Exam I Flashcards
1
Q
Viruses store DNA in what form
A
RNA
2
Q
why is it called “deoxy” ribose in DNA
A
no OH on the 2’ carbon
3
Q
3 parts of a nucleotide
A
deoxy or oxy ribose sugar, 1 phosphate group, and nitrogenous base (ATCG)
4
Q
backbone linkage on DNA
A
covalent phosphodiester bonds, between triphosphate and the 3’carbon
5
Q
what direction does DNA pol read and write strands
A
reads 3’–> 5’ synthesizes 5’–>3’
6
Q
direction of exonuclease activity, why?
A
3’–>5’ because if we cut from 5’ end we lose triphosphate..which we need to grow the strand
7
Q
RNAse H
A
chews out single ribonuscleoside in between okazaki fragments
8
Q
ssbinding poteins
A
keep DNA that has just been unzipped to stay apart
9
Q
enzymes req what to get DNA pol at every primer
A
multi enzyme complex, DNA helices, clamp and clamp loader, DNA polymerase
10
Q
DNA origin of replication usually have what sequence and proteins?
A
AT rich because these only have 2 H bonds
proteins are bound here: cycline dependent kinases, loads DNA helicase nearby
11
Q
How many rep forks are made in DNA
A
2, replication bubble
12
Q
When does DNA synthesis occur in cell cycle
A
S phase
13
Q
chromatin
A
nuclear DNA with proteins assoc with it. lots and lots of protein. beads on a string. histones and non histonal chromosomal proteins
14
Q
nucelosome
A
DNA wrapped in proteins and histones. Protein core with 8 different histones
15
Q
fifth histone protein H1
A
located outside of nucleosome and holds it together
16
Q
histone tails
A
lysine and arginine (+) charges to interact with DNA(-)
17
Q
2 types of chromatin
A
10nm fiber and
30nm fiber from H1 interaction–>makes it a condensed structure
18
Q
Want to transcribe DNA sequence, how do we unravel it from 30nm fiber form?
A
acetylation that will cause binding to the lysine and argentine bases so we can access the DNA. prevent 30nm fiber from forming
19
Q
chromosomes
A
condense chromatins into chromosomes using non histone proteins.
20
Q
epigenetic inheritance in DNA synthesis
A
50% parents histones(methylated) are passed down to daughter cells
21
Q
termination of synthesis on lagging strand
A
use telomerase, which using reverse transcriptase(RNA template to make DNA)
short tandem sequence added. elongates 5’–>3’ of parental strand
22
Q
overhang from telomerase activity
A
“tucked in” to prevent form degradation
23
Q
Central dogma
A
DNA–>RNA–>proteins
24
Q
gene expression
A
DNA synthesis, transcription and translation
25
differences in RNA and DNA
RNA: Uracil, extra OH on 2', single stranded
26
RNA polymerase II is able to do what with no help
can bind, begin without primer and make many mistakes--> not as big of a deal because transcripts can be degraded.
27
RNA pol 1, 2 ,3
RNA pol I--> rRNA synthesis: makes proteins
RNA pol II--> mRNA: protein coding genes, siRNA miRNA: silencing
RNA po lII--> tRNA, rRNA, snRNA
28
What does RNA pol II need
General Transcription factor: TFIID, recognizes TATA box, AT rich sequence. This is before promoter and causes aggregation of more transcription factors that will help to open DNA and begin transcription
29
CTD tail
On C terminal domain of RNA pol II, going to be phosphorylated, functions to make changes to emerging mRNA molecule
30
mRNA is transcribed where
in nucleus
31
What needs to happen to move mRNA out of nucleus
1: methylated GMP cap at 5' because this emerges first(5'-->3')
2: splicing of introns- snRNPs
3: Poly A tail at 3'
32
Sites for splicing
edges and intersections of exons/introns
| 5' site, branch point, 3' site
33
ribonucleotide protein hnRNPs
ribose sugar with nucleotide with a protein
| so it can complementary base pair with NT
34
Poly A tail initiation
sequence coding for termination, causing cleavage, Poly A polymerases add tons of As
requiring a lot a lot of energy
35
rRNA
80%. Pol I No CTD tail, no capping no Poly A tail
many subunits come together to make this molecule
snoRNAs help to post transcriptionally modify rRNA
small and large subunits assembled outside before brought back in
36
most genes encode for what
mRNA--> proteins
37
charged tRNA
carries aa, and anticodon that codes for that aa its carrying
38
wobble position
3rd nucleotide space of codon has some variability and still codes for same aa-- Silence mutation
39
2 important areas in tRNA
charged aa at 3' end
