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bio 211 > lecture 5 > Flashcards

lecture 5 Flashcards

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Biology 101 flashcards
1
Q

what makes one cell type different from another

A

what proteins are expressed in the cell (cuz every cell has same DNA + genome)

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2
Q

what specifically makes cells different from one another

A

transcriptional regulators

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3
Q

what leads to diff proteins being expressed

A

not all of the genes in DNA are actually transcribed/produced; some are turned off other are turned on

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4
Q

what’s the main idea of different cells

A

specific cell types are defined by proteins they express; some proteins are universally expressed, some are specific to each cell

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5
Q

why are cells different

A

all cells have exact same DNA and genes, but don’t have machinery to express the same genes

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6
Q

what dictates what proteins are expressed in cells

A

presence of regulators

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7
Q

what do Gs proteins lead to

A

generation of cyclic AMP and PKA activation

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8
Q

give example of how signaling can control gene transcription –> cell differentiation

A

active PKA enters nucleus where the DNA is; phosphorylates regulatory machinery that allows target gene to be expressed (in liver cell it wud be aminotransferase gene)

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9
Q

how much % of genes does typical human cell express

A

30-60%

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10
Q

what are 2 control points for regulating gene expression we focus on

A

transcriptional control, protein activity control (phosphorylation)

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11
Q

example of control of mRNA production thru transcription

A

transcriptional regulators

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12
Q

what do transcriptional regulators do

A

once activated, they scan DNA sequence in nucleus, look for specific nucleotide sequences upstream of gene they’re controlling that they can bind to

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13
Q

what 2 things can regulators do

A

activate or block gene transcription; either way you have unique gene expression

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14
Q

what regions of DNA do transcriptional regulators bind to

A

cis regulatory sequences

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15
Q

in other words what do transcription regulators do

A

scan DNA sequence, when it encounters part of DNA close to the gene its controlling, binds and provides docking site for machinery to allow production of messenger RNA

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16
Q

why is it ‘cis’ regulatory sequence

A

cis means close to mRNA sequences they’re gonna be transcribing / gene of interest

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17
Q

what can transcriptional regulators do to downstream gene transcription

A

either activate or repress

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18
Q

how do transcriptional regulators interact w/ DNA exclusively through

A

major grooves

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19
Q

why major and not minor grooves

A

b/c major grooves have more nucleotides for transcriptional regulators to interact with

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20
Q

what are all transcriptional regulators

A

dimers; always function as a pair

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21
Q

when scanning DNA for appropriate cis reg sequence to recognize (active/repress downstream gene), how do trans regulators do this

A

with 2 sets of protein-DNA binding regions

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22
Q

what is nanog

A

prefers T to C, next 2 must be A, next 2 prefers T to G, prefers G to A, equally C and G

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23
Q

what is the point of this nanog

A

cis sequence isn’t always gonna be identical; more wiggle room

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24
Q

if monomeric transcriptional regulator has no problem binding DNA sequence, then why do we have dimers?

A

dimers double amount of DNA needed to be recognized; like short vs long password

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25
Q

what does dimerizing allow

A

more specificity on where transcription regulators bind to a sequence; reduces chances that regulatory sequence is gonna be found in genome anywhere else BUT upstream of target

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26
Q

what is needed for DNA to be packed into nucleus

A

highly organized by being wrapped around histone proteins

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27
Q

what is the problem w/ histones

A

when DNA strand is wrapped around histone, it can hide cis reg sequence –> hinders ability of trans reg to get onto cis reg sequence

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28
Q

how does it deal with it

A

breathing and cooperative unbinding

29
Q

what is breathing

A

1/20th of the time DNA is gonna naturally slip off the histone; once it falls off cis reg sequence is exposed and it binds

30
Q

what happens once cis reg sequence falls of histone and binds to trans regulator

A

once it binds other machinery is recruited, histone is temporarily removed so mRNA can be regulated appropriately

31
Q

what is cooperative unbinding

A

cis reg sequence is exposed, trans reg binds to it & recruits additional machinery to help remodel/reorganize histone-DNA complex, allows subsequent cis reg sequences to be exposed to allow additional trans regs to bind

32
Q

describe breathing

A

kinda random, occasionally falls off, when cis sequence is on end of histone

33
Q

describe cooperative unbinding

A

cis reg sequence is in center, multiple trans regs being recruited, more purposeful mechanism

