Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochem 2 > Lectures 5-8 > Flashcards

Lectures 5-8 Flashcards

1
Q

RNA = only macromolecule that acts as both information/genetic ___________ and ____________

A
  • transmitter
  • catalyst
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what is a transcriptome?

A

sum of all RNA molecules produced in cell under given conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Purpose of microRNA?

A

bind to specific nucleotide sequences to regulate expression of genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

RNA polymerase requires (3)

A
  • DNA template
  • all 4 ribonucleosides triphosphates
  • Mg2+
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

movement of transcription bubble requires ? of nucleic acid molecules

A

strand rotation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

5 RNA polymerase core subunits in bacteria + extra subnit! + functions

A
  • 2 x alpha –> assembly and building of upstream promoter elements
  • beta –> main catalytic subunit
  • beta prime –> responsible for DNA binding
  • omega –> appears to protect polymerase from denaturation
  • sigma –> directs enzyme to promoter
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Typical Pol II promoter (eukaryotes) have 2 sequences in common

A
  • initiator sequence at +1
  • TATA box consensus sequence at -30
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

which RNA pol (1, 2 or 3) synthesize mRNA, tRNA and rRNA (+ specialized RNA)

A
  • Pol 1 –> rRNA
  • Pol 2 –> mRNA + specialized RNA
  • Pol 3 –> tRNA + 5sRNA + specialized RNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

major difference between bacteria and eukaryote RNA Polymerase –> what is it?

A

eykaryote Pol has carboxyl terminal domain!
- CTD = many repeats of consensus heptad aa sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

functions of
- Pol II
- TBP
- TFIIA
- TFIIB
- TFIID6
- TFIIE
- TFIIF
- TFIIH

A
  • Pol II: catalyze RNA synthesis
  • TBP: recognizes TATA box
  • TFIIA: stabilize binding of TBP and TFIIB to promoter
  • TFIIB: Binds to TBP + recruits Pol II-TFIIF complex
  • TFIID6: required for initiator at promoters lacking TATA box
  • TFIIE: recruits TFIIH + ATPase and helicase activity
  • TFIIF: binds to Pol II + binds to TFIIB to prevent binding of Pol II to nonspecific DNA sequence
  • TFIIH: unwinds DNA at promoter + phosphorylates Pol II (within CTD)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

5’ cap = residue of ________ linked to __ terminal residue of mRNA through unusual __,__-triphosphate linkage
- occurs at __-__ bp

A
  • 7-methyguanine
  • 5’
  • 5’-5’ linkage
  • 20-30 bp
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

3 functions of 5’ cap

A
  • protect mRNA from degradation by ribonucleases
  • binds to specific cap-binding complexes of proteins
  • participates in binding of mRNA to ribosome to initiate translation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

poly(A) tail = string of ____________ residues added to __-end of most eukaryotic mRNAs

A
  • adenosine residues
  • 3’end
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

2 functions of poly(A) tail

A
  • serves as binding site for specific proteins
  • may help protect mRNA from enzymatic destruction/degradation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How is poly(A) tail added to RNA?
- both proteins are tethered to ?

A

1) endonuclease cleaves RNA at a point 10-30 nt 3’ downstream of sequence (5’)AAUAAA(3’)
2) synthesis of poly(A) tail by polyadenylate polymerase (80-250 nt of A) beginning at cleavage site
- Carboxyl terminal domain! poly(A) tail is also tethered to the CTD!

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Pol II synthesizes RNA before or after site of cleavage/(5’)AAUAAA(3’) ?

A

after!

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

4 classes of introns? require ATP?

A
  • group 1 and 2 –> self-splicing = no ATP and no enzymes
  • spliceosome introns –> removed by large ribonucleoproein called spliceosome
  • group 4 –> protein catalyzed introns are removed by enzymes
    *spliceosome and group 4 require ATP!
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

RNA splicing for group 1 introns (usually in _________ genes): what part of what molecules attacks what?

A
  • 3’OH of free guanosine group attacks phosphodiester bond between U and A or exon-intro junction
  • 3’OH forms bond with 5’ of intron
  • 3’OH of exon acts as nucleophile on 3’ end of intron to rejoin pieces
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what are snRNP?
- found where?
- act as?

A

small nuclear ribonucleoproteins
- make up spliceosome
- act as catalysts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what marks start/end of splicing? for spliceosome splicing

A

GU at 5’ end of intro + AG at 3’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Membranes define _________ of cells/organelles + control __________

A
  • boundaries
  • traffic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

membranes are permeable to (2) + impermeable to (2)

A
  • permeable to small polar solutes + non polar compounds
  • impermeable to large polar solutes and ions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what is almost all the mass of biological membranes?

