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bio 541 > final exam 4 biochem! > Flashcards

final exam 4 biochem! Flashcards

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1
Q

what inhibits insulin and glucagon secretion?

A

somatostatin

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2
Q

alpha cells secrete ________

A

glucagon

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3
Q

beta cells secrete _______

A

insulin

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4
Q

δ-cells secrete ______

A

somatostatin delta

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5
Q

α-cells, β-cells, & δ-cells are found where?

A

in the islets of Langerhans cells in the pancreas (regions of the pancreas that contain it’s endocrine aka hormone cells)

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6
Q

β-cells secrete insulin in response to _________ blood glucose levels

A

increased

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7
Q

what are the four alkylating agents?

A

S-Adenosylmethionine, Dimethylnitrosamine, Dimethylsulfate, nitrogen mustard

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8
Q

what are the three well- understood ribonucleic acids roles in living cells?

A

messenger RNAs (mRNA), transfer RNAs (tRNA), ribosomal RNAs

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9
Q

beta-D-ribofuranose is a pentose in what kind of nucleotide?

A

RNA

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10
Q

beta-2’-deoxy-D-ribofuranose is a pentose in what kind of nucleotide?

A

DNA

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11
Q
A
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12
Q

how are ribonucleic acids synthesized?

A

in cells, using DNA as a template in transcription

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13
Q

most eukaryotic ribonucleic acids are processed after synthesis, this means they go through what?

A

elimination of introns + joining of exons; poly-adenylation of the 3’ end and capping the 5’ end

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14
Q

as transcription E. Coli is being transcribed, the synthesis of the new chain is catalyzed by …? how much does it make?

A

by the enzyme RNA Polymerase, covering ~35 bp long segment of DNA

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15
Q

RNA Polymerase binds to what to begin transcription? does it require a primer?

A

a promoter, it does not require a primer

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16
Q

RNA Pol generates positive supercoils ahead of the DNA strand, what relieves this?

A

topoisomerases

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17
Q

does the transcription bubble form before or after transcription is initiated?

A

before

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18
Q

what are the two types of termination in E. Coli and give a breif description.

A

p- independent: has three U’s on 3’ end of transcript, forms a hairpin 15-20 nt before 3’ end (used to make RNA Pol PAUSE and dissociate aka leave)

p- dependent: less understood, but has a Calcium-rich sequence called a Rut site where the helicase p protein binds to. p protein continues until termination site is reached.

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19
Q

what is RNA Polymerase I known for?

A

synthesizes pre-ribosomal RNA (precursor for 28S, 18S, and 5.8 rRNAs)

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20
Q

what is RNA Polymerase II known for?

A
  • responsible for synthesis of mRNA
  • very fast (500-1000 nuc per sec)
  • specifically inhibited by mushroom toxin
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21
Q

what is RNA Polymerase III known for?

A

makes tRNA and some small RNA products

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22
Q

what is RNA Polymerase IV known for?

A

in plants, responsible for the synthesis of small interfering RNAs (mitochondria have their own RNA Pol for that… RNA Pol III)

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23
Q

when RNA Pol gets to the promoter, it is initiated by what? does the promoter also take part?

A

TATA-binding protein (TBP), yes, it requires the promoter!

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24
Q

what is the most important protein that is part of the multisubunit complex TFIID?

