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Bio 107 > Midterm 2 > Flashcards

Midterm 2 Flashcards

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Biology 101 flashcards
1
Q

What is a constitutive gene

A

A gene that is always expressed

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2
Q

What is a consensus sequence

A

Most common sequence that binds RNA polymerase efficiently

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3
Q

Negative regulation

A

A gene is expressed until it is repressed

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4
Q

Positive regulation

A

A gene isn’t expressed until activated

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5
Q

What is the function of LAC Y/ Galactoside permease

A

transport lactose into the cell

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6
Q

What is the function of Lac Z/ b-galactosidase

A

Cleaves lactose into glucose and galactose

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6
Q

How is the LAC operon negatively controlled

A

The lac operon has a repressor that can bind to its respective operator region. This repressor will be removed when allolactose binds to it

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7
Q

What is the inducer for the LAC Operon

A

Allolactose

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8
Q

Allolactose will bind to the repressor whether its bound or free (true or false)

A

true

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9
Q

Why is IPTG used in blue white screening

A

it cannot be broken down and has similar inducing effects as allolactose

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10
Q

What kind of protein is the LAC repressor (what kind of subunits)

A

tetramer

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11
Q

What do rising cAMP levels correlate with

A

decreasing levels of glucose

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12
Q

How does the LAC repressor block LAC activation

A

the repressor prevents the transition to the open complex. However, it is important to know that the RNA polymerase and repressor can both bind at the same time.

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13
Q

What are the positive control methods for LAC activation

A

Low glucose and the cAMP/CAP binding

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14
Q

How does the cAMP/CAP complex respond to repression

A

the complex can overcome repression and can even continue LAC transcription in the presence of glucose

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15
Q

What does the cAMP/CAP complex allow for (in terms of RNA interacting with DNA)

A

formation of the open complex. Without the CAP complex we will not see the formation of the open complex.

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16
Q

Which domain of the RNA polymerase binds to the cAMP/CAP complex

A

the C terminal of the alpha subunit of rna polymerase

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17
Q

What does the trp operon encode for (in terms of metabolism)

A

anabolism/ building tryptophan

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18
Q

What kind of control is the TRP operon under

A

negative control

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19
Q

Under which conditions is the TRP operon turned off

A

high levels of TRYPTOPHAN

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20
Q

Why is attenuation of the TRP operon necessary

A

TRP repression is weak

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21
Q

Which polymerase type encodes for mRNAS and non coding RNAs

A

polymerase 2

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21
Q

How does attentuation work

A

high trp
many trnas loaded with trp
ribosome can quickly transcribe two consecutive trp codons and thus the hairpin can form

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22
Q

Which polymerase type encodes for major ribosomal rna

A

Polymerase type 1

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23
Q

which polymerase type encodes for trnas

A

type 3

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24
Q

Which polymerase types are only present in plants

A

4 and 5

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25
Q

where is the TATA box most frequently found

A

-25 to -35bp upstream of the transcription start site

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26
Q

What kind of genes tend to not have a TATA box

A

housekeeping genes and developmentally regulated genes

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27
Q

What is the primary function of transcription factors

A

to increase the frequency of transcription initiation

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28
Q

Where does TFIIB bind

A

to the TBP at the c terminal and the RNA polymerase at the N terminal

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29
Q

What are the two forms of RNA Pol 2

A

IIA (unphosphorylated)
IIO( phosphorylated)

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30
Q

Where is RNA POL 2 phosphorylated and by what (during the initiation stage)

A

Serine 5 in the carbon terminal and by TF11H

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31
Q

Where does TBP bind

A

to the minor groove of the TATA box

32
Q

Where is RNA POL 2 phosphorylated during the elongation stage

A

serine 2

33
Q

Is TFIIH sufficient enough to cause phosphorylation

A

yes but other transcription factors aid in enhancing the phosphorylation

34
Q

What are the two essential components of DNA activators

A

DNA binding domain and activator domain

35
Q

Zinc fingers domain type and structure

A

Zinc fingers are a dna binding domain with a zinc ion present that bind to the major groove of DNA

36
Q

What is the purpose of leucine in the bZIP dna binding domains

A

facilitates dimerization

37
Q

Homeodomains structure and function

A

dna binding domain that binds to both major and minor grooves of DNA.

