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[MT 6319] Molecular Biology & Diagnostics Lecture > [2S] UNIT 4 Genomes and Variant > Flashcards

[2S] UNIT 4 Genomes and Variant Flashcards

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1
Q

Study of totality of genome of a living organism

A

Genomics

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2
Q

Total nucleic acid sequences and what will it be translated into a living organism, including viruses

A

Genome

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3
Q

the coding material; distinct sequence of
nucleotides, forming part of a chromosome

A

Genes

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4
Q

Compact bacterial chromosome

A

Nucleoid

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5
Q

About a third of the volume of the cell

A

Bacterial genomes

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6
Q
  • supercoil loop of DNA
  • randomly distributed
A

chromosomal domains

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7
Q

T/F: Bacterial chromosomes are majority circular and some are linear

A

T

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8
Q

Multiple 1-Mb chromosomes

A

Borrelia spp.

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9
Q

8-Mb chromosomes

A

Streptomyces spp.

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10
Q

T/F: In prokaryotic cells, since there are no membrane-bound organelles (ex. nucleus and mitochondria), the genome is packaged into a nucleoid

A

T

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11
Q

_____ with DNA bridging, wrapping, or bending activities contribute to the organization of the chromosome

A

Nucleoid-associated proteins (NAPs)

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12
Q

T/F: Viruses are composed of both RNA or DNA

A

F; Viruses are composed of either RNA or DNA (never both)

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13
Q

VIRAL GENOME

Nucleic acid genome

A

RNA or DNA (never both)

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14
Q

VIRAL GENOME

symmetrical or quasi symmetrical

A

capsid

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15
Q

VIRAL GENOME

a protein that encodes the nucleic acid (DNA / RNA)

A

capsid

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16
Q

virus that infects bacteria and archaea

A

bacteriophage

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17
Q

bacteriophage greek term meaning

A

bacteria eater

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18
Q

how many base pairs are in a human genome?

A

3.4 billion base pairs

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19
Q

a type of packaging for complex viruses wherein the viral capsid is constructed first, then the genetic material enters

A

Phage lambda maturation

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20
Q

average gene of a human genome

A

3000 bases, vary in size

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21
Q

Largest known human gene ______ at 2.4M bases

A

dystrophin

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22
Q

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

A

T

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23
Q

HUMAN GENOME

T/F: Unknown function: 50% of discovered genes

A

T

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24
Q

T/F: The more complex the cell gets, their genetic material becomes shorter but it does not necessarily mean that they contain more functional units

A

F; longer

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25
Q

DNA packaging and the various packing capacities involved to fit eukaryotic DNA into the nucleus

A

Nucleosome structure

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26
Q

The process of phage lambda maturation begins with a change in the shape of the _____ head, which fills with DNA and expands.

A

empty

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27
Q

Counterpart of histones in eukaryotes

A

Nucleoid-associated proteins (NAPs)

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28
Q

CORE HISTONE VARIANTS IN VERTEBRATE DEVT.

Number of Gene Copies: 2
Cell Cycle Exp: RI
Loc: Throughout the genome
Function: Gene activation and silencing
Knockout Pheno: Embryonic infertility

A

H2A.Z

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29
Q

CORE HISTONE VARIANTS IN VERTEBRATE DEVT.

Number of Gene Copies: 15
Cell Cycle Exp: RD
Function: Core Histone
Knockout Pheno: Not determined

A

H2A

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30
Q

CORE HISTONE VARIANTS IN VERTEBRATE DEVT.

