Genetic Exam 2 Flashcards
1
Q
The normal chromosome complement of a cell in mitotic metaphase: Human male:
A
22 pairs of autosomes + X + Y
2
Q
The normal chromosome complement of a cell in mitotic metaphase: Human female:
A
22 pairs of autosomes + 2 Xs
3
Q
What are sex chromosomes
A
Chromosomes that specific es sex (X and Y in humans)
4
Q
What are autosomes chromosomes?
A
All other non-sex chromosomes
5
Q
What is the human Karyotype? (4x)
A
- Represents the chromosome complement
- Produced as a metaphase spread
- Trad method: Giemsa staining
- Mod method: chromosome painting
6
Q
What is Giemsa staining
A
Dyes like Giemsa (and others) stain smaller segments of the chromosomes
7
Q
When using Giemsa staining what regions stain darker
A
G-bands, gene poor, heterochromatin
8
Q
When using Giemsa staining what regions stain lighter
A
R-bands, gene rich, euchromatin
9
Q
Are banding pattern specific to each chromosome when using Giemsa staining
A
Yes
10
Q
What is a major different between Chromosome painting and Giemsa staining
A
Chromosome painting color each chromosome a different color while Giemsa staining results black or white staining on all chromosomes
11
Q
What is Chromosome painting
A
Makes DNA probes specific to each chromosome which are then labeled with fluorescence
12
Q
Which technique is this?
Make DNA probes specific to each chromosome
Label DNA probes with fluorescence
Hybridize the probe to the metaphase spread (squash)
Wash off unbound probes
Examine the slide on fluorescent microscope
A
Chromosome painting
13
Q
What does 9q34 refers to?
A
Chromosome 9, long arm, band 34
14
Q
What does Xp28 refer to?
A
Chromosome X, short arm, band 28
15
Q
Bands and inter bands are assigned with numbers
A
True
16
Q
How do we ensure genes on the X chromosome are expressed at similar levels in both sexes?
A
Unequal dosage in different sexes by increasing the activity of genes in the Chromosome X for males or reducing the activity of genes in X chromosomes for females
17
Q
How do mammals compensate for dosages of X linked genes
A
X chromosomes inactivation in females
18
Q
How do Drosophila compensate for dosage of X chromosomes
A
Increase transcription activity on X chromosomes in males
19
Q
How does C elegans compensate for dosage of X chromosomes
A
Decrease transcription activity in both X chromosomes in females
20
Q
What are complex traits?
A
Affected by the alleles of 2+ genes (genetic factors) as well as by environmental factors
21
Q
What are 3 categories of complex traits
A
Continuous traits (quantitative traits)
Categorical traits
Threshold traits
22
Q
What are categorical traits
A
The phenotype corresponds to any one of a number of discrete categories
23
Q
What is an example of Categorical traits
A
The number of puppies in a litter; flower colors; animal fur colors
24
Q
What are threshold traits
A
A few phenotypic classes, determined by multiple genes & the environment. When a threshold is reached, it shows one phenotype; otherwise, it shows another phenotype
25
What is an example of threshold traits?
Adult onset diabetes
26
Flower color is an example of what complex trait
Categorical traits
27
Animal fur color is an example of what complex trait
Categorical traits
28
Adult onset diabetes is an example of what complex trait
Threshold
29
Heights and weights is an example of what complex traits
Continuous traits
30
Blood pressure in humans is an example of what complex trait
Continuous traits
31
A large variance means what
The distribution is spread out
32
A small variance means what
The distribution is clustered around the mean
33
What is normal distribution
When the data are symmetrical, the distribution can be approximated by a smooth, bell shaped curve
34
A feature of normal distribution is that one standard dev is ______%, two standard dev is ______%, three standard dev is ______%
68%, 95%, 99.7%
35
What are causes of variation (4x)
1. Genotypic variation
2. Environment variation
3. Variation due to genotype-by-environment interaction
4. Variation due to genotype-by-environment association
36
What is Genotypic variance?
Differences in genotype that cause phenotypic variance
37
What is Environmental variation?
differences in the environment that cause phenotypic variance
38
What assumptions are made for the Segregation of 3 genes affecting a quantitative trait
Each Uppercase allele adds one unit to the phenotype
Each lowercase has no effect
39
What is the results of the segregation of three genes affecting a quantitative trait?