| read transcript 5'-->3' so the anticodon loop is read 3'-->5'
40
amino acyl tRNAse
add aa to tRNA using ATP 3' OH group on NT interacts with OH on aa
aa on C terminus carries activation energy to link next aa
41
direction of protein synthesis
begins N terminus--> C terminus
42
subunits of rRNA
small is responsible for recognition of codon
| large: addition of peptide bond, adding aa to protein
43
4 sites of ribosome
mRNA binding site, A(arrival) site, P(peptide), E(exit
44
where is peptide synthesis in rRNA
A site
45
how do tRNA get to A site
chaperones, elongation factors
46
ribozyme
ribosomal molecule that catalyzes a reaction
47
Initiation peptide synthesis
Start codon: AUG -methionine met-tRNAi
met usually removed afterwards
binds into P site in small subunit when finds AUG
(initiation factors leave at this point)
48
Termination of translation
Stop: UGA UAA UAG
molecular mimicry- don't code for aa
bind in A site and peptidyl transferases add a OH to C terminus to release peptide
49
Protein structure vs function
structure equals function!
50
Structures of Proteins
primary: aa sequence
secondary: alpha helices and beta sheets: covalent bonds
tertiary: final form of protein
quaternary: multiple tertiary structures
51
Molten globules state
secondary structure needing chaperones to shift into tertiary structure
52
Protein folding chaperones
Help with correct confirmation, usually assoc with ribosome. Heat shock proteins (inc heat= incorrect folding so inc production of these proteins)
look for hydrophobic patches on exterior, should be on interior.
53
Hsp70
bind protein as emerging from ribosome if locate hydrophobic patches
54
Hsp60
forms a barrel or protective environment for correct protein folding (molten globule states)
55
if protein is incorrectly folded
no functioning properly usually degraded by proteasome that has a cap to recognize protein (poly ubiquital chain)
56
Ubiquitin cascade
E1 activate ubiquitin, activates E2 by transferring the ubiquitin to it then this takes it to target. E3 recognizes which protein needs to be degraded.
E3 has E2 attached and adds ubiquitin to lysine side chain to make ubiquitin tag
57
E3 activation/inhibition
ligand, another subunit, also can unmask degradation signals(removing subunit), cause destabilizing N terminus(removing 12 aa sequence)
58
cytoskeleton units
microtubules, intermediate filaments, microfilaments
59
microtubules
dimers of alpha and beta subunits. oligomers of dimers
60
protofilaments
huge chains of oligomers, form in sheets-->tubulin sheet which roles and folds into a tube
grow at one end via adding dimers, degrade at another
61
2 groups of microtubules
stable: permanent like cilia and flagella. don't degrade very quickly
centrioles or MTOC are stable as well
dynamic: the mitotic spindles. come and go, always in flux.
62
structure of stable microtubule
ex cilium: 9+2 with dynein arms and in middle are two microtubules. Covered by cell membrane (bilaminar phospholipid)
63
centriole structure
basal body is anchoring structure. 9 triplet structure: more stable
g-tubulin proteins to help integrate cilia into basal body
64
cilia
move stuff, line epithelia tract.
65
centrosomal area components
pericentriolar mass and centriole
66
dynamic microtubules are found
cytoplasm, pave roads for like dynein motor proteins and kinesin
67
kinesin
brings structures to where they need to go in the cell. like vesicles or NT
68
microfilaments
actin or myosin(muscle) 5-8 nm
| surround nucleus
69
actin
cell contraction! and locomotive processes
70
tropomodulin structural protein
caps actin so can't grow
71
cofilin
severs actin
72
filamin
cross links actin filaments-->gelatinous structure
73
tropomysin
stabilizes actin filament-->skel m contraction
74
Intermediate filaments
6 classes of IFs very specific
75
Type I and II IFs
keratins and prokeratins
epithelial cells
specific keratin can be associated with cancers
76
Type III IFs
desmin, found in all mm cells.
vimentin, found in non muscle cells-mesoderm derived
glial fibrillary: astrocytes, stabilize neurons
77
Type IV IFs
neurofilaments. found in neurons
78
Type V IFs
lamins--> structure to nucleus and help form nuclear pore(transcription regulation)
79
Type VI IFs
developmental. ex nestin, usually found in islet beta cells to indicate formation of beta cells, then disappear.
