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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
Q

Which enzymes do NSAIDS inhibit? –> resulting in which eicosanoids that are inhibited?

A
  • cyclooxygenase 1 and 2 (COX 1 and 2)
  • thromboxane and prostaglandin
26
Q

Which enzyme does prednisone inhibits? –> resulting in which eicosanoid that is inhibited?

A
  • phospholipase A2
  • leukotriene
27
Q

Steroids mainly affect _______ ___________ through _________ receptors

A
  • cellular transcription
  • nuclear receptors
28
Q
  • cholecalciferol
  • 7-dehydrocholesterol
  • 1a,25 dihydroxycitamin D3 (calcitriol)
    which becomes what? which is active vs inactive?
A

7-dehydrocholesterol becomes cholecalciferol (vit D3) through UV light in skin –> inactive
- cholecalciferol becomes calcitriol (active) through liver and kidney

29
Q

vit A deficiency leads to (3)

A
  • growth retardation
  • night blindness
  • dry skin
30
Q

tretinoin (retin-A) used to treat (2)

A
  • acne
  • wrinkled skin
31
Q

tocopherols (also _______ lipids) act as __________

A
  • prenol lipids
  • cofactor
32
Q

which vitamin is a blood clotting cofactor? –> cofactor to ____________ which converts soluble ________ to insoluble ________ = ____________

A
  • vit K
  • prothromin
  • soluble fibrinogen
  • insoluble fibrin
  • blood clot
33
Q

7 levels of gene regulation (4 + 3 protein…)

A
  • transcription initiation
  • post transcriptional
  • RNA stability/processing
  • post translational
  • protein transport
  • protein modification
  • protein degradation
34
Q

2 types of genes + fct

A
  • housekeeping genes: required at all times
  • regulated genes: protein levels rise or fall in response to molecular signals
35
Q

where does DNA polymerase bind to DNA?

A

promoter

36
Q

regulatory proteins have DNA-binding motifs –> 3 characteristics

A
  • 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
Q

most common amino acids involved in regulatory proteins (5)

A
  • Asparagine (Asn)
  • Arginine (Arg)
  • Lysine (Lys)
  • Glutamine (Gln)
  • Glutamic acid (Glu)
38
Q

helix-turn-helix domain:
- ___ aa with 2 short _________ separated by _________
- 1 __________ acts as ________ _________-

A
  • 20
  • 2 short alpha helices
  • beta turn
  • 1 alpha helix acts as recognition helix
39
Q

Zinc finger
- ____ aa
- loops cross-linked with _____ –> function?
- DNA binding is stronger or weaker? –> results?

A
  • 30 aa
  • zinc –> stabilizes structure of motif
  • weaker –> proteins might have more than 1 zinc fingers
40
Q

Leucine zipper:
- 2 different region functions?
- ______ w/_____ occurs at every ____th position

A
  • DNA binding region + zipper region (for protein-prot interaction domain)
  • alpha helix with Leucine every 7th position
41
Q

which enzymes remodel chromatin to form eurochromatin? (2)

A

SW1 and SNF

42
Q

chromatin remodeling depends on (3)

A
  • position of nucleosomes
  • presence of histone variants
  • covalent modifications of nucleosomes
43
Q

5 covalent modification of nucleosomes

A
  • acetylation
  • methylation
  • phosphorylation
  • ubiquination
  • sumoylation
44
Q

histone acetylation regulated by (2)

A
  • histone acetyl transferase (HATs)
  • histone deacetylase (HDACs)
45
Q

2 activation regulatory proteins that help in assembly of pre-initiation complex

A
  • High mobility group (HMG) –> allows DNA looping so protein complexes can interact directly
  • Upstream activator sequence (UAS) –> enhancer
46
Q

hormone response elements recognized by what? which are what?
- each consensus has __ ___ nt sequences

A
  • transcription factors –> steroid/nuclear receptors
  • 2 six nt sq
47
Q

Steroid hormone receptor has (3)

A
  • binding site for hormone (always at carboxyl terminus)
  • DNA-binding domain (2 zinc fingers)
  • region that activates transcription of regulated genes
48
Q

hormone receptor complex binds to DNA as a _______ w/ _______ ________ domains of each monomer that recognize 1 of ___ nt sequence

A
  • a dimer
  • with zinc finger
  • 1 of 6 nt sequences
49
Q

similarities/differences between RNA metabolism in bacteria and eukaryotes

A

(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
Q

what is catalytic cleft?

A

region in kinase that contains ATP and substrate

51
Q

where do translational repressors bind?

A

to specific 3’UTR region of mRNA
- UTR = untranslated region

52
Q

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

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
Q

what is RNA interference?

A

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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