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Genetics > Lecture 4: DNA/RNA, chromosomes and transposable elements > Flashcards

Lecture 4: DNA/RNA, chromosomes and transposable elements Flashcards

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1
Q

The heterozygote exhibits a phenotype that’s intermediate between the corresponding homozygotes

A

Incomplete dominance

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2
Q

used much more when discussing human diseased

A

Haploinsufficiency

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3
Q

Explain the process of floruescent hybridization?

A
  1. Mitotic chromosomes are headed up, strands separate, and H bonds are broken.
  2. Mix in probe and cool down DNA
  3. When you reneal the DNA, one copy outcompetes another strand—can see probe in genome
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4
Q

shows the DNA sequence genome by taking DNA sequence and adding fluroescent chemicals

A

flourescent hybridization?

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5
Q

Result of Translocation producing Philadelphia Chromosome detected using

A

FISH

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6
Q

What procedure was used for reciprocal translocation

A

FISH

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7
Q

Why do translocations occur so much between 9 and 22 chromosomes?

A

Domains are close by in the nucleus

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8
Q

Shows the different domains in the nucleus, every chromosome colored differently

A

Spectral Karyotyping

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9
Q

Allodiploid vs. allotetraploid

A

allodiploid are sterile, no tetrads in meiosis I
allotetraploid have twice as many chromosomes, viable and fertile

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10
Q

Fused haploid radish and haploid cabbage produced…

A

allodiploid

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11
Q

Fused diploid radish and diploid cabbage produce…

A

allotetraploid

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12
Q

Synaptonemal complex gets broken, two chromosomes of each species moving to opposite poles in: allotetraploid or allodiploid

A

allotetraploid

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13
Q

How many metacentric, submetacentric, and acrocentric chromosomes do humans have?

A

metacentric: 1
acro: 5
submet: most

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14
Q

In Robertsonian Translocations the long arms of two ___ chromosomes have fused.

A

acrocentric

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15
Q

One example of a Robertsonian translocation is

A

Familial Down Syndrome (14 and 21)

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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

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17
Q

In DNA or RNA, no phosphate present on sugar is known as

A

nucleoside

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18
Q

The RNA nucleotides that are precursors to RNA polymers have….

A

3 phosphates

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19
Q

Two RNA nucleotides can ___ undergo the reaction shown below because it i
thermodynamically favored

A

spontaneously

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20
Q

If you mix RNA precursors, what do you get?

A

pyrophosphate (2 phosphates released) and RNA dinucleotide

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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

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22
Q

RNA most stable in what envrionment

A

acidic

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23
Q

In the RNA world, you just need what for RNA to self replicate

A

RNA nucleotide

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24
Q

RNA can act as___ in the rna world

A

Polymerases

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25
Q

Hydrogen bonds in RNA are only located when….

A

strands are opposite in direction

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26
Q

The 3D structure of RNA is needed for…

A

catalytic activity

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27
Q

Why did the RNA World recruit protein?

A

protein has greater catalytic potential than RNA

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28
Q

Proteins are synthesized by…

A

RNA

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29
Q

The enzyme that attaches amino acids to a growing amino acid chain is called the

A

ribosome

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30
Q

In bacteria and eukaryotes: what’s the ratio of RNA and protein in the ribosome

A

60% rna, 40% ribosome

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31
Q

The amino acids are Brought to the enzyme by

A

trna

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32
Q

The amino acid sequence is coded in the

A

mrna

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33
Q

determines the template of amino acids

A

mrna

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34
Q

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?

A

can still get activity, vs. get nothing if RNA not present

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35
Q

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

A

DNA

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36
Q

Scientists propose that an ancestral RNA molecule had the ability to synthesize DNA using RNA as a template: what enzyme

A

Reverse Transcriptase

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37
Q

Enzyme evolution of proteins outcompetes….

A

RNA

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38
Q

What enzyme is very abundant in the RNA world

A

RNA polymerase

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39
Q

There needs to be an RNA enzyme that synthesizes DNA using…

A

RNA template

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40
Q

DNA vs RNA nucleotides

A

DNA: A, G, C, T
RNA: A, G, C, U

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41
Q

Differences in deoxyribose and ribose

A

deoxyribose has an H, ribose has an extra O on C 2

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42
Q

DNA is more stable than rna because

A

extra O

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43
Q

Uracil vs. thymine

A

uracil lacks a methyl

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44
Q

connects the 5’ carbon of one nucleotide to the 3’ carbon of another

A

phosphate

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45
Q

The nucleotide strands have direction from

A

5 to 3

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46
Q

The phosphates and sugar
molecules form the…

A

backbone of nucleic acid strand

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47
Q

Link the 1st Carbon and base (ex. Guanine) in DNA or RNA dinucleotide

A

glycosidic bond

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48
Q

Links phosphate to O of the next molecule in a DNA or RNA dinucleotide

A

phosphodiester bonds

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49
Q

RNA nucleotides originate?

