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Chapter 12 Flashcards

1
Q

DNA polymorphisms

A

two or more alleles at a locus. The sequence variations of a DNA polymorphism can occur at any position on a chromosome and may (nonanonymous polymorphism), or may not (anonymous polymorphism), have an effect on phenotype.
Differences in DNA sequences among individuals

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2
Q

reasons why very few differences in DNA sequences between two people alter the amino acid sequences of proteins.

A

Natural selection might lead to the disappearance of deleterious mutations.
A very small percentage of the human genome consists of codons within genes.
Many mutations within codons are silent.

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3
Q

Anonymous DNA polymorphisms

A

differences in genomic DNA sequence with no effect on gene function.
sequence differences between genomes that do not affect the nature or the amount of any protein in the body

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4
Q

DNA marker

A

an identifiable physical location on a chromosome with DNA sequence variants whose inheritance can be monitored.
if a polymorphism has no effect on phenotype, it may still be useful as a it
serve as signposts in the genome.

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5
Q

The National Center for Biotechnology Information has cataloged more than 100 million SNPs that are found in human genomes. How many of these are considered to be common in human genomes?

A

15 million

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6
Q

genetic variants in order from most (at the top) to least frequent in the human genome.

A

SNP – Single nucleotide polymorphism
DIP – Insertion/ deletion
SSR – simple sequence repeat
CNV – Copy number variant

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7
Q

SNP (single nucleotide polymorphism)

A

A genetic variant involving the change of a single base pair
a single nucleotide locus with two naturally existing alleles defined by a single base pair substitution. SNP loci are useful as DNA-based markers for genetic linkage analysis.
are particular base positions in the genome where alternative nucleotides distinguish some people from others.

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8
Q

Most SNPs in human populations are represented by how many alleles

A

2

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9
Q

The most common type of genetic variants are ____.

A

SNPS

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10
Q

derived allele

A

an allele that arises through mutation.

SNP occurred more recently

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11
Q

ancestral allele

A

the allele carried by the last common ancestor of two species.
More ancient SNP

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12
Q

If you and a friend share a derived allele at an anonymous SNP locus, it means ______.

A

you likely got that allele from the same ancestor

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13
Q

How is the relative frequency of DIPs related to their length (if at all)?

A

Longer DIPs are much less frequent than shorter DIPs.
DIPs relative frequency declines in relation to their length
The longer the DIP the less frequent it is.

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14
Q

simple sequence repeat (SSR)

A

genomic locus that consists of one or a few bases repeated in tandem up to 100 times. Different alleles have different repeat numbers. The human genome contains ∼100,000 SSR loci. Also called a microsatellite locus.

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15
Q

Simple sequence repeats (SSRs) arise from _____.

A

rare, random events

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16
Q

InDel (or DIP) deletion-insertion polymorphism

A

a genomic DNA polymorphism caused by insertion or deletion.

Genetic variations involving short insertions or deletions of genetic material

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17
Q

copy number variant (CNV)

A

a category of genetic variation arising from large regions (from 10 bp up to 1 Mb) of duplicatior deletion. Size is variable

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18
Q

Problems with DNA [] such as slipped mispairing or [] cause simple sequence repeats (SSRs) to expand into longer sequences.

A

Replication; stuttering

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19
Q

Polymerase chain reaction was developed by _____.

A

Kary Mullis

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20
Q

New alleles of a CNV locus are often produced from unequal [] during []

A

Crossing over; meiosis 1

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21
Q

Primer

A

Short oligonucleotides that flank the region of DNA to be amplified by PCR
define the ends of the target region of DNA
chosen for PCR based on the DNA sequence on both sides of the target region
bind to denatured (single-stranded) template DNA

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22
Q

Knowing the sequence of base pairs ______ the target region of DNA allows scientists to design appropriate primers.

A

on the ends of

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23
Q

In PCR, the template DNA is ______.

A

the DNA to be amplified

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24
Q

PCR involves denaturation of target [] into single strands, hybridization of [] and polymerization by DNA []

