Class Three Flashcards
1
Q
why is phosphoric acid inorganic
A
doesn’t contain carbon
2
Q
unique quality of phosphoric acid
A
can donate three protons
3
Q
how is pyrophosphate formed
A
two orthophosphates (aka normal phosphates) bound together via an anhydride linkage
4
Q
example of a high energy phosphate bond
A
P-O-P bond in pyrophosphate
5
Q
hydrolysis of pyrophosphate is..
A
thermodynamically favourable
6
Q
why is the hydrolysis of pyrophosphate very favourable in the cell
A
cells have higher concentrations of ATP than ADP and P
7
Q
reasons why phosphate anhydride bonds store a lot of energy (3)
A
when phosphates are linked together, their negative charges repel eachother
orthophosphate has more resonance forms → lower free energy than linked phosphates
orthophosphates have a more favourable interaction with water than linked phosphates
8
Q
building blocks of nucleic acids
A
nucleotides
9
Q
nucleotides contain..
A
a ribose (or deoxyribose) sugar group
a purine/pyrimidine base at C1
1 or 2 or 3 phosphate units at C5
10
Q
RNA precursor
A
ATP
11
Q
universal short term energy storage molecule
A
ATP
12
Q
energy extracted from food is..
A
immediately out into the phosphoanhydride bonds of ATP
13
Q
UTP - glycogenesis
A
activates glucose-1-P
14
Q
DNA aka
A
deoxyribonucleic acid
15
Q
RNA aka
A
ribonucleic acid
16
Q
why are DNA and RNA called nucleic acids
A
found in the nucleus and have many acidic phosphate groups
17
Q
building block of DNA
A
dNTP
18
Q
deoxyribose vs ribose
A
deoxyribose is missing an OH
19
Q
the purines are..
A
guanine and adenine
20
Q
the pyrimidines are..
A
cytosine and thymine
21
Q
purine vs pyrimidine
A
purine: double ring structure (6-membered and 5-membered ring)
pyrimidine: single 6-membered ring
22
Q
can purines and pyrimidines H bond
A
yes
that is why in dilute solutions, they won’t bond to each other (will bond with the water - RNA)
23
Q
what is a deoxynucleoside composed of
A
deoxyribose and an aromatic base
24
Q
backbone of a nucleic acid
A
sugar-phosphate portion → invariant
25
adenine
26
guanine
27
cytosine
28
uracil - RNA only
29
thymine - DNA only
30
nucleotides in nucleic acids are covalently linked by..
phosphodiester bonds
31
phosphodiester bonds are between..
the 3' hydroxyl group and the 5' phosphate group
32
why is the polymerization of nucleoside triphosphate energetically favourable
pyrophosphate is released & hydrolyzed → drives the polymerization reaction forward
33
Watson-Crick model
DNA is a right-handed double helix held together by H bones and hydrophobic forces between bases
34
ds-DNA
2 polynucleotide chains H-bonded in an antiparallel orientation
35
A is always H-bonded to..
T
36
G is always H-bonded to..
C
37
H-bonded pair in DNA always contains..
a purine + a pyrimidine
38
GC pair is held together by..
3 H-bonds
39
AT pair is held together by..
2 H-bonds
40
when are two chains of DNA complementary
if the bases in each strand can H-bond when the strands are oriented in an antiparallel fashion
41
annealing/hybridization
binding of 2 complementary DNA strands into a double-stranded structure
42
melting/denaturation
separation of DNA strands
43
Tm - DNA
temperature at which a solution of DNA molecules is 50% melted
44
double helix of DNA is stabilized by..
van der Waals foreuse between the bases
45
hydrophobic interactions between bases..
stabilize the double helix
46
when does the helix pattern repeat itself
every 10 base pair (34 angstroms)
47
what is a genome
sum of an organism's genetic information
48
how many chromosomes do humans
46 chromosomes - 23 from each parent
49
prokaryotic genomes are composed of..
