked eye is a human egg cell.
Why are they limited in size?
o Specific cells for specific functions.
o They could fall apart if theyre too big.

Cell size: Small cells are more efficient because of the high surface area to
volume ratio.

Eukaryotic Cells (plants, animals, fungi, protists)

Eukaryotic Cells

Eukaryotic Cells: Have a nucleus and other organelles.

Animal Cells

Have all the following structures/organelles:

o Cell (plasma) membrane:
Regulates what enters/exits the cell.
o Cytoplasm:
Cells interior; water with stuff dissolved in it.
o Cytoskeleton:
Provide internal structure within the cell.
Microtubules Tracks for transporting vesicles.
Microfilaments Support, muscle contractions.
Intermediate Filaments Holds things in place.
o Ribosomes:
Help build proteins.

Organelles

Organelles Membrane bound structures.

o Nucleus:
Contains DNA, controls the cell.
Nucleolus:
Makes ribosomes.
o Endoplasmic Reticulum (ER):
Rough ER: Contains ribosomes; transports proteins.
Smooth ER: Makes fats; breaks down toxins.
o Golgi Apparatus:
Modifies proteins from Rough ER.
o Vesicles:
Transports materials through cell; rides on tracks of
cytoskeleton.
o Lysosomes:
Digests materials not needed by the cell.
o Mitochondria:
Produce energy for the cell (powerhouse of the cell).

Plant Cells

Plant cells have all of the above (animal cells) PLUS

o Vacuoles:

o
o

Store material (water).

Plant cells and some protists.
Cell Wall:
Protective barrier; supports cell shape.
Chloroplasts:
Produce energy by photosynthesis.

Animal Cell

DNA inside
nucleus

Plant Cell

Prokaryotic Cells

Prokaryotic Cells
o Ex: Bacteria
o Smaller than eukaryotic cells.
o Contain no membrane bound organelles, only:
Cell membrane
Cytoplasm
Ribosomes
Ribosomes are pieces of RNA. RNA are pieces of rewritten
DNA.
Nuclear Material
DNA
RNA
Cell Wall

Other Cell Structures

Modes of Locomotion (movement):

o Flagella: Long, whip-like tails.
o Cilia: Short hair-like projections.

Cell Transport

Cells regulate movement of materials across their membrane.

o This maintains internal balance (we call this homeostasis) despite
changes in their environment.
Cell (plasma) membrane: regulates what can enter or exit a cell
o Selectively permeable: Only certain substances may pass through.
Fluid-Mosaic Model Name scientists use to describe the structure of the
cell membrane.
o Membrane acts more fluid than solid.
Components:
o Phospholipids
Head: Hydrophilic (polar) (loves water)
Two fatty acid tails(long Hydrocarbon chains): Hydrophobic (nonpolar) (hates water)
Lipid Bilayer: Two layers of phospholipids, move laterally.
If you added phospholipids to a mixture of oil and water, where
will they align?
Heads facing the water, tails facing the oil.
o Proteins: Perform various jobs within the membrane
Peripheral Proteins: Act as enzymes; NOT embedded in bilayer,
on the surface.

Integral Proteins: Regulate transport across membrane, serve as

markers; extend across entire membrane. Fully embedded in
membrane.
Polar ends, non-polar mid section.

Membrane Transport

Equilibrium: Molecules move until the concentration is the same throughout a

space.
Concentration gradient: A difference in concentration of a substance across a
space.
Passive Transport: When molecules move from a high concentration area to a
low concentration area.
o The movement of molecules, across the membrane, that does NOT use
energy.
o Substance moves down the concentration gradient (from high to low
concentration).
o 3 main types:
Diffusion
NET movement of molecules from high to low
concentration.
o Ex: food coloring, perfume, sugar cube
Osmosis
The diffusion of water.
Solvent molecules can diffuse across a membrane.
Set up Eggs
o Types of Solutions
Hypotonic: Solution with less dissolved
particles than the inside of the cell.
Hypertonic: Solution with more dissolved
particles than inside of the cell.
Isotonic: Solution with the same amount of
dissolved particles as the inside of the cell.
Turgor Pressure: The pressure that water
exerts against the cell wall.
Plasmolysis: Loss of pressure when cell
shrinks away from cell wall.
Cytolysis: Animal cells bursting due to water
diffusing into the cell.
Facilitated diffusion
Diffusion of molecules across a membrane using a
channel or carrier proteins.
o Carrier proteins: Similar to enzymes, in that a
specific shape allows a specific molecule to pass.
o Channel Protein: An open passage for molecules to
pass through.