38
Q

Histones are highly ___

A

basic/positive

39
Q

What are the types of chromatin remodeling that can occur

A

nucleosome sliding, remodeled nucleosomes, nucleosome displacement, and nucleosome replacement

40
Q

H1 histone function

A

helps further compress DNA and

41
Q

what does MNASE allow you to do

A

digest linker DNA and ultimately map nucleosome position

42
Q

What effect does acetylation have on DNA ttranscription

A

activation

42
Q

Why does acetylation cause activation

A

reduces the positive charge of the histone tails, weakens histone association to DNA, and thus allowing for more transcription.

43
Q

Where does acetylation happen on histone tails

A

lysine

44
Q

What effect does methylation have on transcription

A

activation and repression

45
Q

What does the SWI/SNF complex do

A

nucleosome displacement and remodeling

46
Q

What does the ISWI complex do

A

nucleosome sliding

47
Q

How does the TR RXR complex work

A

TR binds to RXR forming a dimer. In the presence of TH, this dimer recruits HAT. In the absence of TH this dimer recruits HDAC

48
Q

What does cytosine methylation do

A

causes the silencing of genes

49
Q

How are reader-writer complexes related to methylation

A

Reader writer complex can help to spread methylation across a genome

50
Q

What enzymatic activity does TAF 1 have

A

HAT and protein kinase

51
Q

What is the difference between rho dependent and independent terminators

A

dependent does not have the T repeats

52
Q

Where is the trp operator

A

in the trp promoter

53
Q

Why is phosphorylation of the RNA POL 2 CTD required?

A

Phosphorylation weakens affinity to TBP which allows for the elongation stage to begin

53
Q

DNA elements where proteins bind to enhance transcription

A

enhancers

54
Q

Where do activators bind to

A

enhancers

55
Q

Which activator types have to form dimers to function

A

leucine zipper and helix loop helix

56
Q

Why is chromatin condensation necessary

A

without it DNA would be far too long to package into cells.

57
Q

What kind of a structure do the core histones form

A

an octamer
h3 and h4 form tetramer and h2A and h2b form two heterodimers. 2+2+4=8

58
Q

What does H3K9AC do ( study guide says to remember at least one code)

A

causes acetylation/activation

58
Q

What are the three main histone modifications

A

Acetylation, Methylation, and Phosphorylation.

59
Q

What does H3K9m2 do (study guide says to remember at least one code )

A

repression

60
Q

What is the difference between epigenetic and genetic inheritance

A

genetic inheritance is mediated by the sequence of dna bases passed from parent to offspring. Epigenetic inheritance is the passing of chemical alterations of histone and dna structure (without affecting the bases) to offspring.

61
Q

How is cytosine methylation different from methylation at the histone tail

A

cytosine methylation occurs on dna while methylation at the histone tail is at the histone tail.

62
Q

Which kind of genes are associated with methylation of gene bodies

A

constitutively active genes

63
Q

How do we identify cytosine methylation

A

Bisulfite sequencing and methyl sensitive restriction enzymes+souther blotting

63
Q

How does bisulfite sequencing work

A

all cytosines that are not methylated will be switched to uracil. This allows us to detect where the points of methylation are.

64
Q

What binds to the AAUAAA region

A

CPSF

65
Q

What is the 5 prime splice site

A

GU

66
Q

What is the 3 prime splice site

A

AG

67
Q

What is the branch point

A

A

68
Q

what recognizes the 3 prime site

A

U2AF

69
Q

What recognizes the A branch point

A

U2

70
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71
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72
Q
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73
Q
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74
Q
A

Bio 107 (2 decks)

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