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Human Genetics > Exam III Review > Flashcards

Exam III Review Flashcards

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Biology 101 flashcards
1
Q

Overdominance

A

Heterozygote advantage- heterozygotes are favored over homozygotes and have reproductive advantage
-Equilibrium will be reached

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2
Q

Underdominance

A

Heterozygotes selected against- heterozygote has a lower fitness than both homozygotes. This leads to unstable equilibrium

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3
Q

The frequency of a recessive allele at equilibrium is equal to what

A

The square root of the mutation rate divided by the selection coefficient

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4
Q

The frequency of a dominant allele at equilibrium is equal to what

A

The mutation rate divided by the selection coefficient

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5
Q

Four forces that (in the short term) cause changes in allelic frequencies

A

Mutation
Migration
Genetic drift
Natural selection

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6
Q

Genetic drift will eventually lead to

A

Fixation of one allele

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7
Q

What populations are good for studying rare variants in allelic frequencies for certain diseases

A

Small populations

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8
Q

Evolution occurs through

A

Genetic change within populations

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9
Q

Biological species concept

A

A group of organisms whose members are capable of interbreeding with one another but are reproductively isolated from members of other species

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10
Q

What must be present for evolution to take place

A

Genetic variation

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11
Q

Anagenesis vs Cladogenesis

A

Anagenesis is evolution within a lineage with the passage of time
Cladogenesis is the splitting of one lineage into two

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12
Q

3 Types of variation talked about

A

Molecular variation
Protein variation
DNA sequence variation

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13
Q

Molecular variation methods

A

Can be used with all organisms
Can be applied to huge amount of genetic variation
All organisms can be compared
Quantifiable
Provide information about the process of evolution

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14
Q

Prezygotic reproductive isolating mechanisms

A

Ecological- Differences in habitat- individuals do not meet
Behavioral-Difference in mating behavior
Temporal- reproduction at different times
Mechanical- anatomic differences
Gametic- gametes are incompatible

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15
Q

Postzygotic reproductive isolating mechanisms

A

Hybrid inviability- hybrid zygote does not survive
Hybrid sterility- hybrid is sterile
Hybrid breakdown- F1 hybrids viable/fertile but F2 are not

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16
Q

Phylogeny is

A

The evolutionary relationships among a group of organisms

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17
Q

The variability selection hypothesis

A

Key events in human evolution were not shaped by any single type of habitat, but rather by environmental instability

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18
Q

Allopatric vs sympatric speciation

A

Allopatric has geological barrier to gene flow b/w two species, sympatric does not

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19
Q

Parsimony phylo tree approach

A

Favors tree that has the fewest necessary changes to explain evolution

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20
Q

Rates of evolution include

A

Rates of nucleotide substitution
Nonsynonymous and synonymous rates of substitution
Substitution rates for different parts of a gene

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21
Q

The molecular clock

A

The rate at which a protein evolves is roughly constant over time
Therefore, the amount of molecular change that a protein has undergone can be used as a clock

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22
Q

Exon shuffling

A

Type of genome evolution

  • Function domains encoded by exons can be shuffled to create new genes of different but related function
  • can be caused by crossover or transposons
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23
Q

Continuous/quantitative characteristics

A

Phenotypes vary continuously

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24
Q

Discontinuous characteristics

A

Traits posses only a few phenotypes

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25
Q

GWAS

A

An examination of many common genetic variants in different individuals to see if any variant is associated with a trait

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26
Q

Polygenic inheritance

A

Occurs when one characteristic is controlled by two or more genes
i.e. height, skin color, weight

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27
Q

Did mendel study continuous or discontinuous traits

A

Discontinuous

If he studied continuous- there would be a range of phenotypes instead a few, easily distinguishable ones

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28
Q

Quantitative characteristics

A 
Exhibit complex relationship b/w genotype and phenotype
Likely polygenic
Important environmental influences
Overlapping phenotypes
Cannot use standard methods to analyze
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29
Q

