ABS

Definitions:
Hypothesis: A guess without evidence based on prior knowledge
Law: Something that WILL happen based off of calculations and proved with equations
and evidence, no exceptions. Is descriptive
Theories: Common thought, with evidence, an explanation with no exceptions
A hypothesis can become a law or a theory, there is no hierarchy
Falsifiable: testable to see if it is false

Evolution as a theory has changed a lot, but it still explains

Evolution Explains:

change over time

why genetic mutations survive in organisms
explains similarities between organisms
distribution of organisms
BASED ON
common ancestry

Homologous structures
Similar shape
same make up
similar development
CAN have same function
gives evidence of common ancestry

ABS 1
 Analogous: same function ONLY, evidence of adaptations

Vestigial: not functional, had a function in the past, also gives evidence of common
ancestry, similar to structures that are functional in other organisms

St. Error
formula: STDEV/ square root of n
n= # of
samples

p<.05, reject H0
There is/There is not a statistically significant [difference, correlation, dependance]
between (sample 1) and (sample 2) (stat=, df=, p=)

Isolated system: No exchange of matter or energy

Open system: We eat and gain energy transfers between system and surroundings.

From a biological standpoint, equilibrium is not good. There’s no food coming in and no
energy is being burned, so the organism is no more

ABS 2
 Cellular pathways

Series of steps
consecutive open systems like a turbine flowing into another turbine, each one is
dependent on what is happening before it, can use more energy

Catabolic vs. Anabolic

Catabolic: Breaks down molecules, energy becomes available (Cat breaks down fish)
Anabolic: Build larger molecules, uses energy (Ana knits a big blanket)

More energy- more capacity to work- less stable

Entropy - randomness, continuously decreases

Equilibrium, maximum stability. Low amount of free energy, no work is happening

Catalyst, something caused a spontaneous reaction

Free Energy

(delta)G=(delta)H-T(delta)S
H=Heat/enthalpy(change

T=Temp in Kelvin
S=entropy(change)

negative (delta)G=spontaneous
Ratio of products to reactants=(delta)G

Catalyst makes sure a reaction happens when and where it’s needed

ATP→ADP+Pi -(delta)G=spontaneous

ABS 3
 v
Glucose+Pi→[glucose]-P=non spontaneous

Coupled: ATP+Glucose→ADP+[glucose]-p= overall spontaneous

If one way is spontaneous, the reverse is nonspontaneous.

LEO says GER

OIL RIG

Loss of electron (oxidation)

Gain of electron (reduction)

NAD^+ is a common electron carrier

NAD++H++2e- → NADH

Drop off NADH→NAD+

Goes back and forth

Oxidation event that puts electron in, reduced and turns around and passes the electron
on and is oxidized again, can work like multiple turbines

2 halves to a REDOX reaction

Things that photosynthesis still go through cellular respiration

Glycolysis starts in the cytoplasm

energy from atp must be added for glycolysis

creation of ATP is non-spontaneous

Starting to break down the six carbon glucose.

Input: Glucose, ATP, oxidized electron carrier

ABS 4
 Output: 2 3carbon pyruvates(Krebs/CA cycle), 4ATP, reduced NADH(→ETC),
Water(Waste)

Citric Acid Cycle

Into Mitochondria
Carbon dioxide splits off pyruvate and remaining atoms connect to coenzyme A

Input: 3C pyruvate, Coenzyme A

Output: 2C+CoA+Acetyl+CoA

Co2→waste

CAC= Continue to break down carbon molecule to harvest e- (small amount ATP made)

4 remaining carbon atoms will soon be released as carbon dioxide

Makes Oxaloacetate and is recycled

Major Input: Acetyl-CoA, NAD+, FAD+

Output: 2 carbon dioxide, NADH, FADH

^ (electron transport chain)

Electron Transport Chain, lots and lots of them in the mitochondria

Cell uses NADH and FADH to make a lot more ATP, energy production comes from this
phase.

dropping off, picking up

Step 2

Series of coupled reactions,

spontaneous : movement of electrons through redox reactions

higher affinity(drawn to) pulls down chain

oxygen is final electron acceptor

ABS 5
 Fermentation

Produces less energy, regenerate NAD+

Makes alcohol and Wine

induced fit
active site

enzymes change shape of substrate

Temperature raised to denature dna so the pcr can anneal, temperature lowered so the
pcr can attach and regular temp for extend

3 cycles, get a short strand before you can start to get copies
16s rRNA= ribosomal RNA differentiate bacteria

ABS 6
 Break hydrogen bonds and proteins, cytoplasm, etc. DNA removed from cell for
isolation

Purpose of electrophoresis: see the bands separating because of primers with different
sizes of isolated pieces depending on primer type. Band size determined what bacteria
we had.