7 phenotypic categories, mean = 3, variance 1.5
40
The distribution of phenotypes as determined by 3 genes or 30 genes are not alike (T/F)
False
41
In the absence of environmental variation, the distribution of phenotypes alone provides what information?
Limited info about the # of genes involved and no info on dominance relations
42
If genotype and environment separately and independently affect phenotype, how can you calculate phenotype variance?
variance(p) = variance(g) + variance (e)
43
If genotype and environment do not act separately and independently they are what variance
G-E Interactions or G-E Associations
44
What are G-E interactions?
Environmental effects on phenotype differ according to genotype
45
What are G-E associations?
Different genotypes are not distributed at random in all possible environments (certain genotypes are preferred with certain environments)
46
What is an example of G-E associations?
Framers feed their cows in proportion to their milk production levels
47
What is an example of G-E interactions?
Strain A is superior when environmental quality is low, but strain B is superior when environmental quality is high
48
What are 3 methods to identify genes affecting complex traits?
1. Linkage analysis in mapping QTLs
2. GWAS
3. Candidates genes for complex traits
49
What is Quantitative trait Loci mapping?
Identifying QTL through linked genetic markers
50
What is Quantitative trait Loci?
A gene that affects a complex trait
51
Can QTLs be identified in pedigrees?
No
52
Common alleles affecting complex traits account for a small fraction of total heritability (T/F)
True
53
How many GWAS were identified for Chron's disease?
71
54
How many % does 71 loci account for phenotypic variation in Chron's disease
23%
55
What are candidate genes
Genes we suspect could contribute to a complex trait that we test the function of
56
What are some examples of candidate genes?
SLC6A4 is an candidate gene for depression that encode a serotonin transporter
57
What is serotonin?
A neurotransmitter that influences anxiety and depression
58
What is the function of Serotonin transporter SLC6A4
Transport serotonin from neurons that make it to neurons that receive it; also recycles serotonin (uptake)
59
The target of antidepressant drugs are
SLC6A4 which will inhibit uptake
60
S form is
the short allele
61
L form is
the long allele
62
How do S and L forms differ
in # of tandem repeats in the promoter region
63
L/L genotype does what
cells make more mRNA and in turn more SLC6A4 protein
64
S/L and S/S genotypes do what
have a higher risk of depression
65
What is the G-E interaction for depression?
Among Ecstasy users (environment factor) depression scores highest in S/S genotype which means ecstasy results in the biggest difference in S/S genotype
66
What is euploid
possessing a normal complement of chromosomes
67
What is aneuploid
possessing an abnormal number of one chromosome (or region of chromosome)
68
What is monosomy
Only possess one copy of chromosome
69
What is trisomy
Possess 3 copies of chromosome
70
What is polyploid
contains extra complete set(s) of chromosomes (triploid, tetraploid, etc)
71
In human pregnancies, which type of aneuploid is most common
monosomy
72
In humans which type of aneuploid is most harmful
monosomy
73
Down syndrome is what type of aneuploid
Trisomy 21
74
How common is Down syndrome
1 in 750 live births
75
What is the most common cause of Down syndrome?
nondisjunction during meiosis
76
What is the least common cause of Down syndrome?
chromosomal translocations
77
What are some symptoms of Down syndrome?
intellect disability
physical abnormality (heart defect)
characteristic facial appearance
78
Occurrence of Down syndrome _________ as women ag
increases
79
What are some examples of environmental effects on nondisjunction?
Bisphenol A (BPA), alcohol, smoking, pollutants, oral contraceptives
80
Why are sex chromosome abnormalities more common than trisomy 21
Dosage compensation ensures extra X chromosomes are inactivated and Y chromosomes only contain a small # of genes
81
47 XXY
Klinefelter syndrome: male, tall, sterile, mild impairment
82
45X
Turner syndrome: female, short, no sexual maturation
83
47 XXX
female, mostly normal, mild impairment (more frequent)
84
47 XYY
male, mostly normal
85
What is chromosomal deletion
a segment of a chromosome is missing
86
The bigger the deletion, the more harmful (T/F)
True
87
How can chromosomal deletion occur
1. chromosomal breakage and reunion
2. ectopic recombination between direct repeats
88
What are direct repeats?
