exam II Flashcards
1
Q
semiconservative DNA replication
A
when both parent strands attatch to new daughter strands so one of the original is always in each new duplex
2
Q
deoxynucleotide monophosphates addition to new chain
and what bond
A
dNTP have Ps cleaved by DNA poly when adding to the chain with a phosphodiester bond btwn 3’OH of alast group and 5’P of new one
3
Q
direction of DNA synthesis
A
built 5’ to 3’ so it reads template 3 to 5
4
Q
primosome and components
A
protein complex for finding origin and making primer DnaA - DnaC DNA helicase (DnaB) SSB DNA primase
5
Q
leading vs lagging strand
A
leading is when the 3’ end is exposed so it can go toward the unwinding continuously (processive)
laging is when 5’ prime is exposed so needs to make a primer repeatedly and move away chunk by chunk from unwinding site
6
Q
okazaki fragments
A
the discontinuous sections on the lagging strand with individual primers
7
Q
replisome and components
A
found at replication fork for helping polymerase has similar stuff to primosome but allso Poly I DNA ligase Topoisomerase
8
Q
bacterial replication
and enzymes
A
starts at oriC moving bidirectionally
uses primosome proteins
9
Q
eukaryotic DNA polymerase gamma, delta, epsilon
A
gamma - in mitochondria for genome
delta - nuclear lagging elongation and repait
epsilon - nulcear leading elongation and repair
10
Q
which euk DNA polymerase has primase actiivty
A
alpha has primase activity for initiation
11
Q
nucleosome
A
only in euk fundamental unit of chromatin packaging containing histones
its the wound up beads
12
Q
telomers
role of
A
non-coding nucleotide sequence at end of linear chromosomes
has shelterin to protect ends
13
Q
which strand is elongated by telomerase
A
3’ end is elongated because it adds a new telomere repeat to an RNA template on the telomerase then primer can be bound to new 3’ group to build that strand
14
Q
RNA component of Telomerase template or primer
A
template for extending 3’ end so that primer can be added and extnd 5’ group before removal
15
Q
telomerase in somatic cells?
A
no which is why it gets shorter every replicatino possiblity leading to aging
16
Q
semidiscontinuos replication
A
just the idea of a leading sstrand being continusoul and the lagging strand being discontinuous
17
Q
origin of replication
A
the oriC in prok found by primosome has lots of AT
18
Q
replicaiton fork
A
just where strands separate into leading and lagging
19
Q
primers
A
short RNA bound to dna weakly to help bring DNA poly III in
20
Q
proof reading
A
3’->5’ exonuclease activitigy removing incorrect base pairs
21
Q
prok vs euk DNA rep
A
euk has multiple origin sites
more polys
telomerase
22
Q
DnaA
A
binding protein for oriC short repeats usually of AT
initial melting and brings other proteins
ATP yes
23
Q
DnaC
A
brings DnaB
24
Q
DNA helicase
A
is DnaB unwinding duplex
ATP yes
25
SSB
single- stranded DNA binding protein stabalizes single strands
26
DNA primase
DnaG makes RNA primers on DNA for DNA poly
27
DNA poly I
removes RNA primers and fills with DNA
28
DNA ligase
seales nicks between DNA fragments by hydrolyzing ATP
29
topoisomerase
unwind supercoils by breaking and rejoining DNA strands i think makes helicase work
30
histone
positively charged beads forming ionic bonds with negative DNA
31
examples of DNA damage
```
UV
oxygin radicals
damination
alyklation
depurination
drugs, metabolism, poly, tobacco
```
32
sun damage
UV light makes incorrect covalent bonds changing structure making Kink that stops polymerase
thymine (pyrimidine) dimers
33
oxygen damage
reactive oxygen species can alter DNA like changing G to 8-oxoguanine changing behavior to an AT bond instead of GC
34
DNA mutations
gene, chrom, genom
35
gene mut
point
- bas sub
- deletion/insertion
36
chromosomes mut
insertion
deletion
translocation
37
genom mut
loss or gain of entire chromosome
| like how downs has extra 21 causing trisomy
38
damage vs mut
damage is reversible 1 in 1000 becomes mut
| mut is permanent hereditary
39
mismatch repair of e coli
only post DNA replication
MutS is wrapped around backbone sliding until finds distortion from missmath
conformational change brings MutL and MutH
MutL forms a loop
MutH finds methylated GATC and endonuclease makes nick and removes backbone from GATC to after bad base then exonuclease removes bad base
DNA polymerase adds base and ligase seals backbone
40
base excistion repair
any cell cycle stage