Active Transport
o Transport of substance against the concentration gradient.
Molecules move from low concentration to high concentration.
Uses energy and a membrane protein.
Vesicular Transport
o Movement of large amounts of material using a vesicle.
Endocytosis: Moves substances into the cell.
Exocytosis: Moves substances out of the cell.
Unit 3: Energy (Cellular Respiration and Photosynthesis)
Types of Energy

Kinetic Energy Energy of motion.

Potential Energy Stored energy (energy of position).

Laws of Thermodynamics

First Law of Thermodynamics

o Energy cannot be created or destroyed, it only changes forms.
Examples:
Dropping a book.
Dropping an object.
Potential energy Kinetic energy Sound/heat energy.
Converting food energy into usable (ATP) energy in our
cells.
o Heat is given off in every energy transfer.
Second Law of Thermodynamics
o Entropy of the universe always increases.
The universe is always moving closer to chaos (entropy).
Entropy Measure of disorder (randomness/chaos).
o If entropy always increases, why can we clean our rooms?
Room is a closed system.
Use energy to clean.
Put energy into a closed system.
Using energy actually increases entropy.
By putting energy into something (like cleaning your
room) you are increasing the entropy of the universe.
Living things work this way we require an input of energy
therefore we increase the entropy of the universe.
o Heat is a highly disordered form of energy.

Overview of Photosynthesis

Where does all the energy that supports life come from?
o The sun
Sunlight

o
o
o

Photosynthesis converts solar energy into the chemical energy:

6CO2 + 6H2O + Sun C6H12O6 + 6O2
Cellular Respiration
C6H12O6 + 6O2 6CO2 + 6H2O + ATP
Autotrophs: Organisms that can produce their own food.
Example: Plants, algae, and certain bacteria.

Overview of Cellular Respiration

Converts food energy into usable energy, called ATP, for the cell (+heat)
C6H12O6 + 6O2 6CO2 + 6H2O + ATP
Heterotrophs: Organisms that get their energy from another source.
o Example: animals, fungi, bacteria, protists.

Overview of important molecules

ATP Adenosine Triphosphate

o Structure
Adenine (nitrogen base)
Sugar
THREE phosphates
o Energy in bonds between phosphates.
o Function
Provides energy to cell for cellular processes and chemical
reactions.
Entire pool of ATP is recycled once per minute.
o ATP + H2O ADP + Inorganic Phosphate + Energy
ATP Cycle
o ATP breaks down into ADP + phosphate
Use energy!
Movement
Active Transport
Making molecules
o Transport energy from food to replenish the missing phosphate group
Make ATP!
Breakdown of food.
Food molecules: (carbohydrates, lipids, proteins)
o Food contains potential energy.
o By breaking the chemical bonds in the good, we can release energy
and transfer it to other forms.
Food
Release energy quickly producing heat and light
Release energy slowly in the form of ATP
Wait doesnt food provide energy? Why do we need ATP?
o We cannot utilize the energy that directly comes from food, so we need
to convert it into ATP so our body can use it.
Electron Carriers: Temporary energy storing molecules.

