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MT6319 MOLBIO > U4 LEC: GENOMES AND VARIANTS > Flashcards

U4 LEC: GENOMES AND VARIANTS Flashcards

1
Q

Bacterial Genome consists of?

A
  • nucleoid
  • bacterial genomes
  • chromosomal domains
  • bacterial chromosomes
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2
Q

Compact bacterial chromosome

A

Nucleoid

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3
Q

About a third of the volume of the cell, has many independent chromosomal domains

A

Bacterial genomes

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4
Q

Supercoil loop of DNA, randomly distributed

A

Chromosomal domains

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5
Q

Majority are circular, some are linear

A

Bacterial chromosomes

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6
Q

Linear bacterial chromosomes

A
  • multiple1-Mb chromosomes (Borrelia species)
  • 8-Mb chromosomes (Streptomyces species)
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7
Q

Circular bacterial chromosomes are mostly represented by?

A

plasmids

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8
Q

1-Mb chromosomes

A

Borrelia species

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9
Q

8-Mb chromosomes

A

Streptomyces species

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10
Q

These proteins assist in the level of compaction in bacterial genome.

A

Nucleoid-Associated Proteins

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11
Q

How do NAPs help in organization of chromosome?

A

bridging, wrapping or bending, causes level of compaction

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12
Q

NAPs

A
  • HU
  • SMC complex
  • FIS
  • IHF
  • H-NS
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13
Q

NAPs

Small protein subunit that bridges interconnecting sites between genome

A

H-NS

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14
Q

NAPs

H-NS causes ______ with linear DNA and fold with each other

A

bridging

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15
Q

NAPs

Antiparallel coiled hinged domain, wraps around to linear DNA causing it to coil

A

SMC complex

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16
Q

NAPs

Appearance of SMC complex

A

Safety pin appearance

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17
Q

NAPs

Abundant NAP, causes interlinkage between successive joints or part of linear DNA and causes to coil

A

HU

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18
Q

NAPs

Alters and facilitates the formation of loops

A

IHF

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19
Q

NAPs

Causes compact and organization but separate molecule that causes bridging with linear DNA

A

FIS

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20
Q

Capsid is made up of?

A

capsid proteins wrapped around RNA or DNA

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21
Q

Capsid follows general symmetry which includes

A
  • Icosahedral
  • Helical
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22
Q

Capsid follows what structure?

A
  • symmetrical
  • quasisymmetrical
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23
Q

Most common capsid structure

A

helical structure

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24
Q

Virus that attacks bacteria

A

Bacteriophage

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25
Q

Structures of the Bacteriophage

A
  • head (where the genome is located)
  • tail (attachment point)
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26
Q

Virus may possess a capsule made up of?

A

lipid

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27
Q

T/F: Larger organisms have a larger genome.

A

True

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28
Q

How many genes do we have

A

25,000

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29
Q

1 gene will contain how many base pairs?

A

less than 1000

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30
Q

Largest known human gene, facilitates muscle injury repair and found in the X chromosome

A

Dystrophin (2.4M bases)

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31
Q

T/F: 99.9% of nucleotide bases are exactly the same in all people.

A

True

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32
Q

The Human Genome Project only took blood from?

A

5 people

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33
Q

More than _____ genes have an unknown function

A

12,000

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34
Q

Histone protein that has the most modification, most diverse and most variable

A

H2

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35
Q

This refers to when histone is removed, the gene is turned off

A

Knockout

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36
Q

Core histone protein, knockout phenotype

A

H2A

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37
Q

For DNA repair, sperm defect in meiosis

A

H2A.X

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38
Q

Gene activation and silencing, embryonic infertlity

A

H2A.Z

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39
Q

Unique Animal Chromosomes

A
  • Lampbrush Chromosome
  • Polyetylene chromosomes
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40
Q

These chromosomes are found in some amphibians

A

Lampbrush Chromosomes

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41
Q

Lampbrush Chromosomes

Found specifically in what amphibians?

A

Pleurodele amphibians

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42
Q

Lampbrush Chromosomes

Similar appearance to?

A

test tube brush

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43
Q

Lateral loops that extrude from the chromomeres at certain prositions

A

Lampbrush Chromosomes

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44
Q

Lampbrush Chromosomes

Appear at meiosis stage in which chromosomes resemble a?

A

series of beads on a string

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45
Q

Lampbrush Chromosomes

The loop is an _______ DNA segment that is actively _______.

