bio130 test 1 Flashcards
(258 cards)
1
Q
prokaryote doesn’t have but eukaryote does (main thing)
A
nucleus
2
Q
eukaryotes are ___ celled
A
single or multi
3
Q
prokaryotes are ___ celled
A
single
4
Q
plants have but animals dont (3)
A
cell wall, vacuole, chloroplast
5
Q
ectosymbiosis
A
a form of symbiotic behav in which an organism lives on the surface of another organism
6
Q
bacterium model organism
A
e coli
7
Q
eukaryote model organism
A
yeast
8
Q
plant model organism
A
arabidopsis
9
Q
tractability
A
ease of manipulation/modification of an organism
10
Q
animal model organisms
A
worms, flies, fish, mice
11
Q
genome
A
all genetic material in a cell or organism
12
Q
transcriptome
A
all RNA/RNA sequences in a cell or organism
13
Q
proteome
A
all proteins/protein sequences in a cell or organism
14
Q
interactome
A
all protein-protein interactions
15
Q
metabolome
A
all small molecule metabolites in the cell/organism
16
Q
phenome
A
all the phenotypes of the cell/org.
17
Q
why is DNA stable
A
its structure
18
Q
nucleotide is comprised..
A
nitrogenous base, 5C sugar, 1+ phosphate group
19
Q
phosphate is attached to __ carbon and base is attached to __ carbon of the carbon chain
A
5’, 1’
20
Q
phosphate is attached to __ end and the sugar is at the __ end of DNA molec
A
5’, 3’
21
Q
pyrimidine = ___ ring
A
1 ring
22
Q
purine = ___ ring
A
2 rings
23
Q
pyrimidines:
A
C U T
24
Q
purines:
A
G A
25
uracil replaces __
thymine
26
nucleoside
base + sugar
27
DNA is synthesized from...
dNTP
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dNTP aka..
deoxyribonucleoside triphosphate
29
RNA is synthesized from...
NTP
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NTP/rNTP aka
ribonucleoside triphosphate
31
examples of dNTP
dATP, dGTP, ..
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bond b/w nucleotides
phosphodiester bonds
33
A-T = __ H bonds
2H bonds
34
C-G = ___ H bonds
3H bonds
35
how do van der waals forces keep dna together
van der waals act b/w bases
36
how do hydrophobic interactions contribute to the structure of dna
bases are hydrophobic = 'inside', sugars = outside
37
protein contact is typically at the... (DNA)
major groove
38
primary protein struc referes to..
AA seq
39
2ndary protein struc refers to...
local folding
40
tertiary protein struc refers to...
long range folding
41
quaternary protein struc is when
there's >1 polypeptide chain
42
how are peptide bonds formed (chemically)
condensation rxn bw OH (carboxyl group) and H (amino group)
43
what forms peptide bonds (organelle)
ribosomes
44
what are AAs called after peptide bonds have been formed
residues
45
backbone of a polypeptide chain is...
everything except for the R groups (N-C-C-N-C-C...)
46
amino end aka...
N terminus
47
what stabilizes alpha helices?
H bond b/w carbonyl atom and amide hydrogen - 4 AA apart. NOT R GROUPS
48
alpha helix vs DNA helix - R groups
alpha R groups face out, DNA base pairs face in
49
super secondary structures
2 secondary structures interact with each other in some way?? that doesnt count as tertiary... e.g. amphipathic helix
50
amphipathic helix
when R groups on 1 side are hydrophobic and on the other side are hydrophilic -> 2 alpha helices coil around e/o
51
how are beta sheets stabilized
more H bonds b/w carbonyl oxygen and amide group hydrogen
52
2 types of beta sheets
anti parallel vs parallel OR beta sheet made w 1 vs multiple polypeptide chains1
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types of AA (chemical properties)
acidic, basic, uncharged polar, nonpolar
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parts of an AA
alpha carbon, H, amino group, carboxyl group, R group
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CYSTEINE?!?!
draw the structure
CH3--CH2--SH
56
what happens to cysteine in oxidation conditions
H removed from SH-- and it forms covalent disulphide bonds
57
how strong are covalent disulphide bonds
VERY strong!
58
reduction conditions in the cell ?
cytosol
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oxidation conditions in the context of the cell?