two repeated blocks that have the same orientation
89
What is a chromosomal duplication
a chromosome has a region that's duplicated (present twice)
90
What is tandem duplication
the segment is duplicated and is in the same orientation immediately adjacent to another
91
Unequal crossing over between duplication results in
even more tandem copies
92
Human red-green color genes are __________ thus pairings can happen
highly similar (96%)
93
What results in color blindness
the unequal crossover in red-green chromosome
94
What is chromosomal inversion
a chromosome in which linear order of a group of genes is reversed
95
What results in chromosomal inversion
ectopic recombination between inverted repeats
96
What are inverted repeats
two repeats that are in reversed order (opposite to direct repeats)
97
What are translocations
interchange of parts between nonhomologous chromosomes
98
What is reciprocal
two reciprocally interchanged parts
99
What is heterozygous translocation?
one pair interchanged, one pair normal
100
What is homozygous translocation?
both pairs interchanged
101
What is Robertsonian translocation
a special type of nonreciprocal translocation where 2 nonhomologous acrocentric chromosomes fuse their short arms resulting in 1 chromosome with a centromere
102
___ % of down syndrome results from Robersonian translocation
3
103
Segregation of Robertsonian translocation ratio
1/4 (adjacent 1) 1/4 (adjacent 2) 2/4 (alternate)
104
Polyploidy is not common in higher plants (T/F)
False
105
What is polyploidy
Containing multiple complete sets of chromosomes
106
How many flowering plants are polyploidy
30-80%
107
What are some examples of plant polyploidy
corn, wheat, cotton
108
What is the effect of triploid on plants
trouble with meiosis and used to produce seedless crops
109
What type of polyploidy does seedless watermelon have
cross between diploid and tetraploid results in triploid seed
110
What is monoploid
the basic set of chromosomes that's multipled in a polyploid species
111
What is haploid
the set of chromosomes present in the gamete
112
How common is sexual polyploidization
1-40% frequency, under genetic control
113
What is sexual polylploidization
The increase in chromosome number takes place in meiosis through the formation of unreduced gametes
114
What is asexual polyploidization
The increase in chromosome number takes place in mitosis through the doubling of the complement of chromosomes
115
What is autopolyploidy
all chromosomes derive from a single diploid species
116
What is allopolyploidy
sets of chromosomes derive from 2 or more different ancestral species
117
What is Plasmid
nonessential bacterial DNA thats not part of the genome
118
Can plasmids replicate independent of genome replication
Yes
119
How are plasmids passed on
passed on to progeny
120
What is the shape of plasmid
circular or linear
121
How many copies of number do plasmids have
high copy number (50) or low copy number (1-2)
A few kb to a few hundred kb
122
What is F plasmid
1. F factor (fertility)
2. Can be transferred from F+ to F- during conjugation
3. Conjugative plasmid
123
What is conjugation
the joining of 2 bacterial cells in the genetic transfer process
124
Transfer of F plasmid between cells begins as
a single strand
125
What is the results of F+ x F- mating
Transfer is replicative, Donor remains F+ and recipient becomes F+
Only plasmid DNA is transferred
126
What are some useful bacteria; mutants
1. Antibiotic resistant mutants
2. Nutritional mutants
3. Carbon-source mutant
127
What are some examples of antibiotic mutants
Streptomycin-resistant (Str-r) and Streptomycin sensitive (Str-s)
128
What are some examples nutritional mutants
Prototroph: wild type cells (grow in minimal medium)
Auxotroph: unable to synthesize essential nutrient
129
What are carbon source mutants
cannot utilize a particular source of carbon or energy
130
What is an example of carbon source mutant
Lac-mutants cant grow on media that only have lactose as carbon source
131
What is selective medium
Medium that allows the growth of only one type of cell
132
What is nonselective medium
Medium that allows all types to grow
133
How do I isolate mutants that do NOT grow on selective media?
