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BIOL 1105 > 19: Genomics > Flashcards

19: Genomics Flashcards

Module 4, Lesson 2

1
Q

Early efforts in genomics focused on ____ and ____ genes.

A

Isolating and sequencing

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2
Q

The complete human genome was sequenced by….

A

2003

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3
Q

Genomics integrates ____ and ____ genetics to better understand genes.

A

Classical and molecular

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4
Q

List four methods of genomics.

A
  1. Mapping genomes
  2. Sequencing genomes
  3. Genome annotation
  4. Genome analysis
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5
Q

True or false:

Like regular maps, genome maps can be high or low resolution.

A

True

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6
Q

List the two main types of genome maps.

A
  1. Genetic maps
  2. Physical maps
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7
Q

____ are derived from recombination frequency and linkage analysis.

A

Genetic maps

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8
Q

Genetic maps provide the ____ location of genes.

A

Relative

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8
Q

____ feature nucleotide-level resolution.

A

Physical maps

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8
Q

Physical maps show the ____ location of genes.

A

Precise

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9
Q

List two types of “landmarks” that can be used as markers in the DNA sequence.

A
  1. Enzyme cutting sites
  2. Small segments of DNA
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10
Q

Physical maps show the ____ location of a marker.

A

Absolute

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11
Q

On ____ maps, the distance between markers is measured in base-pairs (bp) or kilobase-pair (Kb).

A

Physical

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12
Q

____ map the location of restriction enzyme cut sites.

A

Restriction maps

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13
Q

____ are used by researchers to study entire chromosomes or genes that can move between chromosomes.

A

Chromosome maps

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14
Q

____ maps use staining techniques to identify regions of interest.

A

Chromosome

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15
Q

A major advantage of chromosome maps is that they…

A

Enable researchers to view large pieces of DNA at a glance

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16
Q

____ maps combine high resolution with the ability to view large pieces of DNA at once.

A

Sequence-tagged site
(STS)

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17
Q

A small stretch of DNA found in only one location on the genome that is then amplified using PCR is called a…

A

Sequence-tagged site

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18
Q

Researchers use the presence or absence of STS to organize fragments into…

A

A continuous sequence
(contig)

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19
Q

The highest resolution physical map is a…

A

Base-pair sequence

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20
Q

What three things do all sequencing methods rely on?

A
  1. PCR
  2. Electrophoresis
  3. Chain-terminating nucleotides
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21
Q

Dideoxynucleotides (ddNTPs) are an example of…

A

Chain-terminating nucleotides

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22
Q

ddNTPs are different from normal nucleotides in that they…

A

Lack a 3’ OH group, which prevents additional bases from being added to the chain

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23
Q

____ allow DNA to be sequenced over a series of several reactions.

A

Manual sequencing reactions

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24
Q

True or false:

A ddNTP can have any of the four nucleotide bases (A,C,T,G).

A

True

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25
Q

Manual sequencing reactions were developed by…

A

Fred Sanger

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26
Q

Dideoxy sequencing is a(n) ____ form of DNA sequencing.

A

Automated

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27
Q

List the main steps of dideoxy sequencing.

(five)

A
  1. Begin with strand of unknown sequence
  2. Subject strand to PCR
  3. Incorporate ddNTPs
  4. Separate synthesized fragments via electrophoresis
  5. Use laser and photodetector to identify bases
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28
Q

During automated DNA sequencing, ddNTPs are labeled…

A

With a different flourescent marker depending on whether they are A, C, T, or G

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29
Q

True or false:

When DNA polymerase synthesizes DNA, it randomly incorporates one of the ddNTPs.

A

True

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30
Q

The smallest DNA fragments produced in PCR correspond to the ____ end of the molecule.

A

5’

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31
Q

____ is a form of sequencing that is faster, cheaper, and capable of sequencing large DNA fragments at once.

A

Next-generation sequencing

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32
Q

List the main steps of next-gen sequencing.

(four)

A
  1. Large strand of DNA is fragmented
  2. Single-stranded DNA fragments are attached to a solid surface
  3. Multiple copies are created using PCR
  4. DNA polymerase incorporates nucleotides
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33
Q

Why does next-gen sequencing create multiple copies of the DNA fragment?

