MolBio9-10 - 52

Question 1

What are the 6 points of protein expression control?

Answer 1

Transcriptional control, processing control, RNA transport and localisation, translation control, mRNA degradation control, protein activity control

Question 2

What is the primary purpose of gene control?

Answer 2

The execution of precise developmental descisions so that the proper gene is expressed in the proper cell at a proper time

Question 3

What is the main mode of transcriptional control?

Answer 3

Transcriptional initiation control

Question 4

How do transcriptional activator exert their effect?

Answer 4

Either directly, by recruiting one of the components of the transcriptional machinery, or indirectly, by modulating the chromatin structure

Question 5

What are transcriptional activators and repressors?

Answer 5

Modular proteins containing separate DNA-binding and activation/repression domains

Question 6

What are the 4 most common DNA binding motifs?

Answer 6

Homeodomain, Zn finger, leucine-zipper and bHLH

Question 7

What do cooperative binding and combinatorial control achieve?

Answer 7

Transcriptional efficiency, specificity and yet diversity of responses

Question 8

Describe transcriptional activators

Answer 8

Modular proteins with an activation domain and a DNA-binding domain

Question 9

Give an example of a homeodomain protein

Answer 9

Hox

Question 10

Describe the homeodomain protein

Answer 10

60 aminoacid domain, 3 helices

Question 11

Give an example of a zinc finger protein

Answer 11

Ci (in Hh signalling)

Question 12

Describe the zinc finger

Answer 12

23-26 aminoacid motif (C2H2), 2 cys and 2 his bind to Zn

Question 13

Give an example of a leucine zipper

Answer 13

Fos

Question 14

Describe the leucine zipper

Answer 14

Leu separated by 7aa in a helix, two major grooves separated by 1/2 turn

Question 15

Give an example of a basic helix-loop-helix protein

Answer 15

MyoD

Question 16

What are the two activation effects?

Answer 16

Cooperative binding - increased affinity of RNA polymerase for promoter; allostery - transition from closed to open complex

Question 17

What is the advantage of cooperativity?

Answer 17

Greater specificity

Question 18

What are the four methods of repression?

Answer 18

Competition, inhibition, direct, and indirect

Question 19

What is EMSA?

Answer 19

Electrophoretic mobility shift assay

Question 20

Outline EMSA

Answer 20

Tagged DNA, probe washed through DNA that will bind to regulatory sequences, gel retardation to find where bound

Question 21

What is ChIP?

Answer 21

Chromatin immunoprecipitation assay

Question 22

Outline ChIP

Answer 22

Antibody for specific activator/repressor added in to in vivo sample, and DNA that has formed a complex with that activator/repressor will be precipitated out, and the sequence subsequently identified

Question 23

What does epigenetic mean?

Answer 23

Systems that sit on top of genetic mechanisms

Question 24

What is special about epigenetic alterations to the genome?

Answer 24

Erased in germ cells

Question 25

Where are nucleosomal modifications made?

Answer 25

Termini of lysine, arginine and serine side chains

Question 26

What is a condition of nucleosomal modifications?

Answer 26

Mutually exclusive of one another

Question 27

What are the main 3 nucleosomal modifications?

Answer 27

Acetylation, methylation and phosphorylation

Question 28

What are the main two nucleosomal modification enzymes?

Answer 28

Acetyltransferase and methyltransferase

Question 29

What to acetyltransferases do?

Answer 29

Indeterminately acetylate any lysine residue

Question 30

What do methyltransferases do?

Answer 30

Very specifically methylate specific residues

Question 31

What does acetylation of core hostones do?

Answer 31

Creates binding sites for transcriptional activation factors that contain a bromodomain

Question 32

What does methylation of core histones do?

Answer 32

Creates binding sites for transcriptional repressors that contain a chromodomain, or activators that contain a PHD zinc finger domain

Question 33

What reads the histone modifications?

Answer 33

Histone Code Reader proteins

Question 34

What is the function of histone code reader proteins?

Answer 34

To facilitate attachment to other components in nucleus, leading to gene expression, gene silencing, or other biological functions

Question 35

What is the relationship between histone code readers and code writers?

Answer 35

They can recruit each other, helping spread histone code in chromatin, which impacts on gene expression

Question 36

In what 4 ways do transcription activator proteins work?

Answer 36

Selective nucleosome remodelling, selective histone removal, selective histone replacement or selectin histone modification

Question 37

What does PRC stand for?

Answer 37

Polycomb Repressive Complexes

Question 38

What are PRCs?

Answer 38

Histone Code Writers/Readers that can generate or recognise repressive chromatin modifications

Question 39

Name one example of repressive chromatin modification

Answer 39

H3-K27 methylation by Ezh2 of PRC2

Question 40

Name one example of respressive chromatin modification identification

Answer 40

Pc chromodomain identification and subsequent recruitment of PRC1

Question 41

What is the relationship between DNA methylation and repressive histone methylation?

Answer 41

Close functionally - transcriptionally inactive promoters are frequently rich in methylated CpG dinucleotides

Question 42

Why is mammalian X-chromosome inactivation important?

Answer 42

Equalizes the levels of X-chromosome derived gene products in males and females

Question 43

Outline mammalian X-chromosome inactivation

Answer 43

Essentially dosage compensation: males have XY so only 1 dose; females have XX so 2 doses. One is always silent and once is transcriptionally active, the choice is random, and occurs early embryogenesis, and is then clonally inherited

Question 44

Give a visual example of mammalian X-chromosome inactivation

Answer 44

Tortoise shell cats - XO orange; Xo black. Males are orange or black, females are orange, black or calico. Calico is patchy because of random X-inactivation during early embryogenesis

Question 45

Outline the mammalian X-chromomsome inactivation mechanism

Answer 45

Involves synthesis of a non-coding RNA (Xist) from the X-inactivation centre, which binds to the chromsome in cis and promotes chromatin condensation by recruiting PRC group components

Question 46

What is the Barr body?

Answer 46

Highly condensed inactive X chromosome at the preiphery of the nucleus of female somatic cells

Question 47

What is position effect variegation?

Answer 47

Relocation of two functionally distinct regions of genes - euchromatin and heterochromatin

Question 48

Describe euchromatin

Answer 48

Transcriptionally active genes

Question 49

Describe heterochromatin

Answer 49

Transcriptionally silent genes

Question 50

What does abnormal reanets of euchromatin and heterochromatin cause?

Answer 50

Position effects that affect the transcriptional activity of the euchromatic genes

Question 51

What can aberrant chromsomal rearrangements cause?

Answer 51

If heterochromatin is placed next to euchromatin, it can shut down gene activity - the dominant effect is from the heterochromatin to the euchromatin, effectively spreading the silence

Question 52

Is position effect variegation complete?

Answer 52

No - some transcriptional activity of the euchromatin usually remains