modified bases like oxidative damage, deamination, alkylation
DNA glycosylase finds lesion and removes base making AP site
endo and exonuclease remove deoxyr ribose of backbone
DNA polymerase beta and ligase seal nick
41
BER vs NER
free bases vs oligoucleotides
oxidative and alkylation vs UV induced bulky lesions
one cut vs 2 cut excinuclease
aging and cancer vs defieiency
42
which DNA repair system is error prone
only NHEJ
43
clinical consequences
d
44
HNPCC
hereditary non-polyposiss colorectal cancer
| casued by microsatelie instablitiy and slipped mispairing and extra loops when MMR messes up
45
XP
xeroderma pigmentosum when XP proteins from NER are inactivated by mutations makes super sensitive to UV damage and cancer
46
2 main DNA protection strategies
damage avoidance - ezymes to nuetralize ROS (superoxide demutase then peroxidase catalase)
melinin releases UV as heat
or the 6 types of repair
47
Direct reversal of damage
no nicking, no recruiting
fixes stuff like pyrimidine dimers which can stop replication
DNA photolyase can recognize in dark but only repair in light
(not in placental mammals)
or O6 methyl guanine
one protein (alkyltransferase) used up to remove one methyl
48
global nucleotide excision repair
```
in all organisms, repairs helix distorting DNA damage
like pyrimidine dimers gets recognized
helicase makes bubble
2 cuts by excinuclease (XP protein)
polymerase and ligase reclose
```
49
homologous recombinatino
repairs double strand breaks
copies section from homologous pair then reattatches
happens in S phase so it has chromosome template or G2
RAD 51 mediates pairing
50
non-homologuous end joining
also for double stranded break but during G1 when no sister
end trimmed by exonuclease
DNA-PK
so its trimmed rematched and rejoined ligation
51
base subst
```
point
C->T tumors
G->T lung cancer
transition
transversion
```
52
transition
purines to purine
| pyrimidine to pyrimidie
53
transversion
pyrimidine purine
54
deletions
chrom mut
| leads to truncation
55
translocaiton
2 non homoloougs exchange chunks becoming chimeric
| philly is this for 9 and 22
56
transcription coupled NER
during transcription
| protiens from CSB and CSA which if inactivated cause cockayne syndrome
57
cockayne syndrom
developmental arrest and UV sensitivity but not increased risk of cancer
58
features of transcription
not entire genome
specific genes
gene expression restricted to products needed
regulatory sequences mark begin/end and specify template
59
RNA polymerase vs DNA poly
ribo vs deoxy
no primer (less accurate)
different enzymes
absolutely processive
60
transcriptional unit
where RNA poly and factors interact on DNA
promoter - RNA binds and starts, not transcribed, dictates direction
terminator - cis end where RNA poly falls off
61
key aspects of transcription cycle
initiation
elongation
termination
62
pro vs euk transcr
nuclear membrane in Euk separates transcript/lation
pro=polycistronic
euk = monocistronic
63
general transcription factor functions
initiat transcript and bring euk RNA poly to DNA
for RNA polymerase II called TFIIs
interact at core promoter
64
TF order and effect
TBP binds TATA box
TFIIB stabilizes TBP
TFIIF brings RNA poly II and TFIIE which brings TFIIH
TFIIH unwinds DNA
65
script initiation
sigma helps rna poly find promoter sequence
transcription bubble
bonds 2 dNTPs
promoter clearance
66
script elongation
sigma leaves and poly continues until stop site and polymerase release
67
script termination
intrinsic termination when reaches site missing factors and high GC where RNA self binds making loop
isomerization causes hairpin
weakens affinity for DNA
68
Characteristics of prok gene expression and 3 reg proteins
```
gene clusters called operons on/off
polycistronic - 1 gene for many RNA
specificity factors - alter spec of RNA poly
repressosrs - impede RNA poly access
activators - enhance access
```
69
lac operon
```
on/off
dual control
negative regulation
depressed state
positive regulation
```
70
trp operon
5 genes with single promoter
coordinate control
low trp - all genes transcribed
high - repressor binds to trp and blocks RNA polu
drop in Trp - repressor releases Trp starting back up again
71
mech of euk transcription activation
activators and repressors bind near or far from the gene
| enhancers help recruit machinery independent of orientation and position
72
regulation of TF
```
factor only present in need
factor needs activation
ligand control
