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.