ER and outside of the cell (ECM)
60
what is the role of cysteine in protein
helps proteins hold their shape (like a brace)
61
chaperone proteins
proteins that help tertiary structures fold
62
what connects protein domains
intrinsically disordered sequences
63
what are protein domains
semi-independent areas of a protein that do diff things
64
what are proteinfamilies
proteins w similar AA seq.s and tertiary struc.s
65
methods to study proteins (purification)
purified w electrophoresis, affinity chromatography
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multiprotein complexes
many proteins work together
67
molecular machine
all proteins work together for a particular function
68
hemoglobin structure (subunits)
has 4 subunits where each subunit is a separate polypeptide but counts as 1 protein :D
69
multiple polypeptides = multiple proteins?
NO (counterexample: hemoglobin)
70
what is the genome
all hereditary material
71
what is the genome made of and what does that depend on
DNA: living things and some viruses
RNA: some viruses
72
num base pairs in human genome
3B
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why does any given individual have 6B base pairs
3B from e/ genome and 1 genome from e/ parent
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how many protein coding genes in human genome (for 23 pairs of chromosomes)
20k protein coding genes
75
genome size is not related to ___
complexity, organism size, # of genes
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what % of human genome codes protein
less than 1%
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what % of human genome is repetitive DNA
~50%
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a type of repetitive DNA
mobile genetic elements
79
mobile genetic elements - types?
retrotransposons, DNA-only transposons
80
what are mobile genetic elements aka transposons
elements that can ctrl x, ctrl c, ctrl v themselves in/out of the genome
81
what are types of mobile genetic elements, specifically based on length and found in human genome?
LINEs, SINEs
82
num b.p.s in SINEs
less than 500
83
what does LINE stand for
Long Interspersed Nuclear Elements
84
what is the main role of nonrepetitive DNA that is not in introns or exons
determines which + how many RNAs get transcribed and in which cells
85
types of unique DNA
nonrepetitive DNA not in introns or exons, introns, protein-coding exons
86
types of DNA packaging (prok vs euk)
prokaryotic nucleoid, eukaryotic nucleus
87
FISH, CPH, chromatin, histones, interphase
this is not a real card
88
fish is .. and it does..
fluorescence in situ hybridization, a diagnostic technique to detect presence of a specific sequence
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how does fish work
probe DNA (antiparallel, complementary) labelled w dye, denatured w sample, cooled and ideally probe bound to dna now
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what is cph
chromosome painting hybridization - colour chromosomes
91
what is chromatin
single long dna molec + extra proteins
92
when does chromosome duplication begin
interphase
93
where does chromsome duplication begin (a part of the cell)
centromeres
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how is chromatin organized (how's it wrapped)
wrapped around histone octamers, 1.66 times per octamer
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what is dna not wrapped around histones called and how long is it
linker DNA, 80 bp
96
how long is dna wrapped around e/ histone
~147bp
97
how long is dna (per nucleosome)
~200 bp
98
what is a histone octamer made of
8 proteins: 2 H2A, 2 H2B, 2 H3, 2 H4
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charge of histone octamer
positive
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role of linker histone (H1)
clips the DNA on, not actually in the octamer
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nucleosome core particle =
core histones + DNA wrapped around them
102
role of sequence specific clamp proteins and cohesins
hold tgt loops of interphase chromosome - involved in cell division
103
as cells enter mitosis, what happens to cohesins
condensins replace them to form double loops of chromatin (compact chromosome)
104
does chromatin packaging require atp
yes
105
2 forms of chromatin? (condensity)
heterochromatin (highly condensed), euchromatin (less condensed)
106
most chromatin is in what form
30nm fiber (heterochromatin)
107
quiescent
euchromatin that's not being actively transcribed and thus genes are not being expressed
108
beads on a string is what type of chromatin
euchromatin
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constitutive chromatin is
chromatin that is always heterochromatin
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facultative chromatin is
chromatin that is not always heterochromatin but sometimes is
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when is gene expression expressed? (chromatin)
only active euchromatin
112
where is heterochromatin always found (part of cell ish)
meiotic + mitotic chromosomes, centromere, telomere
113
what happens when a specific gene is being expressed
chromatin shifted to allow RNA polymerase to transcribe it and that specific area is made less condensed
114
interphase chromosomes are in ___ regions of the nucleus
distinct/discrete
115
types of DNA synthesis + explain (this is the theory...)
conservative (old theory, 1 daughter cell gets all new DNA and 1 gets all parental DNA), nonconservative
116
general process of DNA synthesis - what is used to build and what protein does that
dNTPs added to parental strands from 5'-3' by DNA polymerase
117
direction of DNA synthesis vs direction of reading template strand
5' to 3' vs 3' to 5'
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dna replication for eukaryotes and bacteria is _____ growth from __ starting point aka the ____
bidirectional growth, 1 starting point, origin of replication
119
origin of replication is made of.. and why?