A

DNA; primers; polymerase

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25
polymerase chain reaction (PCR)
a fast and inexpensive method of replicating a DNA sequence in vitro when short sequences at each end are known; based on reiterative DNA synthesis that amplifies the products of each previous round of replication. way to copy DNA without vectors or host cells
26
In PCR, DNA polymerase adds nucleotides to ______.
the 3' ends of primers
27
Why does PCR require a special DNA polymerase from a bacterium that grows in hot springs?
After each round of replication, the PCR reaction is heated to melt apart the DNA strands and the polymerase must remain active at this temperature. Final product of PCR It is double stranded; It extends from one primer's 5' end to the position of the other primer's 3' end.
28
Steps in one PCR cycle
Denaturation of target DNA into single strands Hybridization of primers Polymerization by DNA polymerase
29
What is a common technique used to genotype SNPs?
Sequencing of PCR products
30
SNPs and DIPs can be genotyped by _____.
sequencing PCR products amplified from genomic DNA
31
What types of polymorphisms can always be genotyped by performing PCR and then separating the PCR products by gel electrophoresis (without sequencing)?
SSR and DIPs
32
what is the longest DNA region that can be amplified by PCR?
25kb
33
In prenatal genetic diagnosis what type of cells are genotyped?
Fetal cells
34
all that can be genotyped by sequencing PCR products amplified from genomic DNA?
Changes in the number of repeats in SSRs SNPs DIPs
35
Two ways to obtain DNA from a fetus so that it can be genotyped
Cell-free DNA analysis: a procedure where DNA in the blood of a pregnant woman, which contains DNA released from broken fetal cells that leaked into her bloodstream, is analyzed in order to genotype the fetus. Amniocentesis: a medical procedure in which a sample of amniotic fluid is taken from a pregnant woman to determine the karyotype of an unborn baby.
36
Polymorphisms that change the size of a locus can be genotyped directly after PCR without sequencing using _____.
gel electrophoresis
37
preimplantation embryo diagnosis
a process by which human eggs are fertilized in vitro and genotyped for particular disease alleles prior to implantation in a uterus. is a method that tests for genetic disease alleles in embryos produced by in vitro fertilization Embryos produced by in vitro fertilization can undergo genetic testing prior to being placed in the mother's womb.
38
The chance that two random people will have the same combinations of SSR alleles
Decimal of the likelihood ^ number of unlinked positions | Ex: 10% likelihood and 13 unlinked positions is .1^13 or 1 in 10 trillion
39
DNA profiling is performed by PCR-amplifying 13 different SSR loci using 13 pairs of PCR primers. Each primer pair is tagged with a different _______.
fluorescent dye
40
prenatal genetic diagnosis
genotyping fetal cells to determine alleles of disease loci. | involves genotyping fetal cells by methods such as PCR
41
amniocentesis
a medical procedure in which a sample of amniotic fluid is taken from a pregnant woman to determine the karyotype of an unborn baby. obtaining fetal cells that can be genotyped
42
Currently, scientists can obtain a DNA profile for an individual by determining what alleles he or she carries for 13 unlinked, highly polymorphic [] loci
SSR
43
How many SSR loci per person are examined and cataloged in the CODIS (Combined DNA Index System) database?
13
44
To genotype a human, a PCR is performed in which 13 unlinked, polymorphic SSR loci are amplified at the same time. How are the different fragments produced by the PCR separated?
They are separated using gel electrophoresis and identified based on their fluorescence and their sizes.
45
Two siblings, as well as parents and their children, share what percentage of SSR alleles?
50%
46
uses for DNA profiling.
Forensics Identification of human remains Paternity suits
47
Two ways to obtain DNA from a fetus so that it can be genotyped
Cell-free DNA analysis | Amniocentesis
48
nucleic acid hybridization
formation of double-stranded molecules through complementary base pairing of single strands of DNA or RNA.
49
molecules that can undergo nucleic acid hybridization.
Two complementary single-stranded RNAs A single-stranded DNA and a complementary single-stranded RNA Two complementary single-stranded RNAs
50
The CODIS database allows forensic laboratories throughout the United States to compare DNA profiles. These laboratories use the same 13 [] pairs to amplify 13 []
Primer; SSR
51
allele-specific oligonucleotides (ASOs)
short oligonucleotides that hybridize with only one of a pair of alleles distinguished by a single base difference. Oligonucleotides that will hybridize to only one of two alleles at a SNP locus
52
Because siblings, and also parents and children, share 50% of all [] alleles, it is possible to identify the perpetrator of a crime not only by a match to his or her own DNA, but also by a [] match to the DNA of a close relative.
SSR; partial
53
DNA microarray
allows researchers to genotype many SNP loci simultaneously. | takes advantage of allele-specific oligonucleotides
54
nucleic acid hybridization
formation of double-stranded molecules through complementary base pairing of single strands of DNA or RNA. The ability of complementary single strands of DNA or RNA to come together to form double-stranded molecules
55
double-stranded hybrid between an oligonucleotide and a target DNA strand with a mismatched base is significantly [] stable than an hybrid with no mismatches because there may not be enough [] in a row to hold the strands together.
Less; hydrogen bonds
56
disease genes
genes whose mutant alleles cause human genetic diseases.
57
positional cloning
the process by which researchers use linkage analysis to obtain the clone of a gene. Goal is to Identify genetic mutations that are associated with hereditary diseases. Obtain information about the location of the disease by finding polymorphic loci to which the mutation is genetically linked. The first goal is to discover a DNA marker that shows linkage to the disease locus.
