Lectur 7 translation

Question 1

1. What is translation’s role in the central dogma?

Question 2

2. Draw the general structure of an amino acid zwitterion.

Question 3

3. Define “proteinogenic amino acid”. Why are non-proteinogenic amino acids often toxic?

Answer 3

non-proteinogenic AAs are often toxic as these are not one foth biologically functional 20AA’s but have similar r groups which could result in it being incorporated into proteins and yielding them nonfunctional

Question 4

4. If a protein is a homodimer what does that mean? Heterotrimer?

Question 5

5. Give the key features that define primary, secondary, tertiary, and quaternary structure of a protein.

Answer 5

primary: the sequence of amino acids
secondary: the hydrogen bonding of the back bone (beta-pleated sheets and alpha helixes)
tertiary: the r 3d shape of the folded polypeptide and the r groups coming off the backbone
quaternary: 3 d shape of polypeptides interacting to form larger macromolecules

Question 6

6. What stabilizes each level of protein organization?

Question 7

7. What are the 5’ and 3’ UTRs? What functions to they serve?

Question 8

8. How many sequences are possible for a protein with a length of 100 amino acids? (Xy notation is

Question 9

9. What are three functions that are shared by both prokaryotic and eukaryotic ribosomes?

Answer 9

bind mRNA and find the start codon
facilitates mRNA and tRNA base pairing
catalyze peptide pond formation

Question 10

What is the role of IF3 in translation initiation in bacteria?

Question 11

What is the role of IF2 and IF1 in translation initiation in bacteria?

Question 12

How is the authentic start codon oriented to the P site in bacterial mRNA by the ribosomes?

Answer 12

ribodomal rna of the ribosome base pairs with the mrna of the consensus sequence ( shine delgarno sequence) which facilitates the ribosome movement to the start codon into its site.

Question 13

Define consensus sequence.

Answer 13

a portion of the mrna that is complimentary to the ribosomal rna and is upstream of the start codon and helps facilitate the recruitment of the ribosome to the start codon.

Question 14

Suppose a bacterial gene acquired a mutation in its Shine-Dalgarno sequence, what might be an
expected consequence of this?

Answer 14

this would prevent base pairing with the ribosomal rna such that the start codon would not be oriented in the p-site

Question 15

Explain the role of f-Met in translation. Is it present in eukaryotes?

Answer 15

f met is the first amino-acid in prokaryotes

Question 16

What are the roles of eIF1, eIF3, and eIF1A in eukaryotic translation initiation? eIF5? eIF4?

Question 17

Explain the process of “scanning” for the authentic eukaryotic start codon.

Answer 17

small subunit for the ribosome moves in the 5’ to 3’ direction and scans for the start codon which is within the Kozak sequence

Question 18

How does scanning differ from how bacteria identify start codons?

Answer 18

in bacteria the consensus sequence is upstream of the start codon and requires base pairing between the mrna and ribosomal rna

in eukaryotes the start codon is within the kozak sequence and the small ribosomal unit scans for the kozak sequence to thus translate the start codon and begin the translation.

Question 19

What is the Kozak sequence?

Answer 19

consensus sequence in eukaryotes

Question 20

Suppose a mutation causes a Kozak-like sequence (with an AUG embedded within it) to appear
upstream of an authentic start in the 5’ UTR of a eukaryotic gene. What is the expected
consequence?

Answer 20

translation would start way upstream and lead to the translation of unintended/abnormal proteins.

Question 21

The Kozak sequence is generally not “free to vary” from an evolutionary perspective. What does
this mean?

Question 22

What is a leaderless mRNA? What types or organisms have them?

Answer 22

a leaderless mrna is one that lacks a 5’ UTR and ultimately begins with a start codon. present in archaean species therefore they can begin translation without a consensus sequence.

there were independent loss events of leaderless mrna in which the archahen inherited it from luca and bacteria and eukaryotes lost these leaderless mrna due to independently

ancestral state of mrna had 5’utr present in luca however there was an independent gain in archaeans of the leaderless mrna

Question 23

23. What is the role of EF-tu in translation elongation?

Answer 23

it enters the A sit with help of GTP to initiate anticodon and codon basepaire to form the petide bonds between amino acids

Question 26

Eukaryotes have fewer release factors than bacteria. Explain this based on the functional
capabilities of the proteins.

Question 28

28. In eukaryotes transcription and translation cannot happen simultaneously. Why?

Answer 28

prokaryotes do not have a nucleus and eukaryotes do so we need to do mrna processing and nuclear transport so these cannot occur at the same time

Question 30

How does the genetic code evidence a single origin of life on earth? Are there any exceptions?
Do these exceptions cast meaningful doubt on the single origin idea? Why or why not?

Question 34

. Suppose the genetic code were overlapping. What two properties would this introduce in terms of
(1) protein sequence and (2) point mutations?