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Foundations Test 1 > Gene Regulation > Flashcards

Gene Regulation Flashcards

1
Q

Reverse transcriptase

A

Rna to DNA

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2
Q

Functional RNA

A

Ribozymes, long non-coding RNAs, miRNAs

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3
Q

Start codon of translation

A

ATG (DNA)

AUG (RNA)

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4
Q

Stop codon

A

UAA, UAG, UGA (RNA)

TAA, TAG, TGA (DNA)

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5
Q

Introns

A

Removed

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6
Q

Cleae-polyadenylation site

A

Cut at the 3’ end and a bunch of A’s are added…defines end of last exon included

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7
Q

Why is mRNA longer than protein?

A

5’ and 3’ UTR regions

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8
Q

Enhancer/promoter location

A

Promoter - only at beginning

Enhancer - can be anywhere

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9
Q

Upstream vs. downstream

A

Upstream - 5’

Downstream - 3’

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10
Q

What controls expression of genes?

A

Trans-acting transcription factors and cis-acting DNA sites

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11
Q

Cis

A

DNA motifs
Structurally linked to gene
Do not encode proteins but serve as docking sites for trans-acting genes

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12
Q

Trans

A

Protein factors that regulate transcription of target genes…non covalentlybind to cis acting sites in a sequence specific manner

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13
Q

Promoter

A

Adjacent to transcription start site…contains cis-acting site that assembles with RNA polymerase 2 complex…may interact with others

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14
Q

Enhancer

A

Bind trans-acting transcription factors that positively influence chroomatin

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15
Q

Silencer

A

Opposite of enhancer

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16
Q

Trans-acting factor structure

A

Bipartite structure

Activation domain and DNA-binding domain

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17
Q

Changes in amino acid sequence of trans-acting

A

Change affinity of binding to DNA

18
Q

Changes in nucleotides of cis-site

A

Increase or decrease affinity to protein

19
Q

Enhancers are a cluster of

A

Transcription factor binding sites

20
Q

Enhancers can

A

Alter chromatin or influence the recruitment of RNA poly 2 complex

21
Q

Enhancers are DNA elelments that are linked to

A

Increasing rate of transcription initation from a linked promoter

22
Q

Co-activator example

A

CBP/p300

HAT

23
Q

Co-activator

A

Interact with transcription factors (do NOT bind DNA)

24
Q

Co-activators may act as

A

Bridge between DNA binding proteins and Pol 2 transcription initiation complex

25
Q

Co-repressor example

A

HDAC

26
Q

Co-repressors

A

May block bridges between DNA binding proteins and Pol 2 transcription initiation complex

27
Q

Transcription facotrs can

A

Influence assempy of RNA polymerase 2 and associated factors on a promoter
Influence rate of transcription initiation
Interact with cis-acting site that are large distance away from promoters

28
Q

Combinatorial model of gene regulation

A

Interaction of multiple trans-acting transcription factors with multiple cis-acting binding sites will ultimately determine specificity, timing, and level of gene expression

29
Q

One TF can control

A

Multiple target genes

30
Q

Nuclear receptor superfamily of TFs conserved doamin

A

DNA-binding domain

31
Q

Generalized domain structure of nuclear receptors

A

Transactivation
DNA binding (Zn)
Ligand binding

32
Q

Orphan receptors

A

Nuclear receptors for which a ligand has not been ID’d

33
Q

Type 1 NR

A

In absence of ligand, in cytosol as a monomer with chaperone proteins…In presence of hormone, NR dissociates from chaperone, dimerizes, enters nucleus, binds to cis-acting sites of target genes and recruits co-activators and RNA polymerase to activate transcription

34
Q

Type 1 NR cis-binding

A

HRE - Hormone response element

35
Q

Type 2 NR

A

In absence of ligand, heterodimer bound to HRE and associated with co-repressors that repress…in presence of ligand, co-receptors dissociates, co-activators bind NR and recruits RNA polymerase to increase transcription

Stays associated the whole time

36
Q

What do type 1 and 2 NR have in common?

A

Both do not require protein synthesis and are fialry rapid response

37
Q

HNF-4alpha

A

Hepatocyte nuclear factor 4alpha

Orphan receptor controls expression in liver, pancreas, and kidney

38
Q

Nuclear factor kB complexes

A

IKK - IKKgamma/NEMO, IKKalpha, IKKbeta
NFKB - p50:relA heterodimer (others exist)
IkB

39
Q

Nuclear factor kB pathway

A

Stimulus activates IKK complex
IKK complex phosphorylates IkB
Phosphorylated IkB is polyubiquitnated
Polyubiquitanted IkB is degraded by 26s protesosome
NFkB translocates to nucleus and binds cis acting site
RNA pol 2 and associated factors recruited to promoter and transcribe gene

40
Q

Binding site of NFkB on DNA

A

NFkB RE

41
Q

NF-kB effect

A

Pro-survival

No proetin syntesis required

42
Q

Regulation of NF-kB

A

targets IkB…this provides feedback mechanism that can inhibit the NFkB complex

Foundations Test 1 (15 decks)

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