A

extruded, transcribed

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46
Q

Lampbrush Chromosomes

Present in urodele amphibians

A

Oocytes (Diplotene prophase chromosomes)

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47
Q

These chromosomes are found in insects such as common house flies in their larvae

A

Polytene chromosomes

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48
Q

Polytene Chromosomes

Appearance

A

different protruding chromosomes with different synapsis, many arms

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49
Q

Polytene Chromosomes

Usually found at?

A

interphase nuclei

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50
Q

Polytene Chromosomes

Useful for?

A

analysis of many facets of eukaryotic interphase chromosome organization and the genome as a whole

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51
Q

Polytene Chromosomes

Develop from chromosomes of?

A

diploid nuclei by successive duplication of each chromosomal element

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52
Q

Gene Size of Rickettsia prowazekil

A

1.11Mb, 834 genes

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53
Q

Gene Size of Homo sapiens

A

3,300 Mb, 25,000 genes

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54
Q

Unique sequence, only 1 copy per haploid

A

Nonrepetitive

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55
Q

Nonrepetitive represents what regions?

A

coding (exons)

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56
Q

Introns contain?

A

repetitive DNA

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57
Q

T/F: The length of the nonrepetitive DNA increase with overall genome size.

A

True

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58
Q

Increase genome size in higher eukaryotes reflects?

A

increase amount and proportion of repetitive DNA

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59
Q

T/F: Genome size and gene number is weaker in prokaryotic genomes than in eukaryotic genomes.

A

False

weaker sa eukaryotic

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60
Q

Moderately Repetitive Sequences

A
  • Interspersed Elements (Repetitive Transposed Sequences)
  • Tandem Repeated DNA (VNTRs and STRs)
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61
Q

under Moderately Repetitive Sequences

A
  • Transposons
  • SINEs
  • LINEs
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62
Q

Most common moderately repetitive sequences

A

Transposons

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63
Q

selfish or junk DNA

A

Transposons

function on their own pero walang ambag aw

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64
Q

Short sequences of DNA, ability to move to new locations in the genome

A

Transposons

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65
Q

Opposite of transposons

A

Retrotransposons (difference in size)

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66
Q

Retrotransposons include?

A
  • Short interspersed elements
  • Long interspersed elements
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67
Q

<500 base pairs, present in 500 times or more

A

SINEs

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68
Q

200 to 300 base pairs long, dispersed uniformly throughout the genome, potential for transposition within the genome related to chromosome rearrangements during evolution

A

Alu family

69
Q

6kb in length, may be present 850,000 times in human genome

A

LINEs

70
Q

under Tandem Repeated DNA

A
  • Short Tandem Repeats (STRs)
  • Variable Number Tandem Repeats (VNTRs)
71
Q

STRs are under microsatellites with ______ repeats and an array size on the order of _______ units

A

2- to 5- bp repeats, 10-100 units

72
Q

Dispersed throughout the genome and vary among individuals in the number of repeats present at any site.

A

Short Tandem Repeats (STRs)

73
Q

STRs are in the form of?

A

di-, tri-, tetra-, pentanucleotides

74
Q

VNTRs are under microsatellites with ______ repeats and an array size of _______

A

10- to 100-bp (usually around 15-bp), 0.5-30 kb

75
Q

VNTRs

How many base pairs long?

A

15 to 100bp

76
Q

VNTRs

Found?

A

within and between genes

77
Q

T/F: In VNTRs, number of tandem copies of each specific sequence at each location varies from one individual to the next.

A

True

78
Q

VNTRs

Variation in size between individual humans is the basis for?

A

DNA fingerprinting

79
Q

Highly repetitive sequences

A

Satellite DNA (satDNA)

80
Q

Highly repetitive DNA, short sequences repeated a large number of times

A

satDNA

81
Q

satDNA

Variable ______ repeat forms array up to ______

A

AT-rich, 100Mb

82
Q

satDNA

Monomer length

A

150 to 400bp

83
Q

satDNA

Located at?

A

heterochromatic regions

84
Q

satDNA

Mostly in?

A
  • centromeric
  • subtelomeric
  • also at intercalary positions
85
Q

satDNA

Likely involved in?

A

sequence-specific interactions and subsequently in epigenetic processes

86
Q

satDNA

Has a sequence-independent role in?

A

formation and maintenance of heterochromatin

87
Q

satDNA

These produce siRNAs

A

Transcripts

88
Q

satDNA

siRNAs are involved in the posttranscriptional gene regulation through?