stuck in membrane
inhibitory protiens
needs a buddy (dimeric activity)
phosphorylation
```
73
regulation of nuclear steroid/hormone receptors
steoid receptor bound to heatshock in cytosol until steroid comes releasing it so it can enter nucleus bind and activate
hormone receptor already in nuc when ligand comes binds and to receptor activating gene - zn finger
74
E2f regulation
cell cycle regulator
G1->S phase
E2f bound to RB protein until kinase CDK phosphorylates RB remiving it so E2f can activate genes to make S phase happen
CDK activated by growth factors
75
p53
TF
'guardian of the genome' tumor suppressor
stops cell cycle when DNA damage, if still cant fix kills self (apoptosis)
76
negative regulation lac
only glucose
repressor is bound to operator region
gene off
77
depressed state lac operon
glucose and lactose available
lactose isomer removes repressor
low expression because no CAP at promoter
78
positive regulation
```
only lactose
ATP becomes cAMP cuz glucose absetn
cAMP + CAP binds promoter
repressor gone
gene on
```
79
attenuation of Trp operon
normal mRNA has 1-2 and 3-4 loop (3-4 terminates) ahead of the trp gene
low Trp the ribosome stalls at Trp codon so 2-3 hairpin forms preventing 3-4 so the ribosome can make it to the gene
otherwise trp is present so hits 3-4 and leaves
80
diff btween lac and trp operon
when lactose is present repressor is removed so lac gene is active
when trp is present repressor is activeated and gene turns off
makes sense because lac is looking to use extra source while trp is trying not to make too much
81
mechanisms of transcription repression
```
competitive DNA binding
masking activation surface
direct interaction w/ TF
recruitment of chromatin remodeling complex
recruitment of Histone deacetylases
```
82
transcription repression competitive DNA binding
repressor and activator have overlapping binding sites
83
transcription repression masking activation surface
repressor binds to activator when both bound to DNA preventing activators effect
84
transcription repression direct interaction with GTF
binds and prevents GTF assembly
85
transcription repression recruitment of chromatin remodeling complex
returns it to pre initiation hiding the TATA box
86
transcription repression recruitment of histone deacetylases
deacetylases histones so they are positive again and bind tighter
87
dna methylation
```
added to C of CpG islands
interferes with transcription factors not GC pairing
readers writers erasers
hyper - no expression
hypo - expression
cuz more blocks TF
```
88
histone modification
reversible, known as histone code
could be phosph-, meth, or acetylation
main one is acetyl
89
readers meth
recognize and bind to methyle groups
| MECP2, MBD!-4
90
writers - meht
add meth to C
| DNA methyltransferases DNMT
91
erasers meth
modify and remove meth
in active demeth
TET enzyme
92
mechanism of epigenitc regulation and gene expression
just meth and acetyl again
93
epigenetic diseases
Rett syndrome - mut of MECP2 in X linked so female and means stalled development
cancer
94
pros/cons of epigenetics studies
helps link diseases and find cures
| cant account for environment
95
long vs short non coding RNA
both regulate neighboring genes
long deregulate in disease Tsix, chromatin remodeling
short are like miRNA for biomarkers
long interacts with proteins Xist masks a chromosomes
96
exosomes
cell to cell transfer
multi vessicel bodies
bring like proteins and miRNA
also good for biomarkers
97
histone code
modifications read by TF akin to a language
98
histone acetylation
HAT enzyme
hyper - active
hypo - inactive
more acetylation make more negative so less affinity to DNA so easier for TF to bind
99
writers acetylation
HAT
| histone acetyl transferase
100
readers histone a
bromodomain proteins
101
erasers HA
Histone DeAcetylases
102
RNA splicing steps
extron intron extron
intron pinched off
spliceosome of snRNAs
103
role of snRNPs in splicing
U1 finds splice site
U2 binding branch point
U4-6 change shape acting as spliceosome pinching off section between exons
104
splicing fidelity
ordered and coupled with transcriptions so only one set of e-i-e exposed and able to splice at a time
uniform exon length marks start stop
105
5' end processing of mRNA
| elements and time
capping
co
decapped post
106
3' end processing of mRNA
| elements and time
co
happens as cleavage once AAUAA happens
more built after but then cleaved
107
alternative splicing