Meristic characteristics

A

Quantitative- determined by multiple genetic/environmental factors, can be measured in whole numbers
-i.e. animal litter size

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30
Q

Threshold characteristics

A

Quantitative- measured by presence or absence, so only two phenotypes possible. They are quantitative because the underlying susceptibility to the characteristic varies continuously. When the susceptibility exceeds a threshold value, the characteristic is expressed

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31
Q

Population vs sample

A

Population is whole group, sample is a representative group from the population

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32
Q

Variance vs standard deviation

A

Variance- the variability within a group of measurements

SD- Square root of the variance

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33
Q

The mean provides info about

A

The center of a distribution

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34
Q

When regression coefficient is 0.2, a 1 unit increase in x is associated with

A

A 0.2 increase in y

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35
Q

Heritability

A

The proportion of the total phenotypic variation that is due to genetic difference
-An individual does not have heritability, a population does

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36
Q

Broad sense heritability

A

Ratio of total genetic variance to total phenotypic variance

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37
Q

Narrow sense heritability

A

Variation in a phenotypic trait in a population that is due to genetic variation between individuals in a population)

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38
Q

Components of phenotypic variance

A

Genetic variance
Environmental variance
Genetic x environmental variance

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39
Q

Components of genetic variance

A

Additive genetic variance
Dominance genetic variance
Genic interaction variance

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40
Q

Narrow sense- when h2 equals 0, 1, or .5

A

0- no relationship between parent/kid phenotype
1- perfect correlation b/w parent/kid phenotype
.5- genes and environment interact to determine phenotype

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41
Q

Does heritability indicate the degree to which a trait is genetic, and why/why not?

A

No, it measure the proportion of phenotypic variance that is the result of genetic factors in a given environment

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42
Q

Heritability indicates ______ about the nature of population differences in a characteristics

A

Nothing

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43
Q

Natural selection arises through

A

The differential reproduction of individuals with different phenotypes- will increase freq of certain alleles

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44
Q

Artificial selection is

A

Selection by promoting the reproduction of organisms with traits perceived as desirable- also will increase freq of certain alleles

45
Q

Segregation analysis

A

Multiple genes analyzed together

46
Q

Association analysis

A

Small areas of genome examine

Larger areas- false positives more common

47
Q

GWAS uses what to help with mapping

A

SNPs

48
Q

Higher MZ concordance compared to DZ concordance suggests what

A

The disease is familial or that there is a genetic influence

49
Q

Epigenetics

A

Heritable change in phenotype that does not involve changes in DNA sequences

50
Q

Behavioral epigenetics

A

Life experiences, especially early in life, have long lasting effects on behavior

51
Q

The thrifty phenotype theory

A

When environmental conditions are poor for parent, internal biological processes know that the environment will be poor for offspring. With food shortage for parents- biochemical modifications allow pre-adaptation to produce offspring that will be better suited for that environment
-Reproductive advantage in severe environments

52
Q

Methylated DNA vs methylated/acetylated histones

A

Methylated DNA causes silencing- usually M-cytosine
Methylated histones can have variable gene activity depending on which lysine is methylated
-Acetylated histones are activating

53
Q

Critical concept of histone code hypothesis

A

Histone modifications serve to recruit other proteins by specific recognition of modified histone - these proteins then repress or promote transcription

54
Q

Methyl transferase classes

A

I- DNA methyltransferase
II- Histone methyltransferase
III- membrane associated

55
Q

Genomic imprinting

A

The expression of an allele depends on whether it is inherited from the male or female parent

56
Q

Uniparental disomy and Prader Willis syndrome

A

Due to nondisjunction, a fertilized egg receives an extra chromosome, if it is not eliminated quickly, the result is miscarriage.
The extra chromosome could have come from the mom, meaning 2x mom chromosome and 1x dad chromosome
If dad chromosome is deleted, you are left with 2x mom chromosome and this can cause Prader Willis syndrome

