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Biochem 2 > Lectures 1-4 > Flashcards

Lectures 1-4 Flashcards

1
Q

what is the name of receptor that epinephrine binds to?

A

beta-adrenergic receptor

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2
Q

how does adenyl cyclase catalyze formation of cAMP?
What is the reversion reaction catalyzed by?

A

ATP –> cAMP
- catalyzed by cyclic nucleotide phosphodiesterase

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3
Q

what signals through GPCR? (4)

A
  • hormone receptors
  • vision
  • gustation
  • olfaction
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4
Q

What is needed (2) for GPCR self-inactivation?

A
  • GTPase
  • GAP (GTPase activator protein)
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5
Q

what allows localization/nucleation of GPCR?

A

A Kinase Anchoring Protein (AKAP) –> a modulator protein

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6
Q

What does G_12/13 alpha regulate?

A

regulates actin cytoskeleton

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7
Q

What is adenyl cyclase?

A

an effector enzyme!

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8
Q

For inactive tyrosine kinase, what blocks the substrate binding site?

A

activation loop

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9
Q

What is Grb2? what type of protein?

A

growth factor receptor bound protein –> adaptor protein

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10
Q

which residues are phosphorylated for IRS1, MEK and ERK?

A

IRS-1: Tyr residues
MEK: Ser residues
ERK: Thr and Tyr residues

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11
Q

what converts PIP3 to PIP2?

A

PIP3 specific phosphatase (PTEN)

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12
Q

what do excitable cells control? (4)

A
  • muscle and nerve contraction
  • memory
  • learning
  • hormone secretion
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13
Q

ion channels are gated by (2)

A
  • ligands OR
  • changes in membrane potential/concentration
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14
Q

which neurotransmitter receptors are cation channels? (3) vs anion channels?

A

Cation:
- acetylcholine
- serotonin
- glutamate

Anion:
- glycine

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15
Q

toxins on ion channels:
- dendrotoxin (from which animal) –> blocks what?
- tetrodotoxin (from which animal) –> acts on what?
- cobrotoxin acts on what?

A
  • black mamba snake –> potassium channels
  • tetrodotoxin from puffer fish –> sodium channels
  • act on acetylcholine receptor ion channels
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16
Q

which 3 hormones (+1) act through nuclear receptors? Why?

A

steroid, thyroid and retinoid hormones + vitamin D
- bc too hydrophobic to dissolve in blood

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17
Q

what is specific regulatory regions in DNA adjacent to specific genes called?

A

Hormone Response Elements (HRE)

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18
Q

4 major types of biological lipids categories (+ 4 others)

A
  • glycerophospholipids
  • sphingolipids
  • steroid lipids
  • prenol lipids
    + fatty acids, glycerolipids, saccharolipids, polyketides
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19
Q

glycerophospholipids are precursors of ?

A

inositol-phosphates

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20
Q

what stimulates glycogen breakdown?

A

IP3

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21
Q

eicosanoids act as __________

A

paracrine factors

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22
Q

eicosanoids derived from (2) –> one of the 2 released from ? by hydrolyzing its ___________

A
  • arachidonate and eicosapentaenoic acid
  • arachidonate released from glycerophospholipids by hydrolying its ester bond (phospholipase A2)
23
Q

what does prostaglandin regulate (5)?

A
  • blood flow
  • body temp
  • sleep wake cycle
  • reproductive cycle
  • responsiveness of certain tissues to hormones
24
Q

lipoxins are potent ______________________?

