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Biochemistry II > Regulation of Gene Expression > Flashcards

Regulation of Gene Expression Flashcards

1
Q

Overview of regulation of gene expression

A
  1. only a fraction of genes expressed at one time
  2. final product depends on multiple stages of regulation
  3. transcriptional regulation is best understood process
  4. there are housekeeping genes (stable levels), inducible genes (levels can rise), and repressible genes (levels can fall)
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2
Q

housekeeping genes

A

genes for products that are required at all time in stable levels

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3
Q

inducible vs repressible genes

A

gene products for which cellular levels rise (inducible) or fall (repressible) in response to molecular signals

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4
Q

multimeric

A

containing multiple peptide chains

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5
Q

features of eukaryotic gene regulation

A
  1. chromatin structure restricts access to promotors
  2. positive regulation is the norm
  3. regulatory proteins are multimeric
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6
Q

types of repression mechanisms
repressors in bacteria

A

molecular signals binds remove repressor from DNA or binds to activate and bind repressor to DNA
operators (repressor region of promoter, can be bound by a repressor protein or not)
negative regulation

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7
Q

regulatory proteins in eukaryotes include
required for

A

ex. transcription factors, activators and repressors
regulatory proteins are required for RNA polymerase to bind to promotor sequence in eukaryotes
change of sequence will change frequency of transcription

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8
Q

types of activation and repression mechanisms

A

Positive regulation
1) baseline state is on, activator binds to RNA polymerase to activate transcription and molecular signal turns activator off
2) baseline state is off, molecular signal + activator binds to turn transcription on

Negative regulation
1) baseline state is off, with repressor bound, molecule signal binds to dissociate repressor
2) baseline state is on, molecule signal causes repressor to bind

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9
Q

Eukaryotic DNA sequences structure

A

5’ UP element, -35 region, -10 TATA region, RNA start site 3’

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10
Q

operon

A

in bacteria multiple genes transcribed as a unit
a cluster of genes transcribed to a single mRNA

Structure: activator binding area, promoter sequence, repressor binding area, genes to be transcribed

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11
Q

DNA regulatory protein binding motifs in bacteria

Common motif

A

small structures, 60-90 AA, that protrude from protein
H bond interaction between specific residues and nucleic acids

Helix-turn-helix domain is common, 20 AA long, 1 alpha recognition helix

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12
Q

Most common AA involved in DNA binding recognition in regulatory proteins
pairings

A

Asparagine, glutamin, glutamate, lysine, and arginine
Adenine - glutamine/asparagine
Guanosine - arginine

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13
Q

zinc finger domain

A

common domain in eukaryotic transcription factors
30 AA long, loops are cross-linked by zinc
zinc stabilizes the structure
weak DNA binding requiring multiple fingers to bind well
can also bind RNA

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14
Q

leucine zipper

A

alpha helix with a leucine at every 7th position
protein-protein interaction domain, and partial DNA binding domain with Lys/Arg residues

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15
Q

regulatory protein domains

A

protein interaction domains, and DNA binding motifs
interaction with other transcription factors, co-regulators at promoter
mix and match combos to regulate gene expression
1557 TF to 25,000 genes

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16
Q

euchromatin

A

transcriptionally active uncondensed chromatin, revealing nucleosomes (DNA wound around 8 histone proteins)
heterochromatin is condensed and hides promoters

17
Q

chromatin remodeling is dependent upon
chromatin remodeling enzymes

A

positioning of nucleosomes, presence of histone variants, covalent modification of nucleosomes
SWI and SNF enzymes remodel chromatin by removing H1 and changing out for histone variants

18
Q

histone types:

A

H1 (transcriptionally active DNA is deficient in H1)
H2A, H2B, H3, H4
transcriptionally active DNA enriched with H3.3 and H2AZ

19
Q

histone covalent modifications

A

methylation on lysine/arginine
phosphorylation on serine/threonine
acetylation, ubiquitination and sumoylation on lysine (regulated by histone acetyltransferases HATs and histone deacetylases HDACs)

20
Q

DNA can be methylated on

A

cytosine of a cysteine-phosphate-guanosine sequence

21
Q

when does chromatin remodeling happen during pre-initiation complex?

A

After mediator binds to activator/enhancer, chromatin remodeling occurs at the modification and remodeling complex

22
Q

Assembly of pre-initiation complex

A
  1. activators bind to enhancers
  2. mediator + modification and remodeling complex binds to activator
  3. histone remodeling at modification and remodeling complex
  4. mediators facilitate TATA binding protein (TBP) and TF IIB binding
  5. basal TF and RNA Pol II bind at transcription start site
  6. TF IIH initiates RNA Pol II to start transcription
23
Q

high mobility group regulatory protein

A

architectural regulator allowing DNA looping to assist protein complexes to interact
Mediator can connect upstream activator, TF activators and initiation complex
repressors inhibit this interaction

24
Q

hormones as transcription factors
conserved structure

A

they bind to specific hormone response elements (HRE) on DNA

Hormone receptors have highly conserved DNA binding domains (2 zinc fingers), transcription activation sequence (amino side), and hormone binding sequence (carboxyl side)

Hormone receptors bind as dimers, recognizing 1 of 6 nucleotide sequence

25
Q

Ligand regulated transcription factors, type I

A

Type I nuclear receptors in cytoplasm
1. Chaperoned by Hsp70 (heat shock protein 70) which disassociates after hormone binds receptor
2. receptor-hormone complex dimerizes and goes to nucleus
3. binds HRE and acts as transcription factor
4. lncRNA inhibits HRE binding by binding to hormone-receptor complex

26
Q

lncRNA
Hsp70

A

long non-coding RNA
Heat shock protein 70

27
Q

Ligand regulated transcription factors, type II

A

Type II nuclear receptors in nucleus
1. Hormone directly enters nucleus
2. receptor is bound to HRE on DNA but inactive due to corepressor bound to it
3. Hormone binding to receptor (TR or RXR depending) leads to dissociation of corepressor
4. receptor can then function as transcription factor

28
Q

genes with multiple exons

A

95% undergo alternative splicing
multiple poly A tail sites indicate different mRNA coding depending on location in the organism
ex. calcitonin and calcitonin-gene related peptide (CGRP) come from the same gene transcript but different exons

29
Q

regulation of gene expression at translation

A

translational repressors bound to mRNA on 3’ UTR interact with initiation factors or ribosomes to prevent translation initiation

microRNAs and short interfering RNAs silence genes by binding to it and blocking or cleaving (via endonuclease Drosha or Dicer)

30
Q

stRNA mechanism

A

Small temporal RNA
1. transcribed as precursor RNA with internal complementary sequences forming hairpin-like structures
2. cleaved by Dicer endonuclease, forming short 20-25 nucleotide duplexes
3. once cleaved becomes miRNA
4. miRNA binds to target mRNA and silences it (inhibition of translation and possibly degradation)

31
Q

siRNA mechanism

A
  1. duplex RNA molecule corresponding to mRNA, can correspond to nearly any mRNA
  2. Dicer cleaves into short segments called siRNA (short interfering RNA)
  3. siRNA bind to mRNA and result in inhibition of translation or leads to degradation

more general regulation of mRNA expression than miRNA

32
Q

HATs and HDACs

A

HAT: histone acetyltransferases
HDAC: histone deacetylases
chromatin covalent modifying enzymes

33
Q

SWI and SNF

A

chromatin remodeling enzymes

Biochemistry II (22 decks)

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