57
Q

During what time in life is epigenetics most important

A

First 1000 days of life

58
Q

Epigenome

A

Overall pattern of chromatin modifications possessed by each individual organism

59
Q

What is used to detect histone modifications

A

ChIP

60
Q

What are used to detect DNA methylation

A

Restriction endonucleases

Bisulfate sequencing

61
Q

Lead exposure and epigenetics

A

Lead exposure can alter DNA methylation

62
Q

Benign vs malignant vs metastatic tumors

A

Benign- tumor remains localized
Malignant- tumor cells invade other tissues
Metastasis- tumor cells induce secondary tumors elsewhere in body

63
Q

Knudsons multistep theory for cancer

A

Proposed that retinoblastoma results from two separate genetic defects, both of which are necessary for the cancer to develop

64
Q

What is the singular key event in cancer

A

Genomic instability

- it leads to multiple mutations that activate all of the secondary hallmark events

65
Q

Main cause of hereditary cancers

A

Establishment of genomic instability is the initiating event

66
Q

Main cause of sporadic cancers

A

Deregulation of growth-regulating genes may be the initiating event, leading to DNA damage

67
Q

Loss of heterozygosity

A

Person could be heterozygous for tumor-suppressor gene.
Loss of wild type allele through chromosomal deletion will leave only mutant allele and tumor suppressor activity is lost

68
Q

Mutations is Ras pathway contribute to

A

Cancer

69
Q

Lynch syndrome

A

Inherited disorder that increases risk of many types of cancer
-Mutated genes in this syndrome prevent proper repair of DNA replication mistakes

70
Q

t(14;18)(q32;q21)

A

Chromosomal translocation that lead to hyper-upregulation of BCL2 (blocks mitochondrial apoptotic pathway) expression in cancer cells
-Hallmark of follicular lymphoma

71
Q

Epigenetics and cancer

A

Mutations in the three classes of epigenetic modifiers (DNA methylation, nucleosome remodeling, and histone modification) are frequently observed in cancers
-These mutations probably cause genome wide epigenetic alterations in cancer

72
Q

MicroRNA and cancers

A

Deregulation of miRNA can lead to cancer because some mRNAs are able to escape regulation by miRNAs

73
Q

Retroviruses cause cancer by

A
  • Mutating and rearranging proto-oncogenes
  • Inserting strong promoters near proto-oncogenes
  • Inactivating tumor suppressors
74
Q

Rituximab function

A

MAB against protein CD20 on B cells. It selectively targets and destroys B cells in cancers with overactive/dysfunction B cells like lymphomas

75
Q

CRISPR and CAR-T

A

CRISPR can be used to genetically alter the patients T cells so they are better equipped to fight the cancer

76
Q

The cancer genome atlas

A

TCGA researchers will identify the genomic changes in more than 20 different types of human cancers to help us understand what turns a normal cell into a cancer cell.

77
Q

What have we learned from The cancer genome atlas project

A

There are certain areas of the genome commonly affected in several types of cancers
Specific changes allow us to tell one type of cancer from another

78
Q

Elephants and cancer

A

P53 is a tumor suppressor gene and elephants have 20 copies of it

79
Q

What created the FDA animal rule

A

Anthrax

80
Q

CHAMP

A

Cardiac high acuity monitoring program

Helps doctors monitor their HLHS patients more closely to reduce mortality rates

81
Q

Is it possible to sequence a single molecule of DNA

A

yes

82
Q

Restriction enzymes

A

Cut DNA at specific nucleotide sequences
Prokaryotes have restriction enzymes to ward off viral parasites. They methylate their own recognition strands to avoid destroying their own DNA

83
Q

Gel electrophoresis

A

DNA fragments of different sized placed in gel
Electrical current is passed through gel
DNA fragments move toward positive pole, small fragments migrate faster than large
Dye is added, DNA fragments appear as bands