A

TBP - TATA-binding protein

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25
along with the multisubunit complex TFIID, other proteins include...?
TFIIA, TFIIB, TFIIE, TFIIF, TFIIH
26
__________ activity in ___________ unwinds DNA at the promoter
helicase; TFIIH
27
________ activity in __________ phosphorylates the polymerase at the Carboxyl-Terminal Domain changing the conformation and enabling _____________ to transcribe
kinase; TFIIH; RNA Pol II
28
7-methylguanosine acts as what, and does what?
a 5' cap, it links to 5' end via 5,5'-triphosphate link
29
methyl groups derive from S-adenosylmethionine (SAMe), this also does what?
protects RNA from nucleases* & forms a binding site for ribosome
30
spliceosome does what?
removes spliceosome introns
31
in eukaryotes, U1 - U6 are known as what?
the 5 snRNA's
32
what are splicesomomes made of ?
snRNP's - small nuclear RiboNucleoProteins
33
what are the marks that identify the sites of splicing?
GU at 5' end and AG at 3' end
34
what is the first stage of protein synthesis?
activation of amino acids: tRNA is aminoacylated
35
what is the second stage of protein synthesis?
initiation of translation: mRNA and aminoacylated tRNA bind to ribosome
36
what is the third stage of protein synthesis?
elongation: cycles of aminoacyl-tRNA binding and peptide bond formation until a STOP codon is reached
37
what is the fourth stage of protein synthesis?
termination and ribosome recycling: mRNA and protein dissociate, ribosome recycled
38
what is the fifth stage of protein synthesis?
folding and post-translational processing: catalyzed by a variety of enzymes
39
what is the first AA in a peptide?
AUG = Met (eukaryotes) or fMet (prokaryotes)
40
an example of antibiotics that target protein synthesis in bacteria is...
**puromycin (binds to A site of ribosomes, can no longer translocate = dissociate), tetracyclines, chloramphenicol and cycloheximide, streptomycin
41
proteins get targeted via a _________, where then the nuclear envelope can degrade and proteins will need to re-enter nucleus
NLS - Nuclear Localization Sequence
42
nuclear proteins bind what?
alpha, beta, and a GTPase called "Ran"
43
how are proteins linked to ubiquitin in eukaryotes?
by activating enzyme E1, conjugating enzyme E2, and ligating enzyme E3
44
E. Coli's mechanism for degradation is by...?
Lon aka "long form" hydrolyzing defective or short-term peptides
45
what are ubiquitinated proteins cleaved by?
26 proteasome complex
46
when lactose is absent....?
there is no transcription. the repressor stays bound, which means no transcription even when CRP-cAMP bind
47
what gene encodes a repressor called Lac?
Lacl
48
the Lac repressor has its own promoter (P^I), this means what?
transcription of the repressor is independent of transcription of the enzymes that repressor regulates
49
the Lac repressor binds to what three sites?
operator sites, O1-O3
50
Lac repressor binds primarily to what? why?
Operator O1, it is adjacent to promoter and helps prevent RNA Pol from binding to promoter
51
If the repressor binds to a second site, it causes the DNA to do what? how does it affect the process?
the DNA loops between the secondary operator and O1. it reduces transcription, even with its basal rate being as low as it is.
52
when lactose is present.....
transcription depends on glucose levels
53
when lactose is present, transcription depends on glucose level. this means?
the repressor will dissociate, but transcription will only be stimulated significantly if cAMP rises
54
what are the two requirements for strongest induction of the lac operon.
1 lactose needs to be present (reduces repression) 2 glucose must be low = cAMP increases
55
when lactose is LOW, repressor is bound, leading to?
inhibition
56
when lactose is HIGH, repressor dissociates, leading to?
continuous transcription
57
when glucose is LOW, cAMP is HIGH and CRP is bound, leading to?
activation
58
when glucose is HIGH, CRP is not bound, leading to?
dampened transcription
59
which amino acids can form specific H-bonds with Adenine's N-6 and H-7 hydrogens
Glutamine (Gln), and Asparagine (Asn)
60
Arginine can form specific H bonds with?
Cytosine-Guanine base pair
61
what are the most well known motifs
helix-turn-helix (used by lac repressor), zinc finger, leucine zipper
62
what is the pattern recognized in leucine zipper motif?
every seventh residue in helices is Leu
63
