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Genomics > Exam 1 Study > Flashcards

Exam 1 Study Flashcards

1
Q

1871

A

Friedrich Miescher identified the presence of ‘nuclein’

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2
Q

1953

A

James Watson and Francis Crick, Rosaland Franklin and Maurice Wilkins, discover the double helix structure of DNA

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3
Q

1977

A

Frederick Sanger develops a DNA sequencing technique

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4
Q

1983

A

Kary Mullis develops polymerase chain reaction a technique used for amplification of DNA

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5
Q

1987

A

the term genomics first used in scientific literature

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6
Q

1990

A

Human Genome Project is launched

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7
Q

2003

A

Human Genome Project is finishes

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8
Q

2007

A

Illumina “next-generation” sequencer is available

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9
Q

haploid cell number of bases

A

3 million

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10
Q

How much of the mammalian genome is coding

A

2%

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11
Q

Mitochondrial DNA inheritance

A

strictly maternal

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12
Q

Chromatin

A

DNA with a protein scaffolding
DNA is wrapped around histones

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13
Q

Constitutive heterochromatin

A

inactive

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14
Q

Centromeres are used by the cell

A

during cell division to make sure that each daughter cell gets a copy of each chromosome

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15
Q

Centromeres are

A

highly repetitive

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16
Q

Telomeres are located_____ and do what

A

at the ends of chromosomes
protect the ends of the chromosomes

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17
Q

Repetitive DNA is

A

Tandem
Interspersed
Segmental duplications

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18
Q

Lines are what percent of the genome

A

17%
around 5-6 Kb

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19
Q

Sines are what percent of the genome

A

11%
<500 bp

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20
Q

Cytoplasmic genome

A

circular
uniparental inheritance
small compared to nuclear
thousands of copies per cell
heteroplasmy

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20
Q

Segmental duplications

A

low copy repeats
blocks that range from 1 to 400 kb in length
occur at more than one spot in the genome
and typically share a high level of sequence identity
about 5% of the human genome

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21
Q

Centromeres are how may bases

A

100s Kb to Mb

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22
Q

Telomeres are how many bases

A

10s Kb

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23
Q

Three parts of DNA or RNA

A

Pentose sugar
nitrogenous base
Phosphate group attached to the 5’ carbon

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24
Q

DNA uses what sugar
RNA uses what sugar

A

Deoxyribose
ribose

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25
Q

Purines

A

Adenine
Guanine

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26
Q

Pyrimidines

A

Cytosine
Thymine
Uracil

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27
Q

The phosphate group allows

A

two nucleotides to be linked
creates the stream of information that DNA encodes

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28
Q

5’ to 3’ linkage between a phosphate group of one nucleotide and the 3’ carbon of the next nucleotide’s sugar

A

phosphodiester bonds

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29
Q

The two ends of the polynucleotide chain are

A

not the same
5’ end-phosphate group attached to the 5’ carbon of the pentose sugar
3’ end has a hydroxyl group

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30
Q

The polynucleotide chain has

A

polarity
5’ to 3’ ends

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31
Q

A-T bond has how many H bonds

A

2

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32
Q

C-G bond has how many H bonds

A

3

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33
Q

A-U bond is in

A

RNA

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34
Q

Watson and Crick investigated the structure of DNA not by collecting new data but by

A

using all the available information about chemistry of DNA to construct molecular models

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35
Q

DNA Structure-3 main points

A

double helix
strands are antiparallel
base complimentary

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36
Q

What type of bond is between base pairs

A

H bonds
Weak enough to be broken and then used

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37
Q

DNA strands are arranged helically with ___ base pairs between each turn of the helix

A

10

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38
Q

Raw materials of DNA synthesis

A

Template
-single stranded DNA
Enzymes
-DNA polymerase
Raw materials (substrate)
-dNTPs
Mg2+ ions

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39
Q

DNA polymerase does what

A

catalyzes the formation of phosphodiester bonds
joins the 3’-OH group of the last base in the DNA chain to the incoming 5’-phosphate of a dNTP

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40
Q

Synthesis is what direction

A

5’ to 3’