A

It ensures accuracy in sequencing

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34
Q

Next-gen sequencing uses a ____ to begin DNA synthesis,

A

Universal primer

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35
Q

Next-gen sequencing uses special nucleotides to…

A

Terminate DNA synthesis

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36
Q

True or false:

Unlike automated sequencing, next-gen sequencing does not use flourescent markers.

A

False

Both use flourescent markers and lasers to identify bases.

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37
Q

The chain-terminating nucleotides used in next-gen sequencing are…

A

Reversible
(can be changed back into normal nucleotides)

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38
Q

Why is it important that the chain-terminating nucleotides are reversible?

A

It allows each DNA fragment to be sequenced multiple times, with new chain-terminating nucleotides being added each time

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39
Q

After sequencing, gene fragments must be…

A

Assembled into complete sequences

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40
Q

True or false:

Most genomes can be sequenced in a single step.

A

False

Most are too large for this to happen.

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41
Q

Gene fragments are assembled into a contig by…

A

Matching overlapping sequences

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42
Q

In the ____ method, a genome is broken down into large pieces of DNA called clones.

A

Clone-contig

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43
Q

List the steps of the clone-contig method.

(three)

A
  1. Genome is broken down into clones
  2. Clones are arranged using STS landmarks
  3. Clones are broken down into smaller fragments for sequencing
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44
Q

In the clone-contig method, after the small fragments are sequenced, they are used to make…

A

Clone sequences

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45
Q

Clone sequences are combined to make a…

A

Larger contigous segment
(contig)

46
Q

The ____ method does not rely on any genetic or physical maps.

47
Q

In the shotgun method, the entire genome is…

A

Broken into more manageable fragments for sequencing

48
Q

The shotgun method uses computers to…

A

Reassemble fragments using overlap between nucleotide regions

49
Q

True or false:

Both the clone-contig method and the shotgun method are often used to sequence a single genome.

50
Q

The human genome project used ____, ____, and ____ as sequencing methods.

A

Genetic maps, clone-contig, and shotgun

51
Q

The human genome project found that the human genome contains around ____ genes.

52
Q

True or false:

Organismal complexity is not merely a function of genome size or gene number.

53
Q

____ is used to assign information about DNA sequences.

A

Genome annotation

54
Q

DNA sequences and their annotations can often be found in…

A

Online databases

55
Q

A potential gene sequence, such as a start codon + amino acids + stop codon is called a(n)…

A

Open reading frame
(ORF)

56
Q

Databases of gene sequences can be updated as…

A

New information about gene functions are discovered

57
Q

DNA sequences that produce protein or are transcribed into functional RNAs are called…

A

Coding sequences

58
Q

Up to ____% of the DNA in the human genome may be non-coding.

59
Q

DNA sequences that do not code for proteins or functional molecules are called…

A

Non-coding DNA

60
Q

List the seven categories of non-coding DNA.

A
  1. Introns
  2. Segmental duplications
  3. Pseudogenes
  4. Structural DNA
  5. Simple sequence repeats
  6. Transposable elements
  7. Noncoding RNA
61
Q

____ are noncoding DNA segments that make up the majority of a human gene.

62
Q

____ are regions of the genome that have been duplicated.

A

Segmental duplications

63
Q

____ are sequences with characteristics of genes but that are not functional genes.

A

Pseudogenes

64
Q

Pseudogenes are also sometimes called…

A

Inactive genes

65
Q

____ is constitutive heterochromatin located near the centromeres and telomeres.

A

Structural DNA

66
Q

____ are stuttering repeats of a few nucleotides, repeated thousands of times.

A

Simple sequence repeats

67
Q

____ are a diverse group of DNA sequences that can move from one chromosome to another.

A

Transposable elements

68
Q

Transposable elements are also sometimes called…

A

“Jumping genes”

69
Q

True or false:

Transposable elements often copy themselves as they move.

70
Q

List the four categories of transposable elements.

A
  1. Long interspersed elements
  2. Short interspersed elements
  3. Retrotransposons
  4. DNA transposon fossils
71
Q

Long interspersed elements (LINEs) are…

A

Active transposons

72
Q

Short interspersed elements (SINEs) are…

A

Active transposons

73
Q

Each end of a retrotransposon contains…

A

Long terminal repeats (LTRs)

74
Q

____ are RNAs that do not code for protein but have regulatory functions.

A

Noncoding RNA

75
Q

True or false:

Many functions of noncoding RNA are currently unknown.

