Topic 3, Lecture 3

Question 1

What must an mRNA have to be considered export-ready?

Answer 1

Poly-A binding proteins, cap binding complex, exon junction complexes, absence of snRNPs

Question 2

Initiation factors for protein synthesis

Answer 2

eIF4G and eIF4E

Question 3

eIF4G

Answer 3

Scaffolding protein, binds to mRNA allowing recruitment of ribosomes and translation initiation

Question 4

eIF4E

Answer 4

Cap-binding protein, binds to helicase and eIF4G

Question 5

Where is the start codon?

Answer 5

Usually within 100 nucleotides of the 5’ cap

Question 6

Kozak Sequence

Answer 6

ACCAUGG, first A and last G help identify the initiating AUG

Question 7

Leaky Scanning

Answer 7

Two different proteins with different N-termini from the same mRNA

Question 8

IRES

Answer 8

Internal Ribosome Entry Site

Question 9

Polysome

Answer 9

Polyribosome, a cluster of ribosomes held together by a strand of mRNA that each ribosome is translating

Question 10

How is the steady-state level mRNA is determined?

Answer 10

By the rate of transcription and the rate of degradation

Question 11

Relationship between mRNA stability and steady state level

Answer 11

mRNA with a long half-life (slow degradation) can result in translation and protein production long after transcription ceases and mRNA with a short half-life (rapid degradation) can result in rapid changes in protein concentration

Question 12

What is the advantage of a long half-life?

Answer 12

If we needed a consistent concentration of the same gene, we wouldn’t have to keep transcribing it over and over

Question 13

What is the advantage of a short half-life?

Answer 13

If we needed a high concentration of a protein for a very short length of time

Question 14

How is mRNA with a short half-life regulated?

Answer 14

At the level of transcription

Question 15

What is the typical half-life of mRNA?

Answer 15

30 minutes

Question 16

mRNA degradation pathways

Answer 16

1. gradual poly-A shortening
2. decapping for rapid 5’-to-3’ degradation OR continued 3’-to-5’ degradation

Question 17

Decapping Pathway (deadenylation-independent)

Answer 17

Decapping, exonucleolytic decay

Question 18

Deadenylation-dependent pathways

Answer 18

Poly(A)-shortening, decapping OR exonucleolytic decay by exosome

Question 19

Exosome

Answer 19

Enzyme that degrades

Question 20

Endonucleolytic pathway

Answer 20

Endonucleolytic cleave, exonucleolytic decay by exosome

Question 21

Deadenylase

Answer 21

Rapidly eats away at the poly-A tail in the 3’ tp 5’ direction

Question 22

Ferritin

Answer 22

Iron-binding protein, prevent accumulation of toxic levels of iron within the cell, produced at high concentration of iron

Question 23

Transferrin Receptor

Answer 23

Binds to transferrin and brings iron into the cell, produced at low concentration of iron

Question 24

Cytosolic Aconitase

Answer 24

Binding protein for transferrin and ferritin mRNA

Question 25

When do we control ferritin and transferrin production?

Answer 25

Post-translation

Question 26

DCP 1

Answer 26

Decapping enzyme, lots of degradation

Question 27

Argonaute

Answer 27

Slicing enzyme, RNA becomes unstable because of endonucleolytic cleavage

Question 28

P-bodies

Answer 28

Dynamic structures composed of large assemblies of mRNA and mRNA degrading enzymes

Question 29

Stress granules

Answer 29

Contain translation initiation factors, poly-A binding proteins, small ribosomal subunits, and mRNA

Question 30

Three classes of noncoding RNAs that engage in RNA interference

Answer 30

microRNAs (miRNA), small interfering RNAs (siRNA), piwi-interacting RNAs (piRNA)

Question 31

Why does RNA Polymerase II make mRNA and the RNAs that degrade?

Answer 31

Dimmer switch

Question 32

miRNA

Answer 32

Guides that bring target mRNA into contact with exonucleases

Question 33

Cropping

Answer 33

Happens in the nucleus, cuts off cap and poly-a tail

Question 34

Dicing

Answer 34

Chops off the loop

Question 35

Slicing

Answer 35

Slices to promote degradation

Question 36

RISC

Answer 36

RNA induced silencing complex

Question 37

Extensive Base Pair Matching

Answer 37

Slicing and RISC reusable

Question 38

Less Extensive Base Pair Matching

Answer 38

Causes rapid translational repression, deadenylation, and eventual degradation

Question 39

RITS

Answer 39

RNAi induced transcriptional silencing, complex recruits proteins that modify histones and direct the formation of heterochromatin

Question 40

siRNAs

Answer 40

Short inhibitory RNAs, one of the siRNAs binds to the RITS

Question 41

What happens when siRNAs bind to the RITS?

Answer 41

Leads to histone methylation, DNA methylation, and transcriptional repression, cotranscriptional

Question 42

Long non-coding RNA

Answer 42

Scaffolds

Question 43

Anchor Proteins

Answer 43

Holes in the wall that hang onto mRNA

Question 44

Directed transport on cytoskeleton

Answer 44

Proteins act as trains on a track to transport proteins

Question 45

Random diffusion and trapping

Answer 45

Diffusion of mRNA all over cytoplasm