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41
Q

dNTP is

A

selected by the DNA polymerase using the opposing base on the template strand

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42
Q

Key features of DNA replication in Eukaryotes

A

occurs in the nucleus during S phase of the cell cycle
is initiated by RNA primers
Occurs in the 5’ to 3’ direction
semiconservative
Initiated at the same time at many points along the chromosome
heterochromatin replicates later than does euchromatin

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43
Q

All DNA polymerases require a

A

free 3’ OH

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44
Q

Gyrase ds breaks to

A

relieve torsional strain

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45
Q

Helicase breaks

A

H bonds between bases

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46
Q

SSB proteins protect

A

free DNA, prevent secondary structure

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47
Q

Packaging of newly replicated DNA

A

histones must first disassemble to allow DNA synthesis (uses old histones)
Synthesis of new histones is coordinated with DNA Synthesis
then resembled into new chromosomes

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48
Q

1952

A

Hershey-Chase experiments are carried out by Alfred Hershey and Martha Chase to demonstrate that DNA, rather than protein, carries our genetic information

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49
Q

How many years from the identification of nuclein to the demonstration of DNA as the genetic material

A

81 years

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50
Q

How many years from the first sequencing method to HGP start

A

13 years

51
Q

2001

A

first draft of the human genome sequence released 3 Gb

52
Q

How many years between the first bacterium to the Human Genome Project

A

8 years

53
Q

Celera vs Human Genome Project

A

HGP clone by clone approach
Celera whole genome shotgun

54
Q

2007

A

solexa 1G sequencer is available
next generation sequencing

55
Q

Order of bases

A

base pair
kilobase
megabase
gigabase
terabase
petabase

56
Q

Moore’s law

A

the number of transistors incorporated in a chip will approximately double every 24 months

57
Q

Number of copies of target

A

N times 2c

58
Q

Requirements for DNA replication

A

DNA template
DNA polymerase
Nucleotides
Primers

59
Q

PCR three steps

A

Denaturation
Annealing
Extension

60
Q

Keys to PCR success

A

primer specificity
annealing temp
Mg++ concentration

61
Q

Limitations of PCR

A

size
base complexity
secondary structure

62
Q

Sanger sequencing uses

A

4 tubes- one for each base

63
Q

ABI sequencing uses

A

one tube with 4 fluorescent labels

64
Q

Key components needed for transcription

A

DNA template
the raw materials (ribonucleotide triphosphate)
transcription apparatus

65
Q

What has to happen to the DNA in order for a gene to be transcribed

A

uncoiling

66
Q

DNA molecules undergoing transcription exhibit ___

A

christmas tree-like structures

67
Q

Regulatory regions determine

A

what, when, where, how much

68
Q

Regulatory promotors are

A

upstream of core promotor
affect the rate of transcription

69
Q

mRNAs have a

A

5’ cap and 3’ poly A tail

70
Q

Most eukaryotic organisms have

A

introns
non-coding region of DNA

71
Q

In eukaryotes, intron size and number is related to

A

organism complexity

72
Q

Introns have

A

regulatory roles and are longer than exons

73
Q

in order to have collinearity, introns are

A

spliced out by snRNPs in a splicesome

74
Q

All sequences in DNA that are transcribed into a single RNA molecule

A

a gene

75
Q

How many bases are needed to distinguish 20 amino acids

A

4

76
Q

The genetic code is ____ which means it repeats alot

A

degenerate

77
Q

sequencing is a

A

tool to be applied to address a question

78
Q

4 basic steps of Illumina Sequencing

A

1 sample prep
2 cluster generation
3 sequencing
4 data analysis

79
Q

Library fragment size has

A

downstream implications for analysis

80
Q

Patterned flow cells give

A

faster scan times due to ordered cluster positions
less cluster overlap
more clusters

81
Q

Sequence by synthesis

A

one nucleotide is added at a time

82
Q

Problems with sequence by synthesis

A

very accurate but dye can be not cleaved off- see both colors then
quality degrades the longer it is

83
Q

In Illumina sequencing the dye is

A

covalently bonded to the base

84
Q

Illumina sequencing is based on

A

reversible terminator chemistry
Sequencing by synthesis

85
Q

Types of color coding for sequencing

A

4 channel-each nucleotide has its own color
2 channel- uses two colors (Ais green and pink, G has none, T is green, C is pink)
1 channel-will be discussed later

86
Q

Error for Illumina Sequencing

A

Clusters start to condense
less resolution
occurs due to physical properties of SBS
equality differences
SNPs

