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BSCI330 > BSCI330 Exam 3 > Flashcards

BSCI330 Exam 3 Flashcards

1
Q

what does even skipped mean

A

even segments are skipped if gene is mutated

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2
Q

what are the inhibitory factor regulatory proteins

A

giant and krüpel

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3
Q

what are the activating factor regulatory proteins

A

hunchback and bicoid

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4
Q

how do you get expression with regulatory proteins?

A

if you have (+) AFs binding and (-) AFs not binding

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5
Q

where can transcription be regulated

A

initiation and termination

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6
Q

what does transcriptional attenuation lead to

A

premature termination of RNA transcript

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7
Q

what do barrier sequences do

A

bind to proteins, inhibit heterochromatin spread

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8
Q

what do insulator elements do

A

control ability of an enhancer to regulate gene expression

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9
Q

what are examples of mechanisms for gene expression regulation

A

small non-coding RNAs

PTM to regulate protein function

level of proteins can be regulated by degradation by ubiquitin/proteasome pathway

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10
Q

what is the first level of post-transcriptional regulation

A

alternative splicing

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11
Q

what can alternative splicing do

A

change activity of protein by changing which exons are present in final transcript

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12
Q

what is standard form in post-transcriptional regulation

A

the first identified; everything else are splice variants

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13
Q

what decides where the last exon in the transcript is

A

alternative poly-A sites

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14
Q

what is the difference between secreted and membrane-bound transcription

A

their poly-A sites

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15
Q

when is RNA processing complete

A

have 5’ cap, chosen poly-A site, have poly-A tail, decided which exons are being sliced in/out, have mature mRNA

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16
Q

why will transcript remain in the nucleus

A

if transcript isn’t fully spliced; only full transcripts are exported

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17
Q

how does HIV work

A

interferes with normal regulation of export to allow full-length RNA to be exported as virus

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18
Q

what proteins bind iron in response to iron starvation

A

ferritin and transferrin

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19
Q

when do you want more transferrin

A

if low on iron

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20
Q

when do you want ferritin

A

when high on iron (it blocks translation)

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21
Q

what is transferrin receptor regulated by

A

mRNA stability

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22
Q

what is aconitase

A

an iron-binding protein

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23
Q

what do miRNAs associate with?

A

series of proteins forming RISC

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24
Q

what is RISC

A

RNA-induced silencing complex; degrades mRNA when bound to double-stranded RNA

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25
Q

what are two classes of short RNAs

A

small inhibitory RNAs (siRNAs) - mediate RNA interference

double-stranded RNA (dsRNA) - bind to RISC like miRNA to interfere with translation

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26
Q

what is a pro of post-transcriptional regulation

A

it can respond to environmental stimuli more rapidly than transcriptional regulation

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27
Q

what is the open reading frame in mRNA

A

region between AUG and stop codons (contributes to stability and translation efficiency)

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28
Q

what are riboswitches

A

places in RNA that can adopt two or more alternative 3D structures (differentiated by binding or non-binding of small molecule ligands)

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29
Q

what is an initiation factor of ribosome binding to mRNA

A

eIF2 (GTP-binding protein)

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30
Q

how does eIF2 work

A

uses GTPase motif to mediate binding of initiator met-tRNA to small ribosomal subunit

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31
Q

how does ribosome switch from initiation to elongation with eIF2

A

when GTP is hydrolyzed, eIF2 falls off and ribosome switches

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32
Q

Why does eIF2 need a GEF

A

to exchange GDP for GTP after GTP is hydrolyzed - GEF is eIF2B

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33
Q

what happens when eIF2 is phosphorylated

A

it inactivates protein and shuts down translation

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34
Q

what is important for amino acid starvation response

A

uORFs - anything downstream won’t be translated

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35
Q

what happens when reducing eIF2

A

reduce translation of early uORFs and increase likelihood that ribosome will translation downstream

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36
Q

what is the transcription factor ATF4

A

controls expression of proteins like amino acid transporter and synthesis enzymes - is translated as an amino acid starvation response

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37
Q

how can we have multiple AUGs

A

internal ribosome entry sites (IRES) allow 2 independent protein sequences to be derived from mRNA (one at 5’ cap, one at IRES)

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38
Q

what is regulated degradation

A

way to destroy mis-created proteins, regulated by ubiquitination and lysines to degrade into amino acids

39
Q

what is epigenetic regulation

A

heritable differences that don’t rely on change in RNA nucleotide sequence

40
Q

where does protein synthesis initiate

A

cytosol on ribosomes

41
Q

what are the 3 modes of protein transport

A

gated, transmembrane, cotranslational

42
Q

what is gated transport

A

transport from cytosol into nucleus through nuclear pore complex

43
Q

what is transmembrane transport

A

transport into mitochondria via TOM and TIM complexes

44
Q

what is cotranslational transport

A

imports proteins into ER and pushes them across ER membrane as it’s being translated

45
Q

what is vesicle transport

A

traffic from ER to membrane-enclosed organelles and cell surface or exterior

46
Q

which transports occur between topologically similar compartments

A

vesicle and gated (NOT transmembrane)

47
Q

what is topologically similar

A

similar membrane orientations (same side of membrane)

48
Q

why is nuclear localization signal (NLS) important for gated transport

A

interacts on target protein with nuclear import receptor if going from cytosol to nucleus (in reverse is nuclear export receptor)

