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BIO 2600 > Chapter 8 > Flashcards

Chapter 8 Flashcards

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1
Q

examples of housekeeping genes

A

RNA polymerase, ribosomal proteins, DNA repair enzymes, cytoskeletal proteins, etc.

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2
Q

techniques that compare protein composition between cells

A

mass spectrometry and quantitative proteomics

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3
Q

techniques to profile gene expression

A

sequencing RNA and mRNA molecules

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4
Q

cortisol causes for release and effects

A

hormone released by adrenal gland in starvation, stress, exercise
signals to liver to increase glucose production and upregulates gluconeogenesis genes

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5
Q

transcription factor/transcription regulators

A

proteins that bind to specific DNA sequences and regulate transcription and gene expression

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6
Q

general transcription factors

A

help RNA polymerase II locate promoter and initiate transcription
only in eukaryotes (prokaryotes use sigma factor)

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7
Q

specific transcription factors (regulators)

A

activators and repressors influence efficiency/rate of transcription initiation by promoting or blocking RNA polymerase recruitment
eukaryotes and prokaryotes

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8
Q

how do transcription regulators bind to DNA

A

surface features in the DNA can change based on nucleotide sequence
recognize specific 3D features
bind to major groove of double helix

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9
Q

how do transcription regulators usually bind to major groove in DNA

A

form tight noncovalent interactions (ionic, hydrophobic interaction, hydrogen bonding)
bind as dimers (or polymers/clusters) usually to increase tightness

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10
Q

4 common DNA binding motifs (in DNA binding proteins)

A

helix-turn-helix motif
homeodomain motif
zinc finger domain
leucine zipper motif

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11
Q

homeodomain motif

A

involved in regulatory control of developmentally important genes
consists of 3 alpha-helices (cylinders) which fit protein into major groove
helix 3 contacts with DNA bases

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12
Q

helix-turn-helix motif

A

two adjacent alpha helices separated by (90 deg) turn of several amino acids

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13
Q

homeodomain difference from helix turn helix

A

homeodomain has three helices
but action of homeodomain is mediated by helix turn helix motif

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14
Q

Zinc finger motif

A

alpha helix and beta sheet held together by zinc molecule
often found in clusters to allow alpha helix of each finger to contact DNA bases in each major groove (identification)

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15
Q

leucine zipper motif

A

bind as dimers -grip DNA like clothespin
formed by 2 alpha helices (from separate proteins)

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16
Q

benefits of transcription factors binding as dimers

A

doubles the area of contact
increases specificity and strength

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17
Q

operons

A

bacterial clusters of genes transcribed together into single (polycistronic) mRNA because they share the same promoter

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18
Q

tryptophan operon makeup

A

contains 5 genes which encode 5 different enzymes needed to synthesize tryptophan
expression of Trp operon controlled by regulatory DNA sequence (operator) within the promoter

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19
Q

regulation of Trp operon

A

negatively regulated by Trp repressor

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20
Q

in high Trp conditions (feedback inhibition)

A

Trp binds to Trp repressor
Trp repressor binds to Trp operator region
prevents RNA polymerase from binding to promoter

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21
Q

allosteric protein

A

regulated by binding of molecule to a site other than the active site (Trp repressor)

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22
Q

activator proteins

A

transcription regulators that facilitate binding of RNA polymerase to inefficient promoters

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23
Q

lac operon makeup and function

A

three genes and three enzymes to import and digest lactose
allows bacteria to use lactose as energy source when glucose is low

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24
Q

what happens to cAMP levels when glucose is low

A

increase

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25
Q

activator for Lac operon

A

catabolite activator protein (CAP)

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26
Q

how is CAP activated

A

binding of cAMP

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27
Q

purpose of lactose repressor

A

shuts down expression of Lac operon if no lactose is present

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28
Q

requirements for Lac operon activation

A
  1. glucose absent (high cAMP, binding of CAP)
  2. lactose present (no binding of repressor)
29
Q

first gene is Lac operon

A

LacZ - encodes beta-galactosidase which breaks down lactose to galactose and glucose

30
Q

order of components in Lac operon

A

-80: activator (CAP binding site)
-40: promoter (RNA pol. binding site)
1: operator (repressor binding site)
40: LacZ gene

31
Q

when lactose present how does repressor release from DNA

A

allolactose binds to repressor and decreases its affinity for the operator DNA

32
Q

function of chromatin remodeling proteins in eukaryotes

A

these proteins and enzymes covalently modify histones that are the core of nucleosomes

33
Q

how do transcription activators activate expression of DNA

A

can recruit histone modifying enzymes and chromatin-remodeling protein complexes to the promoter to make chromatin more accessible to transcription factors and RNA polymerase

34
Q

histone acetylases

A

add acetyl group to select lysine
makes DNA more accessible and enhances transcription efficiency

35
Q

histone deacetylases

A

remove acetyl group and restores packaging
makes DNA less accessible and inactivates expression

36
Q

gene activation in eukaryotes

A

activators bind to enhancers (regulatory DNA sequences that enhance transcription) located far away from promoter region
binding of activators causes DNA bending and positions activators closer to general transcription factors and RNA polymerase II
(activators interact with mediator -adaptor)

37
Q

how do activators only interact with correct gene regulators and not loop in wrong direction?

