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94 Cards in this Set
- Front
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Define: Genetic Variation |
Differences between DNA sequences of individual genomes |
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Explain: Genetic Variation |
- Occurs both within and between individuals - An individual contains two copies of nuclear genome - Maternal and Paternal - At any genetic locus the two alleles may be identical or have slightly different DNA sequences - Identical = homozygous - Different = heterozygous |
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Define: Constitutional Variation |
Inherited, present in all cells |
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Define: Somatic Variation / Post-Zygotic |
DNAchanges that occur during life |
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Explain: Mutation |
-DNAsequence changes arise - Mutations may contribute to a normal phenotype, disease phenotype, have no effect on phenotype, or have some beneficial effect - Fuel for natural selection |
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What are the endogenous sources of Mutation (great majority)? |
- Errorsin normal cellular mechanisms - DNA polymerase replication errors - Chromosome segregation errors - DNA recombination errors - Spontaneous chemical damage |
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What are the exogenous sources of Mutation (great majority)? |
- Radiation - Environmentalchemicals |
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Explain: Radiation |
- Ionizing radiation (γ-rays and X-rays) can directly break the DNA backbone & generate reactive oxygen species that can damage DNA - Ultravioletradiation primarily generates pyrimidine dimers thatdisrupt base-pairing and prevent DNA replication |
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Explain: Environmental Chemicals |
- In food, drink, inhaled air, chemotherapy, etc. - May produce damage in many way–reactive oxygen species, cross-linking, transfer of chemical groups to DNA bases - Cigarette smoke and automobile fumes contain large bulky aromatic hydrocarbons that can bind to bases & form a DNA adduct |
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What are DNA Polymerase Replication Errors? |
- Insertionof the wrong nucleotide during DNA replication - Majorityare caught & fixed by DNA polymerase - Proofreading: 3' --> 5’exonuclease activity - Replication slippage - Occursin areas with short tandem repeats - Unrepaired errors create a mutation |
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Why do most Mutations do not causes diseases? |
- 98.8% of the genome is noncoding - Many mutations in coding DNA do not change the amino acid - Noncoding functional sequences may be tolerant of sequence change |
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What are Chromosome Segregation Errors? |
- Errors in chromosome segregation produces gametes, embryos, or somatic cells with more or less chromosomes than normal - Altered numbers of whole DNA molecules - In germ line this often causes embryonic lethality, or a congenital disorder such as Down syndrome - Changes in sex chromosomes are better tolerated - In somatic cells, changes in chromosomal DNA copy number are a common feature ofcancer |
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What are Recombination Errors? |
Recombination between misaligned chromosomes: - Duplication o r deletion of genes or larger DNA segments - Translocations - Inversions |
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How do Recombination Errors look like? |
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What are the classes of Chemical Change? |
1. DNA strand breakage 2. Base deletion due to cleavage of the bond between a base and its sugar 3. Base modification produced by altered bonding or added chemical groups 4. Base cross-linking |
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What are examples of DNA strand breakage (Chemical Change)? |
i. Single strand break from simple cleavage of a phosphodiester bond ii. Single strand break with additional damage and nucleotide deletion iii. Double stranded break |
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What happens when there is a basedeletion due to cleavage of the bond between a base and its sugar (Chemical Change)? |
Produces an abasic site |
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What examples of added chemical groups that causes base modification (Chemical Change)? |
i. 8-oxoguanine, which mispairs with adenine ii. Thymineglycol, which blocks DNA polymerase iii. Bulky DNA adducts formed by covalent bonding of carcinogens to bases |
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What are types of base cross-linking (Chemical Change)? |
- Intrastrand cross links - Interstrand cross links |
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Define: Base Cross-linking |
Formation of covalent bonds between two bases |
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Define: Intrastrand Cross Links |