80
blistering, whats going on inside
separation of epithelia cells in skin= fills with fluid
| irritation caused
81
Ritters disease
neonatorum. Staph aureus infection of skin. exotoxin is released from this bacteria. Exotoxin attaches and binds to desmosome and denatures them so epithelial cells lose adhesion to one another.
82
2 phases cell cycle general
Interphase:G1-2n (G0) S-4n and G2-4n
| M phase: mitosis: prophase metaphase anaphase telophase
83
homologues
not connected to each other. diploid
84
signals for cell to go back into G1 from Go
growth factors or mitogens
85
restriction point of cell cycle
G1-->S go into Go
86
G2/M chkpoint
chrom alignment at metaphase, need to know that DNA replicated and environment is good
87
met/anaphase chkpoint
sisterchromatids and spindles formed correctly
88
Cdks
phosphorylate proteins that regulate cell cycle
89
cyclins
bind to Cdks to activate them. Undergo cell cycle dependent production
90
cyclin Cdk
particular kinase. cdk activating kinase
91
wee1
phosphorylation to inhibit Cdk
use cdc25 to remove inhibitory phosphate
92
Cdk inhibitor proteins
bind the complex and inhibit activity
| p27, 21 16
93
E3 ligases in cell cycle
anaphase promoting complex APC, activated by cdc20
94
G1 main events
pre replicative complex
| add DNA helicase, assemble proteins and activate S Cdk by producing S cyclin
95
S phase main events
S-Cdk, centrosome duplicated(semiconservative), cohesins, pre-initiation complexes
DNA synthesis
96
G2 main events
M cyclin -->MCdk CAKinase Pi site or Wee1 inhibits site, so cdc25 can dephos wee1
and condensin gets Pi to condense sister chromatids.
97
(+) ends in spindles
growing out! towards sister chromatids
98
dyneins move what direction
towards (-) so towards centrosome
99
APC/C in M phase
ubiquitilating proteins that need to be degraded.
like securin, to activate separase so sister chromatids can split.
also leads to ubiquitlation of MCdk so cell cycle can terminate
100
Cytokinesis
cleavage furrow--> uses actin because contractile ring
activated through RhoA-GTPase. inactive-GDP Guanine exchange factor-GEF switches out for GTP. leads to myosin light chain contraction= actin contraction
101
basic dyes
| acidic dyes
```
hematoxylin, toluidine blue, methylene blue
all stain (-) structures like DNA, RNA etc
eosin, acid fuschin--> basic structures some basic proteins
```
102
osmolality
total concentration of particles in a container
| water will flow where high [ ] are
103
electroneutrality
charges in every compartment in cells wants to have equal + and - charges
104
negative charge in cells is caused by
impermeable proteins
105
simple diffusion
movement of small particles across the membrane that don't need help. H2O, steroids, gases
[ ] dependent only
106
facilitate diffusion
need protein to move it. carriers can become saturated
107
flux is controlled by
distance need to move, diffusion properties and electrochemical gradients
108
passive movement of H2O
osmosis: hydrostatic P used to move water, always maintain near 0 in cells
osmotic pressure: caused by osmolality like in capillaries
109
aquaporins
little channels for H2O movement and sometimes glycerol and never charged particles
They are in every PM.
110
what side of a cell is Na+ and Cl- high on
extracellular
111
[ ] gradients can be used for what
transporting other solutes against their [ ] gradient
112
Na+/K+ gate
inside of cell, 3 Na+ bind. phosphorylate channel which conformationally changes channel and lets Na+ out into extra cell. 2K+ bind causing conformational change so K+ released into cell
113
Where is Ca2+ low
Cytosol. Ca2+ stored in extracellular stores because passively wants to move into cells! used for many pathways
114
Proton [ ] gradient
wants to move into cells
115
Cl- moves with
HCO3-. bicarb buffer system Cl- tries to balance out extreme + charge on extracellular side
116
membrane potential
separation of charges across a membrane
117
Inhibiting Na+/K+ pump causes?
