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174 Cards in this Set
- Front
- Back
Genetics
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The study of heredity, genes, and variation of organisms
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Diploid
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containing two complete sets of chromosomes, one from each parent. Humans are diploid. NOT the most common
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Somatic cells
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Any cell excluding sex cells
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Germ cells
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gametes, reproductive cells, haploid
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Mitochondrial DNA is passed on through
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The egg (from the mother), because there is very little Mitochondrial DNA in the sperm and lots in the egg
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Genotype:
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genetic makeup of the cell or individual; refers to specific genes/alleles present
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Phenotype:
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a cell or individuals observable or measureable traits
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Three major types of inheritance
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1) autosomal, 2) sex-linked, 3) cytoplasmic
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Autosomes
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all chromosomes with the exception of sex chromosomes
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Dominant
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one trait expressed over another even though both are present.
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Recessive
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not expressed when present with dominant trait.
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Mendel's Explanation of Inheritance (5)
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1. “Particles” carry contrasting phenotypes. Modern explanation – Genes on chromosomes
2. “Particles are paired, can be same or different. ME- Alleles on homologues 3.“Particles are split during gamete formation. ME- Meiosis (diploid to haploid) 4. Equal Segregation- 50% of gametes carry “particle” for each variant 5. Random fertilization- offspring are formed independent of allele and carried by gamete |
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Phenotypic and genotypic ratios in monohybrid crosses
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phenotypic 3:1
genotypic 1:2:1 |
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What genotypic ratio will you get if you cross
1. Hetero x Hetero 2. Homo x Homo 3. Hetero x Homo |
1) 1:2:1
2) 1 (100% same) 3) 2:2 (50:50) |
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Testcross:
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Breed individual of unknown genotype to known homozygous recessive individual (tester).
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Law of equal segregation
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The two members of a gene pair segregate from each other into the gametes; half the gametes carry one member of the pair and half carry the other.
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What do genes do? (2)
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1. Make RNA as final product (some genes stop here, simplest form of a gene)
2. Make RNA followed by protein (most genes do this) |
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Law of Independent Assortment
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genes on different (non-homologous) chromosomes are inherited independently
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Pure breeding tester (true breeding tester):
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the parent is homozygous for the trait. Can be Dominant or Recessive.
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Product Rule
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The probability of independent events occurring together is the product of their individual probabilities. Multiply
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Sum Rule
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The probability of either of 2 mutually exclusive events (one or the other) occurring is the sum of their individual probabilities. Add.
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Chi-squared
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(observed-expected)^2/expected
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degrees of freedom
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number of categories-1
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Null Hypothesis
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observed numbers do not differ from 1:1 ratio. Proposing that they are not going to deviate
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Alternative Hypothesis
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observed numbers differ from 1:1 ratio.
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Convention:
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If P < 0.05, null is rejected and you must pose an alternate to explain results
If P > 0.05, cannot reject the null |
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Propositus:
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the first affected member of a family who comes to the attention of a doctor/geneticist
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Acromesomelic dysplasia
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Autosomal Recessive. form of dwarfism, Not a normal phenotype
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Cystic fibrosis
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Autosomal Recessive. Trans membrane pump (Na/K pump) system is disrupted by a mutant allele causing the development of a viscous mucus (1/25 people are heterozygous for the cystic fibrosis gene)
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Genotypes for an autosomal recessive disorder
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A/A= normal, A/a= carrier, a/a= affected
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clustered phenotype
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no one in the family has the phenotype and then two siblings have it.
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Consanguineous mating
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like blood, relatives mating
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Pseudoachondroplasia
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Autosomal Dominant. Dwarfism, Haploinsufficient
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Progeria
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Autosomal Dominant. accelerated aging, occurs as a random mutation, live till 11 or 12.
pleiotrophic. Caused by a point mutation at codon 608 |
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Huntington’s disease
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Autosomal Dominant. middle age years onset, it is brain atrophy.
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Genotype for an autosomal dominant disorder
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a/a=normal A/a= affected A/A= lethal
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How to determine if a trait is Autosomal recessive (4)?
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1. Trait usually skips a generation
2. Both males and females affected in equal proportions (keeping in mind sample size) 3. if both parents affected all offspring are affected 4. if two normal parents have an affected offspring the trait must be recessive |
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Determining genotypes of autosomal recessive (2)
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1. both parents of an affected individual must be carriers
2. all unaffected offspring of an affected individual must be carriers |
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How to determine if a trait is Autosomal Dominant (3)?