A

polar lipids and proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

most membrane lipids are synthesized in ? –> what carries them to destination?

A
  • endoplasmic reticulum
  • vesicles
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

what is the fluid mosaic model (2)

A
  • proteins and lipids move laterally in plane of membrane = fluid
  • contains different components like proteins, lipids and carbs = mosaic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what are the 3 components of the fluid mosaic model + functions
- membrane also enriched with (2) but no ?

A
  • phospholipids: form bilayer
  • proteins –> embedded/float in bilayer –> hydrophobic domains interact with fatty acyl chains
  • carbs attached to proteins and lipids on extracellular surface of PM
  • enriched with cholesterol and sphingolipids but no cardiolipin
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

is there the same distribution of lipids in inner and outer leaflet?

A

no! asymmetry

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

which phospholipid normally in inner layer? + which one is critical but in minor amount?

A
  • inner layer: phosphatidylserine
  • phosphatidylinositol = critical but minor amount
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

which organelle’s membrane contains low cholesterol and sphingolipid but most of cell’s cardiolipin and phosphatidylglycerol

A

mitochondria membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

3 types of membrane proteins + functions + how to remove?

A
  • integral: traverse membrane (monotopic or polytopic) –> detergent to remove!
  • peripheral: associate with membrane through electrostatic interactions and H bonds with hydrophilic domains –> change in pH, chelating agents, urea or carbonate to break bond
  • amphitropic: associate reversibly with membrane + interact electrostatically or lipid anchored
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

phospholipids can move depending on (2) –> general shape and dimension maintained but (1) allowed to change

A
  • temperature and lipid composition
  • degree of motion
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Bilayer:
- below normal physiological temp = what state? + description
- above normal temperature = what state? + description

A
  • liquid ordered/gel like –> motion is constrained, bilayer is paracrystalline and firm
  • liquid disordered/liquid like –> constant thermal motion of side chains from heat
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

4 factors that affect flexibility of bilayer?

A
  • temperature
  • saturation of FA chain (increase packing = increase order/gel)
  • length of FA chain (increase length = increase order)
  • presence of sterols: interact with phospholipid’s unsat FA chain = compact VS interact with sphingolipids and phospholipids with long sat FA = fluid
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

can cells regulate FA content of their membranes?

A

yes! ex: increase sat FA at high temp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

2 characteristics of lateral diffusion

A
  • uncatalyzed and very rapid!
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

transbilayer diffusion/flip flop –> catalyzed? speed?

A

if no catalysis, very very slow

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

flippase vs floppase vs scramblase
- Need ATP?

A
  • flippase: outer to inner, requires ATP
  • floppase: inner to outer, requires ATP
  • scramblase: moves lipid down concentration gradient depending on type of lipid –> towards equilibrium + no ATP but activated by Ca2+
38
Q

can proteins move in the bilayer?

A

some membrane proteins are anchored to internal structures (ie spectrin) that prevent free lateral diffusion –> form fences
- usually freely mobile but motion can be restricted

39
Q

what stabilizes and modulates structure of lipid rafts?

A

ceramide!

40
Q

Lipid rafts contain (3)
hint:
- clusters of ? enriched with ?
- specific ? in inner leaflet + ? in outer leaflet
- caves

A
  • clusters of glycospingolipids (long chain sat FA) thicker than other regions in membrane + are enriched with lipid anchored proteins and cholesterol
  • specific doubly or triply anchored acylated proteins in inner leaflet + GPI anchored proteins in outer leaflet
  • caveolae (little caves) –> allow membrane to form vesicle that pinches off
41
Q

are lipid rafts more ordered than usual membrane?

A

yes because are more thick

42
Q

membrane fusion requires 6 things/steps

A
  1. triggering signal
  2. recognition of each other
  3. close apposition
  4. local disruption of bilayer structure (increase in curvature of lipid rafts)
  5. hemi-fusion (of outer leaflet)
  6. fusion proteins to form 1 continuous bilayer
43
Q

6 steps of membrane fusion

A
  1. neurotransmitter filled vesicle approaches plasma membrane
  2. vSNARE (assembles on vesicle membrane) and tSNARE (assembled on target membrane) bind to each other, zipping up from amino termini and drawing the 2 membranes together
    *Q-SNARE/SNAP25 are regulatory proteins that are Ca2+ induced
  3. zipping causes curvature and lateral tension between bilayers, favoring hemifusion between outer layer
  4. hemifusion: outer leaflets of both membranes come into contact
  5. complete fusion crease a fusion pore
  6. pore widens; vesicle contents are released outside cell
    *then, NSF proteins disassemble SNARE complex
44
Q

passive vs active transporter

A

passive = high concentration to low
- active = low to high/against concentration gradient

