lec 8

Question 1

are some genes transcribed all the time?

Answer 1

yes
- regardless of cell type/environmental conditions
- genes = “constitutive”

Question 2

transcriptional regulation determines

Answer 2

1. which genes are expressed
2. when they are expressed
3. degree (# of copies of RNA) that they are expressed

Question 3

open reading frame (ORF)

Answer 3

region between translational start + stop/termination codons
- have introns and exons

Question 4

what are the regulatory regions that influence each gene?

Answer 4

1. promoter: upstream
2. enhancer: may be up or downstream or in introns

Question 5

transcription factors (TFs)

Answer 5

1. determine if RNA Pol II gets recruited to gene
2. affect the stability of RNA Pol I and transcription in initiation complex

Question 6

what are the 2 types of transcription factors

Answer 6

1. TFII (general TF)
   - expressed in every cell type
   - req for RNA Pol II to bind to the promoter
   - form a complex at the promoter and work together to recruit RNA Pol II

Question 7

what is needed for transcription to occur?

Answer 7

RNA Pol II and TFIIs

Question 8

promoter

Answer 8

binds transcription initiation complex

Question 9

transcription initiation site

Answer 9

where RNA Pol starts making RNA transcript

Question 10

transcription termination site

Answer 10

where transcription stops

Question 11

exons

Answer 11

the region that codes for proteins
- exit the nucleus, are expressed

Question 12

introns

Answer 12

will be removed from the transcript through splicing after transcription
- do not code for protein
- stay in the nucleus, excised via RNA splicing

Question 13

translation termination codon

Answer 13

where translation stops

Question 14

translation initiation codon

Answer 14

where translation of RNA into peptide begins

Question 15

3’ and 5’ UTR

Answer 15

3’ and 5’ untranslated region
- not translated
- follows transcription
- proteins bind to regulate translation
- part of DNA and mRNA

Question 16

tissue-specific transcription factors (TSTFs)

Answer 16

1. req for transcription
2. bind to enhancers
3. do not have to be upstream
4. bind to enhancer regions and have tissue and cell type-specific expression
5. create binding sites for the TFII family
6. help stabilize transcription initiation complex

Question 17

how do you think it is possible for an enhancer region to affect the recruitment of RNA Pol II and interact with TFIIs if it is located far away from the promoter

Answer 17

DNA can form a folded conformation
- not linear all the time

Question 18

can 1 gene have many enhancers?

Answer 18

yes
- enhancers bind to TSTFs
> different TSTFs = expressed in different cell types

Question 19

T/F TFIIs bind to enhancers

Answer 19

F, promoter

Question 20

T/F a gene can have many enhancers

Answer 20

T

Question 21

T/F neuron-specific enhancer DNA will be present in DNA of muscle cells

Answer 21

T, neurons TSTF will not be expressed

Question 22

T/F TFIIs are expressed in every cell type

Answer 22

T

Question 23

T/F TFII transcribes genes

Answer 23

F, req for transcription gene but RNA Pol II transcribes genes

Question 24

what is one of the contributors to cell specialization

Answer 24

differential gene expression

Question 25

histone mods and epigenetics

Answer 25

epigenetic mechanisms = influence gene expression w/o affecting underlying DNA seq

Question 26

what are 2 examples of histone mods and epigenetics

Answer 26

1. regulation of chromatin structures - how tightly or loosely packed 2. chemical mod of DNA - DNA methylation

Question 27

transcription initiation

Answer 27

RNA Pol II TFIIs TSTF and enhancer

Question 28

chromatin and nucelosome structure

Answer 28

DNA packaged with histone proteins = chromatin nucleosome = basic unit of chromatin - 1 histone octamer and wrapped DNA

Question 29

histones and transcriptional regulation

Answer 29

covalent post-translational mod to histones affect the conformation of DNA - causing to be "open/uncondensed" or "closed/condensed" conformation

Question 30

enzymatic mods of histones can influence what

Answer 30

where transcription machinery has access to enhancers and/or promoters

Question 31

epigenetic change

Answer 31

change in chromatin/DNA structures that affect gene expression - does not affect the gene seq

Question 32

histone acetylation

Answer 32

associated w/ active transcription open relaxed chromatin

Question 33

histone methylation

Answer 33

context-dependent associated with activation and repression of transcription associated w/ DNA silencing

Question 34

histone acetyl transferases (HATs)

Answer 34

acetylate N-terminal of histones - leads to relaxed chromatin > open/accessible to transcriptional machinery = more transcriptionally active adds acetyl groups

Question 35

histone deacetylases (HDACs)

Answer 35

remove acetylene groups - leads to chromatin > more condensed = transcriptional repression

Question 36

if HATs level increased, it is safe to say that the transcription would be active or repressed?

Answer 36

active

Question 37

what do you expect would be the effect on the chromatin structure of applying HDACs inhibitor to cells?

Answer 37

it will loosen the chromatin