Minimal media + penicillin (kills dividing cells)
134
What is replica plating
1. Transfer process: Use sterile velvet to pick up bacteria and then transfer onto replica plate
135
What is DNA-mediated transformation
Recipient cells acquire genes from free DNA molecules in the medium
136
In nature (soil), free DNA can be from lysis of donor cells (T/F)
True
137
What are the two steps of DNA-mediated transformation
1. Taking up the DNA
2. Homologous recomb with recipient DNA
138
Are all species capable of transformation
No
139
If two genes a and b are widely separated, chances of them being co-
transformed are
low
140
If they are close, they often present on _________ then
their co-transformation rate is __________
If they are close, they often present on a single donor fragment, then
their co-transformation rate is close to the frequency of single-gene
transformation
141
The farther apart two genes are, the less likely they will be co-
transformed (T/F)
True
142
How is Hfr plasmid is formed
The integration of F into bacterial chromosome by reciprocal recomb
143
How much of F DNA make up the bacterial chromosome
2%
144
Result of Hfr x F- Mating
1. Donor remains Hfr
2. Recipient does not become F+ because they did not gain the whole F+ dna. Some recipients will become recomb where transferred fragment gets integrated
145
How long does it take for the whole genome to get transfered
100 minutes
146
Do cells usually separate after 100 minutes during transferring of DNA
No
147
What is Time of Entry mapping
based on the order of transfer of genes you can determine the sequence as the further away a gene is, the longer it takes for that gene to get transferred
148
What is transduction
DNA fragment transfer from one cell to another by a phage particle containing the bacterial DNA
149
Where is the DNA contained on a T2 phage particle
Head
150
What is generalized transduction
In generalized transduction, the phage can carry any part of the DNA and transfer to another
151
What are the types of mutations
By tissue of origin, by function, by molecular nature.
152
What are origin mutation
Spontaneous, induced ( presence of known mutagen ),
153
What are cell type mutations
Somatic ( non reproductive cells) & germline ( reproductive cells)
154
Which type of cell type mutation is transmitted to the next generation
Germ line mutation
155
What is nucleotide (nt) substitutions
A nt pair is replaced with another pair
156
What is transitions
T→ C or C → T (pyrimidine to pyrimidine)
A → G or G → A ( purine → purine )
157
Phages carries a _________ piece of any part of the bacterial genome during ____________
small piece, lytic cycle
158
Phages when infecting other bacterium cells, can _______
transduce the new host genome through recomb
158
What do phages do to bacterial cells
lyses (break the bacterial genome)
159
Roughly how many phage particles contain bacterial DNA
1 in 10^6
160
How can generalized transduction be used in mapping
Using Cotransduction, the farther 2 markers are, the less likely they will be contransduced
161
What is Cotransduction
2 markers getting transduced into one bacterium
162
____% E coli phage capable of lytic cycle and ____% undergoes lysogeny
75% and 25%
163
What is lysogeny
When a phage infects a host but doesn't destroy the host
164
What is lytic cycle
When a phage infects a host and destroy the host
165
Phage DNA is integrated into the bacterial genome during
lysogeny
166
Once integrated, the phage is now a _______
prophage
167
After the phage integrates into bacterium, the bacterium is called
a lysogen
168
For lysogeny, phage will cut themselves out of the bacterium to move to another host, which is called
excision
169
Excision is ____% accurate
99.9%
170
What happens when there is an error during excision
Specialized transduction
171
What is specialized transduction
DNA excised from bacterium genome may carry a small piece from host, adjacent from the integration site
172
When a specialized transduction occurs the new host will
May gain a small piece of the previous host
173
Is the gene from specialized transduction random
No, only genes nearby the integration site
174
What is C-value paradox
the noncorrelation between complexity of organisms and genome size
175
What is an example of C value paradox
Salamanders having 30x genome than humans
176
E Coli genomic DNA is ____________ um long, while cell is _ um long
1500 and 2
177
The largest human chromosome is ___mm long
82
178
How does the DNA achieve compactness?
