Contol of gene transcription

Question 1

Changes in gene expression underlie what?

Answer 1

The diversity of cell types in the body

Question 2

All cells have the same … but different sets of …

Answer 2

Genes

Proteins

Question 3

What can affect which genes are expressed?

Answer 3

Responses to signals and other cues in the enviroment

Cells also change gene expression in some disease states

Question 4

What affects the level of translation?

Answer 4

The level of transcription in a cell

High levels of transcription can mean more RNA is produced so more protein is made

Question 5

What is the charge of DNA binding proteins?

Answer 5

They are positive

Question 6

What is the target of DNA binding proteins?

Answer 6

The major groove

Question 7

What is the charge of the phosphate backbone?

Answer 7

Negative

Question 8

Unlike proteins, DNA has a limited what?

Answer 8

Topology

Question 9

Regulatory proteins must recognise what on the DNA?

Answer 9

A specific nucleotide sequence

Question 10

Why does the outisde of the helix contain information?

Answer 10

So that the double helix does not have to open

Question 11

The edge of each pair is exposed at the surface, presenting a distinctive pattern of what?

Answer 11

H-bond acceptors
H- bond donors
Hydrogen atoms
Methyl groups

Question 12

Which groove is marked differently for each pair?

Answer 12

The major groove

Question 13

Give the pattern of the major groove for:
G-> C
A- > T
Know this to know the reverse

Answer 13

G to C
H bond acceptor, H bond acceptor, H bond donor, Hydrogen atom

A to T
H bond acceptor, H bond donor, H bond acceptor Methyl group

Question 14

Molecular recognition usually relies on what?

Answer 14

Exact fit between the two surfaces of a molecule

Question 15

How do gene regulatory proteins recognise a specific DNA sequence?

Answer 15

The surface of the protein is complementary to the features of the double helix in that region

Question 16

Proteins make a series of contacts using which 3 interactions?

Answer 16

Hydrogen bonds
Ionic bonds
Hydrophobic interactions

Question 17

How are interactions between the proteins and DNA strong?

Answer 17

Even though each contact is weak, there are about 20 contacts making them hard to break

Question 18

Where does ROX1 bind?

Answer 18

Known to bind to eight sites in three yeast genes

Question 19

Do all the DNA binding sites have the same affinity for the ROX1 protein?

Answer 19

No

Question 20

Describe the structure of a helix-turn-helix DNA binding motif

Answer 20

2 Alpha helices connected by a short constitute of amino acids
The 2 alpha helixes are held at a fixed angle
The more C terminal is called the recognition helix as it fits in to the major groove of DNA, making specific contacts

Question 21

Helix-turn-helix proteins tend to bind as dimers to what?

Answer 21

Two consecutive major grooves

Question 22

The DNA recognition site for Helix-turn-helix DNA binding motif is what?

Answer 22

Palindromic

Question 23

Describe the structure of the zinc finger binding domain?

Answer 23

Four amino acids which hold the zinc atom
Held by cis-cis-his-his
Has three fingers

Question 24

The alpha helix of the zinc finger can recognise how many bases?

Answer 24

Two

Question 25

Describe the structure of a leucine zipper DNA binding motif

Answer 25

The alpha helical monomers are held together by a hydrophobic amino acid eg leucine Forms a Y shaped structure allowing the side chains to contact the major groove of DNA

Question 26

What do homodimers and herterodimers bind?

Answer 26

``` Homo = symetrical sequences Hetero = Non identical sequences ```

Question 27

What is the purpose of heterodimerisation?

Answer 27

It expands the repetoire of DNA sequences that gene regulatory proteins can bind to

Question 28

The helix-loop helix is related to what?

Answer 28

The leucine zipper

Question 29

What is the effect of DNA binding proteins binding as dimers?

Answer 29

It increases their strength - also known as syngergy

Question 30

What are the domains of a transcription factor?

Answer 30

DNA binding domain Protein binding domain Regulatory domain Activation domain

Question 31

How can DNA binding proteins be identified?

Answer 31

DNAse I footprinting

Question 32

List the steps in DNAse footprinting

Answer 32

1) Radioactively label one end of the DNA 2) Mix DNA with cell extract 3) Add DNAse to partially digest the DNA 4) Heat the sample to destroy DNAse and release the binding proteins 5) Run samples by gel electrophoresis This shows regions DNA protected from digestion due to protein binding

Question 33

DNAse I footprinting can also be used to identify what?

Answer 33

Where a protein binds on a sequence of DNA

Question 34

What is EMSA?

Answer 34

Electrophoretic mobility shoft assay

Question 35

What is EMSA used for?

Answer 35

Identify DNA binding proteins

Question 36

Give the steps in EMSA

Answer 36

1) Radioactively label one end of the DNA 2) Mix with the cell extract (or purified protein) 3) Run samples by gel electrophoresis Lanes with a protein bound will move through the gel slower

Question 37

What are the three forms of transcription factors?

Answer 37

Permissive Specific Regulatory

Question 38

What are permissive transcription factors?

Answer 38

General - neccessary for all transcription | Bind at the promoter

Question 39

How do regulatory transcription factors function?

Answer 39

Interactions with the RNA polymerase complex Altering acetylation of the DNA Binding to other transcription factors

Question 40

Where do regulatory transcription factors bind?

Answer 40

Anywhere around the gene - it can be far away | Or they dont bind DNA directly and bind to a regulatory complex

Question 41

What does DNA looping play an important role in?

Answer 41

Forming DNA/protein complexes

Question 42

Because chromatin does not bend easily it is thought that what is needed for two proteins to interact?

Answer 42

They need to bind directly to neighbouring DNA sequences | OR to two sites that are >500 base pairs apart

Question 43

What is the role of insulators and barriers?

Answer 43

They block regulatory sequences from affecting neighbouring genes

Question 44

Which inputs can alter gene expression by integrating?

Answer 44

Activating proteins | Inhibition proteins

Question 45

Genetic switches respond to what

Answer 45

Extrinsic or intrinsic regulation

Question 46

What is tryptophan repressor protein?

Answer 46

A repressor protein which represses genes required for tryptophan synthesis

Question 47

List ways that a transcription factor could be regulated

Answer 47

a) Protein synthesis b) Ligand binding c) Covalent modification d) Addition of a second subunit e) Unmasking f) Stimulation of nuclear entry via removal of an inhibitory protein allowing it to enter the nucleus g) Release from membrane

Question 48

Transcription factors can interact in what way with each other on the DNA? Give an example

Answer 48

They act syngergistically eg just A = 1 unit of transcription Just B = 1 unit of transcription A + B = 100 units of transcription

Question 49

Binding of transcription factors on the DNA helps to prevent what and also helps with what?

Answer 49

Prevents them falling off the DNA | Helps as binding of one may enable another to bind

Question 50

What are the ways in which transcription factors can regulate the transcription of transcription factors?

Answer 50

Positive feedback = more made Negative feedback = less made Flip flop device - two inhibit each other Feedforward loop