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Bio 107 > Midterm 2 > Flashcards

Midterm 2 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
which polymerase type encodes for trnas
type 3
24
Which polymerase types are only present in plants
4 and 5
25
where is the TATA box most frequently found
-25 to -35bp upstream of the transcription start site
26
What kind of genes tend to not have a TATA box
housekeeping genes and developmentally regulated genes
27
What is the primary function of transcription factors
to increase the frequency of transcription initiation
28
Where does TFIIB bind
to the TBP at the c terminal and the RNA polymerase at the N terminal
29
What are the two forms of RNA Pol 2
IIA (unphosphorylated) IIO( phosphorylated)
30
Where is RNA POL 2 phosphorylated and by what (during the initiation stage)
Serine 5 in the carbon terminal and by TF11H
31
Where does TBP bind
to the minor groove of the TATA box
32
Where is RNA POL 2 phosphorylated during the elongation stage
serine 2
33
Is TFIIH sufficient enough to cause phosphorylation
yes but other transcription factors aid in enhancing the phosphorylation
34
What are the two essential components of DNA activators
DNA binding domain and activator domain
35
Zinc fingers domain type and structure
Zinc fingers are a dna binding domain with a zinc ion present that bind to the major groove of DNA
36
What is the purpose of leucine in the bZIP dna binding domains
facilitates dimerization
37
Homeodomains structure and function
dna binding domain that binds to both major and minor grooves of DNA.
38
Histones are highly ___
basic/positive
39
What are the types of chromatin remodeling that can occur
nucleosome sliding, remodeled nucleosomes, nucleosome displacement, and nucleosome replacement
40
H1 histone function
helps further compress DNA and
41
what does MNASE allow you to do
digest linker DNA and ultimately map nucleosome position
42
What effect does acetylation have on DNA ttranscription
activation
42
Why does acetylation cause activation
reduces the positive charge of the histone tails, weakens histone association to DNA, and thus allowing for more transcription.
43
Where does acetylation happen on histone tails
lysine
44
What effect does methylation have on transcription
activation and repression
45
What does the SWI/SNF complex do
nucleosome displacement and remodeling
46
What does the ISWI complex do
nucleosome sliding
47
How does the TR RXR complex work
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
What does cytosine methylation do
causes the silencing of genes
49
How are reader-writer complexes related to methylation
Reader writer complex can help to spread methylation across a genome
50
What enzymatic activity does TAF 1 have
HAT and protein kinase
51
What is the difference between rho dependent and independent terminators
dependent does not have the T repeats
52
Where is the trp operator
in the trp promoter
53
Why is phosphorylation of the RNA POL 2 CTD required?
Phosphorylation weakens affinity to TBP which allows for the elongation stage to begin
53
DNA elements where proteins bind to enhance transcription
enhancers
54
Where do activators bind to
enhancers
55
Which activator types have to form dimers to function
leucine zipper and helix loop helix
56
Why is chromatin condensation necessary
without it DNA would be far too long to package into cells.
57
What kind of a structure do the core histones form
an octamer h3 and h4 form tetramer and h2A and h2b form two heterodimers. 2+2+4=8
58
What does H3K9AC do ( study guide says to remember at least one code)
causes acetylation/activation
58
What are the three main histone modifications
Acetylation, Methylation, and Phosphorylation.
59
What does H3K9m2 do (study guide says to remember at least one code )
repression
60
What is the difference between epigenetic and genetic inheritance
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
How is cytosine methylation different from methylation at the histone tail
cytosine methylation occurs on dna while methylation at the histone tail is at the histone tail.
62
Which kind of genes are associated with methylation of gene bodies
constitutively active genes
63
How do we identify cytosine methylation
Bisulfite sequencing and methyl sensitive restriction enzymes+souther blotting
63
How does bisulfite sequencing work
all cytosines that are not methylated will be switched to uracil. This allows us to detect where the points of methylation are.
64
What binds to the AAUAAA region
CPSF
65
What is the 5 prime splice site
GU
66
What is the 3 prime splice site
AG
67
What is the branch point
A
68
what recognizes the 3 prime site
U2AF
69
What recognizes the A branch point
U2
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Bio 107 (2 decks)

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