A

chromosomes arranged in loops - TADs (topological associated domains) held together by protein clamps

38
Q

factors in combinatorial control

A

general transcription factors: assemble at promoter, always the same
transcription regulators: location of binding sites and regulators themselves different
mediator: assembly place for factors, regulators, chromatin modifying proteins
COMBINED effect of all of these determines rate of transcription of a gene

39
Q

how do eukaryotes control expression of more than one gene at once without operons

A

the same transcription factor can regulate the expression of multiple genes if the genes have regulatory sites that recognize the same transcription factor
e.g. cortisol binds to cortisol receptor which activates many different genes

40
Q

how does cell differentiation occur during development

A

different combinations of gene regulatory proteins cause cells to differentiate

41
Q

pluripotency

A

developmentally flexible- can give rise to different cell types (embryonic stem cells)

42
Q

how many different types of cell types can an organism with three transcription regulators create?

A

2^3 = 8
(one with 0, 3 with 1, 2 with 2, 1 with all three)

43
Q

master regulators

A

regulate all cells in an organ and regulate expression of other regulators
- produce a cascade of other regulators

44
Q

Ey transcription master regulator in flies

A

control differentiation of cells that form the eye
-mutation in Ey -> no eyes
-some of genes regulated by Ey encode other transcription regulators for more genes

45
Q

effect of expressing Ey in precursor leg cells in flies

A

cause formation of non functional eye structures on leg

46
Q

iPCs

A

induced pluripotent cells- by set of 3 transcription factors that induce de-differentiation of fibroblasts

47
Q

myoD

A

muscle specific transcriptional regulator

48
Q

can specialized cells be induced in culture

A

yes

49
Q

terminally differentiated cells

A

do not divide; skeletal muscles, neurons

50
Q

differentiated cells that can divide

A

liver, skin

51
Q

cell memory

A

pattern of gene expression profile responsible foe given cell identity (skin cell division gives more skin cells)

52
Q

three ways a cell maintains its identity

A
  1. positive feedback loop (most prevalent)
  2. condensed chromatin
  3. DNA methylation
    ALL epigenetic changes
53
Q

epigenetic changes

A

no changes in DNA nucleotide sequence

54
Q

positive feedback loop cell identity

A

master regulator activates its own transcription at every division generating a self sustaining circuit of gene expression
generates cell memory because protein produced stimulates its own production
e.g. MyoD directs cells to become muscle cells

55
Q

condensed chromatin cell identity

A

chemically modified histones passed from parent to daughter cell
- modified histones are distributed randomly between daughter cells and enzymes fill in the blanks based on neighboring histones to restore parental modification
(same X chromosome in mammalian females inactive through many cell generations)

56
Q

DNA methylation cell identity

A

covalent modification (methylation of cytosine) by maintenance methyltransferase maintains DNA methylation in parent to daughter cells: methylates only CG sequences that are base paired with methylated CG sequences
generally turns OFF transcription

57
Q

types of post-transcriptional controls

A

operate after RNA polymerase has begun translation
- alternative splicing
- mRNA sequences that control translation (5’ and 3’ UTR)
- regulatory RNAs control gene expression

58
Q

ribosome binding sites

A

place on the mRNA where ribosome binds; important for positioning the ribosome

59
Q

bacterial translational control on ribosome binding sites

A

bacteria have proteins that bind to ribosome binding site and repress translation of specific mRNAs
proteins recruited by 3D structure of mRNA itself

60
Q

thermosensor in L. monocytogenes

A

RNA sequence that controls translation of infectious genes due to temp.
elevated temp inside host changes 3D structure of mRNA (H bonds dissociate) and exposes ribosome binding site to translate infectious genes

61
Q

microRNA

A

direct destruction of target mRNA
-precursor miRNA transcribed in nucleus and exported to cytosol where it forms mature miRNA with help of nuclease Dicer
- RISC protein binds with antisense single stranded miRNA and searches for match
- when match is found mRNA is degraded by nuclease within RISC and RISC released

62
Q

RISC

A

RNA induced silencing complex
a “scanner”

63
Q

RNA interference (RNAi)

A

type of gene silencing where siRNAs bind to mRNA and target degradation
-foreign double stranded RNA cleaved by Dicer to create siRNAs
-assemble with RISC proteins and sense strand discarded so that more foreign RNA can be destroyed

64
Q

RITS

A

RNA induced transcriptional silencing

65
Q

RNAi and transcriptional silencing

A

siRNA can assemble into RITS complex to search for complementary RNA emerging from RNA polymerase
- attracts histone modification proteins resulting in heterochromatin formation and transcriptional repression
-resembles adaptive immune response

66
Q

CRISPR

A

clustered regulatory interspaced short palindromic repeats

67
Q

CRIPSR system function

A

small noncoding RNA system that provides bacteria with immunity from viral infections by integrating viral DNA into bacterial genome and transcribing RNA and binding to Cas protein; now able to identify and cleave viral DNA

68
Q

long noncoding RNA

A

roles are not clear
Xist (X-inactive specific transcript) initiates and maintains epigenetic silencing of one copy of X chromosome in females by promoting heterochromatin formation
some serve as scaffolds to bring proteins together that function in same processes

BIO 2600 (15 decks)

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