OVERVIEW STUDY SHEET FOR BIO 34.

1
Levels of biology
o Biosphere- most regions of land that contain living organisms and organic
compounds.
o Ecosystem - all living things in a certain area and non-living things that interact with
life.
o Communities- a set of populations is an area.
o Populations- a set of individuals living w/in the bounds of a area- specific
o Organisms a uni or multi-cellular being that can functions basic of life.
o Organs and Organs systemo Organs- a group of tissue that have similar function.
o Organ system- a group of organs that also have similar function.
o Tissues- a group of cells with the same function.
o Cells- the fundamental unit of life.
o Organelles- parts of the cell
o Molecules- a chemical structure that have 2 or more atoms.
Major Biological Areas
o Orgasmic Area
1. Zoology
2. Botany
3. Microbiology
Comparative physiology- A) comparative discourse of the nature of organism
B) the comparative study of how living things function.
Organism- any multi or uni-cellular being capable of performing lifes basic function.
ARE MADE UP OF CELLS !!!!!!!!!!!!

HYPOTHETICO- DEDUCTIVE METHOD - Also known as the Scientific Method

o Make an observation
o Ask a question and formulate a hypothesis- an educated possible answer.
o Good Hypothesis
Consistant w/what is already known
Capable of being TESTED AND FASIFIED w/ CERTAIN
EVIDENCE
Is written as IF-THEN predictions
o Break-Down
make observation create a hypothesis test the hypothesis by
experiments refine hypothesis.
Experimental Design
o need a sufficient sample size to prevent chance event.
o Control group and treatment group (no on knows in what they r in)
o Control group- does not get treatment nut a placebo sugar pill
o Repeat
o Statistical testing- be sure the diff. bet. Groups was not an accident
o Peer review
Groups of Organisms
o Domains of Organism
A) Arehea B) Bacteria C) Eukarya
- Animal
-Plants
- Fungi

The types of Eukarya are called the

KINGDOMS.

Cell- is an enclosed in a cell or plasma membrane

o Are fundamental, structural, units of living things.
o 2 types of cells
o Prokaryotic- does NOT have an enclosed nucleus or INTERNAL
MEMBRANE. The DNA is located in the nucleiod region (No membrane)
o Eukaryotic- have an enclosed nucleus have interal membranes.
Homeostasis- the body normally returns to a state of equilibrium by itself.
o An organism needs to be able to detect of something is wrong.
o Acclimation- the imitate attempt of the body to response to stress on the body
o Adaptation- inherited characteristic of an organism that enhances its survival and
reproduction in specific environment.
o ONLY OFFSPRINGS ADAPTS

Metabolism All the chemical reactions in the body. ( will be later studied)
o A+BC anabolism sum of all building reactions.
o CA+B catabolism sum of all decomposition/ break-down reactions.
Chemical Reactions
o Occurs when atoms combine w/other atoms to form molecules break-down.
Synthesis
Decomposition reaction
A+BC
AB A+B
CHEMICAL REATIONS CELLS ARE PART OF METABOLIC PATHWAYS
3 TYPES OF METABOLIC PATHWAYS
a) Simple linear pathway
b) Branch pathways
c) Cycle

Feedback- regulate metabolism.

o There are enzymes to help regulate the chemical reactions (metabolism)
o One specific enzymes for EACH REACTION

In a feedback the enzyme report the amount of product of the reaction from the
beginning of the reaction to the end.
o HOWEVER IN A FEEDFOWARD the enzyme from the end of the reaction
report back to the beginning of the reaction.
o Negative- stops
o Positive- speeds up the reaction.
o

ACTIVATION ENERGY

Energy is absorbed to start reaction.

Energy is releases as new bonds form.

o The enzyme speeds up a reaction by lowering it activation energy.

o The activation energy is received from the surrounding environment.
WHAT IS MOLECULE?
Molecule 2 or more atoms that are chemically bonded together.

Atom- the smallest particle of an element.

Chemical bonds- forces holding 2gether the atoms of a molecules 2gether.
TYPES OF CHEMICAL BONDS
1. Covalent- bonds are formed bet 2 UNCHARGED atoms. E- ARE ONLY ONLY
BEING SHARED
2. Ionic- bond are formed bet. 2 OPPOSITLY CHARGED IONS
3. Hydrogen Bonds- when a PARTICALY POSITIVE H atom w/in a molecule that
is PARTIALY NEGATIVELY charged atom.
o NO IONIC b/c it is PARTIALLY charged NOT COMPLELTY LIKE AN
ION.
o Happens bet. 2 or more molecules.
WATER (H2O) IS THE ESSENTAIL OF LIFE
o Water is polar- b/c it has two different poles. (positive and other negative)
o Can dissociate to O from proton (H+) and hydroxyl; ion (OH-)
o Absorbs large amount of heat b/c the hydrogen bonds are strong to break.
o Water is a good solvent
o H+ ions determines the pH of water.
o pH- the measurement of the concentration of H+ ions to log[H+]

0-6 is Acidic.
Acidic solution- the H+ (proton)
exceeds the amount of hydroxides (OHin a solution.
7= Neutral. OH- equals H+
8-14 is basic.
Basic solution the OH- exceeds the
amount of H+ in a solution.

Hydrophilic- molecules that like water

o could know if there is an OH- , ionic compound, NH group, Sulfur

,polar
Hydrophobic- molecules that does not like water
o could know if it is Hydrocarbon, Carbon, Hydrogen, non-polar.
ORGANIC
----- molecules always contain C atoms and are held together by covalent bonds.
o Other element that are found in organic molecules
1. Hydrogen
2. Oxygen
3. Nitrogen
4. Phosphorus
5. Sulfur
C2H6- ethane- C2 molecule
C3H8- protane- C3 molecule
C4H10- butane C4molecule
C6H12O6- glucose- C6 glucose
MAJOR CLASSES OF MOLECULES
1. CARBOHYDRATES
2. LIPIDS
3. AMINO ACID
4. NUCLEIC ACIDS
1) CARBOHYDRATES- include both sugars and polymers of sugars
o Monosaccharides- glucose, fructose, galactose (milk sugar) ribose (C5)
dihydroxyacetone
o Disaccarides
o Risacharides
o Polysaccharides- starch( plants cells), glycogen, cellulose (plant cells wall)

The boxes at the top and bottom are CH2OH.

