Lecture 4: DNA/RNA, chromosomes and transposable elements Flashcards
(149 cards)
1
Q
The heterozygote exhibits a phenotype that’s intermediate between the corresponding homozygotes
A
Incomplete dominance
2
Q
used much more when discussing human diseased
A
Haploinsufficiency
3
Q
Explain the process of floruescent hybridization?
A
- Mitotic chromosomes are headed up, strands separate, and H bonds are broken.
- Mix in probe and cool down DNA
- When you reneal the DNA, one copy outcompetes another strand—can see probe in genome
4
Q
shows the DNA sequence genome by taking DNA sequence and adding fluroescent chemicals
A
flourescent hybridization?
5
Q
Result of Translocation producing Philadelphia Chromosome detected using
A
FISH
6
Q
What procedure was used for reciprocal translocation
A
FISH
7
Q
Why do translocations occur so much between 9 and 22 chromosomes?
A
Domains are close by in the nucleus
8
Q
Shows the different domains in the nucleus, every chromosome colored differently
A
Spectral Karyotyping
9
Q
Allodiploid vs. allotetraploid
A
allodiploid are sterile, no tetrads in meiosis I
allotetraploid have twice as many chromosomes, viable and fertile
10
Q
Fused haploid radish and haploid cabbage produced…
A
allodiploid
11
Q
Fused diploid radish and diploid cabbage produce…
A
allotetraploid
12
Q
Synaptonemal complex gets broken, two chromosomes of each species moving to opposite poles in: allotetraploid or allodiploid
A
allotetraploid
13
Q
How many metacentric, submetacentric, and acrocentric chromosomes do humans have?
A
metacentric: 1
acro: 5
submet: most
14
Q
In Robertsonian Translocations the long arms of two ___ chromosomes have fused.
A
acrocentric
15
Q
One example of a Robertsonian translocation is
A
Familial Down Syndrome (14 and 21)
16
Q
Any chromosome, not X or Y, will give rise to a ____ if embryo has one chromosome or 3 copies (besides trisomy 21)
A
miscarriage
17
Q
In DNA or RNA, no phosphate present on sugar is known as
A
nucleoside
18
Q
The RNA nucleotides that are precursors to RNA polymers have….
A
3 phosphates
19
Q
Two RNA nucleotides can ___ undergo the reaction shown below because it i
thermodynamically favored
A
spontaneously
20
Q
If you mix RNA precursors, what do you get?
A
pyrophosphate (2 phosphates released) and RNA dinucleotide
21
Q
In the backbone of RNA, the 5’ end has no ____ and the 3’ end has what attached to the 1st C and 3rd C?
A
5’= no nucleotide
3’ 1st C: base attached
3’ 3rd C: phosphate and another nucleotide attached
22
Q
RNA most stable in what envrionment
A
acidic
23
Q
In the RNA world, you just need what for RNA to self replicate
A
RNA nucleotide
24
Q
RNA can act as___ in the rna world
A
Polymerases
25
Hydrogen bonds in RNA are only located when....
strands are opposite in direction
26
The 3D structure of RNA is needed for...
catalytic activity
27
Why did the RNA World recruit protein?
protein has greater catalytic potential than RNA
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Proteins are synthesized by...
RNA
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The enzyme that attaches amino acids to a growing amino acid chain is called the
ribosome
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In bacteria and eukaryotes: what's the ratio of RNA and protein in the ribosome
60% rna, 40% ribosome
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The amino acids are Brought to the enzyme by
trna
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The amino acid sequence is coded in the
mrna
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determines the template of amino acids
mrna
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If you get rid of proteins and are left with RNA, what happens to the enzymatic activity? If you get rid of RNA and are left with proteins, what happens to the activity?
can still get activity, vs. get nothing if RNA not present
35
As volcanic activity diminshed, there would have been a strong selection for the inclusion of ___ which is a much more stable molecule for storing information
DNA
36
Scientists propose that an ancestral RNA molecule had the ability to synthesize DNA using RNA as a template: what enzyme
Reverse Transcriptase
37
Enzyme evolution of proteins outcompetes....
RNA
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What enzyme is very abundant in the RNA world
RNA polymerase
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There needs to be an RNA enzyme that synthesizes DNA using...
