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Genetics - unit 3 - James C. > Genetics > Flashcards

Genetics Flashcards

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1
Q

What are the Hardy-Weinberg assumptions?

A

Large population, random mating, no mutation, no migration, no natural selection

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2
Q

What are the Hardy Weinberg equations?

A

p+q= 1

p² + 2pq + q² = 1

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3
Q

What is the fitness equation?

A

Fitness= mean # offspring for specific genotype/ mean # offspring for most prolific genotype
Fitness will be between 0 and 1

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4
Q

What is the selection coefficient and what does it represent?

A

Selection coefficient= 1-Fitness

Selection coefficient is the intensity of selection against a genotype.

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5
Q

What is epigenetics?

A

How a genotype is transduced to produce a phenotype

“Heritable” but does not involve changes to the DNA

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6
Q

What is the thrifty phenotype?

A

Assumes that when environmental conditions are poor for the
parent, they are likely also to be poor for the offspring. Therefore, when the parent experiences food shortage, biochemical modifications allow pre-adaptation to produce offspring that are metabolically thrifty, eating as much as possible, minimizing energy expenditure, and hoarding/conserving calories.

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7
Q

What is evolution?

A

∆ in gene (ƒ) frequency over time in a population, leads to speciation & divergence, success measured by offspring.

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8
Q

What is a population?

A

Group of interbreeding, sexually reproducing individuals w/ common set of genes.

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9
Q

What does DNA methylation do?

A

gene repression, addition of methyl groups to nucleotide bases, cytosine to 5-methylcytosine, maintained through DNA replication

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10
Q

What do acetylated histones do?

A

Generally associated with gene activation.

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11
Q

What is Behavioral epigenetics:

A

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

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12
Q

An example of epigenetic changes induced by maternal behavior?

A

Increased licking and grooming as pups led to changes in DNA methylation which changed stress response and made less fearful adult rats.

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13
Q

An example of X-inactivation?

A

Xist RNA coating an X chromosome to inactivate it, one X-chromosome randomly inactivated throughout female cats body leads to calico cats

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14
Q

What can differentiated adult cells be reprogrammed to as induced pluripotent stem cells (iPSCs)?

A

Endoderm (internal layer): lung cells, thyroid cells, pancreatic cells
Ectoderm (outer layer): neurons, skin cells of epidermis, pigment cells
Mesoderm (middle layer): cardiac muscle cells, skeletal muscle cells, tubule cells of the kidney, red blood cells, smooth muscle cells

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15
Q

What is genomic imprinting?

A

The epigenetic phenomenon by which genes are expressed in a parent-of-origin-specific manner, eg. Prader-Willi syndrome (paternal) and Angelman syndrome (maternal). May be due to differential male/female imprinting due to male waning increased fetal growth vs female wanting to have decreased fetal growth.

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16
Q

What are epigenetic effects of environmental chemicals?

A

Pb change’s DNA methylation, eg. Agouti mouse as a test for epigenetic mutagens

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17
Q

Totipotent Cell

A

Ability of single cell to divide and produce all of the differentiated cells in an organism (only the morula’s cells are totipotent able to become placenta and all )

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18
Q

What is determination?

A

When a cell becomes comitted to a praticular cell fate (unipotentcy)

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19
Q

What is pluripotent?

A

Embryonic stem cells originate as inner mass cells within a blastocyst. These stem cells become any tissue in the body except a placenta

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20
Q

What are hematopoietic stem cells?

A

They are an example of multipotency. When they differentiate into into myeloid, or lymphoid progenitor cells, the lose potency and become oligopotent cells with the ability to give rise to all cells of its lineage

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21
Q

What cell type is needed for animal cloning and what are the steps involved?

A

To clone an animal totipotence must be reestablished.

1) donor cell taken from sheep’s udder and fused via electric shock to an egg cell
2) fused cell begins dividing normally and becomes an embryo
3) embryo is placed in the uterus of foster mother

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22
Q

What determines the dorsal-ventral axis?

A

Dorsal gene

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23
Q

Determination of the anterior-posterior axis is by what?

A

Biocid gene, nanos gene, hunchback gene

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24
Q

What is apoptosis?

A

Controlled programmed cell death

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25
Q

What is necrosis?