a single circular chromosome
50
DNA gyrase function
only in prokaryotes → makes it more compact & sturdy
enzyme that uses ATP to break DNA and twist the two sides of the circle around each other → creates supercoils
51
eukaryotic DNA is wrapped around..
histones
52
nucleosomes
DNA wrapped around a group of 8 histones
53
fully packed DNA is called..
a chromatin → closely packed nucleosomes
54
are histones basic or acidic & why
they are basic → need to be attracted to the acidic exterior of DNA double helix
55
basicity of histones come from..
arginine & lysine (abundant in histones)
56
heterochromatin
darker, denser regions of chromosomes
57
euchromatin
lighter, less dense regions of chromosomes
58
why do lighter regions of chromosomes have higher transcription rates
higher transcription rates → higher gene activity
this is because the looser packing makes the DNA accessible to enzymes and proteins
59
what is a centromere
region of a chromosome where spindle fibers attach during cell docosopn
60
spindle fibers attach to centromeres via..
kinetochores (anchor attachment sites for spindle fibers)
61
centromeres are made up of..
heterochromatin and repetitive DNA sequences
62
what determines the ratio between p (short) and q (long) arms
position of the centromere
63
what is a telomere
protective caps at the end of DNA that make up chromosomes
64
repeated units of telomeres
6-8 base pairs long & guanine rich → stabilizes the end of chromosomes
65
function of telomeres
prevent chromosome deterioration & prevent fusion with neighbouring chromosomes
66
do prokaryotes have telomeres
no → circular genomes
67
RNA vs DNA (3)
RNA is single-stranded
RNA has uracil instead of thymine
pentose ring in RNA is ribose, not deoxyribose
68
why is the RNA polymer less stable than DNA
the 2' OH group (only present in ribose) can nucleophilically attack the backbone phosphate of an RNA chain
69
function of messenger RNA
type of coding RNA
carries genetic information to the ribosome → translated into protein
70
types of non-coding RNA (2)
transfer RNA
ribosomal RNA
71
transfer RNA function
# translate the genetic code
carries AAs from the cytoplasm → ribosome to be added to a growing protein
72
ribosomal RNA function
major component of ribosome
73
ribozymes
catalytic RNAs → perform specific biochemical reactions
74
the human genome contains..
24 different chromosomes (22 autosomes & 2 sex chromosomes)
75
what is an intergenic region
region composed of noncoding DNA → no known functions
76
major components of intergenic regions
tandem repeats & transposons
77
what is a gene
DNA sequence that encodes a gene product
includes regulatory regions and a region that codes for a protein or a noncoding RNA
78
single nucleotide polymorphisms
single nucleotide changes once in every 1,000 base pairs → essentially a mutation
79
where do SNPs most commonly occur
in noncoding regions → but can also lead to specific traits and phenotypes
80
copy number variation (CNV)
structural variations in the genome that lead to different copies of DNA sections
associated with cancer and other diseases
81
CNV vs SNP
changes with CNVs apply to much larger regions of the genome compared to SNPs
82
tandem repeats
short sequences of nucleotides are repeated one after another
83
when can tandem repeats be unstable
when the repeating unit is very short or very long
84
unstable tandem repeats..
can lead to chromosome breaks and disease
85
what are rich in tandem repeats
heterochromatin, centromeres and telomeres
86
what is transcription
process of reading DNA and writing the information as RNA
87
outcomes of transcription
generation of a final gene product or a messenger molecule (to construct protein)
88
what is translation
the synthesis of proteins using RNA as a template
89
what is a ribosome
massive enzyme composed of many proteins and pieces of RNA
organizes translation
90
Central Dogma
process in which the instructions in DNA are converted into proteins
DNA → RNA → protein
91
language used by RNA and mRNA to specify the building blocks of proteins
genetic code
92
genetic code is written in __ letter words
3
93
what is a codon
a nucleic acid word (3 nucleotide letters)
94
which nucleic acid actually encodes proteins during translation & what does this mean
RNA - has U instead of T
95
how many stop codons are there
3/64
96
function of a stop codon
to notify the ribosome that the protein is complete and cause it to stop reading the mRNA
97
stop codons aka
nonsense codons
98
switching the third nucleotide in a codon..
