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BIOL 3421 - molecular biochem > gene expression regulation > Flashcards

gene expression regulation Flashcards

1
Q

list the 7 cellular processes that can help regulate gene expression levels

A

transcription, mRNA processing, mRNA degradation, translation, post-translational modifications, protein targeting and transport, protein degradation

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2
Q

what are housekeeping genes

A

genes constitutively expressed at a constant level at all times in almost all cells of the organism

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3
Q

define regulated gene expression

A

gene expression that increases or decreases in response to molecular signals

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4
Q

define induction

A

when molecular signals increase expression of a gene

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5
Q

define repression

A

when molecular signals decrease expression of a gene

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6
Q

role of specificity factors + give an example

A

alter the specificity of RNA polymerase for a given promoter (ie sigma)

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7
Q

role of repressors

A

impede access of RNA pol to the promotor

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8
Q

role of activators

A

enhance pol-promotor interaction

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9
Q

where do repressors bind

A

to operators

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10
Q

where are operators located in regards to the promoter

A

downstream of promoter

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11
Q

repressor binding is regulated by small molecules/proteins called ____

A

effectors

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12
Q

where do activators bind

A

to activator binding sites

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13
Q

T or F: like repressors, activators are also regulated by effectors

A

true

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14
Q

which type regulation is more common in eukaryotes: positive or negative? explain

A

positive is more common in eukaryotes: without activators, genes will have little transcription because chromatin is more densely packed = inaccessible genes

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15
Q

other than activator binding sites, where can activators bind to in eukaryotes

A

enhancer sites

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16
Q

where are enhancer sites located in regards to the promoter

A

several thousand base pairs away from the promoter

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17
Q

since the enhancer site is so far from the promoter, how do we bring the two sites together

A

DNA looping occurs, which requires co-activators or architectural regulators as well

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18
Q

role of co-activators?

A

assists in DNA looping to bring the enhancer and promoter together

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19
Q

where is DNA binding in regulatory proteins more likely to occur; major groove or minor groove

A

major groove

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20
Q

describe why DNA binding to regulatory proteins occurs in the major groove

A

the exposed groups (ie H donors or acceptors or methyl groups) will differ in the major groove depending on the sequence (ie G-C vs C-G). This doesn’t occur in the minor groove. In the major groove, the protein is able to distinguish between G-C and C-G

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21
Q

define motif

A

a tiny collection of secondary structure

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22
Q

which is larger: motif or domain

A

domains are larger

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23
Q

structure of helix-turn-helix motif + how it binds to DNA

A

20 amino acids in 2 helical segments that are separated by a b-turn. One is the recognition helix and protrudes out the protein surface and binds to specific DNA sequences

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24
Q

example of a molecule that has a helix-turn-helix motif

A

Lac repressor has 4 of them

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25
Q

structure + function of the homeodomain

A

helix-loop-helix part of a larger 60 residue domain. Critical for embryonic body planning

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26
Q

structure of zinc finger motif + how it binds to DNA

A

30 aa in a loop held together by a Zn2+ ion bound to 2 H and 2 C residues. Zn stabilizes the structure, not binding with DNA.

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27
Q

describe the purpose of the RNA recognition motif

A

binds to noncoding RNA instead of DNA. However, both can fit, so DNA and RNA can compete with eachother to bind

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28
Q

why might a regulator need a protein binding domain

A

so it can bind to proteins like polymerases to regulate transcription

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29
Q

structure of leucine zipper motif

A

dimer of amphipathic a helices that interact through hydrophobic regions. The helices coil around each other. Leu repeats every 7th residue. There is a DNA binding domain with many + charged Lys or Arg residues to interact with - DNA backbone

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30
Q

structure of the basic helix-loop-helix motif

A

50 aa that allow for DNA binding and dimerization. The region forms two short amphipathic a helices linked by a loop. the motifs of two polypeptides can interact to form a dimer. Leu helps with dimerization. DNA binding is mediated by basic residues in the recognition helix

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31
Q

define operon

A

a cluster of bacterial genes that function together on a chromosome, along with a promoter and other regulatory elements

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32
Q

T or F: operons are transcribed together through a single promoter

A

true

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33
Q

list everything that the operon includes

A

activator binding site, promoter, operator (repressor binding site), and all the genes required to make amino acid

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34
Q

what genes does the Trp operon include

A

the 5 genes needed to convert chorismate to tryptophan

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35
Q

describe the structure of the Trp operon

A

has a repressor, which is a homodimer

36
Q

what does the Trp repressor bind to

A

tryptophan

37
Q

describe what happens to the Trp operon when tryptophan is present

A

the homodimer repressor binds to tryptophan and then binds to the operator. This blocks RNA pol from binding to the promoter, which prevents gene transcription

38
Q

T or F: the Trp repressor is included in the Trp operon

A

false; it is not part of the operon

39
Q

define transcription attenuation

A

when transcription starts but is halted before reaching the start codon

40
Q

what type of sequence is involved in transcription attenuation

A

attenuation sequence

41
Q

where is the attenuation sequence located (Trp operon)

A

in the leader region in the promoter

42
Q

describe the 4 relevant parts of the leader region of the trp operon mRNA

A

has a sequence that encodes the leader peptide, and has 3 regions that can form secondary structures (denoted 2,3 and 4)

43
Q

in the trp operon, which two sequences halt transcription when they pair

A

3:4

44
Q

what is the name for the 3:4 pairing in the trp operon promoter sequence

A

3:4 pairing is called the attenuator sequence

45
Q

when would you get 3:4 pairing in the promoter of the trp operon? explain

A

when trp is present. ribosome zooms through and covers sequence 2, forcing 3 and 4 to pair. Transcription stops because a hairpin is formed

46
Q

when would you get 2:3` pairing in the promoter of the trp operon? explain

A

when trp is absent. The ribosome doesn’t cover sequence 2, so 2 and 3 can pair. No hairpin forms, so transcription continues

47
Q

function of SOS genes?