NADH and FADH2; NADPH

NADH (Nicotinamine Adenine Dinucleotide)
FADH2 (Flavin Adenine Dinucleotide)

Energy in Heterotrophs making ATP

Overview:
o 3 Methods to make ATP.
Phosphocreatine
Glycolysis and (Lactic Acid) Fermentation
(Aerobic) Cellular Respiration
o Track two things:
What energy transfers are occurring?
Where are the carbon atoms?
Phosphocreatine: Enzyme that adds Pi (Phosphate) directly onto ADP to make
more ATP.
o Used for quick energy.
o Anaerobic (doesnt use oxygen)
o Stored in muscles.
o Only works for ~30 seconds!
1. Glycolysis: The partial breakdown of glucose.
o Features:
Used for short term energy production.
Anaerobic
Occurs in the cytoplasm.
o Process:
Priming: ATP is used to add phosphates to glucose.
Cleavage: 6C unit split into 2 3C units.
Energy Recovery: Production of ATP and NADH.
Ends with 2 molecules of Pyruvate (AKA Pyruvic Acid).
Electron Carriers:
o NADH is formed to temporarily hang on to energy before making ATP.
Nicotinamine Adenine Dinucleotide.
o NAD+ and NADH are recycled over and over again!
Glycolysis Summary
o Inputs
Glucose
2 NAD+
2 ATP
4 ADP + 2 P
o Outputs
2 Pyruvate
2 NADH
2 ATP (NET gain)
After Glycolysis, the fate of Pyruvate depends
o Oxygen Absent
Fermentation

Oxygen Present
Cell Respiration

Energy in Heterotrophs Fermentation

If oxygen is NOT available, fermentation occurs.

o Fermentation Anaerobic process (does not require oxygen).
o In animals Lactic Acid Fermentation
Pyruvate is converted into Lactic Acid.
o In plants and yeast Alcoholic Fermentation
Pyruvate is converted into ethyl alcohol (ethanol) and CO 2.
Why go through Fermentation? Why not just stop and wait for Oxygen?
o To regenerate the NAD+.
o Need Glycolysis to take place even when theres no Oxygen.
o Fermentation regenerates NAD+ from NADH so that Glycolysis can
repeat.
Recall: NET of 2 ATP produced in Glycolysis!
Why is Fermentation cool
o Alcoholic Fermentation.
If the plants are dead, what is alive that undergoes Glycolysis?
o Bacteria or yeast consumes the cells of the dead plant and it
undergoes Glycolysis.

Energy in Heterotrophs

Fate of Pyruvate
o Oxygen absent
Fermentation (in cytoplasm)
o Oxygen present
Cellular Respiration (transition into mitochondria)

Energy in Heterotrophs Cellular Respiration

If oxygen IS available, cellular respiration continues in the mitochondria:

o 4 main steps of Cellular Respiration:
1. Glycolysis
2. Transition reaction
3. Krebs Cycle
4. Electron Transport Chain
Features:
o Used for long term energy production.
o Aerobic (requires oxygen)
o Occurs in mitochondrial matrix
o Can use glucose, fats or proteins as fuel.
The Mitochondria:

2. Transition Reaction

Occurs between cytoplasm and the mitochondrial matrix.

o Pyruvate combines with Coenzyme A (CoA) to produce Acetyl-CoA.
o 2 CO2 released
o 2 NAD+ is reduced to 2 NADH
End of Transition Reaction
o So
Where is the potential energy of glucose now being stored?
Some of it is in the NADH, and some of it is in the AcetylCoA.
In addition to ATP and NADH from Glycolysis.
Where are the 6 carbons we started with?
2 C exhaled as CO2
Other 4 C in Acetyl-CoA (2 each)

3. Krebs Cycle (Citric Acid Cycle)

Acetyl-CoA combines with a 4C molecule.

The 6C molecule releases a CO2, and NAD+ is reduced to NADH.
The 5C molecule releases another CO2, and NAD+ is reduced to NADH.
ATP is generated.
FAD+ and NAD+ are reduced to FADH2 and NADH.
The 4C molecule is recycled.
Happens two times.
NET Output of Krebs Cycle (per glucose molecule)
o 6 NADH
o 2 FADH2
o 2 ATP
o 4 CO2
End of Krebs
o So
Where is the potential energy of glucose now being stored?
NADH, FADH2, ATP