Cell is going to swell because accumulation ions in cell
118
hypertonic.hypotonic environments
hypertonic external: cell shrinks because water leaves
| hypotonic external: cell swells because water comes in
119
Cell response to acute cell shrinkage
activation of Na+/H+ exchanger. takes in Na+ extrude H+, the extrusion of H+ is going to activate the HCO3-/Cl- pump because cell is getting too basic. Net uptake NA+ and Cl- so increase [ ] so water will follow
120
Cell response to acute cell swelling (too high [ ])
open K+ and Cl- channels, diffuse out via [ ] gradient
121
long term changes in solute [ ] (dehydration or drinking too much H2O)
creates ideogenic osmolytes in the cell in response to shrinking because need to bring H2O in
122
cytoplasmic pH
7.0-7.3
123
Intracellular metabolic acidosis/alkalosis
acidosis low pH(move H+ out) alkalosis high pH (inhibit moving H+ out and start to pump HCO3- out)
124
Intracellular respiratory acidosis
increase CO2 in blood will be driven into cell which produces carbonic acid and H+ and OH- ions. so drop pH because [H+] increased
Na/H exchanger to raise pH then when reached pH it inhibits itself
Cl-HCO3- exchanger lowers pH and when reached pH it inhibits itself
125
Intrinsic buffers
Intracellular, cannot escape cells. so like charged residues on proteins that can donate H+
126
how to proteins get to where they need to be?
sorting signals, found within the aa sequence
sorting patches
detected by charge
127
describe the various types of protein transport
gated: selective (nuclear pore) topologically equivalent
transmembrane: protein has to transport across membrane: topologically distinct
vesicular: using budding then fusion
128
signal sequences
N terminus 15-60 bases long. Usually cleaved after sorted
129
signal patch
1 sequence or different parts of a protein that come together in 3D form
130
direction of proteins in nucleus
proteins in, for transcription
| mRNA out
131
Nuclear pore
nuclear porins that form an octagonal ring with cytosolic fibers to direct molecules in, and a basket at other end
small molecules freely diffuse
proteins need assistance by chaperones
132
nuclear localization signal
proteins sequence to be directed into nuc pore, arginine and lysine because (+) charges. charges interact with cytosolic fibrils
133
nuclear import R
2 binding sites specialized for cargo proteins,1: nuclear localization signal and 2: FG repeats that allow Receptor to bind and move through pore
134
nuclear import adaptor
in between nuclear import R and cargo protein
135
mitochondrial proteins
synthesized in cytosol.
136
HSP70s role in mitochondrial proteins
keep protein unfolded until transported into mitochondrial. has an N terminal sequence alpha helix-ampipathic, recognized by mitochondrial membrane Receptors
137
Intermembrane mitochondrial proteins
N terminal seq directs to mito,
| Internal sequence is a seq to insert protein into membrane. Need stop transfer sequence
138
Stop transfer sequences
hydrophobic because destined to the membrane
139
rER responsible for
beginning of protein trafficking. same as free ribosomes, but the sequence on protein is making ribosome translocate to rER
140
cotranslational import
as protein emerges from mRNA, the N terminus has signal to interact with R on rER to be inserted into lumen of rER
141
sequence on N terminus for rER insertion
signal recognition particle(srp) will bind N term sequence and pause translation so it can insert N term into membrane of rER via Signal recognition particle Receptor. srpR
142
ER resident protein
have C terminal signal to keep them in ER "KDEL"
143
protein glycosylation
happens in ER, tells protein to be in extracell membrane or cytosol. Blood types vary because of glycosylation. enzymes build oligosaccarides but then different enzymes chop down these sugars
signal that protein is folded correctly
144
responses to misfolded proteins
heat shock response and unfolded protein response which happens on ER: initiate signals to increase chaperone amount and mRNA splicing for chaperone production or can reduce translation to influence flow of misfolded proteins
145
GPI anchor
attaches in ER, used for PM proteins
146
Vesicular transport
exocytosis: from ER to golgi to lysosome or PM or endocytosis: from PM or extracellular components
147
membrane markers
on transport vesicles that tell vesicle where to go. transport vesicles use cytoskeleton to travel
148
Cathrin coated vesicles go/from where
from PM, clathrin triskelions
149
COPI
from golgi
150
COPII