A

action of RNA-induced silencing complex (RISC)

89
Q

Noncoding RNAs have been found to play an important role in?

A

neuronal functions

90
Q

Appear to turn over rapidly, but can be strongly influenced by positive selection.

A

MicroRNAs

91
Q

These are dead genes, may evolve functions in regulating expression of related genes and may regulate parenteral genes.

A

Pseudogenes

92
Q

Pseudogenes are DNA sequences representing?

A

evolutionary vestiges of duplicated copies of genes that have undergone significant mutational alteration

93
Q

Genome will evolve because of?

A

errors it may encounter during central dogma

94
Q

What dictates the pace of evolution of an organism?

A
  • how often does the organism have a mutation
  • how efficient is the organism to fix the mutation
95
Q

In homo sapiens, rate of fixation is ______ and rate of mutation is _______

A

high, low

96
Q

In bacteria, rate of fixation is ____ and rate of mutation is ______

A

low, high

97
Q

Introduction of Mutation

A
  • replication error or DNA damage
  • protein-coding region
  • substitution mutation
98
Q

Second step, over successive generations, molecular change a feature of the entire phylogenetic unit such as population, species, or lineage

A

Fixation of Mutation

99
Q

Fixation of Mutation is predictable by?

A

probability (selectively neutral or near-neutral)

100
Q

Random changes in the frequency of a mutational variant in a population

A

Genetic Drift

101
Q

Genetic Drift

A variant may be either?

A

lost or fixed

102
Q

Genetic Drift

Usually in the form of?

A

nucleotide substitutions

103
Q

This is a combination of the mutation rate and the rate of fixation

A

Evolutionary Rate

104
Q

Substitution rate is _________ mutation rate

A

equal to

105
Q

Overall influence that a life history trait has on sequence evolutionary rate is largely a result of?

A

magnitude and directions of its effects on mutation and fixation rates

106
Q

Mechanisms of Genome Evolution

A
  • Gene duplication
  • De novo origination
  • Horizontal gene transfer
  • Gene Recombination
  • New Gene Regulatory Systems
  • Transposable Elements
  • Molecular Evolution of Repetitive DNA Sequences
  • Evolution Rate of Repetitive DNA Sequences
107
Q

Evolution of Prokaryotic Genome

A
  • The Streamlining Hypothesis
  • The Muller Ratchet
108
Q

First theory for genome evolution for prokaryotes

A

Streamlining Hypothesis

109
Q

Streamlining Hypothesis

If an organism evolves, it will prefer a?

A

smaller genome, less use of energy

110
Q

Streamlining Hypothesis

Natural selection will favor?

A

genome reduction and low GC content

111
Q

Streamlining Hypothesis

Faster change in DNA if there is?

A

low GC content *has stronger bonds)

112
Q

Streamlining Hypothesis

Most common explanation for genome reduction in?

A

free-living bacteria

113
Q

Streamlining Hypothesis

Organisms do this selection by?

A

cellular economization

114
Q

Streamlining Hypothesis

Mainly determined by?

A

intracellular environment

115
Q

This theory states that the effect of mutation is cumulative.

A

Muller Ratchet

116
Q

This refers to small mutations one point at a time, and gradually overtime will accumulate and lead to a full-blown evolution.

A

Muller Ratchet

117
Q

In populations undergoing constant bottlenecks and no recombination, genome reduction occurs through?

A

accumulation of slightly deleterious mutations

118
Q

Muller Ratchet

Typical characteristics of these genomes, such as their large _____ content reflect known mutational biases rather than adaptations evolved by selection.

A

A+T

119
Q

Impact of Genome Reduction on Host-Associated Bacteria

Modifications of some genes coded in the ______ genome could allow the ______ to cope with loss of otherwise essential genes

A

reduced, endosymbiont

either the genome is already present sa host or sa bacteria

120
Q

Impact of Genome Reduction on Host-Associated Bacteria

The presence of __________ in the genomes of cosymbionts (if any) may compensate for _______ in the endosymbiont

A

complementary genes, gene losses

endosymbiont retains genome, cosymbiont loses it

121
Q

Impact of Genome Reduction on Host-Associated Bacteria

Genes coded in the genome of the ____ compensate for gene losses in the genome of the ______

A

host, endosymbiont

122
Q

under Impact of Genome Reduction on Host-Associated Bacteria

A
  • host origin
  • from the endosymbiont and transferred to the host
  • horizontally transferred from unrelated organisms not participating in the symbiosis to the host genome or its endosymbionts
123
Q

The mitochondrial genome is particular to what lineage?