usually doesn't have an affect
usually all 4 of the codons with the same first 2 molecules encode the same AA
99
two or more codons coding for the same AA are..
synonyms
100
when a genetic code has synonyms, it is..
degenerate
101
each codon specifies..
only a single AA
102
how can viruses make DNA from RNA
with the use of the enzyme reverse transcriptase
103
conservative replication theory
the parental ds-DNA would remain as-is while an entirely new double-stranded genome was created
104
dispersive replication theory
both copies of the genomes were composed of scattered pieces of new and old DNA
105
semiconservative replication
after replication, one strand of the new double helix is parental and one strand is newly synthesized daughter DNA
106
DNA replication is..
semiconservative
107
helicase function
unwinds the double helix and separates the two strands
108
origin of replication
the place where the helicase begins to unwind
109
which protein finds the ORI in prokaryotes
DnaA
110
finding the ORI in eukaryotes
three proteins find it together (2 of them are destroyed once the S phase begins) → links DNA replication to the cell cycle so DNA replication doesn't initiate during other phases
111
topoisomerase function
cut one or both of the strands & unwrap the helix to release the excess tension created by the helicases
112
single-strand binding proteins (SSBPs) function
protect DNA that has been unpackaged & help keep the strands separated
113
importance of RNA primers
RNA that initiates DNA synthesis → DNA polymerase can only add not start so RNA primer is needed
114
how is RNA primer synthesized
RNA polymerase called primase (part of a set of proteins aka primosome)
115
DNA polymerase function
catalyzes the elongation of the daughter strand using the parental template → adds dNTPs to the 3' end
116
polymerization always occurs in..
the 5' to 3' direction
117
DNA pol requires..
a primer
118
template stands are read..
3' to 5'
119
daughter strands are elongated..
5' to 3'
120
leading strands
elongate continuously right into the widening replication fork
121
lagging strands
must wait until the replication fork widens before beginning to polymerize
122
Okazaki fragments
small chunks of DNA comprising the lagging strand
123
replication of the leading strand is..
continuous
124
replication of the lagging strand is..
discontinuous → resulting in Okazaki fragments
125
RNA primers are replaced by..
DNA
126
what joins DNA fragments
DNA ligase
127
DNA pol III function
found in prokaryotes
responsible for the fast, accurate elongation of the leading strand
can also move backward to chop off newly added nucleotides → proof reading function
128
DNA pol I function
only found in prokaryotes
adds nucleotides at the RNA primer
goes slowly, job gets taken over by DNA pol III
also has exonuclease activity (proofreading)
can also repair damaged DNA
129
theta replication
replication of prokaryotes' genome
130
what happens when telomeres become too short
chromosome can no longer replicate
131
Hayflick limit
number of times a normal human cell type can divide until telomere length stops cell division
132
telomere shortening - disease
age related diseases are linked to this
133
what happens when the telomeres' length is too short
cells activate DNA repair pathways or
enter a senescent state (alive but not dividing) or
activate apoptosis
134
telomerase function
enzyme that adds repetitive nucleotide sequences to the ends of chromosomes to lengthen telomeres
135
what is telomerase composed of
it is a ribonucleoprotein
contains an RNA primer and reverse transcriptase enzyme (read RNA templates and generate DNA)
136
telomerase - cancer
cancer cells can express telomerase → helps cells to immortalize
137
how does one get a genetic mutation
inherited or acquired through life
138
genetic mutation
alteration of the DNA sequence of an organism's genome
139
germline mutations
mutations that can be passed to offspring → occur in germ cells
140
somatic mutations
cannot be passed onto offspring, occurs in somatic cells
141
example of a physical mutagen
ionizing radiation (X-rays, alpha particles and gamma rays)
142
ionizing radiation can cause..