76
Q

The ____ was created to identify all functional elements in the human genome.

A

ENCODE project
(Encyclopedia of DNA Elements)

77
Q

The ENCODE project claimed that ____% of human DNA is functional.

78
Q

ENCODE researchers defined “functional” as…

A

Any sequence with reproducible biological activity

79
Q

List three reasons why some disagree with ENCODE’s findings.

A
  1. “Biological activity” alone is not enough to call DNA functional
  2. Sites of enzymatic activity are not necessarily functional
  3. Evolutionary biology focuses on DNA that has been selected for over time
80
Q

____ focuses on identifying the roles and purpose of DNA elements.

A

Genome analysis

81
Q

List the three primary approaches to genome analysis.

A
  1. Comparative genomics
  2. Functional genomics
  3. Proteomics
82
Q

____ reveals conserved regions of DNA.

A

Comparative genomics

83
Q

Comparative genomics uses information from one genome to…

A

Learn about a second, related genome

84
Q

Comparative genomics is based on…

85
Q

____ is the conserved arrangement of DNA in related genomes.

86
Q

Conserved regions of DNA are also called…

A

Syntenous regions

87
Q

List three applications of comparative genomics.

A
  1. Predict gene function
  2. Locate similar genes
  3. Predict evolutionary relationships
88
Q

____ can be derived from comparing physical maps.

89
Q

____ uses biotechnology to highlight connections between the genotype and phenotype.

A

Functional genomics

90
Q

List the three main categories of functional genomics.

A
  1. Study of all the RNA molecules produced by the genome
  2. Study of all proteins produced by genome
  3. Study of interactions between proteins
91
Q

All the RNA molecules produced by the genome are called the…

A

Transcriptome

92
Q

All the proteins produced by the genome are called the…

93
Q

The study of the proteome and the interactions between proteins is called…

A

Proteomics

94
Q

List two methods of studying the transcriptome.

A
  1. DNA microarrays
  2. RNA sequencing (RNA-seq)
95
Q

Researchers use ____ to determine which genes are expressed at a particular location or time.

A

DNA microarrays

96
Q

The dots on a microarray chip represent…

97
Q

The different colors of dots on a microarray chip represent…

A

The level of gene expression

98
Q

Knowing if a gene is expressed can provide insight into…

(two)

A
  1. The function of the gene
  2. Its interactions with other genes
99
Q

____ uses next-generation technology to capture all the mRNA transcripts created at a particular time.

100
Q

RNA-seq allows researchers to…

A

Collect information on all gene expression, not just the genes of interest

101
Q

True or false:

All mRNA that are successfully transcribed will be translated into proteins.

A

False

Just because an mRNA is transcribed does not mean the protein product will be translated.

102
Q

____ is the study of the collection of proteins encoded in the genome.

A

Proteomics

103
Q

List two reasons why it is difficult to predict a protein’s structure from DNA sequences alone.

A
  1. Alternative splicing
  2. Post-transcriptional modification
104
Q

List two techniques used in proteomics.

A
  1. Mass spectrometry (mass spec)
  2. Protein microarrays
105
Q

Mass spectrometry is used to calculate…

A

The charge-to-mass ratio of each peptide in a protein

106
Q

How does mass spectrometry identify proteins or amino acids?

A

It compares the charge-to-mass data to a database

107
Q

Protein microarrays contain ____ that are used to identify a protein.

A

Antibodies

108
Q

____ uses computer programming, math and modeling to analyze data.

A

Bioinformatics

109
Q

Applying bioinformatics techniques to proteomics enables…

A

Rapid identification of proteins

110
Q

Bioinformatics can predict protein structure using…

(two)

A
  1. Chemical properties of amino acids
  2. Principles of how amino acids interact
111
Q

List two applications of genomics.

A
  1. Synthetic biology
  2. Diagnostics
112
Q

____ involves creating biological organisms to solve problems.

A

Synthetic biology

113
Q

In medicine, diagnostics can be used to…

A

Identify harmful genes

114
Q

In forensics, diagnostics can be used to…

A

ID remains and weaponized pathogens

115
Q

List two areas of genomics that have created ethical concerns.

A
  1. Research of infectious diseases
  2. Gene patenting

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