Chapter 7 - Control of Gene Expression

Question 1

Post-transcriptional control

Answer 1

Operate after RNA polymerase has bound to the genes promoter and has begun synthesis

Question 2

Transcription attenuation

Answer 2

Expression of genes I nhibited by premature termination of transcription.

In some cases, the nascent RNA chain adopts a structure that causes it to interact with RNA polymerase in such a way as to abort its transcription.

Question 3

Example of protein attenuation

Answer 3

HIV

Question 4

Riboswitches

Answer 4

Short sequences of RNA that change their conformation on binding small molecules, such as metabolites.

Probably ancient form of gene control

Question 5

Where are Riboswitches usually located?

Answer 5

5’ end of mRNAs and fold while the mRNA is being synthesized - blocking or permitting progress of RNA polymerase

Question 6

Where are Riboswitches particularly common?

Answer 6

Bacteria - sense key metabolite and adjust gene expression accordingly

Question 7

Key features of Riboswitches

Answer 7

High specificity and affinity with which each recognizes only the appropriate small molecule.

In many cases, every chemical feature is read by the the RNA completely.

Strong binding affinity

Question 8

Important functions of riboswitches

Answer 8

Controls transcription elongation and regulate other gene expression

Question 9

Is the 3’ end of eukaryotic mRNA molecules formed by the termination of RNA synthesis?

Answer 9

No

Question 10

How does the 3’ end form in eukaryotes?

Answer 10

RNA cleavage reaction catalyzed by additional proteins while the transcript is elongating.

Question 11

What do B lymphocytes do to activate antibody production?

Answer 11

Increase concentration of CstF protein so that cleavage occurs at suboptimal site and the shorter transcript is produced

Question 12

Define RNA editing

Answer 12

Alteration of a nucleotide sequence of RNA transcripts once they are synthesized

Deanimation of adenine by inosine (A-to-I editing) and deanimation of cytosine to produce uracil (C-to-U editing).

Question 13

Effects of RNA editing on coding region

Answer 13

If RNA editing is done in coding sequence, it can change the amino acid of the protein or produce a truncated protein by creating and early stop codon.

Question 14

Effects of RNA editing outside coding region

Answer 14

Can effect:

1. The pattern of pre-mRNA splicing
2. The transport of mRNA from nucleus to the cytosol
3. The efficiency with which the RNA is translated
4. Or the base pairing between microRNAs (miRNAs) and their mRNA targets

Question 15

Which form of RNA editing is particularly frequent in humans?

Answer 15

A-to-I editing

Approximately in 1000genes

Question 16

What enzymes perform A-to-I editing?

Answer 16

ADARs (adenosine deaminases acting on RNA).

Question 17

How do ADARs work?

Answer 17

Identify a ds RNA formed through base pairing between the site to be edited and a complementary sequence located somewhere on the same RNA strand

Structure of the ds RNA specifies whether the RNA should be edited and where it should

Question 18

A-to-I editing example at transmitter-gate ion channel

Answer 18

Alters a glutamine to an arginine found on the inner walls of the channel

Affects Ca2+ permeability of the channel

Mutant mice that cannot make edit are prone to epileptic seizures

Question 19

C-to-U binding

Answer 19

Examples

Question 20

About how much of the RNA actually leaves the nucleus?

Answer 20

1/20

Question 21

How does HIV overcome the hosts natural block to the nuclear export?

Answer 21

Encode a protein, called Rev, that binds to a specific RNA sequence (called Rev response element (RRE)) located within the viral intron.

rev protein interacts with nuclear export protein (Crm1), which directs the movement of viral RNAs through the nuclear pores into the cytosol despite introns being present.

Question 22

Where are most localization signals concentrated on the mRNA?

Answer 22

On the 3’ untranslated region (UTR) - region that extends from stop codon to start of poly-A tail.

Question 23

Normal function to eIF2

Answer 23

Forms a complex with GTP and mediates the binding of the methionyl initiator tRNA to the small ribosomal subunit, which then binds to the 5’ end and begins scanning along the mRNA.

When AUG codon is recognized, the eIF2 protein hydrolyzes the bound GTP to GDP causing conformation change in protein and releasing it from the small ribosomal subunit.

Large subunit then joins small subunit to form ribosome and begin protein synthesis

Question 24

Function of eIF2B

Answer 24

eIF2 binds tightly to GDP. eIF2B causes GRP release so that a new GTP molecule can bind and eIF2 can be reused.