DNA breaks
143
single-strand vs double-strand break
single strand: can be easily patched up
double strand break: more difficult to piece back together
144
UV light - physical mutagen
causes photochemical damage to DNA
if two pyrimidines are beside each other, can cause them to be covalently linked
distorts the DNA backbone + mutations in DNA replication
145
what are cross-links
abnormal covalent bonds between different parts of DNA
146
intercalating agent
compounds that insert themselves between base pairs → cause mutations
147
biological agents of mutation (3)
DNA polymerase making a mistake in proofreading
viruses
transposons
148
types of mutations (7)
point mutations
insertions
deletions
inversions
amplifications
translocations and rearrangements
loss of heterozygosity
149
what is a point mutation
single base pair substitution
150
transition vs transversion point mutation
transition: substitution for a purine/pyramidine for a correspondent
transversion: substitution of a purine for a pyrimidine & vice versa
151
missense mutation
causes an AA to be replaced with a different AA
may not be serious if the AAs are similar
152
nonsense mutation
a stop codon replaces a regular codon and prematurely shortens the protein
153
silent mutation
a codon is changed into a new codon for the same AA so there is no change in the protein's AA sequence
154
insertion
addition of one or more extra nucleotides into a DNA sequence
155
deletion
removal of nucleotides from a sequence
156
frameshift mutations
mutations that cause a change in the reading frame
157
inversion
when a segment of a chromosome is reversed end to end
158
insertions, deletions and inversions can be caused by..
transposons
159
start codon
AUG
160
stop codons (3)
UAA
UAG
UGA
161
chromosome amplification
when a segment of a chromosome is duplicated
162
translocation
when recombination occurs between nonhomologous chromosomes → gene fusion
163
balanced and unbalanced translocations
balanced: no genetic material is lost
unbalanced: where genetic information is lost or gained
164
\_\_\_\_\_ is a common occurrence in many types of cancer
translocation
165
what is a transposon
DNA sequence that can change its position within a genome
166
3 transposons
IS element
complex transposon
composite transposon
167
IS element
composed of a transposase gene flanked by inverse repeat sequences
168
complex transposon
contain additional genes
169
composite transposon
two similar/identical IS elements with a central region in-between them
170
transposase
has “cut and paste” activity
donor site → new genetic location
171
chromosome with two transposons in the same direction..
transposons line up → parallel so they loop around
172
DNA segment between direct transposons is \_\_\_\_
deleted
173
if a chromosome has two transposons with inverted orientations..
the DNA segment between the two transposons becomes inverted
174
what happens with parallel transposons
deletion and chromosomal rearrangements (one transposon and DNA segment leave to integrate into a different genomic site)
175
loss of heterozygosity
deletion of the normal copy of a gene and mutated version of the other copy
176
why do mutations on sex chromosomes have greater effects
autosomes are present in double copies, sex chromosomes are not
177
hemizygosity
haploid expression in a diploid organism → increases effect of mutations on these chromosomes
178
gain-of-function vs loss-of-function mutations
gain of function: increases the activity of a certain gene product - gains a new/abnormal function
loss of function: gene product having less or no function
179
haplosufficiency
diploid organisms only having a single functional copy of a gene - not enough to support normal state
180
gene dose
expressing a gene is not enough - need to express enough of the gene to maintain good health
181
example of beneficial mutation in humans
mutation in Hb gene - causes sickle cell anemia BUT makes them more resistant to malaria (important in Africa etc.)
