Translation

Question 1

explains why multiple codons code for one amino acid

Answer 1

wobble hypothesis

• nontraditional base paiting of the 1st base on anticodon with the 3rd base of codon

Question 2

what are teh 4 characteristic of genetic code?

Answer 2

1. specificity
   
   1. specific codon alwasys codes for the same AA
2. universality
   
   1. conserved from early staged of evolution
3. redundancy
   
   1. given AA may have more than one codon
4. nonoverlapping and commaless
   
   1. read fixed starting point as continues sequence of bases, three at a time

Question 3

describe the difference between point mutation, indels and frameshift

Answer 3

1. point mutation
   
   1. silent
      
      1. doesnt change the AA
   2. missense
      
      1. generates a different AA
   3. nonsense
      
      1. generates a stop codon
2. insertion, deletions-> frameshift
   
   1. unless its the entire codon. then its just a deletion/insertion

Question 4

James finds a missense mutation in patient gentic workup. It happens to be on the beta-globulin gene. Whats the disease?

Answer 4

Sickle cell anemia

Question 5

what energy sources are used during translation?

Answer 5

• ATP
  
  • used to attach AA to tRNA
• GTP
  
  • used for binding of aminoacyl-tRNA to A site and for translocation step

Question 6

James is unable to metabolize the attachment of an AA to the tRNA, what enzyme is he deficient/defunct in? How does it attach? What is it responsible for?

Answer 6

aminoacyl tRNA synthetase

1. requires ATP
2. attaches to the 3’ side of the tRNA
3. responsible for
   
   1. specificity
   2. proofreading
   3. high difelity of translation

Question 7

Describe the 3 functional sites of the ribosome.

Answer 7

• A site
  
  • binds incoming aminoacyl tRNA and specifies next AA
• Psite
  
  • occupied by peptidyl tRNA, this tRNA carries syntehsized peptide
• E site
  
  • occupied by empty tRNA as it is about to exit

Question 8

descrive initiation of translation between prokaryotes and eukaryotes

Answer 8

• prokaryotes
  
  • 16srRNA contains sequence that is complementary to the SHINE-DALGARNO sequence of mRNA
    
    • binding these two sequences posistions mRNA on 30S subunit
  • first message recognized is AUG, for N-formylated methionine
    
    • NF-Met is the first, all other AUG’s get regular Met
• eukaryotes
  
  • 40S subunit binds to the cap structure of mRNA
  • Met is not formylated in humans

Question 9

list the four steps of translation and the steps involved in each

Answer 9

• initiation
  
  • initiation factors aid in formation of the 30S initiation complex
  • GTP is cleaved and initiation factors are released when the 50S subunit arrives to form the 70S
• elongation
  
  • elongation factors direct the binding of the appropriate tRNA to the codon in the empty A-site.
  • peptidyltransferase, a component of the 5-S ribosomal subunit transfers the AA (or peptide chain) from the P-site onto the AA at the A-site, and catalyzed peptide bond formation
  • the ribosomes move a distance of three nucleotides along the mRNA in the 5’-3’
• termination
  
  • once growing peptide is complete a termination codon is recognized by a release factor, which activates the release of the newly synthesized peptide and dissolution of the synthesizing.

Question 10

how do the following affect translation?

1. streptomycin
2. tetracycline
3. chloramphenicol
4. clindamycin/erythromycin
5. diphtheria toxin

Answer 10

1. streptomycin
   
   1. bind to 30S subunit and distort its structure
   2. stops initiation
2. tetracycline
   
   1. interacts with 30S in complex, and blocks tRNA attachment
   2. stops at elongation
3. chloramphenicol
   
   1. inhibits prokaryotic peptidyltransferase
   2. stops at elongation
4. clindamycin/erythromycin
   
   1. irreversibly binds to the 50S P or E site, inhibiting elongation
   2. stops at elongation
5. diphtheria toxin
   
   1. inactivates (ADP ribosylation) the eukaryotic elongation factor, eEF2.
   2. stopping translocation- at elongation

Question 11

what assists the protein foldeing correctly? families, and bonds are catalyzed by.

Answer 11

• chaperones - bind to growing polypeptides
  
  • Hsp40 or Hsp70
• disulfide bond formation between cys residues
  
  • protein disulfide isomerase (PDI)

Question 12

list the process/steps in degrading a defunct/old protein

Answer 12

polyubiquitination

1. three step process
   
   1. ubiquitin activating E1
   2. ubiquitin conjugating E2
   3. ubiquitin ligating E3
2. lastly, is the degradation by 26s proteasome

Question 13

How does a protein know where to go/be delivered in the cell?

Answer 13

targeting signal sequences

1. contain a specific AA sequence that direct them to their final location
2. two to know
   
   1. nuclear proteins
      
      1. ​nuclear localization signal
   2. mitochondrial proteins
      
      1. ​mitochondria entry signal

Question 14

list the locations of the following processes in translation

1. synthesis
2. elongation
3. completion of protein (before postmods)

Answer 14

1. synthesis begins in cytosol
2. elonation finishes on ER
3. completed protein is released inside of ER

Question 15

fate of proteins produced on ER

3 main options distcussed

Answer 15

1. lysosomes
   
   1. capable of breaking down different molecules
      
      1. peptidases
      2. nucleic acids
      3. carbohydrates
      4. lipids
2. secretory vesicles
   
   1. contain molecules destined for secretion outside the cell
      
      1. gastric acid
      2. digestive enzymes
      3. lung surfactants
      4. sebum to lubricate skin and hair
3. extracellular vesicles
   
   1. that can carry protein and nucleic acids
      
      1. can be considered as another type of cell signaling

Question 16

Post translational modifications

1. Ser, Thr and Tyr
2. Lys and Arg (on histones)
3. Pro and Lys (for collagen)
4. blood coagulation (clot formation)
5. anchor protein in membrane
6. Ser, Thr or Asn residue of membrane and secreted proteins
7. Lys in carboxylases

Answer 16

1. phosphorylation/dephosphorylation of Ser, Thr and Tyr
2. methylationof Lys and Arg
   
   1. involvev in the regulation of transcription
3. Hydroxylation- Pro and Lys undergo this in collagen to maintain stability
4. attachment of fatty acids to anchor protein in membrane
5. glycosylation of Ser, Thr, or Asn residues of membrane or secreted proteins
6. biotinylation of Lys in carboxylases

Question 17

what do post translational modifications add to the proteom?

Answer 17

Post-translational modifications increase proteomic diversity

Question 18

which is larger, the genome or proteome and why?

Answer 18

the genome= 20k-25k, proteom >1million.

the increase is achieved at the lever of transcription** and **post-translational modification