Number of Gene Copies: 1
Cell Cycle Exp: RI
Loc: Throughout the genome
Function: DNA repair
Knockout Pheno: Sperm defect in meiosis

A

H2A.X

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31
Q

CORE HISTONE VARIANTS IN HUMAN DISEASE

No. of Gene Copies: 1
Cell Cycle Exp: RI
Mutation & Exp Patterns: Reduced expression
Tumor Conseq: Inc cancer progression in p53 KO mice

A

H2A.X

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32
Q

CORE HISTONE VARIANTS IN HUMAN DISEASE

No. of Gene Copies: 2
Cell Cycle Exp: RI
Mutation & Exp Patterns: Over progression (oncogene)
Tumor Conseq: Numerous cancers

A

H2A.Z

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33
Q

CORE HISTONE VARIANTS IN HUMAN DISEASE

No. of Gene Copies: 2
Cell Cycle Exp: Possibly RI
Mutation & Exp Patterns: Reduced expression (tumor sup.)
Tumor Conseq: Melanomas and numerous cancers

A

MacroH2A

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34
Q

CORE HISTONE VARIANTS IN HUMAN DISEASE

No. of Gene Copies: 10
Cell Cycle Exp: RD
Mutation & Exp Patterns: K27M in H3
Tumor Conseq: Adult and pediatric glomas, including GBMs

A

H3.1

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35
Q

LAMPBRUSH CHROMOSOME

Appear at the meiosis stage in which the chromosomes resemble a series of beads on a string

A

Chromomeres

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36
Q

Lateral loops that extrude from the chromomeres at certain positions.

A

Lampbrush chromosome

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37
Q

LAMPBRUSH CHROMOSOME

Extruded segment of DNA actively transcribed

A

Loop

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38
Q

LAMPBRUSH CHROMOSOME

Urodele amphibians

A

Oocytes

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39
Q

Diplotene prophase chromosomes

A

Lampbrush chromosome

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40
Q

Usually found at the interphase nuclei of some tissue of the larvae of flies

A

Polytene Chromosome

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41
Q

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

A

Polytene Chromosome

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42
Q

Develop from the chromosomes of diploid nuclei by successive duplication of each chromosomal element (chromatid)

A

Polytene Chromosome

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43
Q

Cells with polytene chromosomes differ in many ways from mitotically dividing cells

A

Polytene Chromosome

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44
Q

T/F: Genome size is not necessarily related to the gene number in EUKARYOTES

A

T

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45
Q

a primer set has a target locus

A

Pathogenicity islands

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46
Q

THE FEATURES OF GENOMIC SEQUENCES

Has nonrepetitive DNA

A

Prokaryotes

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47
Q

have pathogenicity islands, which are DNA segments (10-200 kb) present in genomes of pathogenic species but are absent in genomes of nonpathogenic variants of the same species

A

Pathogenic bacteria

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48
Q

THE FEATURES OF GENOMIC SEQUENCES

Moderately Repetitive & Highly Repetitive Sequences

A

Repetitive DNA

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49
Q

THE FEATURES OF GENOMIC SEQUENCES

Repetitive Transposed Sequences

A

MODERATELY REPETITIVE DNA: Interspered Elements

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50
Q

THE FEATURES OF GENOMIC SEQUENCES

VNTRs and STRs

A

MODERATELY REPETITIVE DNA: Tandem Repeated DNA

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51
Q

Sequences that are unique: only one copy in a haploid genome

A

Nonrepetitive DNA

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52
Q

T/F: Length of the nonrepetitive DNA decrease with overall genome size

A

F; increase

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53
Q

Usually corresponds to the protein coding genes

A

Nonrepetitive DNA

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54
Q

T/F: In nonrepetitive DNA, the increase in genome size for higher eukaryotes, usually reflects the increase in the amount and proportion of repetitive DNA

A

T

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55
Q

THE FEATURES OF GENOMIC SEQUENCES

One copy in a haploid genome and varies widely among taxonomic groups

A

Nonrepetitive DNA

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55
Q

T/F: Variation in genome size results from the differences in the amount of repetitive DNA, and therefore the relationship between genome size and gene number is stronger in eukaryotic genomes than in prokaryotic genomes

A

F; weaker

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56
Q

THE FEATURES OF GENOMIC SEQUENCES

DNA that do not carry critical information

A

Repetitive DNA

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57
Q

THE FEATURES OF GENOMIC SEQUENCES

Genomes of plants and amphibian, 80% of the genome

A

Repetitive DNA

58
Q

THE FEATURES OF GENOMIC SEQUENCES

The amount of DNA in the unreplicated genome, or the haploid genome, of a species is known as the?