Noticed that each polysaccharides have them at specific
places.

2) LIPIDS- FAT MOLECULES

o Made out of fatty acid and glycerol.
o All hydrophobic
o Fat is use for storage
o Type of Lipid --- Phospholipids.

as shown the head are hydrophiliclike water and the tail are hydrophobic.
Also the head are lipophobicdon like lipid and the tail is lipophilid.
when the lipids are put in water the head will be in the water and tail will be out
of the water. upside down
if there are many lipids the tails will attach to each other to block out the water.

This bilayer is the build up for cell membrane and

also membranes in organelles.
The tail are NOT COMPLELTLY hydrophobic.

TYPES OF FAT
A) Saturated fatthe hydrocarbons and Carbon are bonded BY SINGLE BONDS.
a. SOLID AT ROOM TEMP.
B) Unsaturated fat- the hydrocarbons and Carbons are bonded by Double Bonds.
a. LIQUID AT ROOM TEMP.
Steroids
A type of lipid

 Cholesterol- a steroid that forms an essential component of animal cells

membranes the precursor molecule.

3) AMINO ACIDS, PEPTIDES, PROTEINS

Amino acids- building blocks for proteins.
Organic molecules possessing carboxyl and amino acids.
Amino acids are proteins
BUT not all proteins are enzymes.
Enzymes act like catalysis chemical agents that selectively speeds up chemical
reaction W/O being consumed on the reaction.
-- pH impacts enzymes
STRUCTURE OF PROTEINS
1) Primary structurea long chain of amino acids.

2) Secondary Structure
a. Beta pleated sheet
b. Alpha helix

3) Tertiary structure- BOTH AND COMPINATION beta pleated sheets and alpha
sheet.

4) Quaternary structure- multiple proteins in one structure.

TYPES OF PROTEINS
1. Enzymatic proteins- selective acceleration of chemical reaction.
2. Structural proteins- support
3. storage proteins- storage of amino acids
4. transport protein- transport of other substances
5. hormonal protein coordination of an organisms activities
6. receptor protein response of cell to chemical stimuli
7. motor protein- movement
8. defensive protein protection against disease
4) NUCLEIC ACIDS : DNA & RNA
o nucileotides- basic building block for nucleic acid.
o 2 TYPES OF NUCILETIC ACID
o Ribose- ribonucleic acid RNA
o Deoxyribonucleic DNA
4 TYPES OF NITROGENIOUS BASE
1. cytosine ( C) at
2.Thymine ( T) ake
3. adenine (A) pples

4. guanine

(G) oodies

In RNA the thymine is replace by Uracil

DNA
RNA
A-T
A-U
C-G
C-G

DNA- carrier of the genetic info

o Basic structural unit of DNA is the nucleotide contain a C5 sugar & PO43- to
nitrogenous base.
RNA- transfer genetic info from the DNA to ribosomes when protein synthesis occurs.
o 3 types of RNA
1. rRNA- ribosomal RNA
2. mRNA- messenger RNA
3. tRNA- transfer RNA
A TOUR OF THE CELL
Cell- the fundamental unit of life.
All Living cells must be able to do 4 things
1. use energy (metabolism)
2. respond to stimulus
3. reproduce
4. grow
Cell fractionation- a technique for studying cell structure and function.
o Take cells apart and separate the major organelles.
COMPARING PROKARYOTIC & EUKAROTIC CELLS.
BOTH CELLS HAVE:
a) cytosol
b) chromosomes

c) ribosome
d) plasma membrane
e) cytoplasm

ANIMAL CELL

A. plasma membranemembrane enclosing the cell

B. cytosol- the area bet. The organelles and where cellular metabolism occurs.
C. cytoskeleton- a network of fibers extending throughout the cytoplasm
o 3 components of the cytoskeleton
o Microtubules (thickest) , microfilament (thinnest) , intermediate filaments
(fibers)
o MICROTUBULES grow out a centrosome a region near the nucleus
microtubule organizing center
o Hollow rods measuring 25nm
o The wall is made out of tubulin- globular protein 2 types gamma and
beta the tubulin helps the microtubules grow in length by adding more
tubulin.
D. flagellum- locomotion organelle present in some animal cells.
o Extension of the plasma membrane
o In an animal cell ATP is use

E. Mitochondrion- DOUBLE MEMBRANE POWEROUSE OF THE CELL .

Where cellular respiration and metabolic
processes occur ( will be discuss later).
ATP is generated- where energy come from.
ATP ( adenosine triphosphate) the energy is
released when the bonds between the PO43- is
broken.
The mitochondrion has 2 MEMBRANES
The outer is smooth
The inner is folded and called cristae
Cristae- the interfolding of the inner membrane of
the mitochondrion.

--in the INNER MEMBRANE there is the

Mitochondria Matrix
o The matrix has a pH of neural or
basic
The space bet. The 2 membranes (membrane
o Contains the mitochondrial DNA
space) has an acidic level.
and free ribosome
o The enzymes in the matrix catalyze some steps of cellular respiration.
o The metabolic reaction in the Matrix is the Krebs cycle or the Citric Acid.
o Krebs Cycle cellular energy and e- transfer chain ( will be explain later)
F. THE NUCLUESDOUBLE MEMBRANE- INFO CENTRL

The nucleus contains most of the gene in the

Eukaryotic cell.
Nuclear envelope- encloses the nucleus that
separates it from the cytoplasm.
--DOUBLE MEMBRANE is the membrane
-- member the membrane is made out of lipids.
w/in the nucleus the DNA is organized into
chromosomes--- carry the genetic info.
Chromosomes are made up of chromatin
protein
Humans have 46 chromosomes23 in sex
cells.

