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BIO 142 > Gene Regulation in Eukaryotes > Flashcards

Gene Regulation in Eukaryotes Flashcards

1
Q

the most rapid form of regulation of the amount of protein

A

the degradation of proteins

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2
Q

what is used by eukaryotes that is not used by prokaryotes in gene regulation?

A

RNA splicing and chromatin remodeling

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3
Q

what does RNA splicing allow?

A

different traits to be produced from the same gene due to the sequence that it is stitched in

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4
Q

HDACs

A

histone deacetylases

remove acetyl groups

example of negative control because they re-condense chromatin

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5
Q

HACs

A

histone acetylases

add acetyl groups

example of positive control because they decondense chromatin

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6
Q

how do acetyl groups de-condense chromatin?

A

they neutralize the positive charge on lysine residues which makes less force of attraction between the negatively charged DNA and the lysine. opens up.

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7
Q

DNA methylation

A

negative control

the added methyl groups allow proteins to bind to the DNA that condenses it

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8
Q

why do histones bind tightly to DNA?

A

histones are positively charged and DNA is negatively charged

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9
Q

differential gene expression

A

responsible for creating different cell and tissue types

all cells have the same genes but express them differently

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10
Q

3 steps to regulate gene expression within the nucleus

A
  1. Chromatin remodeling (degree of which chromatin is coiled)
  2. Transcriptional regulation
  3. Alternative splicing
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11
Q

Stain and chromatin

A

areas that are unwound will stain lightly. indicates they will be expressed at high levels. (euchromatin)

areas that are wound will stain dark, indicates they will be expressed at low levels (heterochromatin)

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12
Q

x chromosomes and DNA methylation

A

since females have 2 X chromosomes, one is condensed by DNA methylation

random which of the chromosomes will be affected. means that on an organismal level there will be a 1:1 ratio of alleles present overall.

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13
Q

Barr body

A

stain that is produced by X chromosome that is wound by DNA methylation

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14
Q

Mosaicism

A

different cells exhibit different traits

occurs when female is heterozygous for X-linked trait

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15
Q

example of mosaicism

A

tortoise shelled female cats (heterozygotes)

some cells exhibit the black allele, while others exhibit the orange all due to random condensation of X-chromosome

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16
Q

can male cats be tortoise shelled?

A

yes

nondisjunction (failure to separate normally) can occur and XXY male can have mosacism

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17
Q

DNA methyltransferases

A

add methyl groups to chromatin

results in condensed chromosomes

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18
Q

Nucleosomes

A

repeating bead-like structures that consist of DNA wrapped around histones

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19
Q

DNAase treatment

A

tests for open chromatin because it only degrades open chromatin

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20
Q

H1 protein

A

maintains the structure of each nucleosome

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21
Q

30-nanometer structure

A

H1 proteins interact to form a tightly wound fiber

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22
Q

Acetylation

A

Acetyl groups neutralize the positive charge on lysine and loosen the interaction between positively charged histones and negatively charged DNA

this loosens the chromatin

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23
Q

Histone acetyl transferases

A

put acetyl groups on DNA

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24
Q

Histone deacetylases

A

remove acetyl groups on DNA

DNA tightens

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25
Q

Epigenetic inheritance

A

inheritance not due to differences in gene sequences

26
Q

What is an example of epigenetic inheritance?

A

inheritance not due to differences in gene sequences

27
Q

What do all eukaryotic genes have?

A

a common promoter

28
Q

TATA binding protein

A

binds eukaryotic promoters to the TATA box

29
Q

Where is the promoter found?

A

at the beginning of

30
Q

TATA box

A

sequence of DNA that is at the core of the promoter

where the TATA binding protein binds

31
Q

Promoter proximal elements

A

DNA regions upstream of the promoter that are UNIQUE to specific genes

32
Q

Enhancers

A

located far away from the promoter either upstream (5’) or downstream (3’)

different enhancers are associated with different genes

33
Q

Activator proteins

A

bind to enhancers and stimulate the transcription complex

34
Q

Silencers

A

similar to enhancers but repress gene expression

35
Q

Classes of proteins that bind to the regulatory sequences of eukaryotic genes

A

Basal transcription factors

Regulatory transcription factors

36
Q

Basal transcription factors

A

do not regulate transcription, but are required to start transcription

they are general

37
Q

example of a basal transcription factor

A

TFIID protein that binds directly to TATA box

38
Q

regulatory transcription factors

A

bind to enhacers, silencers, and promoter-proximal elements

responsible for the expression of particular genes in particular cell types at certain stages of development

unique to particular genes

39
Q

How are regulatory transcription factors triggered?

A

extracellular signals can trigger them

40
Q

What can regulatory transcription factors do?

A

they can get histone acetylation to occur and certain genes to be expressed

can recruit the basal transcription complex to bind to a specific promoter

41
Q

What completes the basal transcription complex?

A

RNA polymerase II

42
Q

What happens when chromatin decompresses?

A

the promoter is exposed

43
Q

How can enhancers control genes far away?

A

DNA looping

44
Q

Alternative splicing

A

removes introns and splices exons together

allows one gene to code for many different things

45
Q

snRNPs

A

bind to consensus sequence at the 5’ exon-intron boundary. another snp binds to 3’ boundary.

together they physically loop the introns

46
Q

Spliceosome

A

complex that cuts the RNA, releases introns, and joins exons

47
Q

Example of how alternative splicing can promote diversity

A

the gene for the muscle protein tropomyosin is spliced in five different ways for different tissue types

48
Q

what percent of genes have alternate splicing?

A

90%

technically humans have less genes than wheat

49
Q

RNA interference (RNAi)

A

can result in rapid degradation of mRNA in the cytoplasm

targets specific mRNAs based on single-stranded microRNAs

50
Q

microRNAs

A

transcribed in the nucleus, but are not translated

bind to RNA-induced Splicing Complex where they become single stranded

then, single stranded microRNAs can bind to mRNA with help of RISC

51
Q

RISC

A

binds microRNAs to mRNA

enzyme inside RISC cuts the mRNA to degrade it

52
Q

Protein kinase rapamycin (mTR)

A

phosphorylates translation initiation factors

these factors recruit the ribosome

under stressful conditions, protein kinase rapamycin activity is blocked

this prevents most translation

general form of regulation

53
Q

3 examples of post translational control

A
  1. localization
  2. modifications
  3. degradation
54
Q

Localization

A

post-translational control

proteins can have a signal sequence to quickly change their cellular location

55
Q

Ex of localization

A

transcription factors are sequestered in the cytosol until given a signal to move to nucleus

common mechanism for hormone receptors

56
Q

Modification

A

post-translational control

Covalent modifications to proteins (like the addition of a phosphate group) can be used to quickly change the 3D shape and function of a protein

57
Q

Ex of modification

A

CDKs add phosphate groups to target proteins to begin mitosis

58
Q

Degradation

A

post-translational control

regulating the lifetime of a protein is a way to control its actions

59
Q

Proteasomes

A

control random degradation of proteins by preventing hydrolytic enzymes from floating around cytoplasm and degradating proteins

60
Q

Ubiquitin

A

polypeptide that is often linked to proteins designated for degradation

this ubiquitin-protein complex then binds to a complex called a proteasome

61
Q

What happens once ubiquitin-protein complex binds to the proteasome?

A

Protein is cleaved from ubiquitin and proteases digest the protein

BIO 142 (14 decks)

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