45
Q

4 types of passive transporters:
- simple diffusion
- facilitated diffusion
- ion channel
- ionophore-mediated ion transport

A
  • simple diffusion: small nonpolar compounds
  • facilitated diffusion: need protein for polar molecules
  • ion channel: may be gated by ion or ligand
  • ionophore-mediated ion transport: small molecules mask charge of ions and allow them to diffuse through bilayer
46
Q

active tranporters:
- primary vs secondary

A
  • primary: energy provided directly by chemical reaction –> driven by ATP
  • secondary: couple uphill transport of 1 substrate with downhill transport of another
47
Q

types of transport system:
- uniport
- cotransport
- symport
- allport

A
  • uniport: molecules move singly one at a time in one direction
  • cotransport: S1 cotransports S2 when it moves across –> symport or allport
  • symport: move than 2 molecules move together in same direction
  • allport: more than 1 molecule move in opposite directions
48
Q

which type of transporter are glucose transporters in erythrocyte?

A

uniport

49
Q

3 steps for glucose transport in erythrocyte

A
  1. T1: glucose binds to transporter
  2. conformational change to T2 –> Glucose is released inside the cell
  3. another conformational change to go back to T1
50
Q

GLUT 1, 2 and 4 –> where and function?

A

GLUT 1: erythrocytes + most tissues at low level –> basal glucose uptake
GLUT 2: liver, pancreatic islets, intestine, kidney –> role in liver and kidney
GLUT 4: muscle, fat, heart –> basal glucose uptake + high turnover number

51
Q

Insulin dependant glucose transport (5 steps ish)

A
  1. glucose transporters are stored in vesicles in cells
  2. when insulin interacts with receptors, vesicles move to surface and fuse with PM (PKB) = increase number of transporter in PM
  3. when decrease insulin, GLUT are removed from PM by endocytosis –> forming small vesicles
  4. smaller vesicles fuse with larger endosome
  5. patches of endosome enriched with GLUT bud off to form small vesicles
52
Q

what type of transport is electroneural transport of anions?

A
  • facilitated passive transport
  • cotransport –> antiport!
53
Q

CO2 = ___________ in blood –> converted to ___________ to affect ____ and allow ________________ of hemoglobin to bind and release ____

A
  • not soluble in blood
  • bicarbonate (HCO3-)
  • pH
  • conformational change
  • O2
54
Q

in erythrocytes of respiring tissues –> what enters and what leaves?
VS in lungs?

A
  • CO2 enters
  • HCO3- leaves as Cl- comes in = chloride bicarbonate exchange in protein
    Lungs:
  • bicarbonate enters as Cl- leaves
  • CO2 leaves
55
Q

Describe 2 steps of active transport (examples with symport/antiport)

A
  1. S1 moves out using ATP (1st active transport)
  2. then, S1 flows back in = provide energy to drive cotransport of S2 to go against gradient
    ex.: symport: (Na+ & glucose) and (Na+ & aa)
    allport: (Na+ & K+ & ATPase) and (Na+ & H+ in kidneys)
56
Q

active transport through P-type ATPase (4 steps)

A
  1. transporter binds 3 Na+ from inside the cell
  2. phosphorylation/use of ATP makes conformational change to P-Enz-II
  3. transporter releases 3 Na+ outside and binds 2 K+ from outside
  4. dephosphorylation leads to Enz I shape –> transporter releases 2 K+ inside
57
Q

Proton transport through F-type ATPase
- F-type role?
- high proton gradient supplies what?

A
  • F-type ATPase uses energy of ATP to pump protons across membrane
  • supplies energy to drive reverse reaction –> ATP synthesis by ATP synthase
58
Q

what type of ATP pump does mitochondria use?

A

F-Type –> energy coupling factors to synthesize ATP

59
Q

what does ABC transporter stand for?

A

ATP binding cassette

60
Q

are ATP transporter active or passive transporters?

A

active! use ATP to go against concentration gradient

61
Q

describe process of ABC transporters

A
  1. substrate binds to transporter + ATP is bound to NGB/NBD sites
  2. conformational change occurs when substrate bind + when ATP hydrolyzed to ADP
  3. substrate diffuses away from transporter
62
Q

most enzyme catalyzed reactions are regulated in order to ?

A

regulate metabolic pathways (that are all interconnected)

63
Q

cells need a _______ __________ of energy –> __________

A

constant supply of energy
- homeostasis

64
Q

what depends on body’s needs/metabolic pathways (2)?