G. ENDOPLASMIC RETICULUM (ER) DOUBLE MEMBRANE.

The ER is continues with the
nuclear envelop.
The ER is wavy because it need
a large surface area. Therefore
the wavyness increase the
surface area.
Also where Ca is store.
2types- SMOOTH AND
ROUGH ER.
Rough is first.

FUNTION OF THE ROUGH ER.

o Have ribosomes attached to it.
o The ribosomes make proteins.
o Glycoprotiens- proteins that have carbohydrates covalently bonded to them.
o also have vesicle that is use for transport. (In both I think)
FUNCTION OF THE SMOOTH ER
o synthesis with lipids mostly to detoxify drug and poison
H. GOLGI APPARATUSSHIPPING AND RECEIVING CENTER POST OFFICE .

After thing leave the ER from

the transport vesicles goes to
Gogi
The product r then modified
and is send to different
locations.
Looks like & is consist of
flattened sac called cistemae
However the sacs r not
connected
F. LYSOMES
Lysosmes are membranous sacs that
has enzymes for DIGESTION.
Work beast in acidic environment.

G, RIBOSOMES PROTEIN FACTORIES

o look like dots in the cytosol.
o Made of ribosomal RNA
o Major for protein synthesis- making proteins
o 2 locations
o Free among the cytoplasmcall Free ribosome
o Attached to the ER- bound ribosome.

H. PEROXISOME
Peroxisome does metabolic functions
in lipid metabolism.
Mostly function as a detoxification.

PLANT CELL

A. cytoskeleton
B. ribosome
C. Endoplasmic Reticulum
o In a plant cell the ER extends the plasodesmata and enters into a neighboring cell.
D. Plasmodesmata- channels through cell ways to connect to another cell.
E. Nucleus 2 Membrane
F. Gogi Appartus

G. Mitochondrion- 2 Membrane
H. Peroxisome
I. Plasma Membrane
J. Cell wall
o The outer layer
o Maintains the cell shape & protects.
o Primary cell wall
o Middle lamella
o Secondary cell wall
K. Chloroplast 2 membranes

o Contains green pigment

o Function in the photosynthesis production of sugar
o Inside the inner layer
o There are thylakoids
o Enclose the luman system of vesicles
o Thylakoids looks like flattended sacsthe sacs are called granum.
o Where photosynthesis happens
o Stroma- is the fluid outside the thylakoids.
o Have free ribosome and the chloroplast DNA
L. CENTRAL VACULOE
use for storage, breakdown of waste
products.
Usually the largest organelle in a plant cell.
The larger it is the more efficient it is.

PROKARYOTIC CELL

o Neucleoid- region where the cells DNA is located (NO ENCLOSED

MEMBRANE)
o Ribosome- synthesize proteins are free roaming
o Capsule- jellylike outer coating of many proteins.
o Flagellum/ flagella- attachment structure on the surface of some prokaryotes
could be use for locamotion.
o Plasma membrane- layer under the capsule
o Cell wall- layer under the capsule NOTE NOT ALL PROKARYOTIC CELL
HAVE CELL WALLS

o Fimbriae- helps the prokaryotic cell attach themselves to other cells.

o Plasmid- an extra chromosomal DNA molecule

Cell Cycles
in the process of mitosis the cell divide into 2 or more that becomes
tissues.
Mitosis- the dividing of cells
Meiosis- the diving of cells the daughter cell have half the
chromosomes.
o Tissue- a group of cells w/a common function, structure. That are able to
recognize and communicate with each other.
o 4 types of tissues
o EPITHELIAL- cover the outside of the organism or lining of the organs,
Epithelium- cells of an epithelial tissue shaped like dice
o CONNECTIVE TISSUE- bind and support other tissues.
6 types
1. Loose
2. cartilage
3. fibrious
4. adipose
5. blood
6. bone
o MUSCLE TISSUE
o body movement
o most abundant
o 3types
1. skeletal
2. cardiac
3. smooth muscle
o NERVOUS TISSUE
o Sense stimuli and transmit signal neuron- nerve cell
o Glial cells or glia- nourish, insulate, and replenish the neurons
o Brain- the concentration of nerves.
AS TISSUE MUTIPLE IT FORMES ORGANS --- WHICH THEN TURN TO ORGAN
SYSTEM

ORGAN SYSYTEM
1. DIGESTIVE- mouth, pharynx, stomach, intestines, liver, pancreas, anus
a. Function: food processing
2. CIRCULATORY- heart, blood vessels, and blood
a. Function: distribution of materialsoxygen
3. RESPIRATORY- lungs, trachea
a. Function: gas exchange
4. IMMUNE AND LYMPHATIC- bone marrow. Lymph nodes, thymus, white
blood cells, and lymph vessels
a. Function: body defense
5. EXCRETORY- kidney, bladder.
a. function: disposal of metabolic waste
6. ENDOCRINE- pituitary, thyroid, pancreas, and other glands
a. Function: coordination of body activities.
7. REPRODUCTIVE- ovaries or testes
a. function: reproduce
8. NERVOUS- brain, spinal cord, nerves, sensory organs
a. Function: to sense things
9. INTEGUMENTARY- skin and it parts
a. Function: protects against injury, infection, drying out
10. SKELETAL- skeleton
a. Function: body support, movement, protection of internal organs
11. MUSCULAR- skeletal muscle
a. Function: locomotion and other movement
COORDINATION AND CONTROL
o Animals tissues, organ, and organ system must act in
conjunction w/ others.
o They can use hormones
o Hormones- signal molecules broadcast throughout the body by
the endocrine system.
o Diff, hormones have difference effects and slow-acting
Cells can also interact with each other through intercellular junction- ONLY
ANIMAL CELLS
o TIGHT JUCTIONS

The plasma membrane of neighboring cells are pressed together

bound by specific proteins.

o ANCORHING JUCTION (DEMOSOMES)

o Fasten cells together into strong sheets.
o Use in muscle cells

o GAP JUNCTION COMMUNICATION JUNCTION

o Provide cytoplasmic channels from one cell to another.