Supercoiling
179
Relaxed DNA molecule has _ base pair per helical turn
10
180
What is relaxed DNA
no twisting other than helical twisting
181
What is supercoiling of DNA
the segments of double stranded DNA are twisted around one another
182
Underwinding the helix creates
bubbles and supercoils
183
Bubble of unpaired bases compensates for
underwinding
184
Underwound DNA can also compensate by forming
negative supercoils
185
What is Topoisomerase I
relaxes supercoiled DNA to remove helical constraints that can otherwise hinder DNA replication and transcription (+/- linking #) doesn't require ATP
186
What is Topoisomerase II
Topoisomerase II is an enzyme that is able to break and rejoin double-strand DNA molecules (+/- 2 linking #) requires ATP/NADH
187
What is Topoisomerase also known as
Gyrase (super unwound -2) or reverser Gyrase (super wound +2 )
188
What is topoisomerase
breaking one or both strands, changing the bp number per turn and rejoining the broken strands
189
Bacterial genome structure (3x)
1. DNA is compacted due to supercoiling
2. Also due to protein that wrap, bend, or compact the molecule
3. DNA is a condensed unit called nucleoid
190
What is a nucleoid
a set of looped domains (supercoiled DNA attached to a protein core)
191
What is chromatin
DNA associated with numerous proteins in a stable and ordered aggregate
192
What is Histone
the major class of proteins that associate with DNA
193
What are Eukaryotic genome structure
1. Chromatin
2. Histone
194
How many amino acids are in Histone
100-200
195
What are some characteristics of histones (4x)
1. rich in lysine and arginine (+ charged)
2. attracted to negatively charged phosphate groups in DNA backbone
3. H1, H2A, H2B, H3 and H4
4. Sequences highly similar among different organisms
196
Chromatin shows a _______ structure under electron microscope
bead-like
197
Nucleosomes
the bead-like unit in chromatin
198
The average length of DNA fragment _________ per nucleosome
~200bp
199
The average length of core DNA ___ per core particle
~145 bp
200
Histone Tails (amino ends) are subject to modifications (5x)
1. Acetylation
2. Methylation
3. Phosphorylation
4. Certain mods are associated with double strand break during recomb and DNA repair
5. Other mods regulate gene activity (transcription levels)
201
The internal structure of nucleosomes contain
H2A, H2B, H3, H4 (2 each)
202
Chromosome condensation during cell division (early prophase)
1. form loops
203
Chromosome condensation during cell division (late prophase)
2. shortens
204
Chromosome condensation during cell division (metaphase)
3. Compresses laterally
205
Proteins that help with condensation:
1. Cohesions
2. Condensins
3. Topoisomerase II
206
Nucleosomes further from _______
coils
207
The eukaryotic genome contains:
______%: unique sequences
______%: high repetitive sequences (__________ per repeat, as many as 10^5 copies)
______% middle repetitive sequences (______ copies)
30-75%: unique sequences
5-45%: high repetitive sequences (5-300 per repeat, as many as 10^5 copies)
1-30% middle repetitive sequences (10-1000 copies)
208
How many unique sequences do viruses and prokaryotes have
almost all unique sequences
209
How many unique sequences do sea urchins have
40%
210
How many unique sequences do humans have
over 50%
211
How many unique sequences do drosophila have
70%
212
Highly repetitive sequences are what sizes and also called what
mostly are fairly short (aka satellite sequences)
213
Where are highly repetitive sequences located in
heterochromatin
214
Where is heterochromatin
1. adjacent to centromeres and near chromosome arms ie telomere
2. are interspersed with euchromatin and contains a small # of genes
215
Which contains more genes Euchromatin or Heterochromatin
Euchromatin
216
Euchromatins are where in relation to a chromosome
In between the Heterochromatin
217
What are middle repetitive sequences
Contains genes coding for groups of genes (rRNA, tRNA, histones, etc)
Contain transposable elements (TEs)
218
What are transposable elements
contains terminal repeats that, allow transposase to bind or allow themselves to be recognized and ligated to target insertion sites
DNA sequences that move from one location on the genome to another
219
What is transposase
an enzyme that carries out the transposition
220
In the human genome, how many TEs are not able to transpose
50%
221
TEs always own active transposase
False
221
TEs may encode their own transposase
True
221
What types of repeats may TEs have
terminal direct repeats, inverted repeats, or no terminal repeats
222
What are direct repeats
sequences that have the same 5' to 3' polarity and are in the same DNA strand
223
What are inverted repeats
sequences that are opposite DNA strands in order to preserve the same 5' to 3' polarity
224
What are non-long terminal repeats
Have no terminal repeats, include LINE and SINE and are most abundant ones in mammalian genomes
225
What is LINE