In addition to ATP and NADH from Glycolysis and

Transition.
Where are the 6 carbons we started with?
All 6C exhaled as CO2

4. Electron Transport Chain (Electron Transport System)

Whats involved?
o Electron carriers: NADH and FADH2 are temporarily storing energy.
o Electron transport proteins: Membrane proteins (part of the
mitochondrial membranes).
H+ Pumps: Membrane protein to pump a proton against
concentration gradient.
ATP Synthase: Protein that uses energy released by movement
of protons down concentration gradient to make ATP.
This process is called Chemiosmosis.
o Oxygen: An input and final electron acceptor of the process.
Catches electrons and binds to H+ to form water.
Process
o How many ATP does each NADH yield?
3 ATP
o How many ATP does each FADH2 yield?
2 ATP

Aerobic Cellular Respiration

C6H12O6 + O2 H2O + CO2 + ATP

C6H12O6 Glycolysis
O2 ETC
() +H+ + eH2O ETC
CO2 Transition (2) Krebs (4)
ATP

Energy in Heterotrophs Making ATP

End of electron transport chain:

o Where is the potential energy of glucose now being stored?
ATP
o Where are the 6 carbons we started with?
Exhaled as CO2

Energy in Autotrophs: Photosynthesis

Light Energy:
o Light is a wave.
Wavelength () Distance between two peaks.

Small wavelength = higher energy

Large wavelength = lower energy
Different wavelengths reflect different colors.
o Pigments: Molecules that absorb/reflect sunlight.
Examples:
Chlorophyll (absorbs red, reflects green)
Carotenoids (absorbs violet/blue, reflects yellow/orange)
How they work:
Molecules absorb a photon of light.
Electrons become energized and jump to a higher energy
levels.
Electrons typically fall back down, but in photosynthesis
they are caught by electron carriers and are used to do
work.
Photosynthesis:
o Takes place in the Chloroplast:
Thylakoid: Flattened disc; contains chlorophyll.
Stroma: Fluid filled region.
Grana: Stacks of Thylakoids.

2 Reactions
1. Light-dependent reactions
Occurs in Thylakoid membrane.
2. Light-independent Reactions (AKA Calvin Cycle)
Occurs in Stroma.
Also known as Carbon fixation.
Process
Light-dependent Reactions:
1. Sunlight excites e- in chlorophyll of photosystem II and
caught by an e- acceptor.

2. e- transferred along an electron transport chain (ETC).

3. Sunlight excites e- in photosystem I and again, it is
caught by an e- acceptor.
4. e- are transferred along the ETC and will eventually
combine with NADP+ to make NADPH.
5. Restoring Photosystem II:
o Enzyme in Thylakoid splits water into protons,
electrons, and oxygen. (H2O e- + H+ + O2)
o Electrons replace photosystem II; protons are left
inside Thylakoid; oxygen gas diffuses out.
6. Synthesis of ATP:
o Chemiosmosis: Build up of a H+ concentration
gradient (high in Thylakoid space).
o ATP Synthase: Located in the Thylakoid membrane,
makes ATP as H+ moves down the concentration
gradient.
Order of pigments is photosystem II, then photosystem I.
Light-independent Reactions (AKA Calvin Cycle):
1. CO2 enters and combines with RuBP to form PGA.
2. ATP and NADPH provide energy and H+ to convert PGA
to PGAL.
3. Most PGAL is converted back to RuBP, but some is
eventually used to make GLUCOSE!

Cell Reproduction
Human (Eukaryotic) DNA

Storing DNA
o Nucleus:
Nuclear Envelope: Double membrane surrounding the nucleus.
Nuclear Pores: Small holes in the membrane.
o Packaging DNA
Chromatin Long, thin, uncoiled DNA.
Histone Proteins DNA wraps around to help coil.
Chromosomes DNA coiled, thick (stored this way for
replication).
Chromosome (cont.)
Replicated Chromosomes
Chromatin replicates itself into 2 identical pieces of
chromatin.
Chromatin condenses and forms 2 identical chromosomes.
Chromosomes connect together at a structure called
centromere. When they stick together at the centromere,
it creates one big chromosome made up of two identical
chromatids.

Sister Chromatids Exact copies of DNA

Centromere Connects sister chromatids.
Karyotype: Photograph of all chromosomes in a cell.
o Homologous Chromosomes Two chromosomes that carry the same
type of information, but are not identical.
Autosomes Non-sex chromosomes (22 pairs).
Sex Chromosomes Usually XX or XY; determines sex (1 pair).