HOMOSTASIS - steady state or internal balance in the organism

o Mechanism of Homeostasis
o Setpoint- a variable that the body tries to keep temperature
o Stimulus- a variable above or below the setpoint that cause a change.
Sensor- detect the stimulus and triggers a response
THEMOREGULATION part of homeostasis
o The process by which animals maintain an internal temp. in a tolerable range
o Endothermic- heat generated by metabolism (internal)
o Exothermic- heat generated from an EXTERNAL source.
THE TISSUES AND SYSTEMS OF A PLANT
o The three main parts of the plants: ROOT, STEMS, LEAVES.
ROOTS- a multi-cellular organ that anchors a vascular plant in the soil
Absorbs mineral and water stores carbohydrates (sugar)

Taproot- the main vertical root.

--Gives rise to lateral rootsbranch roots. stores sugars and
starcher.
THE EXCHANGE OF
NUTRIENTS happens in the
ROOT HAIR.
Root hair- one cell extension of
the root.
Meristem- the area of the root
where the primary grows happens
Apical meristem- located at the
tips of roots
Primary growth- allows roots to
extend throughout the soil and
shoots to increase the exposures
to light.
Lateral meristems- thickens the
roots and shoots of woody plants.
Secondary growth- growth
produce by the lateral meristem.

Endodermis- INNER most

layer of the cortex in plants
rootsONE CELL THICK .

VASULAR /CIRULATORY TISSUE SYSTEM OF THE PLANTS

o Important for the transport of nutrients
o XYLEM &PHOLEM
o Use to transport of nutrients in the cells
o Xlem- water and ion up
o Pholem- sugars & other organics down

o the cells in the phloem & xylem are dead cells (kinda)
o kinda b/c it still contain a plasma membrane BUR NO NUCLEUS
o WHY ARE THE CELLS DEAD?
As states before diffusion can be use to transport nutrients through
cells BUT THIS A LONG PROCESS B/C OF THE
ORGANELLS IN THE WAY.
THEREFORE, the xylem and phloem has to be as open as possible
so the transport would be easy as possible.
The xylem & phloem are surrounded by living cells.
o REMEMBER CELLS CAN COMMUCATE THROUGH CHEMCAL &
ELECTRICAL MEANS.
STEMS- an organ consisting of an alternating system of nodes MAIN FUNCTION IS
THE TRANSPORT OF NUTRIENTS
o Nodes- where the leaves are attach
o Internode- the place bet. The nodes
o Auxiliary bud- structure that can form a lateral shout known as a branch

Tissue Organization of Stem

o The epidermis cover the
stem. DERMAL TISSUES
SYSTEM PROTECTIVE
LAYER
o has the xylem and phloem
LEAVES THE MAIN PHTOSYNTHEIC ORGAN OF THE PLANT
o flattened blade and a stalk
o the pertiole joins the leaf to the stem.
o TISSUE ORGANIZATION OF LEAVES
o Has a epidermal barrier epidermis
o In the epidermis there is the stomata
o Stomata- a pore that allow gas exchange bet, the surrounding air and
photosynthetic cells inside the leaf
Basically- regulate the CO2 uptake
Where water is evaporated water is only evaporated at the
leaves.
o In the stomata there are two guard cells.
Guard cells- regulate the opening an d closing of the stomata.
o The ground tissues of a leaf is called mesophyll
o Mesophyll- bet. The upper and lower epidermal layer.

OTHER TISSUES SYSTEMS FOUND IN PLANTS

Ground tissue system
External to the vascular system-- cortex
Respiratory system
Leaves control of gas exchange
The production of O2
Dermal tissue system
Epidermis- ONE layer of cells
Cuticle- a waxy coating on the epidermal surface --- help prevent water lost.
BASIC PRINCIPLES OF ANIMAL FORM AND FUNCTION
EXCHANGE WITH THE ENVIROMENT

Exchange happens as substances dissolved in an aqueous medium w/the plasma

membrane of the cell.
o Exchange of nutrients, waste, & gas.
Cells need to be surround by fluid
o Interstitial fluid- internal body fluids the surrounds cells
Enable the cells to obtain nutrients & get rid of waste.

METABOLISM
Sum of all catabolism & anabolism in biological entity. FOR ALL CHEMICAL
RECACTIONS

Catabolic pathway- decomposition

Anabolic pathway- building reaction

ENYMES
Is a protein ( all enzyme are protein) that work as a catalyst in a chemical reaction
o Speed up metablic reactions. NOT consume by the reaction.
ACTIVATION ENERGY BARRIER
Activation energy- the amount of energy that reactants most absorb before a
chemical reaction happens.
o the energy comes from the breaking of the bonds.
SUBSTRATE SPECIFY OF ENZYMES
substrate- the reactant an enzyme works on
enzyme-substrate complex- a TEMPORARY complex action when an enzymes binds its
substrate molecules.
While the enzyme and substrate are joined the catalytic action begins and a
product is produce.
Enzymes is VERY SPECIFICa enzyme can recognize its SPECIFIC substrate
OR something LIKE IT.
Active site the region where the substrate joins to the enzymes and the catalysis
occurs.
o temp. and pH are factors in the activity of an enzyme
MANY ENZYMES REQUIRE NONPROTIEN HELP FOR CATALYTIC ACTIVITY.
a) cofactor- any NON-PROTEIN molecule or ion that is required for the functioning of
an enzyme.
How does co-factors works
o they bind tightly or loosely to the enzyme or bind to the substrate
o crucial function in the catalysis.
b) coenzyme- an ORGANIC molecule serving as a cofactor.