A

C-value or Constant value

59
Q

THE FEATURES OF GENOMIC SEQUENCES

T/F: Unicellular eukaryotes, most of the DNA is nonrepetitive and only 20% of the genomic sequences are repetitive DNA

A

T

60
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

Short sequences of DNA

A

Transposons / Selfish or Junk DNA

61
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

Ability to move to new locations in the genome

A

Transposons / Selfish or Junk DNA

62
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

Propagate without contributing to the development and functioning of the organism

A

Transposons / Selfish or Junk DNA

63
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

<500 base pairs long and may be present 500,000 times or more in a human genome

A

SINEs (Short interspersed elements)

64
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

■ 200 to 300 base pairs long
■ Are dispersed uniformly throughout
the genome

A

SINEs: Alu family

65
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

Potential for transposition within the genome related to chromosome rearrangements during evolution

A

SINEs: Alu family

65
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

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

A

LINEs (long interspersed elements)

66
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

Retrotransposons

A

LINEs (long interspersed elements)

67
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

Function as retrotransposons in retroviruses. For humans, the function is unknown

A

LINEs (long interspersed elements)

68
Q

INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES

Jumping genes

A

Transposons

69
Q

TANDEM REPEATED DNA – VNTRs and STRs

with 2- to 5-bp repeats and an array size on the order of 10-100 units

A

Microsatellites

70
Q

TANDEM REPEATED DNA – VNTRs and STRs

Di-, tri-, tetra-, and pentanucleotides

A

Short Tandem Repeats (STRs)

71
Q

TANDEM REPEATED DNA – VNTRs and STRs

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

A

Short Tandem Repeats (STRs)

72
Q

TANDEM REPEATED DNA – VNTRs and STRs

Useful for establishing lineages or blood relations

A

Short Tandem Repeats (STRs)

73
Q

TANDEM REPEATED DNA – VNTRs and STRs

Used in forensic DNA profiling to identify missing persons, confirmation of blood relations, and link persons of interest to suspect a crime

A

Short Tandem Repeats (STRs)

74
Q

TANDEM REPEATED DNA – VNTRs and STRs

with 10- to 100-bp (usually around 15-bp) repeats and an array size of 0.5-30 kb

A

Minisatellites

75
Q

TANDEM REPEATED DNA – VNTRs and STRs

■ 15 to 100 bp long
■ Found within and between genes

A

Variable Number Tandem Repeats (VNTRs)

75
Q

TANDEM REPEATED DNA – VNTRs and STRs

Number of tandem copies of each specific sequence at each location varies from one individual to the next

A

Variable Number Tandem Repeats (VNTRs)

76
Q

TANDEM REPEATED DNA – VNTRs and STRs

Variation in size between individual humans is the basis for DNA fingerprinting

A

Variable Number Tandem Repeats (VNTRs)

77
Q

HIGHLY REPETITIVE SEQUENCES

● Highly repetitive DNA
● Short sequences repeated a large number of times

A

Satellite DNA (satDNA)

77
Q

HIGHLY REPETITIVE SEQUENCES

Variable AT-rich repeat forms arrays up to 100Mb

A

Satellite DNA (satDNA)

78
Q

HIGHLY REPETITIVE SEQUENCES

Satellite monomer length

A

150 to 400bp

79
Q

HIGHLY REPETITIVE SEQUENCES

satDNA location

A

Heterochromatic regions (mostly centromeric & subtelomeric but also intercalary posi)

80
Q

HIGHLY REPETITIVE SEQUENCES

Are likely involved in sequence-specific interactions and subsequently in epigenetic processes