182
inborn errors of metabolism
group of genetic diseases that involve disorders of metabolism
183
cause of inborn errors of metabolism
single mutation in a single gene that codes for a metabolic enzyme
184
cancer is driven by..
mutation accumulation
185
carcinogen
mutagen directly involved in causing cancer
186
mutations involved with cancer are usually found in..
oncogenes and tumour suppressors
187
oncogene
gene that can cause cancer when it is mutated/expressed at high levels
188
tumor suppressors
deletion of these or decreased levels can cause cancer
189
direct reversal
type of DNA repair
e.g. enzymes can repair UV-induced pyrimidine photodimers using visible light
190
homology dependent repairs
dependent on using one strand of DNA to repair the damaged other strand
191
excision repair vs post-replication repair
excision: repair that happens before DNA replication
post-replication: repair that happens during and after DNA replication
192
excision repair
type of homology dependent repair
removes defective bases/nucleotides + replaces them
193
mismatch repair pathway
targets mismatched base pairs that were not repaired by DNA polymerase during replication
194
genome methylation purpose
helps bacterial machinery to recognize the older parent chain (will be methylated) and the newer chain that needs to be replaced
195
double strand break repair (2)
homologous recombination and nonhomologous end joining
196
goal of double strand break repair
reattach and fuse chromosomes that have come apart
197
homologous recombination
one sister chromatid helping to repair a DSB in the other
198
purpose of a joint molecule in homologous recombination
where damaged and undamaged sister chromatids cross over
199
when is nonhomologous end joining
used for cells that don't have the option of using sister chromatids
common in eukaryotes
200
nonhomologous end joining process
broken ends are stabilized + processed → connected by DNA ligase
201
cons of nonhomologous end joining
doesn't care about specificity → just reconnects broken chromosomes (usually gets connected in abnormal ways)
202
what is gene expression
process where information contained in genes has effects in the cell
203
mRNA function
carries genetic information to the ribosome → translated into protein
204
5' untranslated region importance of mRNA
this part isn't translated into protein → important in initiation & regulation
205
open reading frame
region of mRNA that codes for a protein
start codon to end codon
206
3' end of mRNA
after the stop codon
isn't translated into protein but contains regulatory regions (influences post-transcriptional gene expression)
207
monocistronic eukaryotic mRNA
one gene = one protein
each piece of mRNA encodes only one polypeptide
208
polycistronic prokaryotic mRNA
mRNA codes for more than one polypeptide
translation, termination & initiation sequence are found in-between the ORFs
209
how does hnRNA become mRNA
addition of a cap & tail
splicing
210
first RNA transcribed from DNA
hnRNA (immature precursor)
211
what is transcription
synthesis of RNA using DNA as the template
212
what uses template driven polymerization
replication and transcription
213
RNA transcript produced in transcription is ___ to the DNA template
complementary
214
driving force for replication and transcription
removal and hydrolysis of pyrophosphate from each nucleotide added to the chain (existing chain acts as the nucleophile)
215
does transcription need RNA primer
no → RNA polymerase
216
does RNA polymerase have exonuclease activity
no - does not possess proofreading abilities
217
promoter region
sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription
218
upstream nucleotide sequences
use negative numbers → toward the 5'
219
downstream nucleotide sequences
use positive numbers → toward the 3'
220
characteristics of prokaryotic RNA polymerase
5 subunits: two alpha, a beta, a beta' and an omega subunit
221
core enzyme for rapid elongation of transcript - prokaryotes
5 subunits of RNA polymerase
222
what makes up the holoenzyme
sigma factor and the 5 subunits of RNA polymerase
223
3 stages of prokaryotic transcription
initiation, elongation & termination
224
initiation of transcription in prokaryotes
RNA polymerase holoenzyme binds to a promoter
225
primary sequences of a bacterial promoter
Pribnow box (-10) and the -35 sequence
226
roles of sigma factor
helps the polymerase find promoters
227
how does sigma factor help polymerase find promoters
increases RNA polymerase's ability to recognize promoters
decreases the nonspecific affinity of holoenzyme for DNA
228
termination of prokaryotic transcription
termination signal (rho protein) & polymerase falls off the DNA and releases RNA
229
eukaryotic vs prokaryotic transcription (location)
p: transcription occurs in the cytoplasm (no nucleus!) - transcription and translation occur simultaneously
e: transcription occurs in the nucleus & then goes to cytoplasm for translation
230
primary transcript in prokaryotes vs eukaryotes
mRNA vs hnRNA
in prokaryotes, they are ready for translation right away (starts before transcription even ends)
231
splicing
to go from hnRNA → mRNA
introns get removed and axons join togehter
232
splicing occurs with..