Question 25

How is eIF2/eIF2B inhibited?

Answer 25

By phosphorylation.

Phosphorylated eIF2 binds unusually tight to eIF2B, inactivating eIF2B

Question 26

In mammalian cells, what is eIF2 especially important for?

Answer 26

Part of a mechanism that allows cell to enter nonproliferating, resting state (G0).

Question 27

Specialized type of RNA sequence that allows cells to initiate translation at positions distant from the 5’ end.

Answer 27

Internal ribosome entry site (IRES)

Question 28

How does IRESs work?

Answer 28

Create hairpin that binds to eIF4G and poly-A-binding protein without needing eIF4E and 5’ cap.

Question 29

IRESs viral use

Answer 29

Some viruses uses IRESs to get their own mRNA molecules translated.

Virus produce protease that cleaves the host-cell translation factor eIF4G making it unable to bind to eIF4E. This shuts down most of the the hosts translation

Question 30

Iron starvation effects on ferritin mRNA

Answer 30

Cytosolic aconitase stays bound to ferritin mRNA and translation is blocked

Question 31

Excess iron effects ok ferritin mRNA

Answer 31

Iron binds to cytosolic aconitase causing the protein to unbind from ferritin mRNA. Allows ferritin to be made

Question 32

Iron starvation on transferrin receptor mRNA

Answer 32

Cytosolic aconitase remains bound to the the transferrin receptor mRNA. Transferrin receptor is made

Question 33

Excess iron effect on transferrin receptor mRNA

Answer 33

Cytosolic aconitase releases from transferrin receptor mRNA when iron binds to protein. mRNA is degraded and no transferrin receptor is made

Question 34

RNAis

Answer 34

Group of short RNAs that carry out RNA interference. (20-30nucleotides)

Question 35

Three categories of small non coding RNAs

Answer 35

miRNAs
siRNAs
piRNAs

Question 36

miRNAs function

Answer 36

miRNAs base-pair with specific mRNA and fine tune their translation and stability.

Question 37

How are miRNAs made?

Answer 37

Precursors are made by RNA polymerase II and are capped and polyadenylated. Then undergo a special type of processing after which the miRNA is assembled with a set of proteins to form an RNA-induced silencing complex (RISC)

Once formed, RISC seeks out target mRNA

Question 38

RISC and Argonaute interaction

Answer 38

Argonaute binds to the 5’ of RISC so that it is optimally positioned for base-pairing.

Question 39

RISC outcome of mRNAs

Answer 39

1. If base pairing is extensive (common in plants but not humans), the mRNA is cleaved by Argonaute removing the poly-A tail
2. If base pairing is less extensive, Argonaute does not cleave mRNA but represses translation and shuttles mRNA to P-bodies where sequestered from ribosomes and eventually undergoes poly-A tail shortening, decapping and degradation

Question 40

How siRNAs are used in cell defense

Answer 40

The presence of ds RNA in cells trigger RNAi by attracting a protein complex containing dicer.

Dicer cleaves the ds RNA into small fragments (siRNAs)

siRNAs are the bound to Argonaute and other components of RISC

RISC is released and catalytically destroys many complementary RNAs (from virus).

Question 41

RNA interference directing heterochromatin formation

Answer 41

Short siRNAs produced by dicer protein are assembled with a group of proteins (including Argonaute) to form the RITS (RNA-induced transcriptional silencing) complex.

ss siRNAs are used as guides and the complex binds to RNA transcripts as the emerge from transcribing.

RITS complex attracts protein that covalently modify nearby histones and eventually direct the formation of heterochromatin to prevent further transcription initiation.

Question 42

What are the siRNAs kept in situ for?

Answer 42

To keep unwanted gene suppressed with a constant positive feedback loop.

Question 43

Where are piRNAs made?

Answer 43

Germ line from genes coding for transposable elements that have been fragmented

Question 44

How do piRNA protect germline?

Answer 44

piRNA complex with Piwi and then seek out RNA targets by base pairing and much like siRNAs, transcriptionally silence intact transposon genes and destroy any RNA produced by then.

Question 45

CRISPR

Answer 45

Bacterial defense system used by humans to genetic engineering experiments

Question 46

Long noncoding RNA

Answer 46

(lncRNA)

RNAs longer than 200 nucleotides that do not code for proteins

Can function as scaffolding RNA molecules - holding together groups of protein to coordinate their function

Can function as guide sequences

Examples include RNA in telomerase, Xist RNA and RNA involved in imprinting