Lectures 1-4 Flashcards
what is the name of receptor that epinephrine binds to?
beta-adrenergic receptor
how does adenyl cyclase catalyze formation of cAMP?
What is the reversion reaction catalyzed by?
ATP –> cAMP
- catalyzed by cyclic nucleotide phosphodiesterase
what signals through GPCR? (4)
- hormone receptors
- vision
- gustation
- olfaction
What is needed (2) for GPCR self-inactivation?
- GTPase
- GAP (GTPase activator protein)
what allows localization/nucleation of GPCR?
A Kinase Anchoring Protein (AKAP) –> a modulator protein
What does G_12/13 alpha regulate?
regulates actin cytoskeleton
What is adenyl cyclase?
an effector enzyme!
For inactive tyrosine kinase, what blocks the substrate binding site?
activation loop
What is Grb2? what type of protein?
growth factor receptor bound protein –> adaptor protein
which residues are phosphorylated for IRS1, MEK and ERK?
IRS-1: Tyr residues
MEK: Ser residues
ERK: Thr and Tyr residues
what converts PIP3 to PIP2?
PIP3 specific phosphatase (PTEN)
what do excitable cells control? (4)
- muscle and nerve contraction
- memory
- learning
- hormone secretion
ion channels are gated by (2)
- ligands OR
- changes in membrane potential/concentration
which neurotransmitter receptors are cation channels? (3) vs anion channels?
Cation:
- acetylcholine
- serotonin
- glutamate
Anion:
- glycine
toxins on ion channels:
- dendrotoxin (from which animal) –> blocks what?
- tetrodotoxin (from which animal) –> acts on what?
- cobrotoxin acts on what?
- black mamba snake –> potassium channels
- tetrodotoxin from puffer fish –> sodium channels
- act on acetylcholine receptor ion channels
which 3 hormones (+1) act through nuclear receptors? Why?
steroid, thyroid and retinoid hormones + vitamin D
- bc too hydrophobic to dissolve in blood
what is specific regulatory regions in DNA adjacent to specific genes called?
Hormone Response Elements (HRE)
4 major types of biological lipids categories (+ 4 others)
- glycerophospholipids
- sphingolipids
- steroid lipids
- prenol lipids
+ fatty acids, glycerolipids, saccharolipids, polyketides
glycerophospholipids are precursors of ?
inositol-phosphates
what stimulates glycogen breakdown?
IP3
eicosanoids act as __________
paracrine factors
eicosanoids derived from (2) –> one of the 2 released from ? by hydrolyzing its ___________
- arachidonate and eicosapentaenoic acid
- arachidonate released from glycerophospholipids by hydrolying its ester bond (phospholipase A2)
what does prostaglandin regulate (5)?
- blood flow
- body temp
- sleep wake cycle
- reproductive cycle
- responsiveness of certain tissues to hormones
lipoxins are potent ______________________?
anti-inflammatory agents
Which enzymes do NSAIDS inhibit? –> resulting in which eicosanoids that are inhibited?
- cyclooxygenase 1 and 2 (COX 1 and 2)
- thromboxane and prostaglandin
Which enzyme does prednisone inhibits? –> resulting in which eicosanoid that is inhibited?
- phospholipase A2
- leukotriene
Steroids mainly affect _______ ___________ through _________ receptors
- cellular transcription
- nuclear receptors
- 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
vit A deficiency leads to (3)
- growth retardation
- night blindness
- dry skin
tretinoin (retin-A) used to treat (2)
- acne
- wrinkled skin
tocopherols (also _______ lipids) act as __________
- prenol lipids
- cofactor
which vitamin is a blood clotting cofactor? –> cofactor to ____________ which converts soluble ________ to insoluble ________ = ____________
- vit K
- prothromin
- soluble fibrinogen
- insoluble fibrin
- blood clot
7 levels of gene regulation (4 + 3 protein…)
- transcription initiation
- post transcriptional
- RNA stability/processing
- post translational
- protein transport
- protein modification
- protein degradation
2 types of genes + fct
- housekeeping genes: required at all times
- regulated genes: protein levels rise or fall in response to molecular signals
where does DNA polymerase bind to DNA?
promoter
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
most common amino acids involved in regulatory proteins (5)
- Asparagine (Asn)
- Arginine (Arg)
- Lysine (Lys)
- Glutamine (Gln)
- Glutamic acid (Glu)
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
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
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
which enzymes remodel chromatin to form eurochromatin? (2)
SW1 and SNF
chromatin remodeling depends on (3)
- position of nucleosomes
- presence of histone variants
- covalent modifications of nucleosomes
5 covalent modification of nucleosomes
- acetylation
- methylation
- phosphorylation
- ubiquination
- sumoylation
histone acetylation regulated by (2)
- histone acetyl transferase (HATs)
- histone deacetylase (HDACs)
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
hormone response elements recognized by what? which are what?
- each consensus has __ ___ nt sequences
- transcription factors –> steroid/nuclear receptors
- 2 six nt sq
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
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
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
what is catalytic cleft?
region in kinase that contains ATP and substrate
where do translational repressors bind?
to specific 3’UTR region of mRNA
- UTR = untranslated region
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
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