A

Injured cells dying in an uncontrolled matter

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26
Q

What are the steps of apoptosis?

A

1) DNA is degraded
2) cell and nucleus shrink; nucleus fragments
3) macrophage phagocytizes apoptotic cells

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27
Q

What are the steps of necrosis?

A

1) cell swells

2) cell lyses and releases cytoplasmic material

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28
Q

How does natural selection lead to enviornmental specialization?

A

It is caused primarily by changing of expression levels of calmodulin

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29
Q

Natural selection leading to enironmental specializaton has what affect on genes?

A

It regulates the expression of many other developmental genes

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30
Q

What patterns and process of evolution arE revealed via development?

A

1) common genes in a developmental pathway

2) Evolution through change in gene expression

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31
Q

What is an antigen?

A

A molecule that elicits an immune reaction

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32
Q

What is an Antibody?

A

A protein that binds antigens and marks them for destruction by phagocytic cells

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33
Q

What is the organization of the immune system?

A

Humoral immunity, cellular immunity, clonal selection

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34
Q

What are the steps in activation of humoral immunity?

A

Antibodies are produced by B cells → the circulating antigens are identified and targeted → the cells producing these antigens are then targeted for destruction by macrophages.

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35
Q

What is cellular immunity?

A

Cellular immunity is produced by T cells and is direced against cells infected with a pathogen and expressing the pathogen’s protein, i.e. the antibody on the host cell surface

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36
Q

What are the steps of humoral immunity?

A

1) lymphocytes originate from stem cells in the bone marrow
2) B-cells mature in the bone marrow
3) B-cells encounter antigens they mature into plasma cells which secrete antibodies that bind to antigen (this is known as humoral immunity)

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37
Q

What are the steps in cellular immunity

A

1) lymphocytes originate from stem cells in the bone marrow 2)T cells mature in the thymus and enter circulation
3) they attack by binding host cells and lysing them (this is cellular immunity)

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38
Q

An immune response to a specific antigen is produced through clonal selection. List the steps of clonal selection.

A

1) in a large pool of B-lymphocytes each is specific for one antigen
2) when an antigen binds to a B-cell the B-cell divides
3) dividing B-cells give rise to a clone of Bcells that are all specific for the same antigen
4) the proliferation of lymphocytes is the PRIMARY immune response 5) some cells differntiate into antibody-secreting plasma cells 6) antibodies are spcific for the antigen
7) memory cells remain in circulation
8) if second exposure of the same antigen occurs
9) the antigne binds to a memory cell
10) this will rapidly give rise to a secondary immune response

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39
Q

How is bioinformatics used to understand biological data?

A

Bioinformatics combines computer science, statistics, mathematics, and engineering to study and process biologial data.

40
Q

What does OMIM stand for?

A

Online Medelian Inheritance in Man. Comprehensive, authoritative compendium of human gene and genetic phenotypes that is free, available and updated daily.

41
Q

Define Gene Expression Omnibus (GEO).

A

Is a public functional genomics database of array and sequence-based expression profiles

42
Q

What is COSMIC?

A

The Catalogue Of Somatic Mutations In Cancer: comprehensive resource for exploring the impact of somatic mutations in human cancer.

43
Q

What is available through the UCSC Genome Browser?

A

This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to ENCODE data at UCSC and the Neandertal project.

44
Q

What is the function of the research consortium ENCODE, the Encylopedia Of DNA Element?

A

To carry out a project to identify all functional elements in the human genome sequence.

45
Q

How does CMH Genome algorithm improve speed and reliability of genetic testing?

A

It makes associations between SNP’s (from the genome of each baby) and identified known genetic variants.

46
Q

What is The Cancer Genome Atlas (TCGA)?

A

Use to comprehensively characterize the genomic and molecular features of ovarian cancer and glioblastoma maltiforme. Largest tumor collection ever to be analyzed for key genomic and molecular characteristics, includes samples from 11,000 patient across 33 tumor types.

47
Q

Describe the structure of immunoglobulin.

A

Each immunoglobulin molecule consists of four polypeptide chains - two light chains and two heavy chains - that combine to form a Y-shaped structure.

48
Q

What is mechanism for generation of antibody diversity?