58
DNA microarray
A silicon chip containing small fragments of single-stranded DNA a collection of oligonucleotides attached to a solid surface. allows researchers to genotype many SNP loci simultaneously.
59
Scientists prepare genomic DNA for microarray analysis by digesting the genome with a [] enzyme and [] an oligonucleotide adapter to the restriction fragments. The adapter is complementary to a PCR primer, which can be used to amplify all parts of the genome.
Restriction; ligate
60
Positional cloning takes advantage of the fact that two loci that are genetically linked _____.
are found close together on the same chromosome
61
When probing a DNA array scientists often need to amplify and fluorescently tag genomic DNA. Why must the genomic DNA be amplified before it is tagged?
A single fluorescently labeled DNA molecule does not generate enough light to be detected.
62
Two genes are [] if they are positioned close together on the same chromosome.
Linked
63
Phase
Another name for the configuration of alleles
64
Positional cloning tracks the disease gene's locus by [] and the marker locus by direct [] of each person.
phenotype; genotyping
65
Based on the rough estimate that 1 cM corresponds, on the average, to 1 Mb, a human disease causing gene would be linked to a polymorphic locus if the two are less than ______ apart from each other.
50 Mb
66
How does the amount of pedigree data affect the resolution of positional cloning?
The more pedigree data is available, the higher the resolution of positional cloning.
67
A Lod score is calculated from the [] of the probability of obtaining a particular set of results in a [] f two loci are linked to the probability of observing the same results if the loci are unlinked.
Ratio; pedigree
68
One limitation to positional cloning is that you must be able to determine the [] of the SNP and disease alleles for the people in the pedigree.
Phase
69
In positional cloning, at least one parent must be a double [] for the cross to be informative.
Heterozygote
70
What human disease gene was the first mapped successfully by positional cloning, due to the availability of a large amount of pedigree data?
Huntington disease
71
disease that best exemplifies allelic heterogeneity.
Cystic fibrosis
72
the Lod score statistic
The ratio of the probabilities of obtaining a particular set of results in a pedigree if the two loci are linked to the chance of observing the same results if the loci are unliked used to determine whether available data are sufficient to conclude with confidence whether a disease gene and a DNA marker are genetically linked.
73
Patients that have one copy of a gene with one mutation, and the other copy of the same gene with a different mutation are called [] or sometimes []
``` compound heterozygotes (trans-heterozygotes) heterozygotes for two different mutant alleles of the same gene. ```
74
A genetic disease that can be caused by a variety of different mutations in the same gene displays
Allelic heterogeneity
75
In whole-exome sequencing, scientists first enrich for genomic DNA fragments that correspond to the exons of all genes by hybridization to ______.
cDNA sequences
76
whole-exome sequencing
sequencing of only the genomic DNA corresponding to exons.
77
High throughput sequencing
The ability to sequence many DNA fragments simultaneously
78
Conditions displaying [] are caused by mutations in two or more different genes.
Locus heterogeneity
79
One of the technological innovations that has made high-throughput sequencing possible is the ability to control base addition [] so that each base can be identified before the next one is added.
Temporally
80
The first step in Illumina sequencing is _____.
attachment of adapters to DNA fragments
81
In a rare dominant condition it is likely that _______.
related patients will have the same rare mutant allele the patient will be heterozygous for the causative allele unrelated patients might have a different mutation in the same gene
82
What new innovations are used in high-throughput sequencing?
Base addition is controlled temporally so that each base can be identified before the next one is added. DNA fragments anchored in one place are replicated by DNA polymerase.
83
Select problems that may impede a geneticist's ability to identify the mutation responsible for a disease.
No genome sequence is 100% accurate or 100% complete. | The amount of variation among human genomes is huge.
84
Nonanonymous DNA polymorphisms.
Genetic variants that affect phenotypes through changes in protein function
85
reasons a mutation may remain unidentified even when a whole-genome sequence is available.
The mutation may affect transcription of the disease gene. | The mutation may affect splicing of the disease gene's transcript without altering splicing consensus sequences.
86
variants that are likely to be nonanonymous polymorphisms.
Nonsense mutation Missense mutations Frameshift mutation
87
Scientists searching for mutations that cause disease first look in the [] because the DNA sequences that regulate transcription and splicing can be more difficult to identify.
Exomes
88
Looking at genetic variants in genes whose sequence has been highly conserved during [] may help scientists determine the mutation behind a rare disease.
Evolution
89
Identification of many disease-causing mutations depends on ______.
knowledge of variants from many other people's genomes
90
Actionable outcome
The identification of a disease gene that provides information on how a condition might be treated
91
Not actionable
When knowing the mutation that causes a disease does not help in the treatment of the disease
92
The progress of human genetics requires that [] remain up to date and that their information is available to all investigators.
Databases

Biotech final (11 decks)

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