A

Satellite DNA (satDNA)

81
Q

NONCODING SEQUENCES

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

A

MicroRNAs

81
Q

HIGHLY REPETITIVE SEQUENCES

Has a sequence-independent role in the formation and maintenance of heterochromatin

A

Satellite DNA (satDNA)

82
Q

HIGHLY REPETITIVE SEQUENCES

Transcripts produce siRNAs
○ Involved in posttranscriptional gene regulation through the action of the RNA-induced silencing complex (RISC)

A

Satellite DNA (satDNA)

83
Q

NONCODING SEQUENCES

Have been found to play a important role in neuronal functions

A

Noncoding RNAs

84
Q

NONCODING SEQUENCES

Dead genes

A

Pseudogenes

85
Q

NONCODING SEQUENCES

○ May evolve functions in regulating expression of related genes
○ May regulate their parental genes, similar to long noncoding RNAs or microRNAs (miRNAs)

A

Pseudogenes

86
Q

NONCODING SEQUENCES

DNA sequences representing evolutionary vestiges of duplicated copies of genes that have undergone significant mutation alteration

A

Pseudogenes

87
Q

Alter the amino acid sequence leading to functional changes in proteins

A

Nonsynonymous Mutation

88
Q

2 Nonsynonymous mutation

A

Missense codon
Nonsense codon

89
Q

Silent mutation

A

Synonymous mutation

89
Q

○ Replication error or DNA damage
○ Protein-coding region
○ Substitution mutation

A

Mutation

90
Q

Do not change the amino acid sequence of a protein

A

Silent Mutation

91
Q

Change 1 amino acid to another

A

Missense Codon

92
Q

frequency at which genetic mutations accumulate over time between different populations or species

A

Rate of Divergence

92
Q

Introduce a premature stop codon, truncating the protein

A

Nonsense Codon

93
Q

Calculates the time of divergence between the 2 members of the family

A

Rate of Divergence (galing s bibig ni maam yn dk gets)

94
Q

GENOME EVOLUTION

Second step

A

Fixation of Mutation

95
Q

GENOME EVOLUTION

Over successive generations

A

Fixation of Mutation

96
Q

GENOME EVOLUTION

Molecular change a feature of the entire phylogenetic unit such as population, species, or lineage

A

Fixation of Mutation

97
Q

GENOME EVOLUTION

Predictable by probability (selectively neutral or near-neutral)

A

Fixation of Mutation

98
Q

GENOME EVOLUTION

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

A

Genetic Drift

99
Q

GENOME EVOLUTION

A variant may be either lost from the population or fixed, replacing all other variants.

A

Genetic Drift

100
Q

GENOME EVOLUTION

Usually in the form of nucleotide substitutions.

A

Genetic Drift

100
Q

GENOME EVOLUTION

A combination of the mutation rate and the rate of fixation

A

Evolutionary Rate

101
Q

GENOME EVOLUTION

T/F: In evolutionary rate, when we compare the rate between species or genes, a portion of the difference comes from the changes in the mutation rate and a portion from the changes in the rate of fixation

A

T

101
Q

GENOME EVOLUTION

T/F: Substitution rate is equal to the mutation rate

A

T

102
Q

GENOME EVOLUTION

The overall influence that a life history trait has on sequence evolution rate is then largely a result of the ______ & _______ of its effects on mutation and fixation rates

A

magnitude and directions

103
Q

GENOME EVOLUTION

_______ _____ will overcome selection to a greater extent in smaller populations, slightly deleterious mutations are more likely to become fixed in species with small effective population sizes

A

Genetic drift

104
Q

ODD ONE OUT: Mechanisms of Genome Evolution

● Gene duplication
● De Novo Origination
● Horizontal Gene Transfer
● Gene Recombination
● New Gene Regulatory Systems
● Transposable Elements
● Molecular Evolution of Repetitive Sequences
● Evolution Rate of Repetitive DNA Sequences
● Mitochondrial Genome

