exam 2 control of gene expression PT regulation

Question 1

what can small non-coding RNAs do

Answer 1

regulate gene expression

Question 2

what PTMs regulate protein function

Answer 2

activation/de-activation, co-localization with interacting molecules, assembly into multi-protein complexes

Question 3

what can protein level be regulated by

Answer 3

ubiquitin/proteasome-mediated degradation

Question 4

what does phosphorylation do

Answer 4

converts an inactive form into an active form and vice versa

Question 5

what are molecular integraors

Answer 5

transcription factors have multiple sites for phosphorylation and other modifications

Question 6

is the GTP-bound form activated or inactivated

Answer 6

activated

Question 7

what does Ras do

Answer 7

phosphorylates and activates first kinase in cascade, which amplifies signal

Question 8

what does the final map kinase do

Answer 8

prosphorylates Elk, which induces transcription and moves into nucleus to continue kinase cascade of phosphorylating things on and on

Question 9

how do PTM regulate TF activity

Answer 9

changes cellular localization

Question 10

what are the varsity of TFs

Answer 10

NF-AT and NF-kappaB

Question 11

what happens with NF-AT and NF-kappaB

Answer 11

regulated by localization: held in cytosol inactive, then PTMs lead release and translocation to nucleus, where nuclear TF is able to regulate gene transcription

Question 12

what is the self-regulating TF

Answer 12

NF-kappaB - induces transcription once in nucleus

Question 13

what can combinatorial control generate

Answer 13

patterns during animal development

Question 14

what is even-skipped expression

Answer 14

even segments are all missing when mutated - expression in one stripe is directed by one DNA molecule

Question 15

what are positive transcription factors

Answer 15

where gene is expressed

Question 16

what are negative transcription factors

Answer 16

boundaries of expression

Question 17

how do different cell types arise to be able to express different TF patterns

Answer 17

• cells in different places in an embryo can sense their locations and activate/express different TFs
• during development, cells can receive different soluble signals that direct TF expression/activation

Question 18

where can RNA levels be regulated at

Answer 18

level of initiation or termination

Question 19

what does transcriptional attenuation lead to

Answer 19

premature termination of the RNA transcript

Question 20

what does a growing RNA chain adopt through transcriptional attenuation

Answer 20

conformation that interferes with RNA polymerase activity - RNA pol pauses and aborts transcription

Question 21

how can transcriptional attenuation be reversed

Answer 21

by binding of specific proteins to the RNA structure, allowing RNA pol to complete transcription

Question 22

what are most eukaryotic genes regulated by

Answer 22

alternative splicing

Question 23

what are splice variants

Answer 23

a gene with even just a few exons can produce many different mRNAs via alternative splicing

Question 24

how does HIV use regulated nuclear export

Answer 24

to allow RNA molecules containing some introns to be exported from the nucleus

Question 25

how can cells use regulated cytosolic localization

Answer 25

to place specific mRNAs at specific locations in the cell, allowing mRNAs and encoded proteins to be concentrated in a particular part of the cell

Question 26

how are genes regulated by mRNA stability

Answer 26

mRNA is rapidly degraded under certain conditions

Question 27

what does aconitase do

Answer 27

iron-binding protein

Question 28

what does endonuclease do

Answer 28

cleaves RNA, leading to degradation = no transferrin made

Question 29

what happens with high levels of iron

Answer 29

want ferritin, don't want transferrin

Question 30

what happens with low levels of iron

Answer 30

want more transferrin and no ferritin

Question 31

what is ferritin

Answer 31

binds to iron in cell to keep it protected

Question 32

what is transferrin

Answer 32

imports iron in cell

Question 33

what forms the RNA-induced silencing complex (RISC)

Answer 33

a short double-stranded RNA is generated after processing and associates with a set of proteins

Question 34

what do miRNAs fold into

Answer 34

hairpin stem-loop structures

Question 35

what happens with the hairpin structure

Answer 35

one strand of RNA is degraded and the other makes base-pairing contacts with an mRNA target

Question 36

what does dicer do

Answer 36

cleaves off loop part of hairpin structure

Question 37

once RNA is sliced, how is it unstable and rapidly degrading

Answer 37

one half has 5'-cap, no poly-A tail and vice versa

Question 38

what do siRNAs do

Answer 38

mediate the process of RNA interference

Question 39

how is dsRNAs formed

Answer 39

formed by base-pairing between complementary regions of separate RNA strands

Question 40

what does dsRNA do

Answer 40

cleaved by dicer nuclease to form siRNA

Question 41

what does siRNA associate with

Answer 41

proteins to form RISC, and target mRNAs are cleaved

Question 42

how does siRNA form RITS complex

Answer 42

associated with different set of proteins

Question 43

what is the RITS complex

Answer 43

inhibits gene transcription by modifying chromatin structure

Question 44

what is dsRNA recognized by

Answer 44

dicer complex and is used to cut up siRNAs to form RITS

Question 45

what advantages might come from post-transcriptional regulation

Answer 45

can respond to environmental stimuli more rapidly than transcriptional regulation - have protein - can quickly turn it on and off when you need it

Question 46

what can info in the 5' and 3' untranslated regions (UTRs) regulate

Answer 46

translation efficiency and mRNA stability

Question 47

what blocks ribosome access

Answer 47

5' UTR RNA structure

Question 48

what inhibits ribosome scanning

Answer 48

RNA structure

Question 49

what can switch translation on and off

Answer 49

riboswitch structure using binding of an ion or small molecule

Question 50

what is required for efficient translation initation

Answer 50

repressors binding to 3' UTR can prevent communication between 5' and 3' ends of mRNA

Question 51

what can phosphorylation of initiation factor eIF2 do

Answer 51

inhibit global protein synthesis by activating eIF2B, a translation initiation inhibitor

Question 52

what does eIF2 use

Answer 52

GTPase motif to mediate binding of initiator met-tRNA to small ribosomal subunit

Question 53

what is eIF2B

Answer 53

GEF that catalyzes exchange of GDP to GTP, activating eIF2

Question 54

what happens in absence of active eIF2B

Answer 54

excess eIF2 remins in its inactive, GDP-bound form and protein synthesis slows dramatically

Question 55

what does IRES (internal ribosome entry sites) allow for

Answer 55

ribosomes to skip the first AUG, which allows two different protein sequences to be derived from a single mRNA

Question 56

what is required for secreted/transmembrane proteins

Answer 56

different initiation sites leading to skipping of signal sequence, switching between cytosolic and secreted form of a protein

Question 57

what allows for independent simultaneous translation of two completely different proteins from one mRNA

Answer 57

IRES sitting between two separate ORFs

Question 58

what is protein turnover

Answer 58

another point of regulation

Question 59

why must damaged/mis-folded proteins be destroyed

Answer 59

to prevent accumulation of malfunctioning proteins

Question 60

what does ubiquitin/proteasome system allow for

Answer 60

regulated destruction of proteins - targeted protein is polyubiquitylated - proteasome recognizes polyubiquitylated protein and degrades it into short peptides