Workshop #9

Workshop #9 

Workshop #9 Solutions!

Sorry for the quality, google can only do so much...let me know if you have any questions!

(if you scroll down - you will see the info!)

Workshop #8

A. Oxygen is a waste product of non-cyclic photophosphorylation because of the breakdown of H2O during the process. H2O breaks down into O2 + H+ + e- and the e- is needed to power the proton pump and carry out the rest of the cycle.

B. The lifespan of red blood cells from athletes is less than that from a sedentary human because athletes breathe more toxic O2 which breaks down biomolecules.

C. The master must have made the soy sauce in an O2 free environment, as it is rich in lactic acid and ethanol. My soy sauce tasted "vinegary" because I made it in an environment where O2 is present and acetic acid was produced.

D. With freely isolated mitochondria, pyruvate, ADP and Pi in solution, ATP is produced. This is because the pyruvate is used to produce acetic acid for the citric acid cycle to produce NADH which powers ETS which produces ATP.

E. An experiment similar to D is conducted but without the presence of pyruvate and ATP is still detected. Why? There are still proton gradients that will still allow the process to continue for some time, but will eventually stop making ATP when the gradients run out of energy.

F. If the proton gradient is unrestricted, the proton concentration will go to Keq and there will no longer be a gradient. If there is no gradient then no ATP will be produced. Mitrochondria in these cells contain this extra complex as another way for electrical energy to generate heat and insulate an animal.

G. The molecules that were radioactive in the student's urine is the H2O. The radioactive O2 was used in a coupled reaction to form H2O in ETS.

H. NEED: ATP/sec + glucose/sec
100,000 PL/1,000 sec x 5 ATP/1 PL = 500 ATP/sec needed to support the generation of a new membrane.
1 glucose transporter/cell. So,
500 ATP/sec x 1 glucose/2 ATP = 250 glucose/sec needed to support that metabolic rate.

Workshop #6

6B) 

• diffuse ions out of the cell
  
• uni-directional transporter wants equilibrium in order to maintain cell's volume 
  

6C) 

• phosphoenolpyruvate has the highest - delta G value
  
• an enzyme with binding sites for ADP and Pe-P
  
• radio label phosphate and filtrate
  
• enzymes work both ways depending on concentration
  

6D) 

1. add radio labeled glucose into the cell without ATP  
   
2. wait
3. filtrate and see if glucse is present:

-if gluscose is present, passive

-if glucose is not present, active

6F) 

• Change polymerase binding sites from RNA to DNA

6G)

• Double stranded DNA needs more energy

6H)

• heating breaks H-bonds between bases
• cooling reforms the double strands

6I)

• its easier to find the codes

Workshop #5, w/solutions

Here is workshop # 5 and its guide.  Use the guide as a reference, DO NOT study from it.  Use your notes and olek's slides - they will be much more useful and informative.  

Workshop #5

Guide

Workshop #4 w/ solutions

Hey guys, here is the workshop, and Caitlin's solutions.  Thanks Cait!

Workshop #4

Workshop #4 Notes

4B) Free Nucleotides + Polynucleotide => Free nucleotides (monophosphates- AMP,GMP, UMP) link together by expending ATP (or any other tri-phosphate) to form a phosphodiester covalent bond. Weak hydrogen bonds form between the base pairs (3 H bonds between A and U or T, 2 btwn C and G) of the polynucleotide and the newly-forming polynucleotide. Template-directed RNA would help to stabilize the reaction and make it occur faster.

4C) A "cell-free" system = E.Coli without membranes in a test tube

How do we get polypeptides? 

Amino Acids bind to tRNA with the expended energy of ATP or another high-energy intermediate

tRNA's anti-codon (3 nucleotide bases) bind to their specific codon (corresponding base pairs) on an mRNA sequence

This process re-occurs with another tRNA binding to mRNA, and the amino acids (attached at the top of the tRNA) are attached by a peptide bond, generating a polypeptide

4D) Codons on mRNA, Anti-codons on aa-tRNA/tRNA

       Also, know that you should associate the amino acid with the correct CODON on mRNA.

4E) AUGUUUGGGCCCUUU => Met- Phe- Gly- Pro- Phe 

       Sequence of mutant mRNA giving rise to the mutant amino acid sequence (shown below)

       AUGUUUAGGCCCUUU=> Met- Phe- Arg-Pro- Phe - There is an A nucleotide base instead of a G.

     Mechanism of Mutation: 

-Know that transcription is template RNA (DNA) to mRNA and translation is mRNA that codes for a protein.

One possible cause for mutation: Transcription error (different base pair codes for a different amino acid)

Another cause for mutation: One of the base pairs is not included in transcription, and the entire protein sequence changes.

4F) -Precursors for the formation of Phospholipids: phosphoglycerol and fatty acids

 -As soon as you make a phospholipid, it is integrated into the protocell boundary membrane. 

 -Lack of an enzyme or inhibited enzyme that separates the phospholipids will limit the growth of the membrane.

4E) For this to occur, : rate of RNA replication > rate of phospholipid formation

 - There must be enough RNA produced before it splits, so that there's enough for both daughter cells  

I emailed Olek and asked about which phospholipid we needed to memorize, the phosphatidly ethanolamine or the phosphotydlcholine, it is indeed the phosphotydlcholine, the one listed in the memorize section, not the one we talked about in workshop.

Workshop #3 Solutions

3B. Looking at the diagram on the back, one would assume that glutamic acid would be more soluble in water than alanine (because of polarity or the fact that it says "hydrophillic/phobic" in the tables. Note: Olek says those are words to avoid...). After careful consideration, however, we can see that alanine is more soluble in water for a rather simple reason- it's size. Glutamic acid is bigger, so it would have to break way more water-water bonds to dissolve in water than alanine would. This means dissolving alanine in water is more favorable in terms of deltaG because it takes more energy to break the water bonds for glutamic acid. 

3C.  1) There are MANY configurations/conformations/tertiary structures (all the same thing). But only the most stable of the structures act as an enzyme. (Derek aside: what are other random things that can affect the structures? temperature, charges, pH).

2) We would have to know BDEs and relative number of conformations in order to predict the largest ratio.

3D. Sucrose (models on BIO 110 site)  {but is a glucose attached to a fructose}.

3E. There are many different conformations for the enzyme, sucrase. The enzymes that are the most stable tend to fit nicely around a sucrose molecule. The sucrase molecule sneaks up on the sucrose molecule and wraps itself around it. How? There are charges on both molecules that attracts them together. Sucrase essentially "pulls" on the attached glucose and fructose molecule, stretching out the bond in between them. This makes the bond weaker so a "less crazy water molecule" can hit it and possibly break it. Now, not only can the "crazier" water molecules that were able to break sucrose before, break the sucrose, but so can the "less crazy." This, in effect, increases the reaction rate of sucrose hydrolysis forming glucose and fructose.

3F. Filter! You could test different enzymes on molecules that you know the size of (and the size of what they would break up into). This way, you could filter out the broken up molecules from the not-yet-broken-up molecules. You can compare the TIME that it takes for each enzyme to break these molecules. 

3G. What you would need to know about these polypeptide chains is that they have charges going along the chain. When they roll up and configure the way that they do, the + and - charges on the chain tend to line up together (because opposites attract). These + and - charges are present on H+s and OH-s. Knowing this, you could engineer the enzyme to effectively wrap around a molecule. 

3H. Yes, it is important! Some proteins are more soluble in water than others because of their size, polarity, etc... You can make a protein relatively insoluble in water but more soluble in a lipid by make it nonpolar. Lipids are nonpolar, so they'd go together great.