bud form ER
151
Golgi apparatus function
sorting station for final destination using coating vesicles. Incoming have signals that say where they need to go. Exit signals have COPII signal
152
how to unfolded proteins not enter vesicles
chaperones in ER cover the exit signals
153
homotypic fusion
fusion of vesicles from same compartment
require t snares and v snares
example: vesicular tubular clusters
154
heterotypic fusion
fusion of 2 vesicles from different compartments
155
ER retrieval signals
C terminal lysine for KDEL sequence, bind COPI or KDEL R and returned to ER from golgi
156
Golgi sides
Cis golgi is the entry side, trans is the exit side. median in the middle
157
lysosomes
degradation. filled with acid hydrolyses- hydrolytic enzymes that require proteolytic cleavage to be active because its so destructive
pH 4.5-5.0
158
how do we get low pH in lysosome
pump H+ via vacuolar H+ ATPase. uses ATP
159
zymogen
enzyme that needs proteolytic cleavage to be activated
160
early endosome
intially endocytosed molecules that contact with lysosomal hydrolyses, some can be recycled back to membrane
161
late endosomes
mildly acidic interior, hydrolytic digestion begins, enzymes not completely active yet
162
endolysosome
fusiong of late endosome and existing lysosomes, decrease pH to the 4.5-5.0 range
163
autophagy
enclosure of organelle with autophagosome to fuse with lysosome and digest the organelles
164
how do we get proteins to lysosome
Mannose residue attached to protein in ER, moved into golgi and enzymatic processes make it Mannose 6P
this signal packages in clathrin to go to lysosome
165
melanocytes
specialized lysosomes will store melanin. the exocytosis of lysosomes bring melanin to surface
keratinocytes will endocytose pigment
166
types of endocytosis
phagocytosis: large molecules in large vesicles called phagosomes
pinocytosis: fluid and small molecules
167
constitutive secretory pathway
exocytosis via exit trans golgi network and secreted into extra cell space, membrane proteins and lipids are added to PM
168
Regulated Secretory Pathway example
NT that signal release of ions. specialized cells that secrete hormone, enzymes etc.
169
majority communication in cells
extracellular, cell signals, ligands, Receptors all that fun stuff
170
cell differentiation
signals that can change the way a cell is forming so it becomes specific. these signals can be combinations
171
Cells have same R in different tissues, how can the result be different?
intracellular cascade is specific to each cell type
172
trophic factors
factors that are required for a cell to survive, without these cell undergoes apoptosis
173
morphogen gradients
important in development, where a cell lies on gradient determines how the cell response
requires signaling centers and responding centers on cell
174
desensitization
prolonged stimulus, cell sequesters the Receptor--> either down regulate(lysosome) or recycle. Can innactivate R. Can inactivate intracellular cascade parts, or induce an inhibitor of the intracellular cascade
175
mitogens
stimulate cell division acivate through restriction site in cell cycle
176
growth factors
not only can stimulate growth but also dictate cellular growth
177
extracellular signaling categories
direct: cell-cell or cell-extracell matrix, gap junctions
endocrine: distance
paracrine: nearby cells
autocrine: works on self
synaptic: in synapse
178
cross talk
interaction of signaling pathways, pos or negative interaction.
179
Steroids
activate intracell R because hydrophobic can cross cell membrane. made from cholesterol
180
R for Steroids
Intracellular Nuclear R superfamily, dimerize upon ligand binding. this directly acts as a transcription factor
181
NO
activates intracell R. very short half life. activates guanylyl cyclase to produce cGMP from GTP= relaxation smooth m
182
Peptides
activate extracell R. have peptide hormones, Growth Factors and neuropeptides
183
Neurotransmitters
small hydrophilic. released from presynaptic membrane to act on post synaptic cell(have R)
ligand gated ion channel or GPCR
184
Eicosanoids
locally. bing cell surface R. clotting and inflammation. Cyclooxigenase I and II inhibited by NSAIDs
185
Ion Channel couple R
ionotropic. rapid signaling with ligands NT. open or close channel, change ion permeability and Mpotential
186
GPCR metabolic
ligand binding on extracell, intracell C term has G proteins(alpha, beta gamma) associated with it.
ligands: eicosanoids, NT, peptide hormones
187
which cell R associated with special sense?