A

Somatic recombination. Diversity is increased by differing combination of light and heavy chains, occasional deletions of nucleotides at the segment junctions.

49
Q

What is major histocompatibility complex (MHC)?

A

Molecule expressed on the surface of cells that is the principle target for immune response

50
Q

How does major histocompatibility complex affect organ transplant?

A

Matching of donor and recipient for MHC antigens has been shown to have a significant postive effect on graft acceptance.

51
Q

Matching of donor and recipient for MHC antigens has been shown to have a significant postive effect on graft acceptance.

A

T cells are activated by binding both to a foreign antigen and to a histocomptibility antigen on the surface on the self-cell.

52
Q

What is the name of molecules released by T cell after binding to cells that present foreign antigen (to lyse these antigen-presenting cells)?

A

Perforin

53
Q

What elements do we use to compare genetic match in organ transplant?

A

ABO red blood cell antigens and MHC antigens; greater the mistmatch, stronger the immune rejection. Rejection is partically inhibited by drugs.

54
Q

What is the most important gene in deciding the fate of transplated cell, tissue, or organ?

A

MHC (the major histocompatibility complex.

55
Q

Where in the genome does the MHC region occur?

A

MHC region occurs on Chromosome 6 (from 6p22.1 to 6p21.3 about 29Mb to 33Mb on the hg19 assembly), and contains 240 genes spanning 3.6 megabase pairs, about half of the genes have known immune functions.

56
Q

What is the Hygience Hypothesis?

A

Proposed by Strachan to explain the increased prevalence of hay fever and eczema in families with small size, and higher standards of cleanliness. Regarding the rural lifestyle, several epidemiological studies in children shown an INVERSE association between growing up on a farm and atopic diseases (allergy).

57
Q

What is the NSIGHT Project?

A

Screens for inborn errors of metabolism through uses of tandem mass spectrometry-based tests that focus on more than a dozen amino acids and 28 acylcarnitines associated with fatty acid disorders.

58
Q

Define primary immunodeficiencies.

A

People with primary immunodeficiency diseases are missing certain types of white blood cells, or those cells don’t work very well. Some affect T-cell function, others affect other arms of the immune system.

59
Q

What is SCID?

A

Severe combined immunodeficiency (SCID) is one of the most severe cases of immunodeficiences. Defects in both B-cell and T-cell function.

60
Q

What is the advantage of Next Gen Sequencing for Newborn screening?

A

Many conditions can be tested with one test vs having to test many conditions with diffferent individual tests.

61
Q

What is a benign tumor?

A

A tumor the remains localized.

62
Q

What is a malignant tumor?

A

Tumor cells that invade other tissues.

63
Q

What is metastasis?

A

Tumor cells that induce secondary tumors.

64
Q

What is genetic evidence for cancer?

A

Carcinogens, chromosomal abnormalities, inheritance

65
Q

What is Knudsons multi step model of cancer.

A

Knudson proposed that retinoblastoma results from 2 seprate genetic defects which are necessary for cancer to develop. He also concluded that multiple mutations are required to produce cancer.

66
Q

What is the clonal evolution of tumors?

A

Tumor cells acquire more mutations that allow them to become increasingly more aggresive in their proliferative properties

67
Q

What determines the hallmarks of origin for a cancer?

A

They vary depending on whether it is hereditary or sporadic.

68
Q

What are the primary and secondary hallmarks of cancer?

A

Hallmarks include genomic instability and consolidate the self sufficency in growth and insensitivity to anti growth signals into activated growth signaling. The secondary hallmarks are oxidative stress and proteotoxic stress

69
Q

What Initiates hereditary cancers?

A

The establishment of genomic instability is most likely the initating event. This then facilitates the establishment of all the other hallmarks.

70
Q

What is the temporal order of sporadic cancer?

A

It starts by deregulation of growth regulating genes. This leads to DNA damage and DNA replication stress, which leads to genetic instability and selective pressure for tumor suppressor p53 inactivation.

71
Q

Mutations in which gene types contribute to cancer?

A

Oncogenes and tumor suppressor genes, genes that control the cycle of cell division, DNA repair genes, genes that regulate telomerase, genes that promote vascularization and the spread of tumors, microRNA’s and cancer

72
Q

What are the 3 primary contributors to cancer?