RNA template
40
DNA vs RNA nucleotides
DNA: A, G, C, T
RNA: A, G, C, U
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Differences in deoxyribose and ribose
deoxyribose has an H, ribose has an extra O on C 2
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DNA is more stable than rna because
extra O
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Uracil vs. thymine
uracil lacks a methyl
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connects the 5’ carbon of one nucleotide to the 3’ carbon of another
phosphate
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The nucleotide strands have direction from
5 to 3
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The phosphates and sugar
molecules form the...
backbone of nucleic acid strand
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Link the 1st Carbon and base (ex. Guanine) in DNA or RNA dinucleotide
glycosidic bond
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Links phosphate to O of the next molecule in a DNA or RNA dinucleotide
phosphodiester bonds
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RNA nucleotides originate?
arise spontaneously
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The two RNA nucleotides vs. RNA dinucleotide energy levels
two individual RNA nucleotides: higher energy
RNA dinucleotide: lower energy
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When an RNA dinucleotide is formed, what is released?
pyrophosphate
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RNA polymerase needs how many templates
1
53
RNA genome diseases with no DNA were the....
1st to exist
54
RNA vs proteins: hydrophilic or hydrophobic
RNA: hydrophilic
protein: hydrophilic or hydrophobic
55
How many nucleotides make up an amino acid
3
56
They tried to build models of DNA using the available
information for DNA structure
Watson and crick
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What are the base pairs that are equally abundant?
a and t, g and c
58
Watson and crick dna double helix led them to discover
that A could hydrogen bond to T and G could hydrogen bond to C
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What was linkage was proposed by w and c
phosphodiester
60
People knew the nucleotide structure before W&C, but not the ___ structure because people....
DNA, purified an enzyme (DNAase) and when DNA was exposed to DNAase, produced 4 nucleotide precursors
61
The dna strands are...
antiparallel and right handed
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There are ____ nucleotides in each strand per complete ___° turn of
the helix.
10, 360 degrees
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The dna bases are oriented so that they are...
flat and facing each other
64
The DNA helix is called a...
B helix (more stable than RNA A helix)
65
What is the advantage of the B helix vs. A helix
Oxygen at the 2nd carbon on the A helix is too bulky
66
C nucleotides would H bond ___ with G nucleotide
3 times
67
a more stable molecule for storing information
DNA
68
Scientists propose that an ancestral RNA molecule had the ability to synthesize DNA using RNA as a template
Reverse Transcriptase
69
The bacterial chromosome is found in a region of the cell called the
nucleoid
70
Domain in the cell with DNA of bacteria
nucleoid
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Shape of bacterial chromosomes
ciricular
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Unlike eukaryotes, the nucleoid is....
not bounded by membrane, in contact with cytoplasm
73
Each bacterial cell can have 1 or more...
chromosomes
74
One origin of replication in...
bacterial chromoosmes
75
Most bacterial species contain how many chromosomes
1 single type
76
Genes are closely spaced together in
bacterial chromosomes
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There are how many repetitive sequences in a bacterial chromosomes
few
78
Bacterial chromosomal DNA is compacted about ____ by ____
1000 fold by proteins into loops
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When bacterial chromosomal dna is compacted, the involves the formation of....
loop domains
80
After loop domains are formed in bacterial chromosomal dna, what occurs to further compact the chromosome? Who does it? Requires what?
DNA supercoiling by gyrase/topoisomerase II (needs energy)
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Promoter of bacterial genes
A/T rich
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The chromosomal DNA in bacteria is
negatively supercoiled
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In E. coli, there is ___ negative supercoil per __ turns of the double helix
1, 40
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Negative supercoiling has two major effects...
1. Helps in the compaction of the chromosome
2. Creates tension that may be released by DNA strand separation
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origins of replication in bacterial chromosomal dna are rich in..
A/T rich (less H bonds than G/c)
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Supercoiling helps separate strands because of
stress
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Introduces negative supercoils using energy from ATP
DNA gyrase
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relax positive supercoils that arise during DNA replication and transcription
DNA gyrase
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Relaxes negative supercoils when there are too many
DNA topoisomerase I
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The competing action of these two enzymes governs the overall supercoiling of bacterial DNA. What enzymes?
DNA topoisomerase I and DNA gyrase
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The ability of gyrase to introduce negative
supercoils into DNA is crucial for…
bacteria to surivive
92
Blocking the function of what enzyme is a way to cure bacterial diseases
DNA gyrase
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Two main classes of drugs inhibit gyrase but not eukaryotic topoisomerases
1. Quinolones
2. Coumarins
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An example of a quinolone is
Cipro (antibotic that kills bacteria)
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Three types of DNA sequences are
required for chromosomal replication and
segregation. what are they?
Origins of replication hundreds or thousands along the chromosome. Human genome has 50,000-100,000 origins.