A

matrilineal

124
Q

Mitochondrial genome

Base pairs and genes

A

17,000bp
32 genes

125
Q

T/F: The mitochondrial gene is not used for studies because it is very small.

A

True

very small din impact sa health ng patient

126
Q

If there is error with RNA splicing, there will be a problem with the?

A

protein

127
Q

Incomplete splicing produces a?

A

truncated protein

128
Q

Only half of the exon is spliced

A

Cryptic splicing

129
Q

This leads to disease.

A

Mutation

130
Q

This can alter the expression of the organism.

A

Polymorphism

131
Q

Refers to the position or location of a gene in the genome

A

Locus

132
Q

Genetic loci are defined by chromosomal location using?

A
  • chromosome bands (G-band or R-band)
  • molecular markers (microsatellites)
133
Q

Separate pairs of genetic expression located on opposite sides of the chromosome, may be homozygous or heterozygous

A

Allele

134
Q

These are related to alterations in the nucleotide sequence of a gene.

A

Allelic differences

135
Q

Refers to one nucleotide change, can be a sequence polymorphism

A

Single Nucleotide Polymorphisms (SNPs)

136
Q

T/F: Tandem repeats are used in the laboratory for crime scenes.

A

True

137
Q

Used for paternity testing

A

VNTRs

138
Q

Used for investigations

A

STR

139
Q

T/F: Each individual has a different number of tandem repeats.

A

True

140
Q

STR dinucleotide repeat is only about ___ the same

A

8%

141
Q

Tetranucleotide repeat is only about ____ the same

A

0.3%

142
Q

T/F: Twins have the same identical VNTR.

A

True

almost the same lang

143
Q

T/F: You may also look at tandem repeats during DNA fingerprinting.

A

True

144
Q

Mutation is present from the very start

A

Germline mutations

145
Q

Acquired mutations

A

Somatic mutations

146
Q

<1% of population, Carrier, Diseased

A

Mutation

147
Q

> 1% of population, not affected, >90% SNPs, not associated with a disease

A

Polymorphism

148
Q

Refers to one nucleotide mutation

A

Point mutation

149
Q

Same type of mutation

A

Transition (pur to pur, pyr to pyr)

150
Q

Purine to pyrimidine

A

Transversion

151
Q

T/F: Polymorphisms can make a person more susceptible.

A

True

152
Q

Genetic Polymorphism

Structural

A
  • gain/loss of chromosome segments
  • translocations
  • rearrangements
  • gene amplifications
153
Q

Genetic Polymorphism

Molecular

A
  • deletions/insertions
  • nucleotide repeats (di-, tri)
  • point mutations (RFLPs, SNPs)
154
Q

Most common type of mutation

A

Substitution

155
Q

Refers to codon changes, affects gene transcript splicing

A

Point Mutations (Base Pair Substitution)

156
Q

This is produced by deletions, insertions, or splicing errors.

A

Frame-shift mutations

157
Q

Refers to change in codon to a different amino acid, transition or transversion substitutions

A

Missense mutation

158
Q

Change in amino acid, but possess same properties

A

Conservative missense mutation

159
Q

Change in amino acid, but the properties are not the same

A

Nonconservative missense mutation

160
Q

This refers to substitution, change in codon but same amino acid and does not cause a change in protein.

A

Silent Mutations

161
Q

This results into a truncated protein due to a change in codon to a stop codon.

A

Nonsense or Stop Mutations

162
Q

Splice Site Mutations

A
  • Exon skipping (incomplete splicing)
  • Intron inclusion
  • Cryptic splicing
163
Q

under Deletion Mutation

A
  • Cystic Fibrosis
  • Duchenne muscular dystrophy
164
Q

70% due to F508

A

Cystic Fibrosis

165
Q

~60% cases due to large deletions, 8% small deletions

A

Duchenne muscular dystrophy

166
Q

Insertion or deletion of nucleotides, reading frame is altered

A

Frameshift mutations

167
Q

When these tandem repeats accumulate, it causes mutations

A

Dynamic mutation

168
Q

Example of Dynamic Mutation

A

Trinucleotide Repeat Expansion

169
Q

Tandem repeats and gene of Huntington disease

A

> 40 CAG, Huntingtin gene

MT6319 MOLBIO (10 decks)

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