49
Q

what are nuclear localization signals

A

a sequence of at least five basic amino acids in a non-random row

50
Q

what does RAN do

A

it’s a GTPase that, hydrolyzed, provides energy

51
Q

what does RAN-GEF do

A

catalyzes the binding of GTP to RAN in nucleus

52
Q

what does RAN-GAP do

A

activates hydrolysis of GTP attached to RAN, causing a gradient

53
Q

which RAN binds to receptors

A

RAN-GTP (receptors can bind to this or cargo but not both)

54
Q

what is import deactivated by

A

RAN-GTP (releases cargo)

55
Q

what is export activated by

A

RAN-GTP (picks up cargo)

56
Q

what is mitochondrial transport

A

mitochondria proteins are synthesized in cytosol and translocated into mitochondria

57
Q

where does TOM complex function

A

outer membrane

58
Q

where do TIM complexes function

A

inner membrane

59
Q

what do proteins going cytosol to mitochondria start with

A

TOM to help insert transmembrane proteins into outer mitochondrial membrane

60
Q

what happens during co-translational translocation

A

proteins enter ER as they’re being synthesized, pushing polypeptide out of ribosome

61
Q

how do uORFs prevent translation under normal circumstances

A

translation initiates upstream and is terminated and ribosome falls off and never gets to main open reading frame

62
Q

what happens in vesicle transport

A

vesicles bud off one organelle and fuse with another, guided by specific coat and targeting proteins

63
Q

what are the three different coat proteins

A

clathrin, COPI, COPII

64
Q

what does clathrin do

A

post-golgi transport (endocytosis and endosomal compartments) - “triskelion” structure

65
Q

what does COPI do

A

retrograde transport from golgi to ER and cisternae of golgi

66
Q

what does COPII do

A

ER to golgi

67
Q

what does recruitment relies on

A

small GTPases!!

68
Q

what are surface markers for identifying vesicles and receptors

A

RAB protein (regulates docking)

SNARE protein (specificity) - V and T SNARE leads to fusion of vesicle and target membrane

69
Q

what are the two paths of secretion

A

constitutive secretory pathway (proteins bud off into secretory vesicles to go to cell surface - no specific signal)

regulated secretory pathway (vesicles concentrate cargo and store it under PM - extracellular signal is sent)

70
Q

what does mannose 6 phosphate (M6P) do

A

recruits clathrin to be transported to lysosome where it activates using coat protein and retrograde transport to return to golgi

71
Q

what are endosomes

A

set of compartments involved in transport between golgi, lysosomes, and PM

72
Q

what are the three main classes of endosomes

A

early (receives cargo and material from golgi to fuse with early endosomes)

later (fuses lysosomes to deliver cargo)

recycling (brings materials from endosomes to PM)

73
Q

what is cellular eating

A

phagocytosis (uptake of large particles through phagosomes)

74
Q

what is cellular drinking

A

pinocytosis (ingestion of fluids and solutes)

75
Q

what are two modes of channels and transporters

A

passive (solutes move down concentration gradient - no energy)

active (solutes move up concentration gradient - requires energy)

76
Q

what do channels allow

A

diffusion down gradient

77
Q

what do transporters do

A

use a conformational change to move a molecule from one side of membrane to another

78
Q

what’s an electrochemical gradient

A

charged substances that have a gradient across a membrane

79
Q

what does delta G of reaction determine

A

if substance will move passively or actively

(+) = delta G is the amount of energy required to move a molecule up gradient
(-) = max amount of energy available
80
Q

what is simple diffusion across lipid bilayer limited by

A

being non-polar, having no charge, and being small

81
Q

what can simple diffusion be regulated by

A

ligand-gated channels, voltage-gated channels, mechanosensitive channels, temperature or light sensitive channels

82
Q

what are the three types of active transport

A

ATPase pumps (hydrolyze ATP to move molecules)

other pumps using energy sources (light)

coupled transporters (movement of one solute up concentration gradient is powered by another solute down its electrochemical gradient)

83
Q

what are the types of coupled transport

A

uniport (transport one type of molecule)

symport (transports two different types of ligands in same direction)

antiport (transports two different molecules in opposite direction)

84
Q

what are the 3 classes of ATP-driven pumps

A

P-type pump (binding of ATP + phosphorylation of pump)

F- and V- type pump (ATP-synthesizing machinery using the gradient to generate ATP)

ABC transporter (multi-subunit proteins that can bind two molecules of ATP and pump lots of small molecules)

85
Q

what are the three structures of the cytoskeleton

A

microtubules (tubulin)

microfilaments (actin)

intermediate filaments (helical proteins)

86
Q

what are filaments made up of

A

repeated copies of a smaller subunit, which self-assmeble into large fibers

87
Q

what does tubulin bind to

A

GTP

88
Q

what does actin bind to

A

ATP

89
Q

which subunit gain monomers with NDP and NTP

A

NDP at (-) = lose monomers

NTP at (+) = gain monomers

90
Q

what are the two states of actin

A

G-actin (monomer)

F-actin (chain)

91
Q

how is actin stabilized

A

treadmilling - gaining and losing at the same time

92
Q

what is polymerization and bundling of filaments regulated by

A

GTPases (Rho family) - act as molecular switches

93
Q

what are the two phases of assembly of microtubules

A

nucleation (small portion of tubule formed at beginning)

elongation (Addition of tubulins and the GTP-cap)

94
Q

where do kinesins move on microtubules

A

from minus end to plus end!! (move vesicles and organelles in nerve cells from cell body to ends of axons)

BSCI330 (15 decks)

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