increases diversity cuz 1 gene many proteins
| skipping or includinding different introns and exons
108
mature mRNA between transcription and translation
d
109
mRNA features and role in gene expression and RNA metabolism
d
110
mRNA degredation
rate of poly A tail degredation determines
| exosome has enzymes
111
hnRNA
heterogenous RNA, includes pre-mRNA
112
pre-mRNA
transcript prior to mRNA
113
snoRNA
small nucleolar RNAs, help process and modify rRNA
114
snRNP
small nuclear RNAs, splicing of pre-mRNA
115
Spliceosome
```
mediates splicing in EUK
5 snRNPs
interacts with hnRNPs
can be ribosome sized
components added sequentially as sites emerge from RNA poly II
```
116
tRNA modification and processing
RNAase P cleaves 5'
exonuclease cleaves 3'
in nucleolus
117
rRNA modification and processing
RNA pol I transcript
| done by snoRNPs
118
mRNA
messenger, code for proteins
119
rRNA
ribosomall, basic structure of ribosome and catalyze protein syn
120
tRNA
transfer, adapter btwen RNA and amino acids
121
RNA processinog steps
```
Capping
splicing
3'polyadenylation
transport
proofreading
```
122
Capping
co-transcriptional
| phosphorylation causing 5'-5' linkage
123
postitive atternative spliing regu
add activator
124
negative alternative splicing regu
add repressor
125
components of general translation of mRNA to protein
amino acids
MRNA template code
tRNA brings aminoacyl-tRNA to ribosome
rRNA nucleic acid, autocatalytic
aminoacyl-tRNA synthetase makes amino acid attatch to tRNA
ribosomes - rRNA + portein making machinery
ATP or GTP
126
stages of protein syn
```
activation of amino acids
initiation
elongation
termination
recycling
co/post processing
```
127
direction of ribosome
reads mRNA 5'to3'
128
codon
3 base pairs signalling amino acid
AUG is start (methionine)
UGA UAA UAG termination/stop/nonsense codons
129
tRNA anticodon to mRNA codon interaction
adaptor hypothesis
| anti codon binds antiparallel to codon
130
direction of sequential adition of amino acids
AA attatched to 3' end
| N to C terminus
131
genetic code
order of bases = which AA made
3 bases per aa
universal
132
degeneracy vs lack of ambiguity
degen= multiple codons per amino acide
| unambiguous - one amino acid per codon
133
wobble hypto
third base codon (so first anticodon) much less important so tRNA can bind to more than one codon
A becomes H so not watson crick
134
altering NT sequence changes protein
mutations like point can be silent if 3rd changed, missense changes charge not AA if 1st or 2nd nonsense if loses stop codon
frameshift will change codons because read in wrong triplets
135
protein syn stage in cytoplasm
activation
136
protein syn stage in ribosome
initiation
elongation
termination
recycling
137
overall structure of tRNA
cloverleaf 2D
3'CCA attaches to amino acid
anticodon binds to codon
138
modified bases of tRNA
idk but they change structure
139
formation of aminoacyl-tRNA
performed by aminoacyl-tRNA synthestase
| 1. ATP~AA=AA-AMP~2tRNA=AA-tRNA
140
function of aminoacyl-tRNA
protects AA on way to ribosome
141
sedimentation coefficients prok
30+50=70
| 16s
142
sedimentation coef euk
60+40=80
small for decoding and fideltiy
large for peptidyl transferases
143
translation initiation
Energy yes
mRNA~small ribosome+aminoacyl-tRNA brings ribosome
eIF1,2
144
translation elongation
energy yes
polypeptide chain formed
guanine exchange factor removes GTP and reactivates EF to restart cycle
ribosomal peptidyl transferase is ribozyme forming pepide bond
145
translation termination
eRF1 finds stop codon and binds with eRF2-GTP to hydrolyze peptide chain
146
translation recycling
ribosomal complex, factors and tRNA release to be reuased
147
euk vs prok translation
prok dont scan mRNA to find AUG
no ATP
just finds SD sequence
coupled with transcription
148
SD sequence
shine-delgarno purine rich sequence that prok finds to line up with AUG instead of scanning for AUG
149
21st AA
selenocysteine
150
22 AA
pyrolysine
151
selocysteine generation
recognized by same aminoacyl-tRNA as serine
| knocks of OH oh selenium and becomes selenocysteine
152
UGA involvement of selenocysteine and selenoprotein
mRNA reaches UGA but 3' non coding region SECIS structure recognized with protein and then EF so it sees UGA as selenocysteine codon and reaches other stop codon
153
pioneering round of mRNA translation
first round when EJC is there and makes upstream stop codon
154
non-stop-mediated mRNA decay
decay when lack of stop codon
