BSCI330 Exam 3 Flashcards
(94 cards)
1
Q
what does even skipped mean
A
even segments are skipped if gene is mutated
2
Q
what are the inhibitory factor regulatory proteins
A
giant and krüpel
3
Q
what are the activating factor regulatory proteins
A
hunchback and bicoid
4
Q
how do you get expression with regulatory proteins?
A
if you have (+) AFs binding and (-) AFs not binding
5
Q
where can transcription be regulated
A
initiation and termination
6
Q
what does transcriptional attenuation lead to
A
premature termination of RNA transcript
7
Q
what do barrier sequences do
A
bind to proteins, inhibit heterochromatin spread
8
Q
what do insulator elements do
A
control ability of an enhancer to regulate gene expression
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
10
Q
what is the first level of post-transcriptional regulation
A
alternative splicing
11
Q
what can alternative splicing do
A
change activity of protein by changing which exons are present in final transcript
12
Q
what is standard form in post-transcriptional regulation
A
the first identified; everything else are splice variants
13
Q
what decides where the last exon in the transcript is
A
alternative poly-A sites
14
Q
what is the difference between secreted and membrane-bound transcription
A
their poly-A sites
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
16
Q
why will transcript remain in the nucleus
A
if transcript isn’t fully spliced; only full transcripts are exported
17
Q
how does HIV work
A
interferes with normal regulation of export to allow full-length RNA to be exported as virus
18
Q
what proteins bind iron in response to iron starvation
A
ferritin and transferrin
19
Q
when do you want more transferrin
A
if low on iron
20
Q
when do you want ferritin
A
when high on iron (it blocks translation)
21
Q
what is transferrin receptor regulated by
A
mRNA stability
22
Q
what is aconitase
A
an iron-binding protein
23
Q
what do miRNAs associate with?
A
series of proteins forming RISC
24
Q
what is RISC
A
RNA-induced silencing complex; degrades mRNA when bound to double-stranded RNA
25
what are two classes of short RNAs
small inhibitory RNAs (siRNAs) - mediate RNA interference
double-stranded RNA (dsRNA) - bind to RISC like miRNA to interfere with translation
26
what is a pro of post-transcriptional regulation
it can respond to environmental stimuli more rapidly than transcriptional regulation
27
what is the open reading frame in mRNA
region between AUG and stop codons (contributes to stability and translation efficiency)
28
what are riboswitches
places in RNA that can adopt two or more alternative 3D structures (differentiated by binding or non-binding of small molecule ligands)
29
what is an initiation factor of ribosome binding to mRNA
eIF2 (GTP-binding protein)
30
how does eIF2 work
uses GTPase motif to mediate binding of initiator met-tRNA to small ribosomal subunit
31
how does ribosome switch from initiation to elongation with eIF2
when GTP is hydrolyzed, eIF2 falls off and ribosome switches
32
Why does eIF2 need a GEF
to exchange GDP for GTP after GTP is hydrolyzed - GEF is eIF2B
33
what happens when eIF2 is phosphorylated
it inactivates protein and shuts down translation
34
what is important for amino acid starvation response
uORFs - anything downstream won't be translated
35
what happens when reducing eIF2
reduce translation of early uORFs and increase likelihood that ribosome will translation downstream
36
what is the transcription factor ATF4
controls expression of proteins like amino acid transporter and synthesis enzymes - is translated as an amino acid starvation response
37
how can we have multiple AUGs
internal ribosome entry sites (IRES) allow 2 independent protein sequences to be derived from mRNA (one at 5' cap, one at IRES)
38
what is regulated degradation
way to destroy mis-created proteins, regulated by ubiquitination and lysines to degrade into amino acids
39
what is epigenetic regulation
heritable differences that don't rely on change in RNA nucleotide sequence
40
where does protein synthesis initiate
cytosol on ribosomes
41
what are the 3 modes of protein transport
gated, transmembrane, cotranslational
42
what is gated transport
transport from cytosol into nucleus through nuclear pore complex
43
what is transmembrane transport
transport into mitochondria via TOM and TIM complexes
44
what is cotranslational transport
imports proteins into ER and pushes them across ER membrane as it's being translated
45
what is vesicle transport
traffic from ER to membrane-enclosed organelles and cell surface or exterior
46
which transports occur between topologically similar compartments
vesicle and gated (NOT transmembrane)
47
what is topologically similar
similar membrane orientations (same side of membrane)
48