- Base cross-linking on the same DNA strand - Most common form of damage from UV sun exposure |
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Define: Interstrand Cross Links |
- Base cross-linking on the complementary DNA strand - Induced by the anti-cancer agent cisplatin |
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What are sources of endogenous Chemical Damage? |
- Hydrolytic damage - Oxidative damage - Aberrant DNA methylation |
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Explain: Hydrolytic Damage |
- Breaking of bonds using water - Maycause depurination, depyrimidination, or deamination - Producesan abasicsite, or alters nucleotide identity |
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Explain: Oxidative Damage |
- Often caused by electrophilic reactive oxygen species - Break covalent bondsin DNA backbone, andproduce modified bases thatbase-pair incorrectly,or block DNA/RNA polymerase |
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Explain: Aberrant DNA Methylation |
- Inappropriatemethylation of adenine or guanine - Distorts the DNA double helix, disrupts DNA-protein interactions or mispairs duringDNA replication |
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What are ways of DNA Repair? |
- Some DNA damage can be repaired by simple reversal - Repairof DNA damage on a single strand - Repairof DNA damage that affects both strands |
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What are examples of DNA Repair by simple reversal? |
- Removal of aberrant methylation - DNA ligase sealing a single broken bond in the DNA backbone |
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What are examples of DNA Repair on a single strand? |
- Base excision repair - Nucleotide excision repair |
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What are examples of DNA Repair on both strands? |
- Homologous recombination - Nonhomologous end joining |
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How does a base excision repair (DNA Repair) look like? |
Repairof a single base that has been modified or lost |
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How does a nucleotide excision repair (DNA Repair) look like? |
Repair of bulky, helix-distorting DNA lesions, including pyrimidine dimers |
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How do homologous recombination (DNA Repair) look like? |
- Repair of a dsDNA break - Requires an intact homologous DNA strand to be used as a template - Ex. sister chromatid - Acts as a template for new DNA synthesis |
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How do nonhomologous end joining (DNA Repair) look like? |
- Ends of broken DNA are fused together - Results in sequence loss - Desperate measure |
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What are examples of Undetected DNA Damage? |
- Deamination of cytosine produces uracil - Abnormal DNA base that is usually recognized & repaired - Deamination of 5-methylcytosine produces thymine - May go undetected - C --> T substitutions are the most frequenttype of single nucleotide change in our DNA |
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How does an Undetected DNA Damage look like? |
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Explain: Defective DNA Repair |
- More than 170 human genes are known to be involved in DNA damage responses and DNArepair - Manysingle-gene disorders result from mutations in these pathways |
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What are common disease features of Defective DNA Repair? |
- Cancersusceptibility - Progeria(accelerated aging) - Neurologicalfeatures - Immunodeficiency |
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Explain: Xeroderma Pigmentosum |
- Autosomalrecessive genetic condition resulting from inherited mutations in genesencoding proteins that functionin the nucleotideexcision repair pathway - Atleast 8 different genes |
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What happens if you have Xeroderma Pigmentosum? |
- Initial symptoms include severe sun-burning and freckling with a minimal amount of sun exposure - Median onset at age 1 – 2 yrs - Continued sun exposure causes premature skin aging, benign and malignant tumours - More thana 1000-fold increase in the frequency of all types of major skin cancerscompared to the normal population - Approximately90% of carcinomas occur on face, neck, and head - 10–20 fold increase in internal neoplasms, including lung and gastric carcinomas - 60–90% of patients also experience ocular (eye) abnormalities - ~18%of patients experience progressive neuronal degradation |
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What are the two goals of Personal Genome Sequencing Projects? |
Next generationsequencing has increasedpersonal genome sequencing 1. Catalognormal human DNA variation - ex.1000 (2500) genomes project - CorrelateDNA variation with phenotype to identify genetic markers of disease - ex. Wellcome TrustUK10K Project |