spliceosome (100+ proteins & 5 small nuclear RNA molecules)
233
how do snRNPs form
half of spliceosome proteins bind to the snRNAs to from 3 snRNPs
234
function of snRNPs
snRNPS H-bond to nucleotides in the intron
two splicing reactions take place
1: attaches one end of the into to the conserved adenine (forms a loop)
2: joins two axons and releases the loop
235
5 conserved nucleotides necessary for splicing
GU, A and AG
236
alternative splicing
different options/patterns of splicing
can increase the complexity of gene expression
237
hnRNA → mRNA (3)
splicing
5' cap (methylated guanine)
3' poly-A tail (100s of adenines)
238
significance of 5' cap
essential for translation
239
significance of cap and poly-A tail
prevents digestion of the mRNA by exonucleases free in the cell
240
why do exonucleases float freely in the cell (2)
mRNA has a very short lifespan (regulation at the transcription level)
viruses inject RNA into the cell (doesn't have a cap or tail)
241
RNA polymerase I, II and III function (eukaryotes)
RNA polymerase I: transcribes most rRNA
RNA polymerase II: transcribes hnRNA (which becomes mRNA)
RNA polymerase III: transcribes tRNA
242
what is translation
synthesis of polypeptides according to the AA sequence by the specific codons in mRNA
243
each tRNA is composed of..
a single transcript produced by RNA polymerase III
244
what stabilizes tRNA
H bonds
245
anticodon function
recognized the mRNA codon to be translation (3 ribonucleotides)
246
tRNA specificity
a tRNA for every codon → tRNA is specific for one AA
247
inosine is derived from..
adenine
248
Wobble Hypothesis
first two codon-anticodon pairs are normal but the third position is more flexible (explains why a smaller number of tRNAs are possible)
249
inosine - Wobble
modified inosine base at the 5' end of an anticodon is very wobbling (can bond to AUC)
250
tRNA loading / AA activation
2 high energy phosphate bones are hydrolyzed to provide the energy to attach an AA to its tRNA molecule
251
breaking the aminoacyl-tRNA bond..
drives peptide bond formation forward
252
step 1 of AA activation
amino acid + AMP → aminoacyl AMP + pyrophosphate
253
step 2 of AA activation
pyrophosphate leaving group → hydrolyzed to 2 orthophosphates (very favourable)
254
step 3 of AA activation
destruction of the aminoacyl-AMP bond to drive tRNA loading forward
255
amino acid activation requires _ ATP(s)
2
256
aminoacyl-tRNA synthetase
specific to each AA
joins AA to the tRNA
257
amino acid activation functions (2)
specific + accurate AA delivery
thermodynamic activation of the AA
258
ribosomes are composed of..
