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KCUMB Molecular Biology > EXAM I Zaidi > Flashcards

EXAM I Zaidi Flashcards

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1
Q

Function of mRNA and miRNA

A

mRNA - RNA molecules copied from genes that direct protein synthesis

Code for proteins

miRNA - MicroRNAs; regulate gene expression by blocking translation of selective mRNA causing their degradation

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2
Q

Function of rRNA and tRNA

A

rRNA - form the core of ribosome and catalyze protein synthesis

tRNA - adaptors that select and hold aa during protein synthesis

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3
Q

Function of snRNA, snoRNA, siRNA

A

snRNA - small nuclear; splice pre-mRNA to form mRNA

snoRNA - small nucleolar; process and chemically modify rRNAs

siRNA - small interfering RNA; regulate eukaryotic gene expression by degrading select mRNA

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4
Q

Function of RNA polymerase; name the ones used for prok and euk transcription

A

Catalyzes the formation of phosphodiester bonds

RNA synthesis has lower fidelity than DNA synthesis due to the mistakes not being transmitted to progeny (RNA is a transient copy)

Prokaryotes - RNA Polymerase

Eukaryotes - RNA Polymerase II (Euks require 3 polymerases)

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5
Q

List the basic steps of transcription

A

Initiation

Elongation

Termination

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6
Q

Describe initiation of transcription in prokaryotes

A

(main regulatory step)

RNA pol slides until locates a promoter

sigma subunit binds to promoter = open promoter complex

Short DNA strand is unwound into a transcription bubble

Rxn is driven forward via the hydrolysis of the nt triphosphates (ATP, CTP, UTP, GTP)

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7
Q

Transcription promoters in proks

Transcription promoters in euks

A

5’ upstream of start site = -35 sequence (TTGACA), -10 sequence (TATAAT)

Euks = TATA box (or CAAT box, GC Box)

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8
Q

Elongation of Prok Transcription; what enzyme releives tension? What causes termination? What is the termination signal?

A

RNA pol & promoter separate, sigma factor dissociates

DNA gyrase releives superhelical tension

GC then AC rich region = hairpin loop with poly(U) tail at the end

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9
Q

Describe initiation of transcription in eukaryotes, what complex is formed; what initiates elongation?

A

TFIID binds to TATA box via the TATA-box binding protein (TBP)

The formation of the transcription initiation complex (TFIIB, TFIIF, RNA Pol II, TFIIE, TFIIH)

DNA is unwound exposing template strand

Elongation initiated with polymerase leaves promoter by CTD phosphorylation by TFIIH

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10
Q

What unique sequence does eukaryote polymerase II contain and what regulates it? What are the general TFs?

A

carboxyl-terminal domain = CTD

Regulated by phosphorylation on Ser residues of the CTD

TFs: TFII - assemble promoter before transcription

positions RNA poly, aids in pulling DNA strands apart, releases RNA rolymerase into elongation mode

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11
Q

Describe transcription elongation in eukaryotes, what prevents the dissociation of RNA pol II? What removes tension?

A

RNA Pol II moves along DNA transcribing RNA along the way

Elongation factors prevent RNA Pol II dissociation

DNA topoisomerase removes tension

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12
Q

What additional proteins are required during euk transcription which allow for initiation to occur due to it being highly compacted?

A
  1. Transcriptional activator - help attract RNA Pol II to transcription initiation start site
  2. Mediator - allows activator proteins to communicate w/ RNA Pol II and general TFs
  3. Chromatin modifying enzymes - provide greater access to DNA with the help of chromatin remodeling complexes and histone modifying enzyme
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13
Q

List the 3 Post-transcriptional modifications in eukaryotes

A
  1. ​5’ RNA cap (7-methyl guanosine) - stabilizes & protects mRNA 5’ from phosphatases & nucleases
  2. RNA splicing - intron removal - exons exit with final mRNA (DO NOT OCCUR IN BACTERIA!!!)
  3. Polyadenylation at 3’ end - poly A tail - important proteins Cleavage & Polyadenylation Specificity Factor (CPSF; binds poly A tail), Cleavage Stimulation Factor (CstF; binds GU rich element) RNA is cleaved & RNA polymerase adds 200 nts where the Poly A binding proteins can assemble
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14
Q

Define the adaptor hypothesis of tRNA

A

The genetic code is read by molecules that can recognize a codon and carry the corresponding amino acid

tRNA is an adaptor that binds to specific codons and brings with it an aa for incorporation into the polypeptide chain

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15
Q

List the 2 important structures of tRNA

A

Anticodon loop - pairs with complementary codon in an mRNA molecule

3’ CCA terminal region - binds the aa that matches the corresponding codon

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16
Q

Function of aminoacyl-tRNA synthetase

What allows it to be accurate?