A

arise spontaneously

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50
Q

The two RNA nucleotides vs. RNA dinucleotide energy levels

A

two individual RNA nucleotides: higher energy
RNA dinucleotide: lower energy

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51
Q

When an RNA dinucleotide is formed, what is released?

A

pyrophosphate

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52
Q

RNA polymerase needs how many templates

A

1

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53
Q

RNA genome diseases with no DNA were the….

A

1st to exist

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54
Q

RNA vs proteins: hydrophilic or hydrophobic

A

RNA: hydrophilic
protein: hydrophilic or hydrophobic

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55
Q

How many nucleotides make up an amino acid

A

3

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56
Q

They tried to build models of DNA using the available
information for DNA structure

A

Watson and crick

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57
Q

What are the base pairs that are equally abundant?

A

a and t, g and c

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58
Q

Watson and crick dna double helix led them to discover

A

that A could hydrogen bond to T and G could hydrogen bond to C

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59
Q

What was linkage was proposed by w and c

A

phosphodiester

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60
Q

People knew the nucleotide structure before W&C, but not the ___ structure because people….

A

DNA, purified an enzyme (DNAase) and when DNA was exposed to DNAase, produced 4 nucleotide precursors

61
Q

The dna strands are…

A

antiparallel and right handed

62
Q

There are ____ nucleotides in each strand per complete ___° turn of
the helix.

A

10, 360 degrees

63
Q

The dna bases are oriented so that they are…

A

flat and facing each other

64
Q

The DNA helix is called a…

A

B helix (more stable than RNA A helix)

65
Q

What is the advantage of the B helix vs. A helix

A

Oxygen at the 2nd carbon on the A helix is too bulky

66
Q

C nucleotides would H bond ___ with G nucleotide

A

3 times

67
Q

a more stable molecule for storing information

A

DNA

68
Q

Scientists propose that an ancestral RNA molecule had the ability to synthesize DNA using RNA as a template

A

Reverse Transcriptase

69
Q

The bacterial chromosome is found in a region of the cell called the

A

nucleoid

70
Q

Domain in the cell with DNA of bacteria

A

nucleoid

71
Q

Shape of bacterial chromosomes

A

ciricular

72
Q

Unlike eukaryotes, the nucleoid is….

A

not bounded by membrane, in contact with cytoplasm

73
Q

Each bacterial cell can have 1 or more…

A

chromosomes

74
Q

One origin of replication in…

A

bacterial chromoosmes

75
Q

Most bacterial species contain how many chromosomes

A

1 single type

76
Q

Genes are closely spaced together in

A

bacterial chromosomes

77
Q

There are how many repetitive sequences in a bacterial chromosomes

A

few

78
Q

Bacterial chromosomal DNA is compacted about ____ by ____

A

1000 fold by proteins into loops

79
Q

When bacterial chromosomal dna is compacted, the involves the formation of….

A

loop domains

80
Q

After loop domains are formed in bacterial chromosomal dna, what occurs to further compact the chromosome? Who does it? Requires what?

A

DNA supercoiling by gyrase/topoisomerase II (needs energy)

81
Q

Promoter of bacterial genes

A

A/T rich

82
Q

The chromosomal DNA in bacteria is

A

negatively supercoiled

83
Q

In E. coli, there is ___ negative supercoil per __ turns of the double helix

A

1, 40

84
Q

Negative supercoiling has two major effects…

A
  1. Helps in the compaction of the chromosome
  2. Creates tension that may be released by DNA strand separation
85
Q

origins of replication in bacterial chromosomal dna are rich in..

A

A/T rich (less H bonds than G/c)

86
Q

Supercoiling helps separate strands because of

A

stress

87
Q

Introduces negative supercoils using energy from ATP

A

DNA gyrase

88
Q

relax positive supercoils that arise during DNA replication and transcription

A

DNA gyrase

89
Q

Relaxes negative supercoils when there are too many

A

DNA topoisomerase I

90
Q

The competing action of these two enzymes governs the overall supercoiling of bacterial DNA. What enzymes?

A

DNA topoisomerase I and DNA gyrase

91
Q

The ability of gyrase to introduce negative
supercoils into DNA is crucial for…

A

bacteria to surivive

92
Q

Blocking the function of what enzyme is a way to cure bacterial diseases

A

DNA gyrase

93
Q

Two main classes of drugs inhibit gyrase but not eukaryotic topoisomerases

A
  1. Quinolones
  2. Coumarins
94
Q

An example of a quinolone is

A

Cipro (antibotic that kills bacteria)

95
Q

Three types of DNA sequences are
required for chromosomal replication and
segregation. what are they?

A

Origins of replication hundreds or thousands along the chromosome. Human genome has 50,000-100,000 origins.
Centromeres
Telomeres

96
Q

in eukaryotic chromosomes, genes are located where?

A

between the centromeric and telomeric regions along the entire chromosome

97
Q

A single eukaryotic chromosome has how many genes

A

usually has a few hundred to several thousand genes

98
Q

Eukaryotic chromosomes are what shape? Occur in?