many polypeptides and rRNA chains
259
Svedberg unit
sedimentation rate - how quickly something will sink
260
70S ribosome
prokaryotic
30S small subunit & 50S large subunit
261
80S ribosome
eukaryotic
40S small subunit & 60S large subunit
262
how many rRNA in prokaryotes
23S
263
how many rRNA in eukaryotes
28S
264
ribozymic activity is found in the __ subunits
large
265
rRNA ribozyme function
link AAs during protein synthesis via peptidyl transferase activity
266
binding sites on ribosomes (3)
A site
P site
E site
267
A site - ribosome
where each new tRNA delivers its AA
268
P site - ribosome
where the growing polypeptide chain (still attached to tRNA) is located during translation
269
E site - ribosome
where the empty tRNA sits before it is released
270
polyribosome arrangement
several ribosomes attach to prokaryotic mRNA and translate it simultaneously
271
characteristic of polycistronic mRNA
ribosomes can start translation in the middle of the chain
272
Shine-Dalgarno sequence
ribosome binding site for prokaryotic translation
located at -10
273
initiation of prokaryotic translation
30S (small) subunit binds to 2 initiation proteins (IF1 & IF3)
this entire process then binds to the mRNA transcript
then the aminoacyl-tRNA, IF2 (bound to a GTP) joins
finally, the 50S subunit joins
274
first aminoacyl-tRNA in pro translation initiation
initiator tRNA
275
first amino acid in all prokaryotic proteins
modified methionine - AUG
276
where does the initiator tRNA sit
in the P site of the 70S ribosome (hydrogen bonded with start codon)
277
when does AUG initiate translation
when a Shine-Dalgarno sequence comes before
278
what happens before the elongation stage of pro translation
initiation factors dissociate from the complex
279
elongation pro translation
2nd aminoacyl-tRNA enters the A site & H-bonds with the second codon (done by elongation factor Tu)
peptidyl transferase of the large subunit catalyzes a bond between fMet and the 2nd AA
280
direction of synthesis pro translation
N → C
since the N of amino acid 2 bind to the C of amino acid 1
281
translocation pro translation
the empty tRNA moves into E site, tRNA #2 (with the growing polypeptide) moves into the P site and the next codon goes into the A site
282
what helps with translocation
elongation factor G (EF-G)
283
purpose of EF-Ts
removes the remaining GDP from EF-Tu → helps it reset
284
termination pro translation
occurs when stop codon appears at the A site
a release facto then enters the A site
causes peptidyl transferase to hydrolyze the bond between the last tRNA and the completed polypeptide
285
RF3 function
GTP-binding protein that doesn't recognize a stop codon but leads to the dissociation of RF1/RF2 after peptide release
286
why can't eukaryotic transcription and translation occur at the same time
needs transport from nucleus → cytoplasm
287
do eukaryotes use Shrine-Dalgarno sequences to initiate translation
no
288
how is translation in eukaryotes started
with 5' UTR sequences - common one is the Kosak sequence
289
eukaryotic translation initiation
initiation complex forms (40S subunit, Met-tRNAMet and eukaryotic initiation factors (eIFs) → recruited to 5' cap
once a start codon is found → 60S subunit is recruited and translation can begin
290
eIF proteins & their functions in initiation (4)
eIF3 prevents premature association with 60S
eIF4A is a helicase and unwinds mRNA
eIF4E binds the 5' cap to mRNA
eIF4G is a scaffold protein (regulator)
291
rate limiting step for translation
eIF proteins
more of them = more translation
292
eukaryotic translation elongation factors
helps with the entry of aminoacyl-tRNA into the A site
and one is a guanine nucleotide exchange factor (releases GDP)
293
eukaryotic translation termination release factors
eRF1 recognizes the 3 termination codons
eRF3 helps to release the completed polypeptide
294
cap dependent translation
eukaryotic translation starting at the 5' end of an mRNA
295
cap independent translation
eukaryotes can sometimes start translation in the middle of an mRNA molecule
296
what is necessary for cap independent translation
transcript must have an internal ribosome entry site
these make sure that cells can make essential proteins under sub-optimal growth conditions
297
principle site of gene expression regulation
transcription (in both eu and pro)
amount of protein made is affected by the amount of mRNA that gets transcribed
298
ways of controlling gene expression at the DNA level (4)
DNA methylation/chromatin remodelling
gene dose
imprinting
X chromosome inactivation
299
DNA methylation - controlling gene expression
prokaryotic & eukaryotic covalently modified by adding a methyl group
300
how does DNA methylation control gene expression (2)
physically blocks the gene from transcriptional proteins