Quiz Time

How many chromosomes do human cells have?

o 46
How many pairs of chromosomes do humans have?
o 23
Autosomes?
o 22
Sex chromosomes?
o 1

Prokaryotic Cell Division

Binary Fission:
o (Remember: no nucleus)
o Single piece of DNA (circular)
o Copies DNA
o DNA moves to opposite sides.
o Cell divides in half.
o Happens very fast.

Eukaryotic Cells

Cell Cycle: Sequence of growth and division of a body cell.

o Importance: Growth, healing, and repair.
o 3 main parts:
Interphase
Mitosis
Cytokinesis
Structures involved:
o Chromosomes: DNA
o Spindle Fibers: Microtubules that attach to the centromere and move
chromosomes.
o Centrioles: Structures that anchor the spindles at opposite ends of the
cells.

Cell Cycle: Interphase

Interphase is the cell carrying out its normal life activities and chromosomes
become duplicated.

G1 Gap between cell division, cell grows.

G0 Gap phase. Cells are NOT undergoing any preparation for cell division
just being.
S Synthesis; DNA is copied.
o When the DNA is copied inside the nucleus. Its preparing for the cell to
divide.
G2 Gap cells prepare for division; Centrioles replicate, spindles form.

Cell Cycle: Mitosis

Prophase:
o Chromatin coils to form visible chromosomes.
o Nuclear membrane and nucleolus disappear.
o Spindle fibers form between Centrioles, which move to opposite ends
of cell.
Metaphase:
o Chromosomes meet in the middle.
o Each chromatid is attached to separate spindle fibers.
Anaphase:
o Centromeres split and sister chromatids separate as they are pulled
apart to opposite sides of cell.
Telophase:
o Nucleus and nucleolus reappear.
o Cells form two new daughter nuclei.
o Chromosomes begin to uncoil
o Cell begins to divide.

Cell Cycle: Cytokinesis

Cytokinesis: Complete division of cytoplasm.

o In plants, cell plate forms and eventually becomes the cell wall that
separates the two cells.
o In animal cells, a protein ring encircles the plasma membrane.
Ring contracts producing a cleavage furrow.

Human Life Cycle

Haploid cells (n): Only one copy of each chromosome.

o Ex: Gametes Egg and sperm cells.
o n = 23 in humans.
(n) = Haploid.
Diploid cells (2n): Two copies of each chromosome.
o Found everywhere except where the egg and sperm cells are produced.
o Found in most body cells.

2n = 46 in humans.

Eukaryotic Division for sex cells

Meiosis:
o Cell division that produces sex cells (sperm/egg).
o This is DIFFERENT from mitosis/the cell cycle (which is used for growth
and repair).

Meiosis

Two Divisions:
o Meiosis I:
Separates homologous chromosomes (the pairs).
Diploid haploid.
Total of 2 haploid cells at the end of division.
1 Diploid cell divides into 2 haploid cells.
o Meiosis II
Separates sister chromatids (the Xs).
Haploid haploid
Total of 4 haploid cells at the end of division.
2 Haploid cells divide into 4 haploid cells.

Meiosis: The Process

DNA is replicated before Meiosis I occurs.

Meiosis I: Separation of chromosomes.
o Prophase I
Synapsis: Pairing of homologous chromosomes.
Crossing Over: Process where regions of DNA are exchanged.
o Metaphase I
Homologous pairs meet in the middle.
o Anaphase I
Homologous pairs pulled apart to opposite poles.
o Telophase I
DNA uncoils and one of each pair of homologous chromosomes
is at each pole.
Cytokinesis occurs.
Haploid cells are formed.
Meiosis II: Separation of chromatids.
o Prophase II
Chromosomes condense again.
DNA does not replicate again.
o Metaphase II
Chromosomes line up in the middle of the cell.
o Anaphase II
Sister chromatids separate.

 Chromosomes are pulled to opposite poles.