regions that are A-T rich (not random areas though, specific sequences) b/c A-T = 2 H bonds vs C-G = 3 H bonds
120
what recognizes the origin of replication
initiator proteins that bind to the DNA
121
euk vs bacteria OOR
euk have multiple, bacteria have 1
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primosome =
helicase + primase
123
replisome is...
molecular machine that's the whole dna duplication process
124
(dna synthesis) what happens after OOR is recognized
initiator proteins bind, and it + helicase-loading protein help the helicase bind
125
(dna synthesis) what happens after helicase binds
helicase unwinds DNA
126
2 types of helicase? (their function not their name)
DNA repair, unwinds 5'-3' along the lagging strand template
127
(dna synthesis) what happens after helicases unzip
single strand binding proteins bind to keep the strangs separated to prevent DNA from sticking to itself
128
hair pins?
caused by DNA H-bonding to itself
129
(dna synthesis) what happens after SSBs bind
primer and primase do their thing
130
what is bound primer and what's special about it
short seq of nt w free 3' OH that lets the DNA polymerase begin
131
what does primase do
synthesises an RNA primer from 5'-3' (same direction as DNAP)
132
(dna synthesis) what happens after primase
DNA polymerase uses dNTPs to synthesize new strand from 5'-3'
133
what is a necessary part of DNA polymerase (another helper protein!)
sliding clamp prevents DNAP from flying off
134
(dna synthesis) what happens after DNA polymerase
nick sealing of okazaki fragments with nucleases
135
how is nick sealing done
DNA ligase seals the fragments by removing the leading strand primer, DNAP fills in the gaps left by the primer and ligase creates a phosphodiester bonds b/w unbonded fragments
136
supercoiling happens when
DNA is unwound and wants to spin due to torsional strain
137
how is supercoiling fixed
topoisomerase cuts a little break in DNA, lets it spin, then re-seals it
138
eukaryote specific dna replication problem? (think.. not circular dna..)
primase is bad at putting the primer at the end of a lagging strand and a removed primer cannot be re-filled
139
how is primase being bad (dna replication issue) solved?
telomerase
140
how does telomerase work
RNA temp[ate sticks to parental strand, extends parental strand (repetitions of template), generates G-rich ends (template C-rich), DNAP alpha then synthesizes that piece
141
where is telomerase less abundant (and why is this a problem)
somatic cells -> aging
142
why is lots of telomerase bad
cancer
143
what happens when dna polymerase screws up - how is it fixed? (2 methods)
3'-5' exonuclease (backspace) and strand-directed mismatch repair
144
what does 3'-5' exonuclease do
removes a wrongly put nucleotide during DNA synthesis at the E site
145
2 sites of DNAP
P and E site (synthesis site and proofreading/editing site)
146
2 proteins of strand directed mismatch repair in eukaryotes
MutS and MutL
147
what does MutS do
is a strand directed mismatch repair protein that identifies and binds to an issue
148
what does MutL do
is a strand directed mismatch repair protein that scans DNA, works w sliding clamp and MutS, identifies nicks and cuts out the area with the problem
149
what happens after MutL cuts out a problem area
DNAP repairs it
150
how is strand directed mismatch repair diff for prok vs euk
prok don't detect nicks, they detect unmethylated adenines
151
what does UV radiation do to DNA
causes pyrimidine dimers
152
pyrimidine dimers are when
2 pyrimidines in a row covalently bind
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how are pyrimidine dimers fixed
NER
154
2 types of spontaneous dna dmg
depurination
deamination
155
depurination is when
h2o hits purine and removes it (dna dmg)
156
deamination happens when
h2o hits cytosine and deaminates it, cytosine turns into uracil (dna dmg)
157
how is spontaneous dna dmg (depurination, deamination) fixed
BER
158
what is BER and how does it work
base excision repair, fixes 1 nt at a time
159
what is NER and how does it work
nt excision repair, fixes multiple nt at a time
160
how is a double stranded break repaired (2 methods)
non homologous end joining (NHEJ) or homologous recombination (HR)
161
molecular definition of a gene
segments of DNA that are transcribed into RNA
162
what RNA is not translated? (example)
mRNA
163
transcription and translation ____ start at the same site
DO NOT
164
non template strand aka the ___ strand
sense
165
template strand aka the ____ strand
antisense
166
(transcription in bacteria) RNA is made ___ to DNA and in _' to _'
antiparallel and complementary, 5' to 3'
167
what does it mean to be made in 5'-3'
add onto 3' end of newly synthesized strand, the template is read 3'-5'
168
ssDNA stands for
single strand DNA
169
diff b/w RNA and DNA polymeras? (related to how they begin doing their thing)
RNA polymerase doesn't require a primer!