A

Mitochondrial Genome - kinuha k lng khit san

105
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Smaller genomes are favored directly by selection as a way to cellular economization

A

The Streamlining Hypothesis

106
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Most common explanation for genome reduction in free-living bacteria

A

The Streamlining Hypothesis

107
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Natural selection directly favors genome reduction and low G+C content in free-living prokaryotes living in low-nutrient environments

A

The Streamlining Hypothesis

108
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Small intergenic regions and small cell size

A

The Streamlining Hypothesis

109
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Mainly determined by the intracellular environment

A

The Streamlining Hypothesis

109
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Genes unnecessary for living in intracellular conditions are not maintained by selection and are lost in the course of evolution

A

The Streamlining Hypothesis

110
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

In populations undergoing constant bottlenecks and no recombination, genome reduction occurs through the accumulation of slightly deleterious mutations

A

The Muller Ratchet

111
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Selection fails to retain gene, which then, by the constant accumulation of mutations, become inactive and are eventually deleted from the genome

A

The Muller Ratchet

112
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- Modifications of some genes coded in the reduced genome could allow the exosymbiont to cope with the loss of otherwise essential genes;

A

F; endosymbiont

112
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

Several of the typical characteristics of these genomes, such as theri large A+T content or their small genomes, reflect known mutational biases (i.e., G:C to A:T mutations and deletions over insertions) rather than adaptations evolved by selection

A

The Muller Ratchet

113
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- The presence of complementary genes in the genomes of cosymbionts (if any) may compensate for gene losses in the endosymbiont

A

T

114
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

T/F: The Impact of Genome Reduction on Host-Associated Bacteria
Genes coded in the genome of the host compensate for gene losses in the genome of the endosymbiont

A

T

115
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- From the endosymbiont and transferred to the host

A

T

115
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

T/F: The Impact of Genome Reduction on Host-Associated Bacteria:
- Host origin

A

T

116
Q

EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION

T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- Vertically transferred from unrelated organisms not participating in the symbiosis to the host genome or its endosymbionts

A

F; horizontally

117
Q

How many nucleotide pairs are in a mitochondrial genome?

A

16,569 nucleotide pairs

118
Q

GENOMIC STRUCTURE

Each DNA molecule is organized into discrete units called

A

chromosomes

118
Q

How many proteins, rRNA & tRNAs are in a mitochondrial genome?

A
  • 13 proteins
  • 2 rRNA
  • 22 tRNAs.
119
Q

GENOMIC STRUCTURE

The total genetic information stored in the chromosomes are referred to as the ______ of the organism.

A

genome

120
Q

GENOMIC STRUCTURE

T/F: The human genome contains approximately 3 x 109 nucleotide base pairs packages into 23 pairs of chromosomes.

A

T

121
Q

GENOMIC STRUCTURE

22 pairs of chromosomes are independent of sex, they are called

A

autosomes

122
Q

GENOMIC STRUCTURE

The total chromosome count in a human is __ autosomes and two sex chromosomes, XX for females and XY

A

44

123
Q

T/F: HUMAN GENETIC VARIATION

The differences (genetic polymorphisms) are what makes each individual unique (except identical twins)

A

T

124
Q

Basic concepts of human genetic variation

A

–Locus
–Allele
–Polymorphism
–Mutation

125
Q

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

A

Genetic Locus

126
Q

are defined by chromosomal location, using chromosome bands (G-band or R-band) or molecular markers (microsatellites) as a point of reference.

A

Genetic Locus

127
Q

is the “version” of a gene that is present at any given locus.

A

Allele

128
Q

T/F: Allelic differences are related to alterations in the nucleotide sequence of a gene.

A

T

129
Q

Position or location of a gene or genetic marker on a chromosome

A

Locus

130
Q

Alternative versions of a gene at a given locus

A

Allele

[MT 6319] Molecular Biology & Diagnostics Lecture (9 decks)

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