Workshop 12: Last workshop (voluntary)

12B.) there are 50 alleles (alleles affect things like eye and hair color and many other things) Uses the equation [N*(N+1)]/2 to find out the combinations of all the alleles.
so the number of alleles is 1275.

12C.)pretty much the intestine or whatever organ is covered in mucus and the mucus is usually water but with cystic fibrosis the mucus dries up because the Cl- channel stops working and so no water follows after the Cl- thus causing the mucus to dry up.

12D.) the steps are pretty much split(uses helikase), copy(polymerase), put back together(DNA replication complex).   yes, the the reproduced bacteria is identical.  even if the bacteria had 4 chromosomes, it would still work but there would be different amounts of chromosomes in some of the daughter cells.

12E.)the radiation would cause a mutation that would make different proteins.  since penicillin, binds to the original protein, this new sequence that exists in the new proteins wouldn't really allow penicillin to bind to it.  this trait would only be in daughter cells if the DNA is affected but if its only local within the cell and not the DNA, then the daughter cells won't be affected.

12F.)
-Protophase-
1.)replicate everything (using DNA replication complex)
2.)condense chromosomes (using condensin complex)
3.)nucleic envelope is gotten rid of so cells can split (using laminase)

-metaphase-
4.)cells line up and mtoc grow microtubioles to the chromosomes' kinetochore

-anaphase-
5.)chromosomes are pulled toward mtoc by the microtubioles disintegrating and becoming shorter

-telephase-
6.)cells start to split. the myosin motor starts to pinch cell.
7.)then two daughter cells are left.

12G.)
cytokinesis is moving out of cytoplasm. the antibody distrupted the process and doesn't allow the myosin to pinch the cells so in the end all the chromosomes are within one cell.

12H.)each chromosome has a 3 loci setting of h,m, and l. in this problem the affinity is also the phenotype and determines how much O2 can pass through.

given: genotypes(settings are supposed to be in subscripts) (affinity)

AmAmBmBmHmHm (1), AhAhBhBhHhHh (1.), AlAlBlBlHlHl (0.5)

ones made in WS:

AmAmBlBlHhHh (averages out to 1)

AlAmBmBmHlHm (around 0.7 since most of it is all m's and only a couple of l's)



on a side note: Derek: "I would like to give birth once." and use the poly in polymerase in lets say polygon.

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)

Workshop #1

Better late than never. 9.12.07

-*lecture lecture lecture* *angry voice*
-Drawing of glucose. Wikipedia - Glucose
-Best kinetic Stability
-Most efficient structure

-Drawing of ribose. Wikipedia - Ribose
dG > 0 => Expending Work / Non Spontaneous
dG < 0 =""> Gives off energy / Spontaneous

dG : Gibbs Free Energy

-No one likes peanuts.

Workshop # 2

In order for molecules to bond with each other, they must be at the correct speed and orientation.

This is where enzymes come in- they lower entropy and make it more likely moelcules will bond!

ATP hydrolysis has FREE ENERGY, so it is delta G NEGATIVE

To make a reaction go, you need activation energy.

polypeptide= amino acid chain...... amino acid chain=polypeptide

PHOSPHODIESTER BONDS connect nucleotides ( C3-O-P-O-C5 )

COUPLING is when you use a delta G negative reaction to fuel a delta G positive reaction

Think: Guy wants to lift weights, which has a positive delta G of 50. He eats a powerpar which contains a negative delta G of 60. Now he can lift the weights, and he releases the extra 10 as heat.

ATP is a high energy intermediate. During hydrolysis, a phosphate group is removed---this releases energy which can be used to bond nucleotides!

The End

Workshop #2

No Fun Fact
No Quote of the Day

Remember this:

BOLD WORDS = KEY WORDS

• Dr. Olek will make the calculations easy
• Ignore extra info like pH 7 @ 25 degrees C
  
• Spontaneous reactions => deltaG is negative at equilibrium
• a negative deltaG means free energy is released and can be used to do other work like COUPLING
  
• Activation Energy is needed to get to the transition state
• a Phosophodiester Bond links nucleotides ==> NOTE: THIS WILL BE ON THE TEST SO KNOW HOW TO DRAW THEM
• polymerization is the joining of nucleotides
  
• polypeptides are amino acid chains (proteins)
• Collision model = slow process because it depends on speed of molecules (energy) and orientation
  
• enymes lower entropy

Problem solving 101

1. list givens
2. draw diagram (may be a waste of time but if it helps do it)
3. find important relationships, proportions, whatever.
4. calculate
   

Thats it

Mooncai

P.S. For Ben and other freshmen. Clubs are for a meals, a side, and a fountain drink. Declining is money only for food and can be used everywhere. Flex or what they are now calling URos is money for everything.

Workshop #1

Fun Fact: Don't download music or else the school will find.

Quote of the day: "To do well in Bio 110 you have to give Olek what he wants" -Derek
......and what might that be ;)

so heres the notes-
*Ring shape is the most efficient
*AMP= adenine monophosphate
*ADP= adenine diphosphate
*ATP= adenine triphosphate

Radio labeling - used to find things later

filter - can be used to separate product from reactant when different sizes

****Important**** DONT include solids and pure liquids (H2O) in reactant for Keq

*6.02x10^23 is molecules per mole

In the Beginning.

Well well well, nice of you to join the party. And by party I mean Biology 110. This is the greatest class EVER, and if you don't agree, I will fight you.1 I'm Derek, your TA. I'll be helping you out this semester, and im really looking forward to working with each and every one of you.2 I hope the semester has started off nicely for you! Please, this blog is for you, so abuse it! Feel free to post any questions, comments or insights you may be having at the time of publication. Im looking forward to having a great semester with ya'll.3


1 I have never once fought someone, ever. (assume this to be a trend)
2 That was a very vague, blanket statement meant to make you feel good inside. By no means is it a personal insight, as I dont know a single one of you. I can assert, however, that by the time you are reading this I will have met you (or soon will) and will have a strong desire to get to know you and make your wildest biology dreams come true. (This is a sincerely genuine comment)
3 I reside in the state of New York, which is in the northeastern United States, where is is very rare, if not wrong, to use the phrase "ya'll". I may or may not continue using it. Because I'm a rebel. I also say "pop"-all the time.