A

Catalyzes the attachment of the correct aa to the corresponding tRNA to the 3’ terminal ribose residue forming the activated aminoacyl-tRNA driven by ATP hydrolysis

Hydrolytic editing - accurate tRNA charging

17
Q

Which direction is protein synthesized in?

A

N-terminal to C-terminal

18
Q

What 4 steps occur during elongation during translation?

A

tRNA binding

peptide bond formation

large subunit translocation

small subunit translocation

19
Q

What must occur for initiation during translation?

A

initiator tRNA carries AUG = Met (methionine)

Initiator tRNA-met complex is loaded onto the small ribosome P site along with other euk initiation factors (eIFs) = eiF4E and eIF4G

Small subunit scans until AUG is reached

Small + Large subunit join = addition of aminoacyl tRNA

20
Q

What elongation factors are involved during translation in eukaryotes & bacteria?

A

EF-Tu, EF-G = bacteria; EF-TU binds GTP and aminoacyl tRNA which monitors interaction b/w anticodon and aminoacyl tRNA & codon of mRNA = Proofreading

EF1, EF2 = eukaryotes

21
Q

What recognizes the stop codon during translation? Where do they bind?

A

Release Factors (RFs)

Bind to A site, catalyzes the addition of water, freeing the carboxyl group from tRNA

22
Q

List the 3 major forms of transport in cells; which organelles are involved in each?

A

Gated - nucleus + cytosol

Transmembrane - from cytosol across an organelle membrane

Vesicular - membrane-enclosed transport intermediates

23
Q

Features of nuclear transport; through which structure do these proteins move through to exit and enter the nucleus?

What is the nuclear localization signal for import into nucleus? What recognizes these signals?

What is the signal for mitochondrial translocation?

ER Signal sequence?

A

Gated, bidirectional, selective

Used for proteins that are needed in the nucleus (histones, DNA, RNA polymerase, topoisomerase, TFs, etc.)

Proteins moving into cytosol = tRNA, mRNA

Nuclear Pore Complexes (NPCs) - fibrils facilitate transport with their FG rich binding site for the import receptors

NLS = (+) lysine and arginine via nuclear import receptors

Mitochondrial contain (+) charged residues on one end and hydrophobic on other end

ER - vary in aa sequence, non-polar aa w/ guided by SRP & SRP receptor

24
Q

What 3 mechanisms involve the controlling of protein transport?

A

Phosphorylation

Proteolysis

Binding to Inhibitory Proteins

25
Q

Where are functions TIM 22 and TIM 23 in mitochondria translocation?

SAM and OXA?

A

TIM 22 - soluble protein —> matrix and helps insert membrane proteins in inner membrane

TIM 23 - subclass entrance into mito (i.e. ATP, ADP, Pi)

SAM - inserts/folds beta-barrel proteins in OM

OXA - protein insertion synthesized in mito

26
Q

How are unfolded proteins maintained during mitochondria translocation?

What cleaves the signal sequence once inserted?

A

Hsp 70

Cleaved via peptidase

27
Q

ER Signal sequence

ER Signal Recognition Particle (SRP)

A

Signal Sequence: Vary in aa; non-polar aa, large hydrophobic pocket

SRP

28
Q

What are the 3 vesicular transport systems? BER

A

Biosynthetic pathway

Endocytic pathway

Retrieval pathway

29
Q

What are the two functions of the vesicular coats? What are 3 types of coats?

A

Concentrates select proteins

Molds the vesicle

Coats are usually discarded before vesicle fuses w/ target membrane

COPI, COPII - ER & Golgi transport (COPII FROM ER EXITS SITES)

Clathrin-coated - Golgi & Plasma membrane transport

30
Q

Role of PI (phosphoinositides) in vesicular trafficking?

A

Undergo rapid cycles of phosph and dephos at 3’,4’,5’ positions

Interconversion = controls recruitment and binding of proteins to specific organelles/domains and regulate vesicle trafficking

31
Q

How does the clathrin coat remove from the vesicle? What protein is involved?

A

Dynamin assembles ring with a PIP2 binding domain and GTPase domain

Pinching

Distortion of lipid bilayer

Hsp70 peels off coat

32
Q

Function of Rab and SNARE in vesicle targeting?

A

Rab - direct vesicle to specific spots on target membrane

Involved in specificity; Rab-GDP = inactive, soluble; Rab-GEFs = active GTP; tightly bound to membrane

SNARE - mediates fusion of vesicle with membrane

33
Q

Rab1

Rab2

Rab3A

A

1 = ER and Golgi

2 = cis golgi

3 = synaptic and secretory vesicles

34
Q
A

KCUMB Molecular Biology (6 decks)

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