Telophase II
Nuclei forms around the Chromosomes.
Cytokinesis occurs.
o Haploid Cells
Four gametes (animal)/spores (plant) are produced.
Pictures on next page.
o

Law of Independent Assortment

Each pair of chromosomes acts independently of the other pairs.

o This leads to endless possibilities of gametes that we can produce!

Fertilization

Haploid Gamete (sperm) + Haploid Gamete (egg) = Diploid Zygote.

23 + 23 = 46

Errors in Meiosis

Changes in Chromosome Number:

o Non-disjunction: Failure of homologous chromosomes or sister
chromatids to separate properly during meiosis.
o Ex: Downs Syndrome Extra 21 chromosome.
o Ex: Turners Syndrome X_ (missing X chromosome)
o Ex: Klinefelters Syndrome: XXY (extra X chromosome)
Changes in Chromosome Structure:
o Mistakes occurs during crossing over.

Deletion Part of chromosome gets lost during crossing over.

Duplication Part of chromosome gets copied during crossing
over.
Inversion Part of chromosome gets flipped upside down during
crossing over.
Translocation Part of chromosome switches places with another
chromosome.
Ex: Cri du Chat
Symptoms
o Small head (microcephaly)
o Unusually round face
o Misshapen voice box cat-like cry as infants.

Sexual vs. Asexual Reproduction

Asexual Reproduction A single parent passes copies of all its genes to each
of its offspring (a.k.a. clone)
o Clones may be produced by:
Binary fission
Mitosis
Fragmentation
Budding
Sexual Reproduction Two parents each form haploid gametes.
o Gametes fuse together to form a diploid zygote.
o Offspring have genetic variation due to the fusion of two different sets
of chromosomes.
o Occurs only in eukaryotes, including humans.

Effect on Genetic Diversity

Asexually reproducing organisms have very little genetic diversity.

o Many offspring in a short period of time.
Sexually reproducing organisms have great genetic diversity.
o Each generation has genetic variation.

Cancer
Cancer Unregulated cell growth.
o Cell cycle continues uncontrollably.
o Keeps dividing and dividing doesnt stop.
Tumor: Cluster of cells from unregulated growth.
o Benign
Not dangerous
Not going to affect the body that much
o Malignant
Dangerous
Malicious

Metastasis
o Occurs in malignant tumors
o Cancerous cells spread to different parts of the body the through
bloodstream.
Risk factors
o Sun exposure (UV rays)
o Smoking
o Family history (genetics)
o Chemical exposure
o Radon
o Radiation
o Asbestos
Unit 5: Genetics
Gregor Mendel (1822-1884)

Austrian Monk
Developed Laws of Inheritance
Studied Pea plants (28,000)
Called the Father of Genetics
Mendel did not know that the physical traits inherited were actually
chromosomes and DNA.

Genetic Terminology

Heredity Passing of traits from parent to offspring.

Genetics Study of heredity.
Traits Any characteristic that can be passed from parent to offspring.
o Ex: Plant height, seed texture, seed color

Experiments with Pea Plants

Pollination
o Pollen is male plant sperm.
o Plants have both male and female reproductive structures.
o Self-pollination:
Flowers are fertilized by own pollen.
o Cross-pollination:
Flowers fertilized by different flowers.
Mendel produced pure strains by allowing the plants to self-pollinate for
several generations.
Parental (P) generation: Purple x White
F1 Generation: All Purple
F1 Purple x F1 Purple
F2 Generation: 3:1 Ratio purple vs. white
Generations: P, F1, F2

More Terminology

Genotype Gene combination for a trait (e.g. RR, Rr, rr)

o TT, Tt, tt
Phenotype The physical feature resulting from a genotype (e.g. red, white)
o TT = Taster
o Tt = Taster
o tt = Non-taster
Alleles Two forms of a gene (dominant and recessive) represented by
letters.
o T = Dominant allele
o t = Recessive allele.
Dominant Stronger of two genes.
o Expressed in the hybrid; represented by a capital letter (R).
Recessive Gene that gets covered up by the dominant trait.
o Represented by a lowercase letter (r).
Homozygous Genotype Gene combination involving 2 dominant or 2
recessive genes (alleles). TT, tt, or RR, rr; also called true- or pure-bred.
Heterozygous Genotype Gene combination of one dominant and recessive
allele (Tt or Rr) also called hybrid.
Law of Segregation A pair of factors is segregated, or separated, during
reproduction.