GPCR sight, smell and taste
188
Resting state GPCR
no ligand, alpha G protein bound by GDP and betagamma complex assoc with membrane
189
Active state GPCR
GDP exchanged to GTP (GEF) on alpha which dissociates subunits.
190
Deactivation GPCR
GTPase activating protein, exchanges GTP for GDP
191
G alpha proteins and what they do
G stimulatory (activates adenlyly cyclase)
Ginhibitory (inhibits adenlyly cyclase)
Gq activate PKC
192
Enzyme coupled R
extracell binding, intracell catalytic domain.
193
R Tyrosine Kinase
Enzyme coupled. ligands: GFs dimerize when ligand binds and cross phosphorylate each other
intracellular cascade induces kinases
194
Tyrosine Kinase Assoc R
act through tyrosine kinases
ligands: cytokines, interleukins and integrins
binding of ligands induce dimerization
195
cytokine R
subclass TK assoc R. JAK/STAT
196
Protein tyrosine phosphotases
inhibits pathway by dephosphorylating
197
R guanylyl cyclase
activates cGMP
198
R serine/threonine Kinases
TGF beta ligand. form heterodimers when active, one chain phosphorylates the other.
Smad pathway
199
Notch
requires downstream proteolysis. developmental!
cell-cell binding of delta to notch
ligand induces cleavage of cytosolic tail-->nucleus to induce transcription
200
Frizzled
Wnt pathway, when activated can induce the release of Beta catenin(stops phosphorylation of betacatenin aka degradation) so it can go into nucleus to act as a transcription factor
201
patched/smoothened
hedgehog ligand. activates patched to activate smoothened which will inhibit Phosphorylation of Ci so Ci can enter nucleus and induce transcription
202
Death R
extrinsic apoptosis. ligands: cytokines, GFs, pathogen assoc molecular patterns
homotrimeric. when one ligand binds the subunits cluster of domains
adaptor proteins with death domains will activate caspases. (8and10)
203
Integrins
At cell-matrix junction. associate with cytoskeleton interiorly and extra cell matrix exteriorly so when sense movement outside can cluster and autophosphorylate FAKs, Focal Adhesion Kinases
these Pi sites serve as binding for signaling proteins
204
second messengers
small intracellular signaling molecules. generated very fast and move very fast
205
cAMP
formed form ATP by adenlyly cyclase, degraded to aMP by cAMPphosphodiesterase
induces PKA which is a tetramer of 2 subunits which will phosphorylate targets
206
cGMP
formed from GTP by guanlyly cyclase, degraded to GMP by cGMPphosphodiesterase
activates protein kinases and ion channels
207
PIP2
inner leaflet of plasma membrane. we use as second messenger
| phospholipase C induces cleavage of PIP2 to IP3 and diacylglycerol (DAG)
208
IP3 activates ligand gated Ca2+ channels
activates ligand gated Ca2+ channels
209
DAG
activates PKC
210
PI3 kinase
works on PIP2 to convert into PIP3
211
PIP3
activates AKT= protein survival and synthesis
212
MAP kinase
GFs and mitogen activated. regulate cell growth and differentiation.
RAS activation--> RAS Raf Mek Erk
213
JAK/STAT
cytokine R, TK assoc. JAK is a nonreceptor tyrosine kinase that phosphorylates STATs
STATs dimerize when Pi and translocate to nucleus to act as transcription factor
214
TGFbeta/SMAD
serine/threonine kinases phosphorylate one another. SMAD translocates to nucleus and acts as transcription factor
215
NF-kB
Receptor is the tumor necrosis factor R.
ligands: cytokines, GFs, TNF
NF-kB is usually bound by inhibitory protein
activation Pi inhibitory protein= ubiquitilation
NF-kB moves to nucleus to act as TF
216
Rho
regulate cytoskeletal changes, like focal adhesions, filopodia etc.
Activated via integrins and GF receptors.
promotes actin polymerization and phosphorylation of myosin light chain= contraction