long interspersed nuclear element
226
What is SINE
short interspersed nuclear element
227
Human genome contains a significant amount of TEs
True
228
What are centromeres
a narrow constriction along the chromosome
229
What is a central component of kinetochore
centromeres
230
What is kinetochore
where spindle fibers bind to pull DNA apart during cell division
231
What are holocentric chromosomes
Centromeric sequences spread throughout the chromosome
232
What is an example of holocentric chromosome
C elegans
233
What is the most common centromeres
Localized centrosomes
234
Centromeres in yeast are big and complex
False (small and simple)
235
What are the lengths of centromeres in other eukaryotes
hundreds of kb in size
236
What are telomeres
a special DNA protein structure at the end of chromosome
237
What becomes shorter with each round of DNA replication without telomerase
telomeres
238
What do telomerase do
adds tandem repeats to the end of the chromosome thus preventing it from shortening
239
The simple sequences in telomeres in human
5' TTAGGG 3'
240
The simple sequence in telomeres in Tetrahymena
5' TTGGGG 3'
241
What is Hayflick's limit
in most cells, telomerase are limited so telomere length limits # of cell divisions
242
Telomere length is restored as fast as it was shortened
False
243
How many divisions can human progenitor cells go for
about 70
244
What is the difference between embryonic stem cells and cancer cells vs progenitor cells
Embryonic stem cells and cancer cells have high telomerase activity
245
What are the 4 stages of DNA replication
1. Initiation
2. Elongation
3. Termination
4. Fidelity
246
What are the key features of DNA replication (5x)
1. Semi conservative replication
2. Proceeds in 5' to 3' direction
3. Catalyzed by DNA polymerases
4. Requires free deoxynucleoside triphosphate (dNTP)
5. Requires free 3'OH group on stand being synthesized
247
What is the semiconservative model of replication
One strand is used as template to make new complementary strand
248
How is free dNTP used as a substrate
1. dNTP is added to growing chain
2. O-P bond forms between phosphate group and 3' OH
3. pyrophosphate is released
4. dNTP (A T G C) is selected according to base pairs
249
Can new dNTP be added to 5' end
No
250
What is initiation
1. starts with RNA primer which is the elongated by adding deoxyribonucleotides to its 3' end
251
What is elongation
1. Chain grows from 5' to 3'
2. requires DNA polymerase
3. Continuous on leading strand
4. Discontinuous on lagging strand
252
What is Fidelity
1. Errors occur 10^-5 where there is a mismatch in base pairs per round of replication (ie 6000 mismatches per cell cycle in humans)
2. Polymerase has proofreading ability
253
Are there different mechanisms in prokaryotes and eukaryotes for termination
Yes
254
What type of replication does E coli have
theta replication
255
Wat kind of replication does F plasmid, phage, and etc have
rolling circle replication
256
What is theta replication
Replication occurs on a continuous DNA, is bidirectional w/ 2 replication forks
257
What is rolling circle replication
Starts with a single-strand cleavage that produces a 3' end and 5' end and results in linear tandem repeats of parental sequences
258
What occurs in late stages of replication od dsDNA phages with circular DNA
Rolling circle replication
259
Replication between F plasmid and Hfr conjugation and recipient E coli is
Rolling circle replication
260
What are the key enzymes/proteins involved in DNA replication (5x)
1. Gyrase
2. RNA primer
3. DNA ligase
4. Helicase
5. SSB protein
261
What is Helicase
an enzyme that uses ATP to unwind the DNA
262
What is SSB proteins (Single strand DNA binding)
binds to and stabilizes the single-strand DNA
263
What is Gyrase
a type of Topoisomerase II: releases torsional stress caused by unwinding
264
Primase
a special RNA polymerase that synthesizes the RNA primer
265
Polymerase
add new nucleotides to daughter molecule
266
267
Transcription
The synthesis of an RNA molecule from corresponding DNA segment
268
Promoter
The region where RNA polymerase and other transcription factors binds to initiate transcription (20-200nt)
269
Translation
Info transfer from the mRNA to amino acid sequences and the chemical run that link the amino acids to polypeptide chain
270
Transcript
The RNA product of transcription
271
Ribosome
Particles in the cytoplasm where translation takes place
272
rRNA
ribosomal RNA, component of the ribosome
273
mRNA
Messenger RNA, template for translation
274
tRNA
Transfer RNA, the RNA that recognizes the codon in the mRNA and transfers the corresponding amino acid during translation
275
Polypeptide
A string of amino acids connected by peptide bond
276
Protein
One or more polypeptide chains folded into a higher order structure
277
TSS
Transcription start site
278
In Ecoli, genes and proteins are
Colinear
279
If genes and proteins are colinear a mutation earlier in the gene results in