why is nuclear localization signal (NLS) important for gated transport
interacts on target protein with nuclear import receptor if going from cytosol to nucleus (in reverse is nuclear export receptor)
49
what are nuclear localization signals
a sequence of at least five basic amino acids in a non-random row
50
what does RAN do
it's a GTPase that, hydrolyzed, provides energy
51
what does RAN-GEF do
catalyzes the binding of GTP to RAN in nucleus
52
what does RAN-GAP do
activates hydrolysis of GTP attached to RAN, causing a gradient
53
which RAN binds to receptors
RAN-GTP (receptors can bind to this or cargo but not both)
54
what is import deactivated by
RAN-GTP (releases cargo)
55
what is export activated by
RAN-GTP (picks up cargo)
56
what is mitochondrial transport
mitochondria proteins are synthesized in cytosol and translocated into mitochondria
57
where does TOM complex function
outer membrane
58
where do TIM complexes function
inner membrane
59
what do proteins going cytosol to mitochondria start with
TOM to help insert transmembrane proteins into outer mitochondrial membrane
60
what happens during co-translational translocation
proteins enter ER as they're being synthesized, pushing polypeptide out of ribosome
61
how do uORFs prevent translation under normal circumstances
translation initiates upstream and is terminated and ribosome falls off and never gets to main open reading frame
62
what happens in vesicle transport
vesicles bud off one organelle and fuse with another, guided by specific coat and targeting proteins
63
what are the three different coat proteins
clathrin, COPI, COPII
64
what does clathrin do
post-golgi transport (endocytosis and endosomal compartments) - "triskelion" structure
65
what does COPI do
retrograde transport from golgi to ER and cisternae of golgi
66
what does COPII do
ER to golgi
67
what does recruitment relies on
small GTPases!!
68
what are surface markers for identifying vesicles and receptors
RAB protein (regulates docking)
SNARE protein (specificity) - V and T SNARE leads to fusion of vesicle and target membrane
69
what are the two paths of secretion
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
what does mannose 6 phosphate (M6P) do
recruits clathrin to be transported to lysosome where it activates using coat protein and retrograde transport to return to golgi
71
what are endosomes
set of compartments involved in transport between golgi, lysosomes, and PM
72
what are the three main classes of endosomes
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
what is cellular eating
phagocytosis (uptake of large particles through phagosomes)
74
what is cellular drinking
pinocytosis (ingestion of fluids and solutes)
75
what are two modes of channels and transporters
passive (solutes move down concentration gradient - no energy)
active (solutes move up concentration gradient - requires energy)
76
what do channels allow
diffusion down gradient
77
what do transporters do
use a conformational change to move a molecule from one side of membrane to another
78
what's an electrochemical gradient
charged substances that have a gradient across a membrane
79
what does delta G of reaction determine
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
what is simple diffusion across lipid bilayer limited by
being non-polar, having no charge, and being small
81
what can simple diffusion be regulated by
ligand-gated channels, voltage-gated channels, mechanosensitive channels, temperature or light sensitive channels
82
what are the three types of active transport
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
what are the types of coupled transport
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
what are the 3 classes of ATP-driven pumps
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
what are the three structures of the cytoskeleton
microtubules (tubulin)
microfilaments (actin)
intermediate filaments (helical proteins)
86
what are filaments made up of
repeated copies of a smaller subunit, which self-assmeble into large fibers
87
what does tubulin bind to
GTP
88
what does actin bind to
ATP
89
which subunit gain monomers with NDP and NTP
NDP at (-) = lose monomers
NTP at (+) = gain monomers
90
what are the two states of actin
G-actin (monomer)
F-actin (chain)
91
how is actin stabilized
treadmilling - gaining and losing at the same time
92
what is polymerization and bundling of filaments regulated by
GTPases (Rho family) - act as molecular switches
93
what are the two phases of assembly of microtubules
nucleation (small portion of tubule formed at beginning)
elongation (Addition of tubulins and the GTP-cap)
94
where do kinesins move on microtubules
from minus end to plus end!! (move vesicles and organelles in nerve cells from cell body to ends of axons)