A

linear, sets (many species are diploid)

99
Q

each chromosome contains a ___ that forms a recognition site for kineticore proteins

A

centromere

100
Q

Contain specialized sequences located at both ends of a linear chromosome

A

telomeres

101
Q

In eukaryotic chromosomes, repetitive sequences are commonly found…

A

by centromere and telomere

102
Q

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

A

Unique or non-repetitive sequences (genes)

103
Q

Found a few hundred to a few thousand times
Includes:
Genes for rRNA and histones Origins of replication
Some Transposable elements

A

Moderately repetitive DNA sequences

104
Q

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

A

Highly repetitive DNA sequences

105
Q

Highly repetitive DNA sequences in eukaryotes are dominated by ____

A

transposable elements

106
Q

Were viruses at one point, stayed in the genome, make DNA copies of RNA genome and insert copies into the genome

A

ERV elements

107
Q

Examples of Highly repetitive DNA sequences

A

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
Q

What two eukarytoic genomes can tolerate ploidys

A

Amphibians and plants

109
Q

Causes for Differences in Eukaryotic Genome Size?

A

DIfferences in number of genome duplications (ploidy) and in the accumulation of repetitive sequences

110
Q

transposable elements probably occur in the genomes of…

A

all species

111
Q

Relationship between transposable elements and fast/slow dividing organisms in various species

A

Slower dividing organisms have an increase in transposable elements

112
Q

involves the integration of small
segments of DNA called transposable elements
(TEs) or transposons into the chromosome

A

Transposition

113
Q

DNA sequences that make copies of themselves

A

transposable elements

114
Q

Most transposable elements come from

A

Line 1 transposon and Alu transposon

115
Q

Three general types of transposition pathways
have been identified

A
  1. Simple transposition
  2. Replicative transposition
  3. Retrotransposition (including LINE-1 and Alu)
116
Q

are small circular independently replicating minichromosomes found in bacteria and yeast

A

Plasmids

117
Q

Plasmids ___ essential for life in bacteria or yeast

A

not essential

118
Q

The best understood bacterial plasmid is the

A

E coli F factor

119
Q

What did the e coli f factor do??

A

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
Q

Plasmids are useful in studying

A

transposable elements

121
Q

Simple transposition is a mechanism called

A

cut and paste

122
Q

Simple transposition is found in

A

bacteria and eukaryotes

123
Q

Simple transolocation mechanism steps…

A

when it moves to another site, it makes a staggered cut, and it inserts somewhere else

124
Q

The enzyme ‘Transposase’ catalyzes the
Excision and Insertion in…

A

simple transposition

125
Q

converts single to double stranded dna

A

dna polymerase

126
Q

dna base sequence targets are in the same direction and are repeated at both ends of the element

A

simple transposition

127
Q

simple transposons in eukaryotes are….

A

dervived from homology and not functional/active

128
Q

What type of transposition confers a selective advantage

A

composite transposons

129
Q

contain additional genes that aren’t necessary for transposition, two copies of simple transposon on either side of gene

A

composite transposons

130
Q

what transposition can move genes around

A

composite

131
Q

Created by two transposons flanking the additional genes
and behaving as one transposon. Transposon sequence may then be
lost turning them into….

A

composite transposons

132
Q

What transposition has one more gene, known as resolvase, not in eukaryotes and only in bacteria?

A

replicative

133
Q

This mechanism involves replication of the TE and insertion of the copy into another chromosomal location

A

Replicative transposition

134
Q

gene is found between the inverted repeats in Replicative Transposition

A

resolvase

135
Q

In replicative transposition, Insertion into the genome causes a short target sequence at the site of insertion to be duplicated to form…

A

Direct Repeats

136
Q

Replicative Transposition Requires what enzymes?

A

transposase and resolvase

137
Q

Replicative transposition has been studied in several bacterial transposons and in…

A

phage u (Mu)

138
Q

The net result of replicative transposition is that a….

A

TE occurs at a new site and the TE remains in its original location

139
Q

In replicative transposition, there are what on the target sequence in the plasmid?

A

staggered cuts by transposase

140
Q

Makes cuts at on the target sequence and transposable element and the strands are exchanged and ligated together in what? By what?

A

replicative transposition, transposase

141
Q

the product of replicative transposition is…

A

a cointegrant

142
Q

Replicative transposons can also give rise to

A

composite transposons

143
Q

large circular chromosome, plasmid inserted into chromosome by transposon

A

cointegrant

144
Q

Some transposons encode a ____, gives a specific homologous recombination to give plasmid and chromosome with transposon

A

resolvase

145
Q

Catalyzes the recombination between two elements of a cointegrant, turning the cointegrant into 2 separate structures, each with a transposable element

A

resolvase

146
Q

Retrotransposition is found in

A

eukaryotes

147
Q

Transposon is copied into RNA, RNA copied in double stranded DNA, then DNA inserts itself elsewhere

A

retrotransposition

148
Q

RNA intermediate in retrotransposition

A

Reverse transcriptase

149
Q
A

Genetics (11 decks)

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