Amino acids positions earlier in protein sequence
280
One strand of DNA is used as template to make
RNA
281
Usually only one DNA strand is transcribed for a particular gene
True
282
Transcription in prokaryotes- Initiation
Need:
The RNA polymerase + promoter sequence
283
Promoter sequence in E. coli starts at what sequences
-35 and -10
284
Consensus sequence
Sequence of nucleotides determined by the majority rule from the actual sequences
285
What does Polymerase does
1. Unwind DNA
2. Bind to unwound DNA
3. Adding nucleotide to the growing rNA chain (require free OH group)
286
RNA polymerase
Synthesizes RNA
287
DNA polymerase
DNA replication
288
Transcription in prokaryotes- Termination
Intrinsic termination
By a terminator sequence in DNA
289
Transcription in eukaryotes- Polymerases
RNA Pol I, Pol II, Pol III
Pol I: rRNA production
Pol II: mRNA (12 subunit holoenzyme)
Pol III: tRNA and 5S rRNA
290
Transcription in eukaryotes- Promoters
TATA box
25-30 not upstream of the transcription start site
291
Transcription in eukaryotes – Transcription factors (TFs)
1. DNA binding proteins that regulate the initiation of transcription
2. 26 general TFs interact with Pol III complex
3. Enhancers and silencers
292
DNA binding proteins that regulate the initiation of transcription
1. General transcription factors (required for transcription)
2. Tissue specific transcription factors (regulate gene expression in a tissue-specific and timing-specific manner)
293
Enhancers and silencers
DNA fragment bound by TFs that are often located far upstream or even downstream of TSS to regulate transcription levels
294
Transcription in eukaryotes - Initiation (2 steps)
1. TATA box binding protein binds and bends promoter DNA
2. Other transcription factors start to bind, unwind and stabilize DNA
295
Transcription in eukaryotes - Elongation
Only one DNA strand is transcribed (template strand)
296
Base pairing specificity comes from:
1. weak hydrogen bond between bases
2. structural changes near the active site of PolII that promote the electron transfer during polymerization
297
Transcription in eukaryotes - termination (3x)
1. No specific terminator sequence known
2. End of transcript established by RNA processing
3. One round does not have to finish to start another round of transcription
298
Primary transcript:
The RNA molecule produced from transcription from DNA template
299
Prokaryotes RNA processing
Primary transcript = mRNA
300
Eukaryotes RNA processing
Primary transcript (processing—>) mRNA
301
RNA processing – 5’ capping
1. Adding a 5’ modified guanosine (a cap)
2. For mRNA to bind to ribosome for protein translation
302
RNA processing – 3’ polyadenylation
1. Adding a poly-A tail at 3’ end
2. Determines mRNA stability
303
RNA processing - splicing
1. Introns
2. Exons
3. Splicing
304
Introns
The segments in primary transcript that are not used in protein translation and need tp be excised
305
Exons
The segments that will form the mRNA sequence
306
Splicing
Cutting out the introns and connecting exons
307
RNA processing: Capping machinery
Is recruited early, when length of pre-mRNA is only 20-40 nucleotides
308
RNA processing: splicing machinery
Is recruited to each intron as the intron is being transcribed
309
RNA processing: Polyadenylation
Introns
Are not necessarily spliced in the same order in which they are transcribed
310
RNA processing: Polyadenylation
Splicing
Recruits proteins to the exon junction that function later to facilitate export of the mRNA
311
RNA processing: Polyadenylation
Is recruited when transcription is terminated
312
RNA processing: Polyadenylation at what step
Terminatio
313
RNA processing: Capping and splicing machinery at what step
Transcription initiation and elongation
314
RNA processing: Release and export at what step
Release and export
315
RNA processing: Release and export what occurs
1. 5’ cap is in place
2. All introns are remove prior to the release of the mRNA
3. Exon are marked with export proteins and first round proteins to detect premature termination condones
4. Poly A tail has been added to 3’ end
316
Protein synthesis - ribosomes
Protein + RNA complex that synthesizes polypeptide chain using mRNA as template
317
ribosomes size (E coli and Eukaryotes)
Small and large subunits
1. E. coli 30S subunits and 50S subunits
2. Eukaryotes 40S subunit and 60S subunits
318
Protein synthesis - tRNA
an RNA molecule that recognizes each triplet codon on the mRNA and transfer a specific amino acid to the growing peptide chain
319
Aminoacyl-tRNA synthetases
enzymes that catalyzes the attachment of each amino acid to its corresponding tRNA molecule
320
Protein synthesis- Prokaryotes
Transcription and translation: simultaneous and colocalized
Polycistronic mRNA: common
321
Protein synthesis- Eukaryotes
Transcription and translation: separate (nucleus and cytoplasm)
Polycistronic mRNA: rare or nonexistent
322
Does nt substitutions always result in a change in protein sequence?