ENZYME INHIBITORS AND REGULATIORS

Inhibitor- look alike substrates that affect the reaction of an enzyme.
2types of inhibitors

competitive inhibitors- look alike substrate that compete for admission into the
active site. enters the active site and prevents the CORRECT substrate of doing
it job.

Non-competitive inhibitors- does not bind in the active site but rather another
part of the enzyme- to stop the reaction.

REGULATION
Allosteric Regulation- change an enzymes shape and the functioning of it active
site by binding elsewhere

Covalent regulation- a molecule that covalently binds to the enzyme ex- PO43o Phosphorlation- adding an PO43- to an molecule.
CANNOT HAPPEN ON IT OWN it need a catalyst
This catalyst s called kinase- do phosphorlation reaction.
o Dephosphoryaltion- take off the phosphalation & perform by enzymePhosphatase

STORAGE OF ENERGY
energy is need for reactions
free energy- the portion of a system energy that can perform work when temp and
pressure are uniform throughout the system.
ATP ( adensine triphophate) contains a nucleic base, sugar, and three PO43o the break of the three bonds in the triphophate gives off energy.
o WHY?
The bond bet. Them is negative so it takes energy to keep them
together so when the bond is broken PLENTY of energy is give
off.
ATPADP

Two ways to make ATP

o Substrate chain phoslorlation- giving a PO43- to a ADP
o done by the catalyst called kinase
o Elertrachemical grandiat- ( oxidative phosphorylation) a molecule is
oxidizes and the energy is use to ATP. Happen in the e- transport exchange
o Use the delta pH in the membrane
CELLULAR RESPIRATION CHAPTER 9
CATABOLIC PATHWAYS AND PRODUCTION OF ATP
o Organic compounds posses P.E. as a result of their arrangement of atoms.
Cellular respiration- catabolic pathway of aerobic and anaerobic respiration
o Break down organic molecules for the production of ATP.
Catabolic pathways- a metabolic pathway that releases energy by breaking down
Complex molecules to simpler compounds.
TYPES OF CATABOLIC PROCESS
Fermentation- a catabolic process that makes a limited amount of ATP from glucouse
W/O AN E- TRANSPORT CHAIN.
Partal degradation of sugars W/O the use of O2

Aerobic respiration- O2 is consumed as a reactant along with the organic fuel

PRODUCE ATP
o Most efficient catabolic pathways in most
eukaryotic cells & many prokaryotic cells.
Anaerobic respiration- use in ONLY INORGANIC MOLECULES and use a substance
OTHER THAN O2 TO ACCEPT E- .
Redox Reaction: Oxidation and Reduction
The principle of redox
o Redox reactions- (or oxidation reduction)
o e- transfers in chemical reactions from one reactant to another.
o Oxidation- loss of eo Reduction- add of e- to another substance
ENERGY HARVEST via NAD+ AND THE E- TRANSPORT CHAIN
cellular respiration does not oxidize glucose in a single step BUT a SERIES of
step.
In the oxidization reaction the proton (H+) travel with an electron.
o But then taken by an e- acceptor, coenyeme, -- NAD
NAD- e- acceptor reduction equivalent- functions as an oxidizing agent during
respiration.
PROCESS OF NAD+
o Enzymes called DEHYDROGENASES remove 2 of H atom from glucose
(or substrate) and oxidizing it.
o DEHYDROGENASES bring the 2 e- and 1 proton to NAD+
o NAD+ is neutralized itself by getting 2 e- and 1 proton.
o NAD+ NADH
Others
o NADP+ + 2e- & 1 proton NADHPH2 (PLANTS, ?)
o FAD+ + 2e- FADH2
Electron transport chain- a sequence of electron carrier molecules that shuttle e- during
the redox reactions that release energy use to make ATP.
Overview of Cellular Respiration
Respiration could go in two directions
Aerobic use Oxygen
1. Glycolysis
2. Krebs Cycle
3. E- transport (oxidation phoslation)

Anaerobic Does not use Oxygen

Fermentaion
1. glycolysis
2. recycling of NADH/ reduction of
pyruate

THE STAGES OF CELLUAR RESPIRATION IN A ANIMAL CELL- Aerobic

1. GLYCOLYSIS
2. THE CITRIC ACID CYCLE
3. OXIDATIVE PHOSPHORYLATION: E- TRANSPORT AND CHEMIOSMOSIS
Glycolsis- sugar splitting breakdown of glucose (C6H12O6)
Glucose- is a stable molecule so ENERGY is need to break it down (ATP is that energy)
o Takes place in the cytosol.
REMEMBER - WITH EACH
ATP the C6 or C3 is pair with a
PO43-.
The end result is PYRUVATE
OR PYRUBVIC ACID.
C6 2 separate C3
Net gain energy
-2ATP
+4ATP
.
2 ATP
2 NAD IS USE .

--before the pyruvate enters the Krebs cycle it is Decarboxlation happens in the
mitochondria
o Decarboxlation- in the presence of Oxygen.
o Takes off one CO2 from an organic molecule.
o It removes the carboxyl group and adds the acetyl CoA in it place. (coenzymes)
o Acetyl CoA- the entry compound for the citric cycle or Kerbs cycle.