87
Q

How much can Illumina NovaSeq X sequence

A

1600 Gb

88
Q

How does Ultima Genomics work

A

like a dvd or cd
wells that are spun around and read by a laser

89
Q

The ability to resolve a repetitive sequence is dependent on

A

the length of the molecules in your library

90
Q

Long Read Technology

A

Oxford Nanopore (ONT)-protein nanopores
pacific BioSciences (PacBio)-SMRT
bionano genomics-optical maps
proximity ligation-assembly

91
Q

Nanopore uses
and can do how much for what price

A

biological nanopores
10-20 Gb in <24 hours
around 600 dollars

92
Q

nanopores have a diameter that are

A

in the same scale as many single molecules, including DNA

93
Q

How does nanopore sequencing work

A

nanopore is embedded in the membrane
-current cannot travel through
-nanopore creates a hole and the current drives things through the pore
-then measure the change in electrical current to determine which nucleotide it is
-each nucleotide has a different structure so it creates a different electrical current

94
Q

Nanopore can sequence how much

A

400 bp/sec

95
Q

nanopore errors

A

homopolymers

96
Q

Nanopore accuracy

A

> 99%

97
Q

Which type of sequencing can detect base modification

A

nanopore

98
Q

PacBio uses what type of sequencing

A

SMRT-single molecule real-time

99
Q

PacBio uses what to do its sequencing

A

Nano-wells called Zero-mode Wave guidlines
polymerase bound to bottom of ZMW
Phospholinked nucleotides
light from nucleotide cleavage detected as polymerase processes DNA

100
Q

PacBio mean read length

A

> 20 kb with a moderate error rate

101
Q

Process of PacBio

A

start with high quality double stranded DNA
prepare SMRTbell libraries
anneal primers and bind DNA polymerase
circularized DNA is sequenced in repeated passes
the polymerase reads are trimmed of adapters to yield subreads
consensus and methylation status are called from subreads

102
Q

PacBio sequencing rate

A

10bp/second

103
Q

PacBio errors

A

homopolymers and indels

104
Q

PacBio accuracy

A

> 99%

105
Q

Error types of
Illumina
Oxford Nanopore
PacBio

A

-SNPs
-Homopolymers
-Homopolymers and Indels

106
Q

HMW DNA is fluorescently labeled at

A

known sequence motifs

107
Q

Bionano genomics process

A

HMW DNA is fluorescently labeled at known sequence motifs
DNA is stretched through nanochannels then imaged
creates a map of those sequence motifs
NOT SEQUENCING

108
Q

HiC

A

order and orients contigs (set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a genomic region)

109
Q

PacBio characteristics

A

increasing read lengths+increasing throughput means decreasing cost
20-30 kb
per base error rate is 10-15%
Most popular long read

110
Q

Oxford Nanopore characteristics

A

extremely long reads but relatively few-expensive
no upper limit on size- huge potential
most promising long read in a few years

111
Q

bionano optical maps characteristics

A

inexpensive
significant improvement of genome assembly
both short and long reads

112
Q

FASTA has how many parts and what are they

A

Two
1) > sequencing name
2) sequence

113
Q

FASTQ has how many parts and what are they

A

1) @sequence name
2) sequence
3) + some other info
4) quality value (phred scale using ascii)

114
Q

FASTA is used when

A

quality is not needed
presents only the sequence itself
chromosomes
gene structures

115
Q

FASTQ is used

A

when quality is needed
sequence reads

116
Q

Differences between FASTA and FASTQ

A

quality included in FASTQ using ASCII coded quality value

117
Q

At a given position in a sequence, the base present is either A/C/G/T but we

A

cannot directly observe that base.

118
Q

The base that is produced from a DNA sequencer is an observation based on some biochemical/physical property that has

A

error

119
Q

QPhred=

A

-10 log10 P(error)

120
Q

FastQC is

A

one of many software tools to evaluate quality
it does not actually do any filtering, provides summary metrics and visuals

121
Q

important metrics

A

base quality
adaptor content

122
Q

K-mers

A

any integer goes for k
it is a polymer

123
Q

what are k-mers used for

A

to make distributions and estimate errors

124
Q

sequence reads are typically how long

A

150 bp or less

Genomics (11 decks)

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