No
323
Synonymous mutations/ silent mutations
No change in protein sequence
324
Nonsynonymous mutations/ missense mutations
A change in amino acid
325
SOS repair found where
In E. coli and other bacteria
326
SOS repair alway active?
No, induced by DNA damage
327
SOS repair
Bypass system that allow DNA replication to happen across pyramiding diners or DNA distortions and maintains the integrity of the genome but produced error prone DNA
328
Template-directed gap repair results in
Error free repair
329
Double-strand gap repair
Non-homologous end joining: error-prone joining of ends
330
DNA damage bypass
The damaged region is skipped over during replication, minimizing harmful effect
331
Photoreactivation
UV-induced pyrimidine dimers can be reversed by enzymes that breaks the bond joining the two Ts using the energy of light
332
Proofreading Function of DNA polymerase
3' to 5' exonuclease activity
Cleaves the unpaired nucleotide and gives a 2nd chance to get it right
333
Okazaki fragments
Lagging strands
334
Joining precursor fragments (4 steps)
1. Junction of 2 fragments with RNA primer present
2. DNA polymerase 1 degrades primer and synthesizes DNA complement to template
3. DNA ligase, seals the resulting nick
4. Intact double helical molecule
335
Where is the termination replication site
opposition to replication origin
336
How long is the termination replication sequence?
23bp repeats
337
What is a termination replication site
bind to a protein that inhibits helicase activity
338
Replication in eukaryotes
1. multiple origins of replication on each chromosome
2. Replication proceeds bidirectionally
339
Does RNA primers have to be removed and replaced with nucleotides
Yes
340
How are RNA primers removed
1. DNA polymerase delta elongates DNA strand from upstream
2. RNA primer for previous lagging strand fragments is encountered
3. Singe stranded DNA binding protein, RPA, flips out RNA and a bit of DNA
4. RPA recruits specific endonucleases to cleave the flipped piece out
341
How are RNA primers replaced
Excised primer RNA and SNA are broken down by exonucleases and Polymerase delta continues until newly synthesized DNA replaces primer and then ligase together
342
The importance of Telomerase in replication
Degradation of RNA results in 2 daughter chromosomes with terminal deletions
Telomerase adds repeat sequences to the end of chromosomes to prevent degradation
343
Sanger sequencing
1. DNA replication-based sequencing tech
2. Uses dideoxy terminators that are fluorescently tagged
3. Still in use for routine small fragments
344
Next generation sequencing (NGS)
1. Highly throughput
2. Synthesis based
3. Short reads (< a few hundred bp)
4. Tens of millions of short reads assembled
345
Mechanism of Next Gen sequencing
1. Prepare genomic DNA samples
2. Attach DNA to surface
3. Bridge amplification
4. Fragments become double stranded
5. Denaturation leaves single strand
6. Complete amplification
346
Contig Assembly
fragments from NGS sequencing are then assembled into the full genome
347
H1 are ______ histone
linker
348
Transverison
T --> A, T--> G, C--> A, C--> G (pyrimidine --> purine)
A --> T, A --> C, G --> T, G --> C (purine --> pyrumidine)
349