certain proteins bing methylate CpG groups & recruit chromatin remodelling proteins to change the winding of DNA around histones
301
gene dose - controlling gene expression
increased copy number of a gene by amplification
allows a cell to make large quantities of a protein
gene deletion = opposite
302
genomic imprinting - controlling gene expression
when only one allele is expressed
epigenetic process
303
X chromosome inactivation - controlling gene expression
females have 2 X chromosomes (one active & one inactive)
different X chromosomes inactivated in different tissues and cells (the cells decide)
304
simple mechanism of bacteria transcriptional regulation
some promoters are stronger than others
(this is preset)
305
anabolic and catabolic enzymes - regulation of transcription in prokaryotes
anabolic enzymes whose transcription is inhibited in the present of excess products → repressive
catabolic enzymes whose transcription can be stimulated by abundance of substrate → inducible enzymes
306
components of a lac operon (5)
P region: promoter site on DNA → RNA polymerase binds here to initiate transcript for Y Z A genes
O region: operator site where Lac repressor binds
Z gene: codes for enzyme beta-galactosidase (cleaves lactose → glucose + galactose)
Y gene: codes for permease (transports lactose into cell)
A gene: codes for tranacetylase (transfers an acetyl group from acetyl-CoA to beta-galactosides
307
crp gene function
codes for catabolite activator protein (CAP)
308
I gene fucntion
codes for Lac repressor protein
309
in the presence of glucose, lac operon will be \_\_
off
310
glucose, adenyl cyclase and cAMP
glucose levels control levels of adenyl cyclase
adenyl cyclase converts ATP → cAMP
311
I gene & transcription
codes for a repressor protein → prevents RNA pol from binding to the promoter and transcribing Z, Y and A genes
312
lac operon in the presence of glucose and absence of lactore
Z, Y and A are not transcribed or translation
low levels of cAMP
313
lac operon in the presence of glucose and lactose
Z, Y and A are transcribed at low levels
decreased cAMP levels
314
lac operon in the absence of glucose and presence of lactose
Z, Y and A are transcribed at high levels
315
in the presence of tryptophan..
trp repressor protein and typotophan bind to the operator together
RNA pol cannot bind to the promoter → trp genes are turned off
316
activator proteins - regulation
point of transcriptional regulation in eukaryotes
enhancer sequences in DNA are bound by activator proteins
317
gene repressor proteins - regulation of transcription in eukaryotes
these proteins inhibit transcription
318
RNA translocation - transcription regulation in eukaryotes
mRNA transcripts aren't translated into proteins until they are localized properly in the cell
nucleus → cytoplsm
important in cells with a high level of polarity
319
mRNA surveillance - transcription regulation eukaryotes
monitoring so only high quality mRNA transcripts are read
defective transcripts are degraded
320
RNA interference - transcription regulation eukaryotes
way of silencing gene expression after a transcript has been made
decreases protein expression
321
protein folding: post-translational modification
newly synthesized protein is folded into 3D shape by chaperone proteins
322
covalent modification: post-translational modification
proteins are covalently modified
e.g. adding acetyl, formyl or alkyl groups
this can change many aspects of a protein (e.g. enzyme affinity for substrate)
323
processing: post-translational modification
cleavage (from zymogens → mature protein)
324
why are protein precursors used
when the mature protein is dangerous to the organism → allows to control how much there is
325
Doppler ultrasound allows to distinguish between..
a stationary and moving object
326
splicing is a…
post-transcriptional modification
327
cytochrome C acts as a ___ electron carrier
1
328
what makes the best primer for PCR
primers with high G and C (esp near the ends)
329
what is PCR
polymerase chain reaction
making lots of copies of a specific segment of DNA
330
in what phase of meiosis does nondisjunction occur
anaphase I
331
high insulin levels leads to..
low blood sugar levels
332
which amino acid is neutral, but zwitterionic at pH 7, despite possessing two nitrogen atoms in its formula
glutamine
333
actin is a..
microfilament
334
colour weakness is due to..
absence/reduction in the number of receptors for the specific colour → fewer signals sent to the brain
335
head of a fatty acid
carboxyl group
336
carbonic anhydrase inhibitor to the RBCs would most likely cause an increase in..
CO2 in the tissues
337
HCO3– concentration in veins vs arteries
higher in the veins
338
lining of the mouth is derived from..
ectoderm
339
according to Mead, the spontaneous and autonomous part of our unified self is the..
I