155
defects related to no-go/stop decay
go-
| stop-
156
nonsense-mediated decay
mRNA with premature termination
| UPF, SMG
157
nonsense-mediated decay
mRNA with premature termination
UPF, SMG
EJC make earlier stop codon activity
158
nonsense decay related defect
same things that helped discover UPF and SMG
159
SMG
suppressorm with morphenaginic defect on genetailia
160
EJC
exon junction complelx
161
EJC
exon junction complex
162
phosphorylation of eIF2
affects levels of eIF2-GTP in response to stress
kinases add P
blocks release of GDP so GTP cant reparticipate in initiation
locks eIF2B in place eIF2b causes GDP release so its stuck not releasing anywhere else either
163
mTOR regulation
```
mechanistic target of rapamycin
mTORc1 activated by good things (AA, ENERGY, etc) for cell, inhibited by bad things
mTORC2 just activated by growth factors
activated by non stress
inhibited by stress
```
164
how mTOR globally regulates
mRNA translation, ribosome biogenesis, autophagy, metabolism
mTORC turned on by good things and turns on good things like growth
turns off 4E-BP which inhibits eif-4e
so mTOR turns on eif4e
165
cystolic polyadenylation
```
CPElement
CPE-binding protein
in cytosol
on an mRNA recruits other factors
PARN limits PolyA tail
add P and tail grows
```
166
cystolic polyadenylation control of translation
CPEB gets P
other factors open up
poly AA extended so eiF4E can come and be initiated
167
subcellular targetting and translation
mRNA brought to specific cell regions by factors
translation localized
BDNF
168
ferritin
it stores Fe so wants to be active when Fe is high
IRE-BP bond to IRE when Fe is low blocking coding region
but IREBP do not bond when Fe is high so ferritiin region is accessible.
169
transferritin
it brings Fe into the cell so when FE is low we want more of it
IRE-BP binds to IRE when Fe is low preventing degredation of mRNA
IRE-BP does not bind when it is high allowing degradation
170
phosphorylation of eIF2
high stress = high eIF2alpha-P, low eIF2-GTP
delayed re-initiation so ATF 4 produced in stress because it takes longer for small 40 s ribosomal subunit to find eIF2GTP so it finds at a later AUG on mRNA
171
IRES
internal ribosome entry sites
| secondary loop that directuly recruits factors without 5' cap
172
AA levels affect mRNA translation
low slow ribosome
speed affects folding
fast prevents aggregation
slow allows coordinated folding
173
tRNA levels affect mRNA translation
low slow ribosome
174
rare codon use affect mRNA translation
high slow ribosome
175
how antibiotics target translation and inhibit mRNA
resemble aminoacyl-tRNA and bind to A sight of ribosome causing premature termination euk and prok
inhibit peptidyle transferases prevent elongation in euk
bind to 30s subunit prevent fmet-tRNA preventing initiation prok
176
pro vs euk antiboiotics
different subunits bound and stages stopped
| know the prok and euk subunits
177
origin and function of siRNA in plants and lower euk
short interfering RNAs
from Dicer cleaaege of longer dsRNAs
RNA interference is its sliencing
degrades with RISC
178
origin and function of miRNA in vertebrates
```
microRNA
processed form RNA Pol II transcripts
same length as siRNAs
incomplete complementary
has own RISC
```
179
biosynthetic pathway of miRNA
RNA pol II transcript makes primary-miRNA
Drosha/DGCR8 microproccessor cuts into pre-miRNA w/ 3' overhang
exportin sees 3' brings to cytoplasm
DICER cuts off terminal loop aided by TRBP and recruites ago making RISC
180
RNA silencing
gene suppression oby small RNAs
| transcript and post transcript
181
RNA processing into miRNA?
same as biosynthetic pathway
182
model for miRNA post-translation gene reg in vertebrates
d
183
determinants of miRNA binding to a target mRNA
d
184
factors affecting streght of silencign by miRNA
d
185
global regulation of miRNA
d
186
selective regulation of miRNA
d
187
miRNA alter expression of target genes
d
188
miRNA biomarkers for disease
d
189
miRNA therapy for disease
d
190
what and where CRISPR-Cas
d
191
origin and function of elements in CRISPR-Cas
d
192
3 phases of CRISPR-Cas
d
193
target recognition and degradation employed by Type II CRISPR-Cas
d
194
dicer
endonuclease from RNase III
cuts up dsRNA into siRNAs
leave 2 nt overhang of 3'end, recognized end then cuts certain length repeat
195
RISC
siRNA+Argonaute
both bind to mRNA
Ago slices RNA and degrades it
196
dsDNA origin
lots but mainly virus