170
what's specific to bacterial transcription? (specirfic protein)
sigma factor
171
purpose of sigma factor (2 main ones)
binds to RNAP and finds the promoter region. synthesizes a few short seq.s until RNAP gets ahold of itself and begins synthesis
172
other names for RNAP
RNA core enzyme, RNA polymerase,
173
RNAP holoenzyme =
RNA core enzyme + sigma factor
174
translation starts at AUG and transcription starts...
anywhere
175
when talking about the promotor sequence, what does + and - refer to
+ = in the direction of the transcription , upstream
- = before the transcription, downstream
176
promotor consensus sequence
most common sequences used for recognition
177
are promoter sequences transcribed
NO!!!
178
in bacteria, how are different promotor sequences recognized
by diff sigma factors
179
how does bacterial transcription stop (full process)
RNAP hits the terminator sequence, transcribes it, then the hairpin bs happens
180
hairpin mech?? (bacterial transcription)
abundance of G's and C's bond to each other, eventually snaps the newly synthesized strand off
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in ___, translation and transcription are coupled
prokaryotes but not eukaryotes
182
___ are absent in eukaryotic finally processed mRNA
introns
183
list out parts of processed mRNA from 5' to 3'
5' cap, 5' UTR, coding sequence, 3' UTR, poly-A tail
184
num of RNAP in bacteria vs eukaryotic
1 vs 3
185
types of RNAP in eukaryotes and their purposes
RNAP I: most of them
RNAP II: protein coding genes (mRNAs)
RNAP III: tRNAs
186
which RNAP is similar to bacterial RNAP
RNAP II, similar but larger b/c of a special domain
187
what's special about RNAP II
special domain! CTD! (carboxyl terminal domain)
188
eukaryotic equivalent of sigma factor
transcription factors (TFxD)
189
diff b/w euk and prok promoter regions for transcription
euk: more variable, can have multiple elements
190
where is the promoter region for prokaryotes usually (number range)
-10,35
191
what are elements
specific locations that are recognized by specific transcription factors to help position RNAPs
192
promoter region corresponding to RNAP II?
TATA box
193
TBP?
TATA-binding protein is a subunit of TFIID that binds to the minor groove of DNA
194
how does TFII work
TBP binds and bends the DNA, then TFIIH (helicase) separates the DNA strands and phosphorylates CTD, then RNAPII does its thing
195
activator proteins?
activate transcription idk
196
what IS CTD???
a stretch of 7 amino acids that is required for transcription to begin. Ser at its tail is phosphorylated to get RNAPII activated
197
eukaryotic mRNA processing process
add 5' cap, remove introns, process and polyadenylate 3' tail
198
purpose of 5' cap
protect RNA from exonucleases
199
why can't exonuclease cut up 5' cap
has like 3 phosphates or something
200
prok mRNA doesn't have ___
introns
201
how are introns removed
spliceosome recognizes intron-exon boundary, 2' OH on adenine attacks the boundary to form a lariat/loop. spliceosome cuts out the intron and joins the exons together
202
important part of spliceosomes
snRNPs = snRNA + proteins
203
exon junction complex
a protein added near where the introns used to be after splicing - relevant to quality control (transcription)
204
snRNPs are...
small nuclear ribonucleoproteins that are building blocks of the spliceosome
205
does the spliceosome cut out the same areas for every cell, why or why not
no b/c it has a diff function (ie brain mRNA and muscle mRNA are cut at diff points)
206
what does poly A tail do
protect from 3'-5' exonuclease
207
1st step of making poly A tail
cleavage signal/sequence (AAUAAA) recognized by 3' end processing proteins (CPSF)
208
how do poly a tail???
AAUAAA, CPSF + CsTF (cleave), PAP=poly-A polymerase (+AAAAAAA), PABP=poly-A-binding protein (stabilize)
209
where is mRNA translated
cytoplasm
210
genetic code is read _'-_'
5' - 3'
211
translation goes from _' to _'
5'-3'
212
where does translation start
5' most AUG
213
effects of mutations (all types - 6)
nucleotide-pair substitution (silent, missense, nonsense), frameshift (nucleotide-pair deletion, nucleotide pair insertion)
214
tRNA structure - key points (# nt, shape, how is it transcribed, special features?)