The carboxyl group is remove from the pyruvate and Acetyl CoA is put in it place
this is deoboxiation.
IF THIS REACTION IS W/O OXYGEN IT IS FERMATIONIN THE CYTOSOL.
2. CITRIC CYCLE (KREBS CYCLE) take place in the mitochondrial matrix
While pyruvate is entering the
mitochondrion it is changes to
acetyl CoA
NEEDS O2 B/C OF THE EACCTCEPTOR SO THIS DOES
NOT HAPPEN IN
FERMENTATION.
1 ATP PER C2 entering the Krebs
cycle. BUT THERE ARE 2 C2 in
the Krebs cycle 2 ATP. ( diagram
shows one C2 because one is down
per cyclewhen the 1st is done it
goes to the next. )

The citric cycle or krebs cycle happens in eight steps

1. Coenzyme A transfers its 2-carbon acetyl group to the 4-carbon compound
oxaloacetate to form the 6-carbon molecule citrate the C4 (at the end of the cycle)
molecule joins the C3 molecule
2. The citrate is rearranged to form an isomeric form isocitrate by removing an adding
water
3. The 6-carbon isocitrate is oxidized by NAD+ and a molecule of carbon dioxide is
removed producing the 5-carbon molecule alpha-ketoglutarate. During this oxidation,
NAD+ is reduced to NADH + H+
4. Alpha-ketoglutarate is oxidized, carbon dioxide is removed, and coenzyme A is added
to form the 4-carbon compound succinyl-CoA. During this oxidation, NAD+ is reduced to
NADH + H+
5. CoA is removed from succinyl-CoA to produce succinate. The energy released is used
to make guanosine triphosphate (GTP) from guanosine diphosphate (GDP) and Pi by
substrate-level phosphorylation (def). GTP can then be used to make ATP
6. Succinate is oxidized to fumarate. During this oxidation, FAD is reduced to FADH2
7. Water is added to fumarate to form malate (see Fig. 24).
8. Malate is oxidized to produce oxaloacetate, the starting compound of the citric acid
cycle. During this oxidation, NAD+ is reduced to NADH + H+
BALANCE REVIEW

-2ATP GLYCOLYSIS
+4ATP GLYCOLYSIS
+2ATP KREBS CYCLE
.
NET = 4ATP IN BOTH GLYCOLISIS AND KREBS CYCLE
2 NADH= GLYCOLOSIS
2NADH= DECORBOXYTION
6 NADH= KREBS CYCLE
.
10 NADH2
o IN A COMPLETE CYLCE ABOUT 30 ATP IS USE
o THAT ATP IS FROM THE NADH2.
o Will be explain in the electron transport chain

2FAD IN KREBS
CYCLE

3) OXIDATIVE PHOSPHORYLATION CHEMIOMOISIS COUPLES ETRANSPORT TO ATP SYNTHESIS- HAPPENS IN THE CRISTAE
Oxidation phosphorlation-( process one to make ATP) ATP synthase- located in the cell
membrane
First let explain e- transport chain since this occurs in the oxidation phosphorlation.
o The e- transport chain is a collection of molecules that are embedded INNER
MEMBRANE of the mitochondrion in eukaryotic ( in prokaryotic in the plasma
membrane)
o In chain exist in multi-protein complexes 1 to 4.
o Bound to them is prosthetic groups (non-protein components for the
catalytic functions of certain enzymes)
THE IMAGE BELOW CONTAIN BOTH THE E- TRANSPORT & ATP SYNATANSE

o In the e- transport exchange the proton H+ are delivered upward ( remember the fluid
between the two membranes of the mitochondria has a low pH (high acid)
o The NADH from the citric acid cycle is transfer to the Complex ONE.
o The proton and e- is remove is from the NADH. ( 2 e- and 2 proton are
removed if it is NADH2)
o CONTIUNING IN COMPLEX ONE the proton that was removed is then
move upward to the matrix bet. The two membranes in the mitochondria.
o The e- is then carried from COMPLEX ONE by the UBIQUINONE (Q) ( the
Q can carry up to two e-)
o The Q carry the electron to Complex THREE
o In COMPLEX THREE also shuffle H+ upwards. HOWEVER the e- is then
brought to the cytochromes.
o Cytochromes- an iron containing protein and a component of the e- transport
Chain in the mitochondria and chloroplast.
o Cytochrome pass the e- to the COMPLEX FOUR where the e- is pass to
oxygen.
o Each oxygen atom also picks up a pair of Hydrogen from the aqueous
solution forming water.
SO HOW MANY ATP CAN BE MADE FROM NADH?
3 ATP CAN BE FROM 1 NADH
BACK TO COMBINATION OF GLOCYLOSIS, DECORBOXYTION, &
CREBS CYCLE
ALL 2GETHER THEY MADE 10 NADHTHEREFORE 30 NADH IS MADE
FROM CELLULAR RESPIRATION.
SO WHAT HAPPENS IN COMPLEX 2

o It takes e- from FADH

o Does not shuttle proton through the membrane.

ATP SYNTHASE- a complex of several membrane proteins that provide a port through
which proton diffuse.
o Make ATP from ADP
o ATP synthase use the energy is from the difference of in concentration of
H+ ( delta pH or gradientREMEMBER THE SPACE BETWEEN THE
TWO MEMBRANE IS ACIDIC THE MATRIX IS BASIC.)
This process is called e- gradient or chemiosome(process two)
o Chemiosome- an energy-coupling mechanism that uses energy stored in
the form of hydrogen ions gradient across a membrane
H+ enter the stator the stator is in the
membrane.
Then the H+ enter the binding site within the
rotor (Fo unit) changing the shape of each
subunit so the rotor spin within the
membrane.
Each H+ make one complete turn before
leaving Fo unit through a exit channel. That
then leaves to the other side of the
membrane.
The spinning of the Fo also cause the internal
rod to spin also.

--ATP synatse use the P.E. store in the

proton gradients and converted it to
chemical energy.

The catalytic knob (F1 unit) turns that

activates catalytic sites in the knob that
produce ATP from ADP.

where does the ATP comes from

o the ADP enters the F1 unit with a PO43- group.
o The F1 group use the energy from the movement of the internal rod to
bond the PO43- to the ADP.
ATp synatse could work in reverse if the are where H+ is low and the other side is
side
o It would pump the H+ upwards instead of downwards while still making
ATP.