34
Q

tryptophan repressor

A

when enough tryptophan in cell, it binds to trans regulator binds to activate it, which binds onto cis-reg sequence and PREVENTS production of tryptophan

35
Q

what activates trans reg

A

tryptophan

36
Q

what happens when tryp activates trans reg which binds to cis reg sequence

A

RNA pol is blocked from accessing DNA when cis reg sequence is bound by trans reg

37
Q

what is this an example of (tryptophan operon)

A

repressing the gene and preventing it from being transcribed

38
Q

what happens if theres less tryptophan in cell

A

repressor remains inactive cuz there’s no tryptphan for it to bind

39
Q

what happens if tryp doesn’t bind to trans reg

A

trans regulator isn’t activated and doesn’t bind to cis regulatory sequence which means RNA pol is free to bind cis reg sequence and produce more tryptophan

40
Q

what else can transcriptional regulators do

A

activate transcription, not just repress

41
Q

example of transcriptional regulators serving as activators

A

signaling molecule activates transcriptional regulator; binds cis reg sequence and actively recruits RNA pol rather than blocking it; allows messenger RNA to be produced

42
Q

which is more complex mammalian or proks

A

mammalian cells have many more nodes of control; multiple cis reg sequences, multiple trans regs, etc.

43
Q

how can reg sequences be 10k+ nucleotides away from gene of interest and still regulate the gene

A

because these things fold in 3D structure, putting them in close proximity

44
Q

during development how are differences between one cell to another defined

A

defined exclusively by which transcriptional regulators are active

45
Q

how many stripes of Eve protein

A

7

46
Q

what are transcriptional regulators also known as

A

complex genetic switches

47
Q

what are the 4 transcriptional regulators that control the regulatory segment in drosophila

A

bicoid, giant, hunchback, kruppel

48
Q

how many regulatory sequences are in Eve gene DNA

A

7 regulatory segments (7 stripes)

49
Q

within stripe 2 regulatory segment binding sites for how many transcriptional regulators

A

4; bicoid, giant, hunchback, kruppel

50
Q

what are the transcriptional repressors in drosophila

A

giant and kruppel

51
Q

what happens if giant and kruppel are active and bound to regulatory 2 stripe

A

they PREVENT expression of eve protein

52
Q

what are the transcriptional activators in drosophila

A

bicoid and hunchback

53
Q

where is eve protein gonna show up in

A

only cells that have BOTH of transcriptional activators and none of trans repressors

54
Q

what is requirement to have stripe region

A

BOTH activators present (hunchback and bicoid) and both repressors absent (giant and kruppel)

55
Q

sum up eve stripe

A

eve stripe 2 is under control of 4 transcriptional regulators; 2 repressors, 2 activators; it will only be expressed when both repressors aren’t there and both activators are there

56
Q

what does combinatorial gene control do

A

creates hella diff cell types; diff combos of trans regulators give rise to many diff cell types [in daughter cells, one cell A has trans expressed other cell doesn’t, each of their daughter cells can have diff ones expressed]

57
Q

just b/c transcriptional regulator is expressed doesn’t mean

A

it’s active

58
Q

what is one way to activate transcriptional regulator

A

phosphorylation (covalent modification), ligand binding, etc.

59
Q

transcriptional regulators are not just controlled by

A

protein expression; may need other things to activate it

60
Q

what are 3 transcriptional regulators for fibroblasts

A

Oct4, Sox2, Klf4

61
Q

what happens if you force fibroblast to express 3 trans regulators and allow them to grow

A

cells de-differentiate to stem cells and can become diff cell types

62
Q

basically what do trans regulators do to cells

A

induce cells to differentiate

63
Q

why are there only 3 trans regulators that do this

A

because they each control hella pathways and an enormous network of genes below theme [basically v small changes lead to v big effects]

64
Q

what do trans regulators control

A

control cell phenotype

65
Q

what do trans regulators recognize & bind to

A

recognize nucleotide sequences, bind to major groove on DNA

66
Q

what can trans regulators do to downstream genes

A

can activate or repress downstream genes

67
Q

a single euk gene is controlled by how many regulatosr

A

10s-100s

68
Q

what can this complexity in regulation allow for

A

protein expression at right place and time during dveelopment

69
Q

what can right combo of transcription factors do

A

reprogram cell fate

bio 211 (18 decks)

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