Mendels Laws and Punnett Squares

Law of Independent Assortment:
o Recall: One pair of chromosomes acts independently of other
chromosome pairs.
o New meaning: Alleles for different traits are distributed to gametes
independently of one another.
Ex: Use Rr to represent one pair of chromosomes and Yy to
represent another pair.
Dihybrid Cross: Cross involving two different traits.
o Ex: Tall (T) pea plants are dominant over short (t). Round seeds (R) are
dominant over wrinkled (r).
TT Tall
Tt Tall
tt Short
------------- RR Round
Rr Round
rr Wrinkled
o Cross a plant that is heterozygous for both traits with another plant
that is heterozygous for both traits.
Parent 1 genotype: Tt, Rr
Parent 2 genotype: Tt, Rr

Keep traits together. In the trait pairs, put the capital

letter first.
Another Dihybrid cross
Cross a Black, short haired guinea pig (BBSS) with a brown, long
haired guinea pig (bbss).

Exceptions to Mendels Laws

Incomplete Dominance: Neither allele is completely dominant; rather they

combine to create a new mixed trait.
o RR = Heterozygous
o RR = Red
o RR = Pink
o RR = White
o Ex: Cross a Pink x Pink
Codominance: Both alleles are expressed equally; both phenotypes are
produced.
o Ex: Human blood type A, B, AB, O Groups
IA, IB, i
IAIA = Homozygous dominant A genotype
IAi = Heterozygous dominant A genotype
IBIB = Homozygous dominant B genotype
IBi = Heterozygous dominant B genotype
IAIB = Heterozygous codominant AB genotype
ii = Homozygous recessive O genotype
IA and IB dominant alleles
i recessive allele
IAIB codominant allele
Rh factor Another type of marker on your cells
o If you have it, youre positive
o If you lack it, youre negative
o Positive is (dominant) over negative (recessive)
o RR = Rh+
o Rr = Rh+
o rr = RhSex-linked traits Genes that reside on the X chromosome; more commonly
found in males.
o Sex chromosomes
Recall: Females XX, Males XY
o Examples:
Colorblindness
Polygenic Traits Traits determined by multiple genes; gives a range of
phenotypes.
o Ex: Skin color, eye color, hair color, height, etc

Simple Probability

Product Rule (AKA AND rule) The probability that two events will both
happen; probability = product of their individual probabilities.
Sum Rule (AKA OR rule) Probability of an event that can happen in
multiple ways; probability = sum of their individual probabilities.

Pedigrees

Family tree that traces inheritance of a certain trait.

o May be autosomal or sex-linked.
Key
o Males = Squares
o Female = Circles
o Shaded = Affected
o Blank = Unaffected
o Half-shaded = Carrier
Not all pedigrees show carriers!

Unit 6: DNA and Protein Synthesis

DNA (Deoxyribonucleic Acid)

Rosalind Franklin and Maurice Wilkins

X-ray diffraction
James Watson and Francis Crick
Created 3D model of DNA

DNA

DNA is composed of strings of chemicals called nucleotides.

Long sequences of these nucleotides are called genes.
Genes are uniquely organized in each individual.
Entire set of DNA are genome.
Full spectrum of genomes is the gene pool.