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Define: Variants |
Mutationsthatresult in alternative forms of DNA (rare variants have a frequency of less than 0.01)
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Define: Polymorphisms |
DNA variantsthat are common in the population (frequencyof more than 0.01 (1%) in the population) |
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Explain what happens in a small scale of Human Genetic Variation (most common)? |
- Involveone or a very small number of nucleotides - Singlenucleotide changes accountfor ~75% of DNA changes - Oftenno obvious effect on phenotype |
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Explain what happens in large scale of Human Genetic Variation? |
Largescale structural variation produces the greatest number ofdiffering nucleotides between individuals |
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Explain: Scale of Human Genetic Variation |
Eithermay produce: - Nonet gain or loss of sequence - Singlenucleotidereplaced with another - Balancedtranslocations & inversions - Net gainor loss of sequence - Insertionor deletion of a single or small number of nucleotides - Insertionor deletion of larger DNA segments - Abnormalchromosome number |
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Define: Single Nucleotide Variants (SNVs) |
- Singlenucleotide substitutions - Most commontype of genetic variation - ex.Either G or C at a particular position |
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Define: Single Nucleotide Polymorphism (SNP) |
- If frequencyexceeds0.01 - SNPsare generally not new mutations and instead differ due to evolutionary ancestry - ~1every 300 bp - Maylead to gain or loss of a restriction site |
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Define: Indel |
- If anucleotide is either present or absent = insertion/deletion variation(polymorphism) - Onenucleotide up to ~50 nt - May lead to gain or loss of a restriction site |
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How would you detect whether SNPs or Indels have lead to gain or loss of a restriction site? |
- Detection with restriction enzymes - Produces a restriction fragment length polymorphism (RFLP) |
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Explain: Variable Number of Tandem Repeats (VNTR) |
- Tandemlyrepeated DNA sequences are unstable - Frequentlyvary in repeat number - Differencesin the number of tandem repeats |
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What are three classes of Tandem Repeat arrays? |
- SatelliteDNA - MinisatelliteDNA - MicrosatelliteDNA |
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Explain: Satellite DNA |
- Arrayof 20 kb–hundreds of kb - Located at centromeres and otherheterochromatic regions |
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Explain: Minisatellite DNA |
- Arrayof 100 bp – 20kb - Primarilyat telomeres and subtelomeres |
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Explain: Microsatellite DNA |
- Array of ~100 bp or less - Widelydistributed in euchromatin- Repeatunitusually 2 – 4 bp - Multiplealleles present in the population - Differin length due to having different numbers of repeats - Polymorphismin repeat length results from strand slippage during DNA replication - Responsiblefor variation in populations, but generally stable enough that length does notchange during meiosis - Usedin DNAprofiling |
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How do Microsatellites DNA look like? |
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How does a strand slippage look like (Microsatellite DNA)? |
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Define: DNA Profiling |
DNA testing to establish identity or relationships |
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Explain: DNA Profiling |
- Originalmethod = DNA fingerprinting - Digestion,gel electrophoresis, and Southern blotting of genomic DNA - Probe= sequence common in minisatellites - Laborious,time consuming, and required a lot of DNA - Oddsthat the sample came from an unrelated member of the population can becalculated from the population genotype frequencies for each locus - Suspectscanbe conclusively eliminated (disproved)if they do not match the DNA profile - Identitycannot technically be proved, but can establish probabilities lowenough that it seems extremely likely - IfDNA evidence is in small quantity, poorly preserved, or highly degraded thenonly a partial profile may be obtained - Reducesstrengthof match probability |
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How to do DNAprofiling using microsatellites? |
- Thenumber of repeats present at a particular microsatellite locus can bedetermined by PCR - Muchless DNA is required - Good microsatellite markers have multiple alleles, each occurring at a low frequency in the population - e.g.D7S820 on chromosome 7 contains between 5 and 16 repeats of GATA - 12possible alleles - PCRproducts will differ in size by 4 bp, depending on the number of repeatspresent |
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What Marker Panels do Canada and US use? |