~80 nt long, clover shape, transcribed 5'-3', modified bases
215
where does AA attach to tRNA
AA attaches to 3' end
216
anticodon?
3 bp area where where tRNA binds to mRNA. note that it is antiparalle and complementary to the mRNA
217
anticodon = 5'-3' GAA then mRNA is 3'-5' ____ and you should look up ___ on the genetic code table
CUU, UUC
218
1 anticodon per ___
codon in the genetic code table (kinda, multiple codons can bind to the same anticodon though), tRNA
219
diff b/w euk and prok wobble pos.
euk is less flexible
220
wobble position is...
the 5' position of the anticodon where other bases can attach (not strict)
221
how is accuracy ensured during translation
aminoacyl-tRNA-synthetase recognizes AA and puts it on the proper tRNA
222
how many types of aminoacyl-tRNA-synthetase are there and why
20 types, 1 per AA
223
how does aminoacyl-tRNA-synthetase identify a match
identifies the anticodon, identifies the n.t. seq of the acceptor, identifies n.t. on other parts of the tRNA
224
aminoacyl-tRNA-synthetase correction mech
hydrolytic editing
225
what are ribosome subunits made of
large and small subunits made of ribosomal proteins and rRNA molecules
226
ribosome sites and purpose
A site (aminoacyl), P site (peptidyl site, peptide bond formed b/w AA in P and E sites), E site (exit site)
227
where are ribosomes located
ER and cytosol
228
purpose of ribosomes in the ER
make proteins that are secreted or go to lumen of some organelles
229
how is peptide bond made during translation and what enzyme is involved
catalyzed by peptidyl transferase activity of the rRNA, can be done b/w of the high energy bond b/w tRNA and AA
230
ribozyme
RNA molecule that possesses catalytic activity
231
what is an EF and why is an EF??
elongation factor, quality control and efficiency
232
how do EFs do quality control
check the aminoacyl tRNA site to make sure that it's the right AA. sticks to tRNA and will take away the tRNA if the pairing is wrong
233
EF types (prok vs euk)
EF-Tu for prok and EF1/EF1A for euk
234
EF and GTP interaction
EF + GTP bring tRNA to the rRNA, if it's the right base pairing then GTP will hydrolyze to GDP and EF will get released
235
euk vs prok in how many proteins mRNA can code for
euk: 1 mRNA codes for 1 protein
prok: 1 mRNA can code for multiple proteins
236
polycistronic mRNA
when 1 mRNA can code for multiple proteins (prok)
237
diff b/w euk and prok mRNA (as it relates to translation)
has non coding regions b/w coding regions called ribosome-binding sites aka Shine-Dalgarno sequences that tell the ribosome where to start binding
238
which EFs help with elongation
EF-G (prok) and EF2 (euk)
239
how do EFs help with elongation
"pulls" the small subunit of RNA so that it's immeidately ready to accept the next AA to speed up elongation
240
at which site is the initiator tRNA positioned?
P site
241
beginning of translation in prok (general process)
initiation bg w shine-dalgarno seq, initoation factors position small subunits, tRNA binds to initiator codon, large ribosomal subunit binds
242
beginning of translation in euk (general process)
small subunit, large subunit and initiation factors are alr together and bind to mRNA, then they jsut go ! starts with Met in the P site
243
translation termination? process
at the stop codon, a diff non-tRNA protein (translation release factor) binds to the A site and initiates dissociation of ribosome and termination of polypeptide chain
244
e.g. post translational modifications
phosphorylation, glycosylation
245
ubiquitin
a small protein that covalently attaches to proteins targeted for degradation
246
how does protein degradation work
ubiquitin does its thing then the proteins are directed to the proteasome where they are degraded by proteases
247
methods to study proteins (AA sequencing)
mass spectrometry
248
methods to study proteins (precise 3D struc)
x-ray crystallography, NMR, cryo-electron microscopy
249
proteins in the same family have similar...
structural domains
250
how is the tertiary structure of a protein held together (what forces)
hydrophobic interactions, covalent disulphide bonds, non covalent bonds
251
where are amphipathic alpha helices/coiled coils found
alpha-keratin of skin and hair, myosin of muscle cells
252
subunits of hemoglobin
2 alpha, 2 beta
253
nucleosome is made up of...
nucleosome core particle (histone octamer + wrapped DNA) + linker DNA + H1
254
proteomics
large scale study of proteins
255
histones are proteins rich in...
lysine and arginine
256
charge of histone and why
positive to neutralize negative charge of DNA
257
how do euchromatin and heterochromatin interchange
RNAP modulates the reversible switching of the 2
258