Centromeres
Telomeres
96
in eukaryotic chromosomes, genes are located where?
between the centromeric and telomeric regions along the entire chromosome
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A single eukaryotic chromosome has how many genes
usually has a few hundred to several thousand genes
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Eukaryotic chromosomes are what shape? Occur in?
linear, sets (many species are diploid)
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each chromosome contains a ___ that forms a recognition site for kineticore proteins
centromere
100
Contain specialized sequences located at both ends of a linear chromosome
telomeres
101
In eukaryotic chromosomes, repetitive sequences are commonly found...
by centromere and telomere
102
Found in two copies (one from mom and one from dad) Includes structural genes as well as intergenic areas
In humans, make up roughly 40% of the genome
Unique or non-repetitive sequences (genes)
103
Found a few hundred to a few thousand times
Includes:
Genes for rRNA and histones Origins of replication
Some Transposable elements
Moderately repetitive DNA sequences
104
Found tens of thousands to millions of times
Each copy is relatively short (a few nucleotides to several hundred in length)
Some sequences are interspersed throughout the genome
Highly repetitive DNA sequences
105
Highly repetitive DNA sequences in eukaryotes are dominated by ____
transposable elements
106
Were viruses at one point, stayed in the genome, make DNA copies of RNA genome and insert copies into the genome
ERV elements
107
Examples of Highly repetitive DNA sequences
Alu transposable elements in humans (11% of human DNA)
LINE-1 transposable elements in humans (20% of human DNA) ERV elements (Endogenous RetroViruses) (8% of human DNA)
108
What two eukarytoic genomes can tolerate ploidys
Amphibians and plants
109
Causes for Differences in Eukaryotic Genome Size?
DIfferences in number of genome duplications (ploidy) and in the accumulation of repetitive sequences
110
transposable elements probably occur in the genomes of...
all species
111
Relationship between transposable elements and fast/slow dividing organisms in various species
Slower dividing organisms have an increase in transposable elements
112
involves the integration of small
segments of DNA called transposable elements
(TEs) or transposons into the chromosome
Transposition
113
DNA sequences that make copies of themselves
transposable elements
114
Most transposable elements come from
Line 1 transposon and Alu transposon
115
Three general types of transposition pathways
have been identified
1. Simple transposition
2. Replicative transposition
3. Retrotransposition (including LINE-1 and Alu)
116
are small circular independently replicating minichromosomes found in bacteria and yeast
Plasmids
117
Plasmids ___ essential for life in bacteria or yeast
not essential
118
The best understood bacterial plasmid is the
E coli F factor
119
What did the e coli f factor do??
encodes proteins causing tubes to come off of bacteria. If another bacteria comes along, it can fuse with membrane and plasmid can fuse through the tube into other bacteria
120
Plasmids are useful in studying
transposable elements
121
Simple transposition is a mechanism called
cut and paste
122
Simple transposition is found in
bacteria and eukaryotes
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Simple transolocation mechanism steps...
when it moves to another site, it makes a staggered cut, and it inserts somewhere else
124
The enzyme ‘Transposase’ catalyzes the
Excision and Insertion in...
simple transposition
125
converts single to double stranded dna
dna polymerase
126
dna base sequence targets are in the same direction and are repeated at both ends of the element
simple transposition
127
simple transposons in eukaryotes are....
dervived from homology and not functional/active
128
What type of transposition confers a selective advantage
composite transposons
129
contain additional genes that aren't necessary for transposition, two copies of simple transposon on either side of gene
composite transposons
130
what transposition can move genes around
composite
131
Created by two transposons flanking the additional genes
and behaving as one transposon. Transposon sequence may then be
lost turning them into....
composite transposons
132
What transposition has one more gene, known as resolvase, not in eukaryotes and only in bacteria?
replicative
133
This mechanism involves replication of the TE and insertion of the copy into another chromosomal location
Replicative transposition
134
gene is found between the inverted repeats in Replicative Transposition
resolvase
135
In replicative transposition, Insertion into the genome causes a short target sequence at the site of insertion to be duplicated to form...
Direct Repeats
136
Replicative Transposition Requires what enzymes?
transposase and resolvase
137
Replicative transposition has been studied in several bacterial transposons and in...
phage u (Mu)
138
The net result of replicative transposition is that a....
TE occurs at a new site and the TE remains in its original location
139
In replicative transposition, there are what on the target sequence in the plasmid?
staggered cuts by transposase
140
Makes cuts at on the target sequence and transposable element and the strands are exchanged and ligated together in what? By what?
replicative transposition, transposase
141
the product of replicative transposition is...
a cointegrant
142
Replicative transposons can also give rise to
composite transposons
143
large circular chromosome, plasmid inserted into chromosome by transposon
cointegrant
144
Some transposons encode a ____, gives a specific homologous recombination to give plasmid and chromosome with transposon
resolvase
145
Catalyzes the recombination between two elements of a cointegrant, turning the cointegrant into 2 separate structures, each with a transposable element
resolvase
146
Retrotransposition is found in
eukaryotes
147
Transposon is copied into RNA, RNA copied in double stranded DNA, then DNA inserts itself elsewhere
retrotransposition
148
RNA intermediate in retrotransposition
Reverse transcriptase
149