A

1) Oncogenes: mutated dominant- acting stimulatory genes that cause cancer -(proto oncogenes): responsible for basic cellular functions in normal cells that when mutated become oncogenes
2) Tumor-suppressor genes: mutated recessive acting inhibitory genes that are inactive (loss of function and loss of heterozygosity)
3) Genes that control the cell cycle

73
Q

What are oncogenes?

A

Mutant alleles that tend to be dominant: one copy of the mutant allele is sufficent to induce excessive cell proliferation.

74
Q

What do tumor suppressor genes do?

A

Normally produce factors that inhibit cell mutation. However when there is a mutation in both alleles (or mutation in one and deletion in one) then the gene becomes inactive. It must be a mutation in both genes or only one allele being expressed because the mutant aleles are recessive

75
Q

What is the seminal effect in follicular lymphoma?

A

Translocation of chromosome 14 and 18 aka t(14;18) which places the bcl2 gene next to the immunoglobulin heavy chain locus, making it constrictively active. Bcl2 encodes an integral ouer mitochondrial membrane protein that blocks the apoptic death of some cells such as lymphocytes and allows them to propagate exponentially. this fusion gene is deregulated , leading to the transcription of excessively high levels of Bcl-2. this helps cells aviod undergoing apoptosis

76
Q

How do retroviruses cause cancer?

A

They mutate and rearrange protoncogenes/ or they insert strong promoters near protooncogenes

77
Q

What is antibody therapy for cancer?

A

Monclonal antibodies target cancer cell specific antigens and induce an immunological response against the target cancer cell

78
Q

What is Retuximab?

A

A chimeric monoclonal antibody against the protein CD20. CD20 is on surface of B-cells and Rituximab destroys B-cells. Therefore Rituximab is used to fight diseases that are characterized by excessive numbers of B-cells. This includes many lymphomas leukemias, transplant rejection and autoimmune disorders.

79
Q

How does Rituximab induce B-cell destruction?

A

1) ADCC: attracts natural killer cells, t cells, and macrophages which are invoved in recognizing and killing antibody labeled target cells which leads to cell lysis
2) CDC binding the antibody recruits complement proteins, which punch holes in the cell membrane, flooding the cell and leading to cell lysis
3) Apoptosis: binding of antibody signals that tell the cell to self destruct
All 3 mechanisms are important contributors of targeted B-cell destruction.

80
Q

What is predictive medicine?

A

The use of the information produced by personal genomics techniques when deciding what medical treatments are appropriate for a particular individual. Precision medicine is focused on a new taxonomy of human disease based on molecular biology.

81
Q

What are examples of the use of predictive and precision medicine?

A

Inherited medical genomics, cancer genomics and pharmacogenomics

82
Q

What is 23andMe?

A

A privately held personal genomics and biotechnology company, named for the 23 pairs of chromosomes in a normal human cell.

83
Q

What is Promethease?

A

A literature retrieval system that builds a personal DNA report based on scientific literature cited in SNPedia and a file of genotype (DNA) data.

84
Q

What is the “real” goal of 23andMe?

A

To hoard your personal Data (wife of Google).

85
Q

What is positive assertive mating?

A

Like individuals mating.

86
Q

What is negative assertive mating?

A

Unlike individuals mating.

87
Q

What is in inbreading?

A

Measure of probability that alleles are identical by descent.
↑ inbreeding in a population= ↑ homozygous population= ↑ deleterious alleles.

88
Q

What does it mean to be identical by descent?

A

Alleles descended from same copy in common ancestor.

89
Q

What is negative assertive mating?

A

Unlike individuals mating.

90
Q

What is inbreeding depression?

A

Increased (lethal & deleterious) traits w/ inbreeding, inbreeding ↑ % of AA & aa in population.

91
Q

What does it mean to be identical by state?

A

Alleles same in structure and function but from different ancestors.

92
Q

What is positive assertive mating?

A

Like individuals mating.

93
Q

What is outcrossing?

A

Avoidance of mating between like individuals.

94
Q

What is overdominance?

A

Heterozygotes are favored over homozygotes.

95
Q

What is underdominance?

A

Homozygotes are favored over heterozygotes.

Genetics - unit 3 - James C. (1 decks)

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