84
Q

Southern vs northern vs western blot

A

Southern- DNA
Northern- RNA
Western- Protein

85
Q

Cloning vector

A

A replicating DNA molecule attached with a foreign DNA fragment to be introduced into a cell

86
Q

Making plasmid vectors

A

Circular DNA plasmid molecule from bacteria
Insert foreign DNA into plasmid using restriction enzyme
Linkers- synthetic DNA fragments containing restriction sites

87
Q

LacZ use in cloning

A

LacZ gene is a selectable marker in the pUC19 cloning vector
It encodes a protein which breaks down x-gal to form a blue precipitate.
When the lacZ gene is interrupted with an inserted piece of DNA it produces a white colony and shows that the bacteria is carrying a recombinant plasmid

88
Q

5 things required for PCR

A 
DNA template
DNA polymerase
Primers
Nucleotides
Reaction buffer
89
Q

PCR technique

A

DNA is heated to 90-100c to separate strands
DNA is quickly cooled to 30-65c to allow primers to anneal to complementary strands
Heated to 60-70c, DNA polymerase synthesizes new strands, doubling DNA amount
Cycle is repeated

90
Q

Uses of PCR

A

Identify genetic variation
Isolate DNA from mammoths
Detect virus in blood sample
Amplify small amounts of DNA from crime

91
Q

Limits of PCR

A

Requires knowledge of at least part of sequence of target DNA for construction of primers
Contamination can be a problem
Taq polymerase is used and cannot proofread

92
Q

cDNA library

A

Consists only of DNA sequences that are transcribed into mRNA

93
Q

Chromosome walking

A

Sequencing fragments from a point near to a gene of interest

94
Q

Chromosome jumping

A

Large fragment is circularized and the junction is sequenced

95
Q

Identifying CF gene

A

Linkage studies identified the CF locus
Clones from region were isolated by DNA walking/jumping
Analysis of genes in clones revealed 4 possible genes
DNA sequencing revealed 3bp deletion in the gene of the CF patient

96
Q

Sanger sequencing

A

Single strand target DNA added
-Primer and all four dNTPs are added with polymerase
One type of ddNTP is added to each tube
Sequences terminate at different positions because ddNTP lacks 3’ OH
Fragments are separted by gel electrophoresis and can be read

97
Q

Metagenomics

A

Involves identification of organisms present in the intestine, sewage, water, dirt etc…

98
Q

What caused the skeleton to be so small

A

Mutations in certain genes previously linked with diseases of small stature, rib anomalies, cranial malformations and osteochondrodysplasia

99
Q

Humanized mice

A

Limitations of development and function of certain lineages of human cells in mice can be overcome by transgenic expression of human HLA molecules, cytokines and other factors by targeting mouse genes to eliminate host MHC antigens and reduce host immunity

100
Q

shRNA

A

Form hairpains back on themselves and can be used to silence genes. Must be introduced via vector

101
Q

Crispr/Cas9

A

Prokaryotic immune system that confers resistance to foreign genetic elements such as plasmids and phages. Combination of Crispr, Cas9, guide RNA and template DNA can induce precise gene editing and the correction of genetic diseases in adult mammals

102
Q

Bioinformatics

A

Develops methods for understanding of complex biological data

103
Q

CMH genome center algorithms do what

A

Dramatically improve the speed and reliability of genetic testing

104
Q

OMIM (online mendelian inheritance in man)

A

Catalog of human genes and genetic disorders and traits. Focuses on gene-phenotype relationship

105
Q

ClinGen

A

Shares genomic and phenotypic data provided by health care providers through centralized database

106
Q

EncODE (Encyclopedia of DNA elements

A

Goal is to identify/map all functional/regulatory elements in the human genome sequence

107
Q

eMERGE (electronic medical records and genomics network)

A

Develops methods for the utilization of electronic medical record as a tool for genomic research

108
Q

Gene expression omnibus (GEO)

A

A public functional genomics database of array and sequence based expression profiles

Human Genetics (13 decks)

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