DNA structure

Double Helix: Nucleotides are arranged like a twisted ladder.

o Sides of ladder: Alternate sugar-phosphate
Held together by covalent bonds.
o Steps: Pairs of nitrogen bases.
Held together by hydrogen bonds.
Nucleotides:
o Sugar
o Phosphate
o Nitrogen Bases
Purines:
Adenine

Guanine
Pyrimidines
Cytosine
Thymine
Guanine will always pair with Cytosine
Adenine will always pair with Thymine
T will always pair with A
C will always pair with G

DNA Replication

What do we mean by replication?

o Make copies of DNA
Why does DNA need to make copies of itself?
o So every single one of new cells have the exact same amount of DNA.
Same as the S phase of the cell cycle.
Occurs in the nucleus
Enzymes involved:
o Helicase Unzips DNA (unwinding DNA)
o DNA Polymerase Adds complementary nucleotides, forming two new
strands of DNA.
DNA Polymerase I Adds complementary nucleotides.
DNA Polymerase II Proofreads new DNA strands.
Ex: Imagine you need to replicate your DNA. Use the following template
strand of DNA to show this process.
o Write the complimentary base sequence of the new strand:
AGCCTAACTCGGGAT
TCGGATTGAGCCCTA
A with T, G with C
What happens if DNA polymerase makes a mistake and adds the wrong
nucleotide?
Mutations: Changes in the nucleotide sequence.
o Occurs when DNA polymerase adds the wrong nucleotide.
o Happens in ~1/10,000 nucleotides
Good news?...
DNA polymerase can proofread and repair mistakes!

**DNA to Protein Synthesis

Quick review
o Describe the structure of proteins
Amino Acids
o What cell structures build proteins
Ribosomes
o What do proteins do
Enzymes
Transport

Amino Acids
20 types of Amino Acids
Arranging these in different combinations HUGE
diversity of proteins.
DNA controls the cell by determining what proteins are made!
So how does it do that?
o In a 2 step process: Transcription and Translation.
Transcription
o Taking the information of DNA and transcribing (rewriting) it to RNA.
Translation
o RNA leaves the nucleus and is translated into a protein.
The process
o Transcription:
Genetic information is copied from DNA to RNA (Ribonucleic
Acid).
Re-writing of DNAs instructions in the form of RNA.
RNA structure
Single stranded
Ribose sugar
Uracil
mRNA, tRNA, rRNA
Occurs in the nucleus.
o

DNA Vs RNA

DNA
o

Sugar
Deoxyribose
o Nitrogen Base
[A, T,] [C, G]
o Function
Contains heredity information
2 strands
RNA (3 kinds)
o Sugar
Ribose
o Nitrogen Base
[A, U,] [C, G]
o Function
mRNA: Provides instruction (messenger RNA)
tRNA: Delivers amino acids (transfer RNA)
rRNA: Combines with proteins to form ribosomes (ribosomal
RNA)
1 strand

DNA to Protein Synthesis (transcription)

Whats involved?
o DNA (the gene)
Promoter Region where polymerase binds.
Termination signal Causes release of mRNA.
o RNA Polymerase: Forms complimentary base pairs between DNA strand
and RNA nucleotides.
o mRNA (messenger RNA) Molecules that will later be read to make
the protein.

DNA to Protein Synthesis: Transcription

Example: Transcribe the DNA base sequence written below

o Hint: Use complimentary base pairing to make a strand of mRNA.
DNA: G G C T T C G A A A T A C T G G T A A
mRNA: CC G A A G C U U U A U G A C C A U U
DNA (transcription) mRNA (translation) Protein

Translation:

Process
o Translation: Assembling proteins from information encoded in the
mRNA.
o Occurs with the ribosomes, located in the cytoplasm/Rough ER.
Whats involved
o mRNA (messenger RNA):
Codons 3 bases of mRNA
o rRNA (ribosomal RNA): Ribosomes Creates the protein by reading
the mRNA.
o tRNA (transfer RNA): Matches mRNA with correct amino acid
Anticodons 3 bases on tRNA, complementary to mRNA.

Mutations

Mutation: A change in the base sequence of DNA.

Four types of mutations:
o Silent mutations
o Missense mutations
o Nonsense mutations
o Frameshift mutations

Types of Mutations

Silent mutation: The change in the base sequence does not change the
amino acids.
Missense mutation: The change in the base sequence causes a different
amino acid to be inserted into the protein.

Nonsense mutation: The change in the base sequence results in a STOP

Codon, which causes the ribosome to stop adding amino acids. Protein
synthesis stops.
Frameshift mutation: A nucleotide is inserted or deleted. All the amino acids
following the mutation are incorrect.