A

anti-inflammatory agents

25
Which enzymes do NSAIDS inhibit? --> resulting in which eicosanoids that are inhibited?
- cyclooxygenase 1 and 2 (COX 1 and 2) - thromboxane and prostaglandin
26
Which enzyme does prednisone inhibits? --> resulting in which eicosanoid that is inhibited?
- phospholipase A2 - leukotriene
27
Steroids mainly affect _______ ___________ through _________ receptors
- cellular transcription - nuclear receptors
28
- cholecalciferol - 7-dehydrocholesterol - 1a,25 dihydroxycitamin D3 (calcitriol) which becomes what? which is active vs inactive?
7-dehydrocholesterol becomes cholecalciferol (vit D3) through UV light in skin --> inactive - cholecalciferol becomes calcitriol (active) through liver and kidney
29
vit A deficiency leads to (3)
- growth retardation - night blindness - dry skin
30
tretinoin (retin-A) used to treat (2)
- acne - wrinkled skin
31
tocopherols (also _______ lipids) act as __________
- prenol lipids - cofactor
32
which vitamin is a blood clotting cofactor? --> cofactor to ____________ which converts soluble ________ to insoluble ________ = ____________
- vit K - prothromin - soluble fibrinogen - insoluble fibrin - blood clot
33
7 levels of gene regulation (4 + 3 protein...)
- transcription initiation - post transcriptional - RNA stability/processing - post translational - protein transport - protein modification - protein degradation
34
2 types of genes + fct
- housekeeping genes: required at all times - regulated genes: protein levels rise or fall in response to molecular signals
35
where does DNA polymerase bind to DNA?
promoter
36
regulatory proteins have DNA-binding motifs --> 3 characteristics
- small structure can stably protrude from protein surface (60-90 aa residues) - interactions depend on H-bon donors and acceptors in bases and amino acids - 2 H-bonds btw Gln OR Asn and thymine N6 and N7 of Adenine cannot form with any other base
37
most common amino acids involved in regulatory proteins (5)
- Asparagine (Asn) - Arginine (Arg) - Lysine (Lys) - Glutamine (Gln) - Glutamic acid (Glu)
38
helix-turn-helix domain: - ___ aa with 2 short _________ separated by _________ - 1 __________ acts as ________ _________-
- 20 - 2 short alpha helices - beta turn - 1 alpha helix acts as recognition helix
39
Zinc finger - ____ aa - loops cross-linked with _____ --> function? - DNA binding is stronger or weaker? --> results?
- 30 aa - zinc --> stabilizes structure of motif - weaker --> proteins might have more than 1 zinc fingers
40
Leucine zipper: - 2 different region functions? - ______ w/_____ occurs at every ____th position
- DNA binding region + zipper region (for protein-prot interaction domain) - alpha helix with Leucine every 7th position
41
which enzymes remodel chromatin to form eurochromatin? (2)
SW1 and SNF
42
chromatin remodeling depends on (3)
- position of nucleosomes - presence of histone variants - covalent modifications of nucleosomes
43
5 covalent modification of nucleosomes
- acetylation - methylation - phosphorylation - ubiquination - sumoylation
44
histone acetylation regulated by (2)
- histone acetyl transferase (HATs) - histone deacetylase (HDACs)
45
2 activation regulatory proteins that help in assembly of pre-initiation complex
- High mobility group (HMG) --> allows DNA looping so protein complexes can interact directly - Upstream activator sequence (UAS) --> enhancer
46
hormone response elements recognized by what? which are what? - each consensus has __ ___ nt sequences
- transcription factors --> steroid/nuclear receptors - 2 six nt sq
47
Steroid hormone receptor has (3)
- binding site for hormone (always at carboxyl terminus) - DNA-binding domain (2 zinc fingers) - region that activates transcription of regulated genes
48
hormone receptor complex binds to DNA as a _______ w/ _______ ________ domains of each monomer that recognize 1 of ___ nt sequence
- a dimer - with zinc finger - 1 of 6 nt sequences
49
similarities/differences between RNA metabolism in bacteria and eukaryotes
(eukaryotes: assembly step of pre-initiation complex) 1. RNA pol binds to DNA and forms transcription bubble (with unwinding steps (E: helicase activity), conformational change) 2. change in conformation to go from initiation form to elongation form (E: phosphorylation of CTD VS B: sigma70 replaced by NusA ish (this is more during elongation for bacteria)) --> promoter clearance 3. elongation until its finished --> dephosphorylation for E and dissociation of NusA for B
50
what is catalytic cleft?
region in kinase that contains ATP and substrate
51
where do translational repressors bind?
to specific 3'UTR region of mRNA - UTR = untranslated region
52
siRNA technology: 1- small temporal RNAs transcribed as ____A_______ with internal complementary sequences forming _____________ structures 2- ____A______ are cleaved by ________ forming _____ _______ ____ (__-__ nt) 3- one strand of processed miRNA is transferred to _______ _______ --> results in (2)
A = precursor RNAs - hairpin-like structures - cleaved by dicers forming short duplex RNA (20-25 nt) - target mRNA - results in inhibition of translation OR degradation of mRNA
53
what is RNA interference?
introduction of duplex RNA molecule corresponding to sequence to virtually any mRNA - dicer cleaves duplex into short segments (siRNA) --> these bind to mRNA --> results in inhibition of translation OR degradation of mRNA

Biochem 2 (8 decks)

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