- Canadaand US use CODIS system - 13microsatellite markers and Amelogenin forsex typing - Average match probability = 1 in 10 trillion |
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What Marker Panel does UK use? |
- UKuses SGM+ system - 10microsatellite markers and amelogenin - Averagematch probability = 1 in 1 billion |
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Explain: DNA Databases & Privacy |
- Boththe DNA profile and the DNA sample of a suspect, or from the crime scene, arekept in a national DNA data bank - Microsatellitemarkers used in CODIS and SGM+ were chosen partially because they provide nopersonal information - Howeverother informative markers exist throughout the genome: - Microsatelliteswith allele frequencies that differ between ethnic groups - Y chromosomemarkers & surname prediction - Genesthat can provide a rough prediction of hair and eye colour - Familialsearching due to close matches is another concern |
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What are the types of Structural Variation in Human Genome? |
- Large scale - Balanced - Unbalanced |
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Explain: Large Scale Structural Variation in Human Genome |
Largescale DNA variation that involves moving or changing the copy number of long tovery long DNA sequences |
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Explain: Balanced Structural Variation in Human Genome |
- SameDNA content but sequences are located in different positions - Chromosomesbreak and rejoin incorrectly, without loss or gain of DNA - Translocations,inversions |
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Explain: Unbalanced Structural Variation in Human Genome |
- Changesin structure with accompanying gain or loss of content - Deletionor duplication - Mayresult in disease, or produce common copy number variations (CNV) thatare found in normal individuals |
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What are the effects of Genetic Variation? |
- Mostgenetic variation has a neutral effect on the phenotype - Normalindividuals (no genetic disease) carry ~120 gene-inactivating variants, withabout 20 genes inactivated on both alleles - Somegenes do not carry out vital functions!(ex. ABO blood type) - Somegenetic variation is harmful and subject to purifying (negative) selection - Occasionallya DNA variant has a beneficial effect & becomes prevalent through positive selection |
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What is an example of neutral Genetic Variation? |
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What is an example of positive Genetic Variation? |
- Selectionfor genetic variants in different human populations has allowed for adaptationto different environments and major dietary changes |
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Explain: Skin Pigmentation |
- VitaminD3 production requires UV radiation, which stimulates a photolytic reaction ina deep layer of the dermis - UVradiation also causes DNA damage that can be reduced by skin pigmentation(melanin) |
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What happens to Skin Pigmentation if UV radiation is reduced? |
InNorthern populations, UV radiation is reduced - Lowerability to make vitamin D3 - Offsetby an adaptation that reduced skin pigmentation - Maincontributor = mutation in SLC24A5 gene, a calcium transporter that regulatesmelanin production |
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Define: Selective Sweep |
Variationin the population will be reduced at immediately neighbouring nucleotidesequences due to positive selection of the favourable DNA variant |
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Explain: Selective Sweep |
- Amutation that is subject to positive selection increases in frequency to becomethe common allele - Chromosomecontaining the mutation is notpassed down as a unit - Recombinationreplaces adjacent sequence -Thesegment containing the favourable DNA variant will be slowly reduced in size |
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What happens before Selection Sweep? |
BeforeselectionDifferentalleles (1 – 4) are present at different loci across the chromosome =significant heterozygosity |
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What happens after Selection Sweep? |
AdvantageousDNA variant plus closely linked DNA have increased in frequency, reducingheterozygosity for the chromosome segment surrounding the variant |
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Explain: SLC24A5 Selective Sweep |
- Selectivesweep in European population for SLC24A5 variant associated with reduced skinpigmentation - Almostall European chromosome 15s share a segment containing this allele, andhitchhiker alleles at MYEF2 and CTNX2 loci |
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What are examples of response to diet? |
Developmentof agriculture led to: - High-starchdiets - Lifelongconsumption of milk |
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Explain: Lactase |
