molecular bio 4

Question 1

SD on prokaryotic mRNA

Answer 1

Shine-Dalgarno sequence; orients on small ribosomal machinery

Question 2

What nucleotides are in the Kozak sequence?

Answer 2

ACCAUG

Question 3

Eukaryotic vs prokaryotic mRNA

Answer 3

SD vs. Zozak, 5’ cap and poly(A) tail, cistronicness

Question 4

What is special about the beginning of translation in prokaryotes? Why?

Answer 4

Initiator proteins recognize specifically formalated methionine to prevent starting translation at an internal methionine. So, the first rRNA brings in fMet

Question 5

3rd codon in anticodon

Answer 5

Wobble codon, could be a different base to produce to the same amino acid

Question 6

A, P, and E sites on srRNA

Answer 6

P- peptyl transfer, E-exit site, A-aminoacyl (entry) site

Question 7

Which direction is mRNA read during translation?

Answer 7

mRNA is read 5’ to 3’ during translation. DNA is read 3’ to 5’ in transcription

Question 8

Initiation factors

Answer 8

Recognizes start codon, recruits ribosome
Binds near A and E sites so that tRNA binds to the P site

Question 9

Elongation factors

Answer 9

help with tRNA translocation and peptide bond formation

Question 10

Release factors

Answer 10

Bind so that no more tRNA are able to bind

Question 11

How does the ribosomal machinery get assembled?

Answer 11

Recruited by initiation factors

Question 12

Sometimes instead of 5’ cap in eukaryotes and viruses

Answer 12

internal ribosome entry sequence (IRES), more stable because of loop structures, used on very important transcripts

Question 13

Methylation on 5’ cap

Answer 13

Can help prevent nuclease activity

Question 14

GTP hydrolysis, not in the steps of elongation

Answer 14

Release initiation factor and promotes attachment of large subunit

Question 15

Elongation steps

Answer 15

tRNA loaded into a site
Older amino acid chain is moved to the new amino acid
tRNA moves over

Question 16

Error rate of translation

Answer 16

10^4 (transcription 10^9)

Question 17

Every amino acid how many energy units

Answer 17

2 GTPs

Question 18

When do RFs come along?

Answer 18

Have specificity to stop codons

Question 19

RRF (pro)

Answer 19

ribosome recylcing factor

Question 20

Truncated mRNA

Answer 20

DNA transcription ends prematurely

Question 21

Non-stop mRNA

Answer 21

mRNA lacks a stop codon (mutation)

Question 22

tmRNA

Answer 22

incorporates amino acids if 3’ end is broken; ribosomal pausing prevented; 10 AAs added are tags for degredation

Question 23

Post-translational modifications

Answer 23

Met sometimes removed; chemical groups added (glycosylation, methylation) (N-terminal acetylation protects chewing, super common); sometimes part is cleaved

Question 24

Why is an aminoacyl-AMP transfered to tRNA?

Answer 24

I think because each tRNA needs to carry an amino acid

Question 25

Where do amino acids get attached on a tRNA?

Answer 25

3' end

Question 26

Shine-dalgarno sequence

Answer 26

prokaryotic; on mRNA; complimentary base pairs to rRNA

Question 27

IRES

Answer 27

IRES more stable than 5' cap; for mRNAs that are regulated in high specificity

Question 28

What energy does translation elongation require?

Answer 28

GTP

Question 29

What are the two steps that require GTP?

Answer 29

Recruitment of tRNA into A slot, moving that tRNA

Question 30

What does the stop codon bind to?

Answer 30

Release factor

Question 31

What is the release factor (or ribosome recycling factor) shaped like?

Answer 31

tRNA

Question 32

What happens if there is a broken 3' end of mRNA in prokaryotes?

Answer 32

tmRNA has an amino acid, tRNA (check?), and some additional mRNA bases

Question 33

What is the equivalent of the shine-delgarno site in eukaryotes

Answer 33

Kozak sequence

Question 34

What is differently formalated across eukaryotes and prokaryotes?

Answer 34

The first Met

Question 35

What happens if there's a broken 3' end of mRNA in eukaryotes?

Answer 35

Ski7 protein chews up the RNA?

Question 36

Deadenylation-dependent mRNA decay

Answer 36

mRNA chewed, starting in 3' end (starts at polyA), then exosome can chew the rest up or decapping enzyme and nuclease

Question 37

Exosome

Answer 37

Chews RNA

Question 38

Deadenylation-independent mRNA decay

Answer 38

decapped then chewed 5' to 3'

Question 39

Endonuclease mRNA decay

Answer 39

Starts with a cut in the middle of the RNA

Question 40

Nonsense-mediated mRNA decay

Answer 40

Happens when stop codon has been introduced; only happens after translation and ribosome has recognized premature stop codon

Question 41

What is the 50-55 nucleotide rule?

Answer 41

If there is a stop codon at least 50 nucleotides upstream of an exon-exon junction, then the mRNA is marked for degredation

Question 42

What does RRF do?

Answer 42

Detaches ribosome subunits in prokaryotes

Question 43

What are key targets for phosphorylation?

Answer 43

Serine, threonine, tyrosine