--As explain earlier 3ATP is made from 1 NADH. How?

-- realized that 3 H+ was shuffle upwards in the e- transport exchange. (Oxidation
phosphorlation)

ALL TOGETHER.

Review
Glycolysis- +2 ATP
Citric cycle- +2 ATP
Oxidative and chemiomois- + 32 or 34 ATP. (from the total amount of NADH)
REVIEW OF PROCESS
In the process called glycolosis ( that takes place in the cytosol) the C6 molecule,
glucose, is split in two. & and is further processed to 2 NADH2 , 4 MOLECULE OF
ATP, 2 MOLECULES OF PRRUVATE.
--But if there is no oxygen in the process FERMENTATION, which also happens in the
CYTOSOL, Fermentation regulate the concentration of NADH+
CHAPTER 10PHOTOSYNTHESIS- the conversion of light into energy
--The chloroplast of plants capture light energy from the sun and convert it chemical
Energy stored in sugars.
Break down to two reactions

 light reactions- happens in the thylakoid membranes of the chloroplast. Convert

the light to chemical energy of ATP and NADPHreleases Oxygen
o ATP
o NADPH2
Dark reactions- the fixation of CO2 on reduction of the fixed Carbon into
Carbohydrate.
o Co2 Calvin Cycle. in the stroma.
Complete reaction
Co2 + H2O + light energy C6H12O6 + CO2
The energy for this reaction is from the photons from the Sun.
Mesophyll cells- where chloroplast are found.
Chlorophyll- has green pigment and is green because it doesnt absorbs green light very
Well.
o Is found in the thylakoidheld down by proteins so it can stay in a fix
position.
LIGHT REACTIONS happens in the chloroplast
--When photon hit the chlorophyll in the thylakoid membrane it get excited and then the
one next get excited and so on & so on. UNTIL that energy ( the cause of the excitement)
hit SPECIAL PAIR of chlorophyll
o The special pair of chlorophyll gives off an eThe green is the chlorophyll

Linear E- flow in photosynthesis -the celluar respiration exchange in the chloroplast.

o Light hit the pigment molecule and the chlorophyll get excited and pass it on
to other chlorophyll ( as stated before)
o Then that energy reaches the special pair in PHTOSYSTEM 2( is call
photosystem 2 because it was discovered 2nd )
o The special pair in Phtosystem 2 is call P680 it absorbed light at 680
wavelength very well.
o P680 then get excited and give off an eo ALSO HAPPENING THE PS2 an enzymes is catalyzes the splitting of water
into 2 e-

o Those e- from the splitting of water is given to P680 one by one

(remember two are given off) when it lose it e- in it excited state.
o SO WHAT HAPPEN TO THE E- THAT WAS GIVEN OFF BY THE P680?
o The e- is then carried by the plastoquinione (PQ) and brings it to the
CYTOCHROME COMPLEX
o The cytochrome complex is another complex.
o As the is going through this complex the energy falls that provide
energy for the synthesis of ATP
o Meanwhile the electron it then taken up by the plastocyamin(PC) (sit
on topn the Cytochrome complex ) and carry the e- to PS ONE.
o When the e- enters PS 1 the special pair P700 ( absorbs 700nm photo very
well)
o The P700 then get excited getting the e- and gives off an e- as well.
o That given off e- is then passes through a series of redox reaction from PS 1
down a second e- transport chain through the protein FERREDOXIN (Fd)
o Then the enter the NADP+ REEDUCUTION. Where the NADP+ is turn to
NADPH.
o Making this molecule have higher energy than water and the e- are
more ready for the Calvin Cycle (dark reactions)
o The H+ that was given off from PS 1 and PS 2 in the thlakoid space goes to the
ATP synthase. Similar to the ATP synthase to the mitochondria.

The ATP ( that was produce from the synthesis) & the NADPH+ (from the PS) goes to the
Calvin cycle (dark reactions)
Calvin cycle formula ( a shorter version of the previous formula)
6CO2 + H2O 2C3 C6
the Calvin cycle uses ATP and NADPH to convert CO2 to sugars.
The Calvin cycle is anabolic builds sugars from smaller molecules and comes
energy
o Unlike the cirtic or krebs cycle that break down sugar.

The CARBON enter the cycle ONE AT A TIME

Phase 1- Carbon Fixation
carboxylationribulose biphosphate rubisco is a C5 sugar that is attached to
EACH CO2 molecule.
The product of this is a SIX CARBON that is unstable making it split in half
which forms 2 3- phosphoglercerate. REMEMBER PER CO2
Phase 2- REDUCTION
each 3- biphosphoglercerate gets a PO43- form an ATP- PER
then a pair of e- from NADPH that makes 3- biphosphoglercerate lose a PO43becoming G3P- EACH (2 NADPH PER 3-biphospoglercerate)
o in the diagram it show for EVERY THREE MOLECULE CO2 that enters
the cycle there is ONE MOLECULE of G3P
o in phase 2 glocose is given off.
o LOST OF ONE CARBON

Phase 3- Regeneration of he CO2 ACCEPTOR

-- the rest of the 5 CARBONS it combines together with the use of ATP.
o 1 ATP per 5 CARBONS.
--regeneration of the CO2 acceptor (RuBP)
however there is a problem with RuBisCO
o it can do both carboxylation & oxygenation.
o How is this a problem
o It can take the product of C5 and break it down to a point that it is useless.
Meaning that the energy use in the Calvin Cycle was useless.
Therefore the cycle has to be repeat again.
-- REMEMBER THREE (3) CO2 MUST PASS INORDER FOR G3P is produce.
Organism Metabolism Identities
Autotroph- (plants) get it carbon by inorganic means. (CO2)
o Calvin Cycle in Plants
Heterotrogh get it carbon by organic means humans
Phototrogh- get it energy by photons (lights) plants
Chemotrogh- get it energy by organic and inorganic means humans
Plants are photo autotroph
Human are -- chemo hetertogh
TYPES OF PLANTS
C3 PLANTS- a plant that uses the Calvin Cycle for the initial steps that incorporate CO2
into organic material, forming a 3-Carbon
C4 Plants- in the Calvin Cycle that has a C4 as it product.
Example: corn and other agriculture plants

CAM PLANTS- C4 that open their stoma at night.