- Inmammals, production of the enzyme lactase declines after weaning - Consumptionof milk causes abdominal pain and diarrhea - Somehumans continue to express lactase as adults = lactase persistence - Varieswidely among human populations - Resultsfrom a DNA variant that changes a cis regulatory element |
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Explain: CNVof AMY1A |
- Salivaryα-amylase is produced by AMY1A gene - Chimpanzeeshave two diploid copies - 1gene - Humansmay have 2 – 15 diploid copy numbers = CNV - Morecopies = higher oral salivary amylase concentration - Copynumber is higher in populations with high historical starch consumptionsuggesting positive selection |
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Explain: Genetic Variation in Immune System |
Adaptiveimmunity involvestwo types of lymphocytes that produce extraordinarily diverse recognitionmolecules - T Cells - B cells |
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Explain: T Cells |
- ExpressT-cellreceptors onthe cell surface - Bindto antigens that are presented to them by MHC proteins onthe surface of other cells |
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Explain: B Cells |
- ExpressB-cell receptors, also known as immunoglobulins - Initiallyexpressed on B cell surface where they bind to pathogens - Antigenrecognition stimulates maturation & secretion of antibodies (soluble immunoglobulins) |
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Explain: Immunoglobulin Heavy Chain Locus |
- Genelocus is made of a series of repeated gene segments that specify discrete partsof the protein - Constantregion: - Definesclassof antibody (IgA, IgD, IgE,IgG, or IgM) - Encodedby differentC gene segments - Variableregion: - Involvedin antigen recognition - Madeof three types of repeated gene segments: - V(variable), D (diversity) and J (joining) - VDJsegments are joined by somaticrecombination - Somaticrecombination of DNA produces different combinationsof gene segments &different proteins |
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What are the mechanisms of Antibody Diversity? |
- Combinatorialdiversity - Junctionaldiversity - Proteinchain combinatorial diversity - Somatichypermutation |
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Explain: Combinatorial Diversity |
- Randomrecombination of VDJ segments in each maturing B cell - E.g.V2D3J2, V4D21J9, V38D15J4 |
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Explain: Junctional Diversity |
- “Messy”somatic recombination mechanisms tend to add or subtract nucleotides at thejunctions |
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Explain: Protein Chain Combinatorial Diversity |
- Eachfunctional antibody has one unique heavy chain + one unique light chain |
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Explain: Somatic Hypermutation |
- StimulatedB cells produce an enzyme that converts cytosines in the variable region to uracils at ahigh rate - Repairpathway converts uracils toone of four bases |
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Explain: MHC Proteins |
- MHC =Major histocompatibility complex - AkaHLA = Human leukocyte antigen - Functionin antigenpresentation to Tcells - MHCproteins exhibit extraordinary diversity in populations |
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What are the classes of MHC Proteins? |
ClassI MHC is expressed on almost all cells - Presentsintracellular protein fragments on cell surface - Recognitionby cytotoxic T cell à Cellkilling ClassII MHC is expressed by some types of immune cells - Presentsexogenous protein fragments that have been internalized - Recognitionby T helper cell --> Immune response |
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Explain: Genetic Diversity of MHC Genes |
- Variationin MHCs is focused on amino acids that form antigen-binding pocket - Differentalleles exhibit different peptide-binding specificities - Positiveselectionpromotesgenetic variation - Heterozygousindividuals are better protected against microbial pathogens & have higherreproductive rates |
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What are the medical importance of MHC? |
Organand cell transplantation - DifferentMHC proteins can cause: - Attackof donor cells by recipient's immune system - Graftvs. host disease (graft contains donor T cells that attack recipient) - Transplantsuccess requires immunosuppressive drugs & MHC (HLA) matching Diseaseassociation: - MHCproteins differ in ability to recognize specific foreign antigens - Individualswith different HLA profiles may show different susceptibility to someinfectious diseases - CertainHLA variants are strongly associated with autoimmune disease - Failureto discriminate self from foreign |
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Explain: HLA Haplotypes |
- HLAgenes are located close together in a cluster on chromosome 6, and aretherefore tightly linked - Haplotype =series of alleles at linked loci on an individual chromosome - Amatch within a family should match at all major loci |
