Translation

Question 1

what does a redundant or degenerate genetic code mean?

Answer 1

• Some amino acids must have more than one codon (64 possible amino acids, but only 20, so multiple codons code for an AA)

Question 2

what kind of mutation is found in CF?

Answer 2

• ΔF508 mutation of CF
  
  • deletion of phenylalanine at amino acid position 508

Question 3

name the stop codons

Answer 3

• yoU Are Away
• yoU Go Away
• yoU Are Gone

Question 4

only 2 AA have one codons…which?

Answer 4

Methionine (Met) and Trytophan (Trp). Except in mitochondria, where Trp has 2 codons

Question 5

describe the structure of a functional ribosome

Answer 5

• 3 binding sites
  
  • A site holds the tRNA that carries the next aa to be added to the chain
  • P site holdes the tRNA that carries the growing polypeptide chain
  • E site is the exit site, where discharged tRNAs leave the ribosome

Question 6

describe the structure of the prok ribosome and the euk ribosome

Answer 6

• Prok: 2 subunits which = 70s
  
  • 50 s = peptidyl transferase activity
  • 30 s
• Euk: 2 subunits which = 80s
  
  • 60 s
  • 40 s

Question 7

describe the tRNA secondary structure

Answer 7

• Resembles a cloverleaf
• The anticodon recognizes 3 bases on the mRNA by base pairing

Question 8

describe the tertiary structure of tRNA

Answer 8

• 3’end where amino acid is attached to

Question 9

explain the Wobble Hypothesis

Answer 9

• Wobble position is the 3rd nucleotide on the codon (most right position)
  
  • Where you can have non-traditional base pairing because of the degenerate genetic code

Question 10

how are AA attached to tRNA?

Answer 10

• 2 step process
  
  • Enzyme bound amino-acid adenylate
  • Formation of the aminoacyl-tRNA (aka charged)
• Reaction is driven by hydrolysis of pyrophosphate
• tRNA attached to amino acid is called the “charged tRNA”

Question 11

what is the first AA in prokes and mitochondria?

Answer 11

• fMet-tRNA
• This special tRNA is recognized differently by the ribosome–allows initiation
• Prokes have 2tRNAs for methionine, one allows formation of fMet, the other recognizes internal AUG codons

Question 12

what is the first AA in euks?

Answer 12

• The first codon also uses Met, and it has a special tRNA for this first codon, but not formylated
• Normal Met-tRNA for internal codons

Question 13

describe the function of the Shine-Dalgarno sequence

Answer 13

• Prokaryotes have a SD sequence which is purine rich and resides a few bases 5’ to the start codon
• Euks don’t have a SD sequence, therefore euk small ribosome binds close to the cap at the 5’end, scans until it encounters the AUG start codon

Question 14

describe the protein synthesis in translation

Answer 14

1. Initiation factors (IFs) aid in the formation of the 30s initiation complex. The charged initiator tRNA is brought to the P site of the 30s subunit by IF-2-GTP
2. GTP on IF-2 is hydrolyzed and initiation factors are released when the 50s subunit arrives to form the 70s initiation complex

Question 15

describe the elongation process in protein synthesis

Answer 15

3. Elongation factor EF-Tu-GTP brings the appropriate charged tRNA to the codon in the empty A site (decoding). GTP on EF-TU is hydrolyzed
4. Peptidyltransferase, an activity of the 23S rRNA of the 50s subunit, catalyzes peptide bond formation, transferring the initiating AA (or peptide chain) from the P site to the amino acid at the A site (transpeptidation).

**Catalyzed by an enzymatic actvity of the RNA portion of the 50s ribosome – a Ribozyme

Question 16

describe the next steps of elongation and termination

Answer 16

5. EF-G-GTP facilitates movement of the ribosome 3 nucleotides along the mRNA in the 5’ to 3’ direction. What was in the P site is now in the E, A now in P, and A is empty.
6. Steps 3, 4, 5 repeated until termination codon in A site.
7. A termination codon is recognized by a release factor (RF-1 or RF-2) which results in release of the newly synthesized protein. GTP on RF-3 is hydrolyzed. The complex dissociates

Question 17

describe the process of protein folding

Answer 17

• Occurs during translation
• Spontaneous or facilitated by chaperones

Question 18

differences between prok and euk translation

Answer 18

• Euk
  
  • first MET is not formylated
  • monocistronic
  • typically start translation at first AUG site
  • may not couple bc of nucleaer membrane
• Prok
  
  • first MET is formylated (fMET)
  • polycistronic
  • may select an internal AUG to start translation
  • translation and transcription are coupled

Question 19

describe the function of diphtheria toxin

Answer 19

• Inactivation of EF-2 (euks) by adding ADP-ribose to it

Question 20

describe the function of stretomycin

Answer 20

• Prevents assembly of ribosome (binds to 30s subunit)
• Inhibits initiation

Question 21

describe the function of tetracyclin

Answer 21

• Four (tetra) ring (cyclic) structure
• Blocks elongation by preventing aminoacyl-tRNA access to the A-site

Question 22

describe the function of erythromycin (macrolide)

Answer 22

• Binds to the 50s subunit of the ribosome
• Blocks ribosome translocation
• macroSLIDES –> blocks translocation

Question 23

chloramphenicol

Answer 23

• inhibits peptidyl transferase activity in proks
• at high levels, may inhibit mitochondrial translation

Question 24

describe the function of cycloheximide

Answer 24

• inhibits euk peptidyl transferase activity
• Used for research in labs

Question 25

describe the function of puromycin

Answer 25

* causes premature termination of translation in both proks and euks

Question 26

describe zymogen activation

Answer 26

* Zymogen (or proenzyme): an inactive enzyme precursor * activated within an organism into active enzymes * activation by enzymatic cleavage of peptide bonds of the zymogen molecules * Cascade of zymogen activation: * caspases to activate apoptosis * blood coagulation * digestion of proteins

Question 27

what is the purpose of protein phosphorylation

Answer 27

* Serine/Threonine * phosphate is transferred from ATP to a protein on a Ser/Thr residue of a protein * More common than tyr phosphorylation * Tyrosine * phosphate is transferred from ATP to a protein on a Tyr reside of a protein * the insulin receptor is a tyrosine kinase

Question 28

explain the process of glycosylation

Answer 28

* may occur as either one type of linkage or with both on the same protein

Question 29

describe the process of lipid anchoring

Answer 29

* Lipid anchoring * have proteins that need to interact with the lipids in the PM; need to add Farnesyl which lets it interact with the lipid bilayer * The cell targets Ras to the PM by a lipid anchor mechanism

Question 30

describe proteolytic processing of insulin

Answer 30

* Insulin and its C-peptide are packaged together into secretory vesicles to be made ready for secretion * C-peptide is essential for proper insulin folding * **C-peptide is a good indicator of insulin production and secretion because its (C-peptide) half-life in the plasma is longer than that of insulin**