White: Control of gene expression 1&2

Question 1

Gene regulation requires

Answer 1

Recognition sites for DNA binding proteins-TATA

Gene regulatory proteins-TFs

Question 2

Recognition sequences can be proximal or distal to first exon: T or F

Answer 2

True- they can be either proximal or distal

Question 3

Transcription factor modules and which of these are required

Answer 3

DNA-binding module–required
Activation module–required
Dimerization module– not required
Regulatory module– not required

Question 4

Helix-turn-helix

Answer 4

Simplest most common DNA binding motif
Two alpha-helices
Longer helix= recognition module–DNA binding module fits into its major groove

Question 5

Zinc finger domain

Answer 5

DNA binding motif includes Zn domain
Binds to major groove of DNA
Found in tandem clusters
Stabilizes interaction with DNA, multiple contact points

Question 6

Leucine zipper motif I

Answer 6

Two alpha-helical DNA binding domain
Grabs DNA like clothespin
Activation domain overlaps dimer domain
Interaction b/w hydrophobic AA side chains (leucines)

Question 7

Leucine Zipper motif II

Answer 7

Dimerizes through leucine zipper region
Interactions b/w hydrophobic AA side chains (leucines)
Leucine residue every 7 AAs down one side of a-helix, forms zipper structure

Question 8

Helix-loop-helix domain

Answer 8

Consists of short Alpha-chain connected to longer alpha chain
Can be Homo or Heterodimers
3 modules- DNA binding domain, Dimerization domain, Activation domain

Question 9

Hereditary spherocytosis and zinc finger domain

Answer 9

HS can be caused by mutation in Zinc finger protein gene Klf1
Mutation is Glu to Asp in exon 3
HS KLF1 binds to opposite strand as the wildtype protein, which will NOT allow transcription to start

Question 10

Identification of transcription factors

Answer 10

Describe one way TFs are identified

Question 11

Gene control region

Answer 11

DNA region involved in regulating and initiating transcription of a gene

Question 12

Gene control region includes

Answer 12

Promotor- TFs and RNA poly II assemble here

Regulatory sequences for binding of regulatory proteins which control rate of assembly process at the promoter

Question 13

Activation of transciption

Answer 13

DNA looping and a mediator complex allow the gene regulatory proteins to interact with the proteins at the promoter
The mediator serves as an intermediary between gene regulatory proteins and RNA polymerase II

Question 14

Transcription factors bind to DNA in _______,

Fact about affinity in this process

Answer 14

Nucleosomes
Transcription regulators bind to DNA in nucleosomes with lower affinity than naked DNA because surface of nucleotide recognition sequence may be facing inward when attached to nucleosome

Question 15

Ways to overcome affinity problem w/nucleosomes

Answer 15

Nucleosome remodeling
Nucleosome removal
Histone replacement
Histone acetylation

Question 16

Gene repressors inhibit transcription in what ways

Answer 16

Competitive DNA binding
Masking of the activation surface
Direct interaction with TF- repressor binds DNA and blocks assembly of TFs
Recruitment of chromatin remodeling complexes
Recruitment of histone deacetylases
Recruitment of histone methyl transferase

Question 17

Proteins can be either activating or repressing depending on

Answer 17

The composition of complexes at gene regulatory sites

Question 18

7 ways gene regulatory proteins are controlled

Answer 18

Synthesis
Ligand binding
Covalent modification-phosphorylation
Addition of subunit
Unmasking
Nuclear entry
Proteolysis
Must be able to describe two of these

Question 19

Negative vs positive control of alternative splicing

Answer 19

Negative control- Repressor molecule prevents splicing machinery access to splice site
Positive control- Activator recruits and helps directs splicing machinery

Question 20

Spatial localization of mRNAs

Answer 20

mRNA leave nucleus through pores
They travel to destination using cytoskeletal motors
Randomly move and can be trapped by special proteins
Non trapped RNA is degraded

Question 21

Regulation by RNA stability

Answer 21

Poly-A tail– once reduced to 25 nucleotides, two pathways converge to degrade mRNA

• Decapping- mRNA degraded from 5’ end
• mRNA degraded from 3’ end through poly-A tail

Question 22

IREs IRAs

Answer 22

IRE- Iron responsive elements- recognition sites for binding
IRP- Iron responsive regulatory protein- Aconitase
IRP binds IRE

Question 23

Effect when IRP binds IRE at 5’ ferritin mRNA vs binding IRE at 3’ transferrin receptor mRNA

Answer 23

Iron starvation
IRP binds IRE at 5’ ferritin mRNA- no ferritin- translation is blocked
IRP binds IRE at 3’ transferrin receptor mRNA- Transferrin receptor made- mRNA stable
What would happen with excess iron?
Remember with excess iron, the iron binds IRP which releases IRP from binding sites

Question 24

microRNAs

Answer 24

Regulatory RNAs that regulate mRNA
Silence expression of specific mRNA targets
Bind to complementary sequences in the 3’ UT end of mRNA and degrade or block translation (depending on strength of complementary binding)

Question 25

Formation of miRNAs

Answer 25

``` Precursor miRNA Cropped in nucleus Forms double stranded loop Further cleaved by Dicer Joins with Argonaute and others to form RISC complex Base pairs with mRNA Cleaves RNA, shuts down expression ```

Question 26

Are changes in microRNA expression causative of disease or responsive to disease

Answer 26

Both

Question 27

Causative miRNA disease

Answer 27

Tourettes syndrome Change in recognition sequence on target SLITRK1 mRNA--> increased miRNA binding--> decreased SLITRK1 expression--> tourettes syndrome

Question 28

3 ways to activate degredation signal

Answer 28

Phosphorylation by kinase Unmasking by protein dissociation Creation of destabilizing N-terminus

Question 29

Proteasome therapy

Answer 29

Proteasome inhibitors used to treat multiple myelomas Proteasome inhibition may prevent degradation of pro-apoptotic factors for cell suicide -leads to cell apoptosis of cancer cells

Question 30

Coordinated gene expression

Answer 30

Expression of critical regulatory protein can trigger battery of downstream genes Example- glococorticoid hormone causes gene expression

Question 31

Decision for specialization

Answer 31

Different options for products of differentiation at each step Example is Hematopoietic stem cells

Question 32

DNA methylation

Answer 32

Silences genes | Can be inherited

Question 33

Genomic imprinting is based on ____, Genomic imprinting definition

Answer 33

Based on DNA methylation | -Differential expression of genetic material depending on the parent of origin

Question 34

Epigenetics definition

Answer 34

Regulation of expression of gene activity without altering gene expression (e.g., methylation)

Question 35

X-chromosome inactivation

Answer 35

One X chromosome is inactivated in females by Heterochromatin- Barr Body