The mesophyll cells store the organic acids the night before in the vacuoles that is

later releases the next night.

MEMBRANE STRUCTURE AND FUNCTION
the biological membrane is made up of a lipid bilayer

 all biological membrane is selective permeable-- the membrane allows some

substances through and others dont.
WHAT SUBSTANCES GO THROUGH THE MEMBRANE WITH EASE ?
o Water
o Small gases ( carbon dioxide, oxygen)
o Uncharged small molecules.
cell membrane are made up of lipids and proteins
o the phospholipids is amphipathic molecule meaning it has both a
hydrophilic and hydrophobic regions.
o Types of Lipids
DAG- diocylglecides made up biological membrane
TAG- Ticyglecides
Sterols
WHY ARE MEBRANE INPORTANT?
o They separate reactions that are happening in the organelle or cytosol
o Separate from the external environment
o Build-up the gradient- which helps in the process of making ATP
TYPES OF PROTEINS IN THE CELL MEMBRANE
o 1. intergral proteins- proteins that penetrate the hydrophobic core
Does not need to be all the way
Tertiary structure- alpha helix
The hydrophilic parts are the parts that are expose to the solution.
o 2. peripheral proteins- NOT embedded in the membrane but bound to the
Surface of the membrane.

TANSPORT ACROSS THE MEMBRANE

Endocytosis - cellular uptake of biological molecules an matter formation of new
vesicles from the plasma membrane
o Process
o A molecule enters the cell as a vesicle new vesicle is formed
o The plasma membrane surrounds the molecule
Making the membrane that cover the molecule OLD plasma
membrane.

Exocytosis the cell gets rid of a molecule by fusing a vesicle to the plasma membrane.

Membrane selectivity
o a biological membrane in very selective of what goes through.
o Factors for movement across the membrane
Charge
Size
If there a need of energy
o Materials that need helpers proteins to transport them.
o The amount of material that need to transport affect the time

2 types of transport
1. Passive transport- diffusion of molecule trough the membrane that DOES NOT
require any energy.
o Goes down the gradient from high to low.
2. Active Transport- diffusion of molecule through the membrane that REQUIRES
Energy (ATP)
o Goes AGAINST the gradient that why energy is used.
o ANYTHING THAT GOES AGAINST THE GRADIENT NEED
ENERGY
o Secondary Active Transport- does not use ATP but uses the gradient as it
engery use to proform the transport.
WHAT IS DIFFUSION?
o Diffusion- the movement of substances DOWN the gradient
o Teacher defa random mixing of substances that occur in a solution b/c
of the substance kinetic energy.
WHAT IS CONCENTRATION GRADIENT?
Concentration gradient a region along which the density of a chemical substance
increases or decreases
osmosis- movement of water DOWN the concentration gradient. ( passive transport)
CLASSES OF PROTEINS
1. CHANNEL- membrane pores
2. CARRIERS- carries the substances from one side to the other
3. PUMPS- use energy to go against the gradient ( primary active transport)

--Ions channel- are one type of channel

o Channels (pores) in the membranes that regulate ions
o How do they work
Like doors open, close, -- or lock these are the stages
--Sodium- potassium pump- a transport protein in the plasma membrane of animal cells
that actively transport sodium OUT of the cell and potassium IN the cell.
4 types of Ion channels
1. Leakage Channel- DOES NOT REGULATE
o Gate randomly closed and open
o The cell can regulate how many of these leakage channel
2 . Voltage-gated Channel ALL CAN OPEN TA THE SAME TIME REGULATE
o Open to response to changes on the membrane potential
o Neuron
o Example of type of channel: Na+, Ca2+, K+.
o When they close they are lock for a period of time. (this period of time
will be explain in material for the final)
3.Ligand-gated channel ( one at a time )
o Opens and closes on response to chemical stimulus such as nerotransmitters,
hormones, and particular ions.
4. Mechanically gated channelso Opens and closes in response to mechanical stimulation in form of vibration
pressure

a. Found in hearing
WHAT IS MEMBRANE POTENTIAL ?
Membrane potential- the diff. of electrical charge across the cell plasma membrane
ACTION POTENTAL not in chapter 7
Resting Membrane Potential (Vrest)
the membrane potential of non-conducting excitable cell w/the inside of the cell
more NEGATIVE than the OUTSIDE
Graded Potential
SMALL CHANGES in the resting potential
o By opeining Ligand-gated channels
Depolarization adding SMALL POSITIVE charges to the INTERIOR of the cell
o Also ligand-gated channel
o Na+ and K+ ion rush in. (neuron with sodium potassium pumps)
Action Potential
a DRAMATIC , LARGE, AND FAST, change in the membrane potential
o Voltage-gated channel (REMEMBER THEY ALL OPEN AT ONCE)
Repolarization
the phase when the cell tries to get back to it resting potential
o the inside get more negative.
o Tries to get rid of Na+ and K+ ions (neuron with sodium potassium pumps
o Voltage-gated are close ant lock
Hyper polarization
Adding SMALL NEGATIVE charges to the interior of the cell
o The cell get to negative and is under the resting potential.
o It uses pumps in order to go back to the resting potential.
PHASES OF ACTION POTENTIAL
Phase 1- resting potential
Phase 2- depolarization- small changes to getting more positive
Phase 3- Action potential
Phase 4- repolarization

Phase 5- hyper polarization

Phase 6- return to resting potential

Extra Notes
Cytoplasmic streaming- movement of fluid within a animal and plants cell.