Workshop 10

allosteric regulation - controlling actions of enzymes to regulate amouts of products and reactants

example: PFK enzyme is used when 3BPG is converted to 1,3 BPG and vice versa.

CITRATE negatively inhibits the forward reaction by blocking anything from binding to the enzyme.
ADP positively inhibits the process by allowing things to bind to the enzyme.

triacylglycerol = fat

GLYCOLYSIS is used to produce ATP needed for short bursts of energy (a running turkey)

CITRIC ACID CYCLE is used when energy is needed for long periods of time (a flying pigeon)

GENE EXPRESSION is a result of one pathway being more likely to happen than another

DNA is packed tightly in cells forming a CHROMOSOME. Histones are proteins with tightly packed DNA.

A GENE codes for a specific squence of nucleotides (a protein)

Steps of DNA replication:

1) UNRAVEL a portion of DNA using "unravelase"
2) UNZIP H bonds between base pairs usiong Helicase
3) DNA polymerase replicates genes

Phosphorylation helps control actions of enzymes
KINASE adds a P group
PHOSPHATASE removes a P group

The End!

Workshop 9

a) There was 02 in the environment thus causing the creation of Acetyl CoA.

b)Mitochondria is making ATP using the Krebb Cycle/TCA cycle:
[PYR + O2 -> Acetyl CoA (2C) ]+ Oxaloacetate(4c) -> 6C Molecule
Releases Carbon in the form of CO2 and finally is back down at a 4C molecule (Oxaloacetate) which is a reactant needed for the initial equation.
+1 for cycles.

Creates the following inside the cell:
ATP
NADH
FADH
FADH2

"lighting a candle with a dynamite... stick" -Derek Crowe

(Too much Energy)

ETS creates proton gradient in between bilayer.
ATP Synthase needs the gradient to have dG < 0 reaction for ADP + Pi
(Sorry. If that was confusing contact Derek Crowe :) )

"in the winter your breath is like a little cloud and its cool" - Derek Crowe

c)There is still acetyl CoA in the cell and the cycle will run until there is none left.

d)The yield of ATP goes down

e) H2O

f) (5 ATP / phospholipid ) (100,00 phospholipids/ 1 cell ) = 500,000 ATPs/cell

(500,000 ATPs / cell )(1 cell / 1000 seconds) = 500 ATP / second

(500 ATP / second) (1 glucose / 2 ATP ) = 250 Glucose / second.

Workshop #7

Let me preface by saying, I lost my notes from this workshop, but since I agreed to be the scribe, I will do my best.

"Transport and ATP synthesis"

Passive transport

• with the concentration gradient
• bidirectional
• how it all goes down:
1. large molecule binds to an integral membrane protein
2. the bond causes a conformation change
3. conformation change causes the molecule to pass through the membrane (switches its side)
4. ready to repeat

Active transport

• against concentration gradient
• unidirectional (use this principle to determine what kind of transporter it is)
• how it all goes down:
1. large molecule binds to an integral membrane protein
2. ATP latches onto the IMP and releases a phosphate group
3. phosphorylation = big conformation change
4. conformation change causes molecule to pass through membrane
5. not ready to repeat until the IMP dephosphorylates

How is ATP made?

Creatine P + ADP -> Creatine + ATP
CP-> C is delta G -50kJ/mol
ADP -> ATP is delta G +30kJ/mol

Couple the reactions = spontaneous! delta G -20kJ/mol

made in an ATP synthase (aka an ion pump working in reverse)
times of large concentration gradients = make ATP
times of small concentration gradients = make bigger concentration gradient

New term of fun:
Iso-osmotic= same amount of stuff on each side and same amount of pressure on each side.

Workshop # 6

6C) the polar heads will bind to one another because of the charges on the head. so no liposomes form.

6D) ammount/time/area=units for permeability, the permeability is going to decreaces becasue the space between phospholipid decreases.

6E) The membrane is a phospholipid bilayer. the bilayer maintains its position by bonds with water, holds structure from integral member proteins

6F)The rate of production of RNA must be faster than the rate of the PL production so the daugheter cells will have enough RNA templates. Need more RNA Polymerase to have RNA template in daughter cell.

6G) The cell size will increase becasue water will come in and forms bonds w/ proteins and other molecules, so less water will the membrane, causing the cell to increase in size until it bursts. In order for a cell to not burst, it needs to have some way of regulating what flows in and out.

Workshop #5

Study workshop questions for the test--workshop questions can be on the test



translation: using mRNA to make protein

transcription: using RNA to make mRNA



template RNA needed for making proten

aminoacyl tRNA is needed for making protien


base pairing: A-U, G-C



replication error can occur and make a different amino acid chain



5 things needed for cell replication:

1. mRNA


2. aminoacyl tRNA


3. aminoacyl tRNA syntatase


4. tRNA


5. ribosome

Workshop #4

*High energy intermediates are needed to form polymers

- the amount of triphosphates limits the number added to the polymer

- a monophosphate can be used to start the chain, but then triphosphates must be used

*RNA polymerase = protein enzyme

- Adding RNA polymerase to a system containing an RNA sequence does not increase the rate of the reaction because there are no binding sites for the template

*Polynucleotides are built from 5’ to 3’

- a phosphodiester bond connects the nucleotides

- weak hydrogen bonds connect the base pairs (A,C,G,U)

*An enzyme that has binding sites for a template and for free nucleotides can rapidly generate copies of RNA

Workshop #3

*For any amino acid chain there are a really big number of different possible 3-D configurations.
(3-D configuration=conformation=tertiary structure)
*Out of these structures there will always be one that is the most efficient.
*Structure of Sucrose: http://http://en.wikipedia.org/wiki/Image:Saccharose.svg
*sucrase = enzyme
*The function of a protein (including enzymes) depends upon its amino acid sequence.
*The most efficient reaction will have the highest Keq, which can be found through radio labeling and filtration.
*Solubility depends on a number of different things:
-polar vs. non-polar
-bond strength
-temperature
-size of molecule
-addition of other things (salts)
-change in pH (add H+ ions/OH- ions)