Coils coiled on other coils: supercoiling so it can fit in the nucleus

Can only be seperated a little at a time

Bubbles in helix strands are origin of replication. They continue to expand until the dna
strand is seperated

Would naturally reform hydrogen bonds, need to hold it open

Step 1: open helix with helicase and ssbp(single stranded binding protein)

Step 2: RNA primers added by primase

Dna polymerase III cannot “start from scratch"

Rna is more stable as a single strand than dna (rna has second OH on the bottom
of the sugar)

Step 3: 3’ extends, now there's nothing to add to 5’ end primase can add another primer
to build off of. This is called semi-discontinuous. Okazaki fragments.
Step 4: rna and dna cannot be together, now replacement must happen. DNA
polymerase III builds complimentary strands in between the primers.

Step 5: DNA polymerase I takes out the RNA and replaces it with DNA
Step 6: there's still gaps in the sugar phosphate backbone. Ligase completes the bonds
in the backbone. Now the bubble should be completely double stranded

PCR Replication

Denaturation Heat Helicase

DNA/flank region of interest, placed RNA/ first one at origin of replication,

Primers
by placed by space
Millions, specific region of interest in One copy, whole chromosome (2
Product
chromosome daughters)

ABS 7
 Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar
and a phosphate. They serve as monomeric units of the nucleic acid polymers –
deoxyribonucleic acid and ribonucleic acid,

N and O are negative

C and H are positive

It's shared equally in non polar so there's no need for charges

ABS 8
ABS 9
 Adenine and Thymine have 2 hydrogen bonds
Guanine and cytosine have 3 hydrogen bonds

Antiparallel
5’ end and 3’ end are opposites on either side of the dna helix

3’ you can add on to

Replication is semi discontinuous because the lagging strand, it starts at the origin and
can only be extended on the 3’ end

Ribosomes make proteins

Directions held in the dna
Eukaryotes have mitochondria and all the membrane stuff, vesicles, ER, golgi body

Rna Polymerase
1) initiation

Rna Polymerase binds to the promoter

Rnap opens the helix

Rnap creates a complimentary strand to the template strand

Conserved sequence

Promoter= Rnap has an affinity for it= BINDING SITE

5’ end is the coding strand

RNA= uracil instead of Thymine

3) termination

ABS 10
 Unbinding
Release

Lets go of RNA

Dna

Closes up behind

ABS 11
 5’ TCGATACTC 3’ (template)

3’ AGCTATGAG 5’ (coding strand)

3’ AGCUAUGAG 5’ (RNA)

This is transcription, RNA strand will be sent to ribosome for translation

Prokaryote- happens in the cytoplasm

Eukaryote- happens in the nucleus

Translation happens in the ribosomes in the cytoplasm and eukaryote in rough
endoplasmic reticulum - golgi - vesicles- exported or membrane bound

Prokaryotes-
Prokaryotes= transcription and translation happen

Eukaryotes - RNa has to leave nucleus and engage with ribosomes in the
cytoplasm/rough er

1) add methyl guanine cap to 5’ end

Help ribosome identify and bind (vs tRNA, rRNA, etc)

2) poly-adenine tail added to 3’ UTR (30-300 As)

Allows RNA to exit the nucleus via the nuclear pores

No tail- no

Also a buffer around translated region

If exo

3) splicing
Parts of rna called exons
Cut off introns to stick exons together

ABS 12
 Introns are non coding- can get recycled, can go on to regulate gene expression

Alternative splicing
1) SR’s: splice regulator

Bind to and mark exons to be kept in

2) snRNA’s - u1 +u
3) >snRNA’s; spliceosome complex cuts and attaches

ABS 13
 Start codon always at 5’ end, promoter always on 5’ end of the coding
read the template strand (complimentary to rna) (coding strand and rna are the same,
with u’s instead of t’s)

Carbon makes 4 bonds

Hydrogen makes 1 bond

ABS 14
 Oxygen 2 bonds
Nitrogen 3 bonds
Phosphorus 3
Sulfur 2

Expanded bonding
Phosphorus 5 bonds

Sulfur 4 bonds

How protein structures are drawn:

Two lines come together to make a point implies a carbon molecule
Sometimes carbon is shorthand, assume hydrogen

Lipids
Hydrophobic

Hydrophillic is polar and can create Hydrogen bonds with other polar molecules and
water

Hydrophobic is non polar and does not interact with water

Electronegativity further apart makes them polar, closer together makes them non polar
Carbon and hydrogen are non polar
Fats are a type of lipid
Phospholipids have polar heads and fatty acid chain bottoms that are non polar

Heads naturally orient themselves to face the water and will connect in a circle to shield
the tails from the water, wether in a micelle or a lipid bilayer

Phospholipids form water-filled vesicles. Lipid bilayer forms around water.

ABS 15
 Phospholipids are in constant lateral motion, but will not flip to the other side of the
bilayer
Membranes are selectively permeable:

Hydrophobic molecules can cross (o2, co2, n2)

Small uncharged polar molecules (h2o, indole, glyceral)

Cannot pass

Ions and large uncharged polar molecules

Double bonds cause kinks in phospholipid, these are unsaturated with hydrogens.
Unsaturated lipid bilayers is more permeable. Needs a balance

Cholesterol also has a polar head and non polar tail, is in the cell membrane
Compartmentalization
Many proteins that function as enzymes and receptors are bound in the membrane

Protein structures and folding

Folding has to do with function
Ribosomes make proteins all the time through synthesis. Proteins need to be modified
to function

Folding is modifying
Shape and function work together

Primary structure
Sequence of amino acids that make up the monomer of the protein held together with
peptide bonds. They form polypeptide chains
Genes determine number and order of amino acids, when one amino acid is changed
can make a big difference
Amino group, acid group, r group

Secondary structure

ABS 16
 Sequences fold in alpha helix or beta pleated sheet, depending on where hydrogen
bonds occur
A helices

Polypeptide has a turn every 3.6 amino acids

N-H is h-bonded to C=O of another peptide bond. Interstrand connections
B pleated sheets
Neighboring chains running in same or opposite directions, intrastrand connections

Tertiary structure
3d shape r group

R group varies
Some are hydrophilic, others hydrophobic
Hydrophilic go on the outside, hydrophobic amino acids curve towards the inside

Quaternary structure
Protein consisting of more than one polypeptide chains. Hydrogen bonds and etc keep
them together

Chaperonins help folding process, has an environment ideal for folding

Each protein has an ideal environment, temp or pH can denature the protein, losing it's
shape

Enzymes
Active sight is specifically shapes for the enzyme
Substrate can be formed together with the help of enzymes
Enzymes usually end in ase
Sugars end in ose

ABS 17
 Lactase breaks lactose down quickly so it's digestable, changes the shapes in the
lactose so it can be smaller in size

Catalyst can be used over and over

Lipase breaks down (lipids)
Amylase (starch)
Protease (proteins)
Cofactors and coenzymes
Bind to substrate or active site so it fits in the enzyme

Enzymes have ideal conditions, pH and temperature

Enzyme becomes denatured

Wild type RNAP Inhibitor CAP

Lactose only Yes No Yes

Glucose only No Yes No

Both Yes No No

Beta gal

Lactose is up, inhibitor is decreased

Glucose is up, cap is decreased
Anywhere there is an inhibitor, rnap cannot bind
Lactose not inhibited, is activated, has highest
Glucose is lowest
Both is middle

Lactose regulation:

ABS 18
 In the absence of lactose, the inhibitor binds to the operator (o) region
Even if it could bind, the protein inhibitor blocks the way for it to do so

With lactose, inhibitor doesn't bind. Y gene (permease) lets lactose into the cell. Binds
to inhibitor and changes shape. Becomes complex, cannot bind to Operator, RNAP can
go through and start transcription
Regulate promoter, regulate whole operons

ABS 19
 Makes b-gal, permease

Beta gal breaks down lactose into glucose and galactose (?)
Lactose binds to I protein
Always making permease and beta gal at a low-level even with no lactose

Beta cells make insulin, travels through blood into muscle and adipose tissues, insulin
goes in, becomes AKT, vesicle with glucose transporters, transporters in cell
membrane. AKT is inhibitor of GS, GS is released and is free to make glycogen and
store glucose
glucagon

ABS 20