role of the attenuator (which is part of the leader)?
determines if transcription will be attenuated at the end of the leader OR if transcription will continue into the genes for Trp synthesis
64
what is the trp operon regulated by?
transcription attenuation
65
where is the attenuator and what does it do?
the attenuator sequence is in the 5' region of a leader sequence and it can make the ribosome stall
66
how to researchers shut down genes artifically? explain.
via RNA interference. any dsRNA that corresponds to an mRNA and is introduced into a cell will be cleaved by Dicer into short segments called small interfering RNAs (siRNAs) that will then bind to the mRNA to silence its translation.
67
what are the RNA's called that are made briefly during development?
small temporal RNAs (stRNA)
68
how do miRNAs silence genes?
by binding to mRNAs - can prevent transcription of the mRNA by cleaving it (via endonuclease Drosha or Dicer) or by blocking it
69
what is the idea of a "Nucleosome Code" or "Histone Code"?
some believe that genomes encode directions for nucleosome organization since nucleosomes seem to occur at specific sequences and covalent modifications seem to occur at specific regions/ sequences
70
the leader region can form different stem-loop structures in its _____ nucleotide long segment
162
71
the leader region has 4 segments total, if segments 2 and 3 base-pair, what happens?
transcription proceeds and the trp synthetic enzymes are made... no attenuation
72
the leader region has 4 segments total, if segments 3 and 4 base-pair, what happens?
they form a hairpin structure that is the attenuation signal
73
the trp operon has a repressor that binds to DNA in the presence of tryptophan. expand.
when trp is abundant, it binds to the trp repressor (homodimer), causing it to bind to operator and slow expression of genes for trp synthesis. has helix-turn-helix motifs that interact with DNA via the major groove
74
chromatin remodeling of transcriptionally active genes involve....
nucleosomes repositioned; histone variants; covalent modifications to nucleosomes
75
methylation of _______ at H3 and ________ at H3 and H4 alters transcription
Lys4 & 36; Arginine (Arg)
76
what 5 proteins are required for RNA Polymerase II
transcription activators (enhancers), architectural regulators to facilitate DNA looping, chromatin modification/ remodeling proteins, coactivators, basal (general) transcription factors
77
what is the second phase of replication?
elongation
78
what are the transitioning steps between Okazaki Fragments?
(1) core subunits of DNA Pol III dissociate from one beta clamp bind to a new one, (2) RNA primer is removed, (3) DNA Polymerase I fills the gap, (4) DNA ligase seals the nick
79
What kind of exonuclease activity does DNA Pol I have?
5' --> 3' IN ADDITION TO THE 3' --> 5' exonuclease activity
80
what is each DNA Polymerases role in E. Coli
DNA Pol I: abundant, has low processivity, primarily for clean-up DNA Pol III: principal replication polymerase DNA Pol II, IV, and V: DNA repair
81
during the second phase of replication, leading strand synthesis consists of what steps?
(1) primase (DNAG) makes RNA primer - the DNAG primase interacts with DNAB helicase, but primase moves in opposite direction of helicase (2) DNA Pol III adds nucleotides - Pol III is linked to DNAB, which is tethered to the opposite DNA strand
82
the first step of beta-cells secreting insulin in response to increasing blood glucose levels is...?
glucose enters beta cells via GLUT2 --> enters glycolysis, ATP increases
83
the second step of beta-cells secreting insulin in response to increasing blood glucose levels is...?
ATP binds to ATP gated K+ channels --> K+ channels close, depolarize the plasma membrane
84
the third step of beta-cells secreting insulin in response to increasing blood glucose levels is...?
depolarized plasma membrane triggers opening of voltage-gated Ca2+ channels --> increased Ca2+ in cytosol triggers release of insulin by exocytosis
85
the endoplasmic reticulum is where what important container forms disulfide bonds?
storage vesicle!
86
glucose regulation of insulin secretion is caused by...
the addition of Ca2+ release from the endoplasmic reticulum on top of the former release into the cytosol. cytosolic Ca2+ is now high enough to trigger insulin release by exocytosis

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