A
  • precursor levels
  • energy requirements
65
Q

cells/organisms maintain a _________ _________ ______ –> what does it mean? ex.:

A
  • dynamic steady state
  • intermediates are formed and consumed at equal rates
  • ex.: rate of glucose entry in cells is regulated
66
Q

when a transient perturbation alters rate of formation/consumption of a metabolite –> what happens?

A

compensating changes in enzyme activities return system to steady state

67
Q

cells regulate their metabolism either by (2)

A
  • changing number of a specific enzyme molecule
  • changing activity of existing molecules
68
Q

6 principles to regulate changing number of a specific molecules (in regulation of enzymes)

A
  1. extracellular signal
  2. transcriptional regulation
  3. mRNA stability
  4. mRNA translation
  5. Protein stability
  6. enzyme localization
69
Q

describe:
1. extracellular signal
2. transcriptional regulation (3)
3. mRNA stability

A
  1. extracellular signal: conformational change –> leads to signaling pathway
  2. transcriptional regulation:
    - activation of transcription factors in signaling pathway
    - TF phosphorylation/dephosphorylation
    - TF interactions with ligand
  3. mRNA stability: resistance to degradation –> rate of synthesis vs degradation
70
Q

describe:
4. mRNA translation
5. Protein stability
6. enzyme localization

A
  1. mRNA translation: rate of translation into proteins
  2. Protein stability: balance between rate of synthesis and degradation
  3. enzyme localization: segregation or sequestration of enzyme = limiting factor
71
Q

4 principles of regulation of enzymes to change the activity of existing molecules

A
  1. changes of levels of substrate
  2. enzyme binding allosteric effectors/ligands
  3. covalent modification (phosphorylation/dephosphorylation)
  4. interaction with regulatory protein that can regulate enzyme’s activity
72
Q

pathways in opposite directions are favored/not favored simultaneously?

A

not favored

73
Q

common regulatory mechanisms at organism level (5)

A
  • pathways in opposite directions are not favored simultaneously
  • maximizes product utilization
  • ability to partition metabolites between alternative pathways
  • draws on fuel/product best suited for the need
  • slows down synthetic pathways when products accumulate = homeostasis
74
Q

various _______ activate or inactivate _________ ________ that act in ________ to regulate ______ _____________

A
  • signals
  • transcription factors
  • nucleus
  • gene expression
75
Q

changes in transcriptome lead to changes in (2)

A

proteome and metabolome of cell

76
Q

in some tRNA, anticodons include a ____________ at __ position –> forms _______ bond with (3 nt) –> creates?

A
  • inosinate (I)
  • 1st position
  • weak H-bonds
  • A, U, C
77
Q

which 2 nt at first position so that the binding is specific/only 1 codon recognized? vs which other. 2nt so binding is less specific/2 different codons may be read

A
  • specific = C and A
  • non specific = U and G
78
Q

what sequence (3 nt) at 3’ end of amino acid arm?

A

CCA

79
Q

what does T(Y)C arm do?

A

interacts with large subunit rRNA

80
Q

5 examples of post-translational modification for proteins

A
  • acetylation of N-terminal residues
  • enzymatic removal of formyl group from 1st residue OR removal of Met/other residues
  • removal of signal sequences/other regions
  • forming disulfite links
  • attaching carbs
81
Q

E1 vs E2 vs E3 for attachment of ubiquitin to target proteins

A
  • E1 = activating enzyme
    E2 = conjugating enzyme
    E3 = ligating enzyme
82
Q

what esterifies aa to corresponding tRNA?

A

aminoacyl tRNA synthetase

83
Q

what are the 2 types of met?

A

Met and fMet

84
Q

A vs P vs E site

A

Aminoacyl site: where aa added to tRNA
Peptide site: aa added to polypeptide chain
Exit site: tRNA released from ribosome

85
Q

release factors replace (2) by (1) resulting in tRNA dissociation

A
  • Ribosome recycle factor (RRF) and EF-G
  • with IF3
86
Q

what serves to define template vs non-template strand?

A

promoter

87
Q

where is TATA box? bacteria vs eukaryotes?

A

bacteria: -10
eukaryotes: -30

88
Q

how many subunits does RNA Pol II has in humans?

A

12!

89
Q

synthesis of 5’ cap carried out by (#) enzymes tethered to the _____ of Pol II –> cap remain tethered through association with ___ ___________ _____________

A
  • 4 enzymes
  • CTD
  • Cap binding complex (CBC)
90
Q

exception: _________ genes don’t have introns

A

histone!

91
Q

U1 and U2 bind to which site? for spliceosome splicing?

A

U1 –> donor site (5’ splice site)
U2 –> branching site

92
Q

ATP required for spliceosome splicing?

A

only for spliceosome assembly

Biochem 2 (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions