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Biology 311 > Lectures II-ii > Flashcards

Lectures II-ii Flashcards

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1
Q

+1 start site

A

transcription start site (present in prokaryotes and eukaryotes)

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2
Q

promoter sequence

A

(-35 TTGACAT and -10 TATAAT) in prokaryotes, (-30 TATA) in eukaryotes

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3
Q

Shine-Dalgarno sequence

A

helps ribosome find the correct start codon-present in prokaryotes

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4
Q

PPE (promoter-proximal elements) + enhancers

A

present in eukaryotes

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5
Q

polyadenylation termination sequence

A

tells transcription when to stop - present in eukaryotes

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6
Q

intrinsic termination and rho-dependent terminator

A

tells transcription when to stop - present in prokaryotes

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7
Q

SNPs and SSLPs can become mutations if they occur in:

A
  1. regulatory sequences important for transcription (promoter, terminator, promoter and PPE/enhancer)
  2. coding regions (anything between start and stop codon)
  3. intron boundaries (applies only to eukaryotes, found within the coding region)
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8
Q

what effect does SNPs and SSLPs in regulatory regions have?

A
  • prevents transcription machinery from recognizing promoter and starting transcription
  • allows transcription machinery to bind more strongly to promoter, enhancing transcriptional rates
  • destroys termination site, preventing proper transcription termination
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9
Q

how do you detect effect of a mutation on transcription?

A

use Northern Blot (isolate RNA and run agarose gel, transfer RNA to filter and incubate with a radioactive probe)

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10
Q

DNA code is degenerate, meaning:

A

there are multiple codons that code for the same amino acid

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11
Q

the last nucleotide position in a codon is known as:

A

the wobble position, SNP’s at the location may or may not cause mutation

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12
Q

what effect does SNPs have in coding regions

A

synonymous/silent mutation, conservative missense mutation (chemically similar amino acid produced), nonconservative missense mutation (chemically dissimilar amino acid produced), nonsense mutation (early chain termination)

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13
Q

how can you detect effect of SNP on protein expression?

A

use Western Blot (isolate proteins and run on a POLYACRYLAMIDE gel, transfer proteins to a filter and incubate with a radioactive probe-antibody)

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14
Q

what effect does SSLPs have in coding regions

A

frameshift mutation (base insertion or base deletion) - this can be detected by Western Blots)

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15
Q

eukaryotes genes are made up of two regions:

A

introns (non-coding junk DNA) and exons (coding region)

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16
Q

post-transcriptional modification removes:

A

all introns before proceeding to translation (done by splicing/spliceosome)

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17
Q

how do spliceosome recognize introns?

A

5’ GU-AG 3’ rule

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18
Q

what effect does SNPs in introns have?

A

can cause frameshift by removing or creating GU/AG sites, results in improper removal of introns which can change phenotype of protein produced

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19
Q

what effect does SSLPs in introns have?

A

could result in changes to splice sites by destroying site, creating new sites, or moving the original site

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20
Q

how can you detect SNPs and SSLPs in introns?

A

Nothern Blot (mRNA changes) and Western blot (detect protein expression)

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21
Q

what mechanisms do cells need for gene regulation?

A

1) able to recognize environmental conditions in which they should activate or repress the transcription of relevant genes
2) able to turn on or off the transcription of each specific gene or group of genes

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22
Q

promoter

A

DNA segment that interacts with RNA polymerase to determine where transcription begins

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23
Q

activator/repressor

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A

DNA segments near the promoter that serve as binding sites for sequence-specific regulatory proteins by controlling accessibility to RNA polymerase

24
Q

operator

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A

binding site for repressors

25
positive regulation
presence of bound protein is required for transcription
26
negative regulation
absence of bound repressor allows transcription to begin
27
DNA binding is effected through the interaction of two different sites in the protein:
1. DNA binding domain (can be functional or nonfunctional) and is determined by.... 2. allosteric site which interacts with allosteric effects that bind to the allosteric site of the regulatory protein in such a way as to change its activity
28
metabolism of lactose requires two enzymes:
structural genes: 1. permease (Z) - transports lactose into the cell 2. B-galactosidase (Y) - cleaves molecule to yield glucose and galactose
29
coordinately controlled
genes whose transcription is controlled by a common means
30
what are the regulatory components for the lac regulatory circuit?
1) gene for Lac repressor (I) - blocks expression of Z Y A 2) lac promoter site (P) - site where RNA polymerase binds to initiate transcription of structural genes 3) lac operator site (O) - site on DNA to which the Lac repressor binds
31
the lac operon consists of
P O Z Y A
32
operon
a segment of DNA that encodes a multigenic RNA as well as the adjacent common promoter and regulatory region
33
characteristics of Lac repressor
- is not part of operon - has a DNA binding site that recognizes operator sequence - allosteric site binds to either allolactose or analogs - binds tightly only on O site of DNA on genes it controls
34
allosteric transition
change in shape of repressor protein when allolactose or its analogs bind to it (no longer has binding affinity)
35
induction
the relief of repression for system
36
inducers
allosterically inactivate the repressor
37
enzyme induction
the appearance of a specific enzyme only in the presence of its substrates
38
constitutive mutations
cause the lac operon structural genes to be expressed regardless of whether inducers were present
39
Oc mutations
repressor cannot bind to operator, always "on," only affects the chromosome it is on "cis-acting"
40
operator only influences:
expression of structural genes linked to it, cis-acting
41
I- mutations
dominant to I+, I+ are trans-acting-can regulate all structural lac operon genes (on same or different DNA molecules, constitutive mutation
42
supperrepressor Is mutations cause:
repression to persiste even in the presence of an inducer (dominant over I+) -alters the allosteric site so that it can no longer bind to an inducer
43
promoter mutations are:
cis-acting, affects transcription of all adjacent structural genes in the operon
44
what are the conditions that must be met for lactose metabolic enzymes to be expressed?
1) Lactose must be present in the environment | 2) glucose cannot be present in the cell's environment
45
catabolite repression
presence of a breakdown product (glucose/catabolite) that represses the system by activator proteins
46
in the presence of high concentrations of glucose...
low concentrations of cAMP
47
in the presence of low concentrations of glucose...
high concentrations of cAMP
48
cAMP
cyclic adenosine monophosphate
49
for activation of lac operon, high concentrations of ......
cAMP are necessary
50
CAP
catabolite activator protein
51
how does CAP-cAMP system work?
cAMP is an allosteric effector that binds to CAP and activates the lac operon, the system binds to DNA promoter and interacts with RNA polymerase to increase enzyme affinity for the lac promoter
52
what do repressor and activator binding sites have in common?
the sequences display rotational symmetry
53
negative control
signal that results in blockage of normal expression | ex. inducer-repressor control of the lac operon
54
positive control
signal that activates the system | ex. CAP-cAMP system
55
the lac operon is:
a cluster of structural genes that specify enzymes taking part in lactose metabolism
56
lac operon genes are controlled by:
the coordinated actions of cis-acting promoter and operator regions
57
the activity of promoter and operator regions is determined by:
repressor and activator molecules specified by separate regulator genes

Biology 311 (6 decks)

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