A

DNA repair

48
Q

when is the SOS response activated

A

when there’s extensive DNA damage

49
Q

what are the two main SOS response players

A

LexA repressor and RecA

50
Q

role of LexA repressor?

A

inhibits expression of DNA repair genes

51
Q

role of RecA?

A

repairs double stranded DNA breaks

52
Q

describe the structure of a chromosome that will need the SOS response (ie where are LexA repressor and RecA located on the chromosome)

A

normally the LexA repressor will be repressing the transcription of DNA repair genes and preventing the SOS response. It has an operator sequence right before each repair gene

RecA is one of the genes that is beside the LexA repressor’s operator. It’s transcription is only partly blocked by LexA

53
Q

describe the activities of the SOS response

A

extensive DNA damage creates single stranded DNA. The small amount of RecA present in the cell will bind to the ssDNA, and can now act like a protease. RecA induces LexA to self-cleave into two parts, causing LexA to be inactive. With an inactive repressor, all the DNA repair genes (including more RecA) can now be transcribed

54
Q

how much of the eukaryotic genome is heterochromatin

A

10%

55
Q

how much of the eukaryotic genome is euchromatin

A

90%

56
Q

which is always transcriptionally inactive: heterochromatin or euchromatin

A

heterochromatin

57
Q

T or F: euchromatin can be either transcriptionally active or inactive

A

true

58
Q

when does chromosome remodelling occur

A

when a chromatin region becomes transcriptionally active

59
Q

list 2 examples of chromosome remodelling

A

change in nucleosome position, changes in covalent modifications of the nucleosome

60
Q

which family of proteins can separate histones from DNA near transcription start sites

A

SWI/SNF complex

61
Q

role of SWI/SNF complex?

A

separate histones from DNA near transcription start sites

62
Q

describe the issues solved by combinatorial control

A

in bigger eukaryotic genomes, there’s a higher chance that a DNA binding sequence for a regulatory protein will appear elsewhere in the genome. Also, you would need so many regulatory proteins to separately regulate tens of thousands of eukaryotic genes

63
Q

describe the basics of combinatorial control

A

you have only a few regulatory proteins, but they bind in different combinations to regulatory sequences. Also you require multiple regulatory sites per gene, lowering the chance that all regulatory sequences will randomly appear elsewhere together

64
Q

describe all the steps of eukaryotic gene regulation, starting with activators and coactivators binding to enhancers

A

after binding to enhancers, activators recruit a large co-activator complex, the Mediator. They also recruit chromatin remodelling complexes to help adjust nucleosomes. They also recruit architectural regulators to loop DNA (ie a family called HMG). Mediator facilitates recruitment of TATA binding protein (TBP) and TFIIB. TFIIB then recruits pol II + other TFs. When pol II arrives, mediator binds to the CTD, and helps stabilize the entire initiation complex

65
Q

in regards to steroid hormones, what does NR stand for

A

nuclear receptor

66
Q

how many nuclear receptor types do steroid hormones have

A

2

67
Q

give 2 examples of type 1 steroid hormone NR

A

estrogen + glucocorticoids

68
Q

give an example of type 2 steroid hormone NR

A

thyroid hormones

69
Q

what do nuclear receptors bind to

A

DNA sequences called hormone response elements

70
Q

what motif do NRs have

A

zinc-finger DNA binding motifs

71
Q

describe type 1 NR in eukaryotic signalling

A

these ones are monomeric and found in the cytosol. They are complexed with heat shock protein (HSP70). Steroid binding to NR causes HSP dissociation, receptor dimerization which exposes a nuclear localization sequence, and migration to the nucleus

72
Q

describe type 2 NR in eukaryotic signalling

A

these are dimers and always found in the nucleus. They’re bound to HRE but also a co-repressor. Steroid binding causes a conformational change in the dimer that leads to co-repressor dissociation

73
Q

what are translational repressors + what do they do

A

proteins that bind to RNA transcripts, usually in the 3’ UTR before the polyA tail. They interact with translation IFs or with the small ribosomal subunit. they impede translation initiation + save time by making the transcript a circle

74
Q

what does miRNA stand for

A

micro RNA

75
Q

what do miRNAs do

A

they interact with mRNA to inhibit translation

76
Q

describe the structure of miRNA

A

25 nt long, have hairpin-like secondary structures, they bind to the 3’ UTR of the mRNA

77
Q

describe briefly how miRNA production and processing occurs

A

they’re initially transcribed as much longer RNA molecules but then are cleaved/shortened by nuclear endonucleases

78
Q

how do miRNA get to the cytosol (out of the nucleus)

A

through nuclear pores via Exportin

79
Q

what occurs to miRNA once it gets to the cytosol

A

it’s released from exportin and picked up by Dicer

80
Q

what two activites does Dicer have

A

endonuclease and helicase

81
Q

describe what dicer does to miRNA

A

cuts miRNA even smaller and unwinds any complimentary sequences that form hairpins

82
Q

what is miRNA called after interacting with Dicer

A

mature miRNA

83
Q

what does mature miRNA do in the cytosol

A

binds to RISC

84
Q

what does RISC stand for

A

RNA-induced silencing complex

85
Q

what does RISC do after miRNA binds to it

A

binds to a target mRNA

86
Q

describe what occurs when miRNA-RISC-mRNA interact

A

if there is complementarity between miRNA and mRNA, RISC can trigger mRNA cleavage

BIOL 3421 - molecular biochem (20 decks)

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