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1. trait usually presents in all generations (keeping in mind sample size)
2. affected person cannot have two normal parents 3. both males and females affected in equal proportions (keeping in mind sample size) |
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Determining genotypes of autosomal dominant (1)
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all normal individuals carry two normal alleles
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how to determine if a trait is sex-linked recessive (3)
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1. mostly male affected
2. affected females must have an affected father and sons of affected mother must be affected 3. daughters of affected females and unaffected males are nto affected |
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how to determine if a trait is sex-linked dominant (3)
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1. more frequent in females
2. all females of affected father are affected 3. no sons of unaffected female are affected |
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how to determine if a trait is sex-influenced (1)
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dominant in one sex and recessive in the other
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how to determine if a trait is sex-limited (1)
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completely absent from one sex
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Autosomal polymorphisms:
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variation for traits within populations (ie. eye colour)
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Can Human pedigrees permit for Mendelian ratios?
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No because the number of progeny is too small.
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How many autosomal chromosomes do humans have?
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22 pairs
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How many sex chromosomes do humans have?
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1 pair
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Hemizygous
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genes effectively present in single copy in males, differential region
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In what region are X and Y sex chromosomes homologous?
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pseudoautosomal regions
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Y-linked inheritance
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Found in males only. Passed on to 100% of male offspring. Females cannot be carriers
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Cytoplasmic Inheritance
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Female organelle phenotype is passes 100% of progeny regardless of male genotype/phenotype. Mitochondrial genes are very important, major part of energy |
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Mitochondrial diseases
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cells cannot function properly
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Generic phenotypic category
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Dominant/Dominant
Dominant/Recessive Recessive/Dominant Recessive/Recessive |
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Mitochondrial DNA
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many copies in a cell, major part of energy, mostly passed on from mother (sperm has very little mitochondrial DNA)
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p-value
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chance occurance, probability of obtaining a test statistic at least as extreme as the one that was actually observed
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Hemophilia
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X-linked recessive
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Chromosome theory of heredity:
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genes that encode for traits are located on chromosomes
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2 important features of Chromosomes:
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1.Chromosome number is identical from cell to cell within an individual
2. Chromosome number is identical among individuals within a species |
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What does it mean to say chromosomes are dynamic structures
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They flip between diffused state and condensed state
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Diffuse state
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occupy space in the nucleus during normal cell function
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Condensed state
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special form taken during cell division
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Histones
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A group of 5 basic proteins that organize DNA into nucleosomes by forming molecular complexes around which DNA winds
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A Chromosome is
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a single DNA molecule densely folded
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Genes
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functional (coding) sequences along a DNA molecule
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Human genome (6 points)
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2 meters of DNA
i)DNA double helix ii) DNA winds into histone proteins iii)DNA-histone complexes coil into solenoid iv) solenoid forms loops attached to central scaffold v) scaffold and loops arranged in a giant super coil |
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Eukaryotic Chromosomes (6)
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1. Chromosomes are hereditary material
2. Chromosomes fluctuate- diffuse and condensed 3. Each chromosome is highly packaged DNA molecule 4. Each chromosome houses many genes 5. Genes are separated by other DNA types 6. Coding sequences (exons) interspersed by introns that do not contribute to product |
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Mitosis
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Single nuclear division, asexual cell division. Chromosome #, genotype of daughter cells constant
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Meiosis:
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two successive nuclear divisions in germ cells. Chromosome number halved; 4 haploid daughter cells. Ploidy changes.
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ploidy (n)
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the number of sets of homologous chromosomes in cells.
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DNA content (c):
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the number of copies of haploid genome in cells
Content doubled during S phase; reduces by half in mitosis and in both meiosis 1 and 2. |
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Hayflick Limit:
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the number of times a cell will divide before it stops and becomes senescent
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Kinetochore:
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point of spindle attachment
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3 major events of mitosis
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1) DNA replication, duplication of chromosomes (2n,2c)
2) Sister chromatid adhesion (2n, 4c) 3) Segregation of sister chromatids into daughter (2n, 2c) |
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6 major events of meiosis
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1) DNA replication, duplication of chromosomes (2n, 2c)
2) Sister chromatid adhesion (2n, 4c) 3) homologous chromosome pairing 4) crossing over (recombination) 5) segregation 1: homologues (n (now a haploid), 2c) 6) segregation 2: sister chromatids into haploid gametes (n, c) |
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Sister chromatids (SC):
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identical copies of same chromosome; share a centromere
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Homologous Chromosomes (HC):
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different copies of same chromosome, 1 from each parent
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What is the main disadvantage to being diploid?
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main purpose of adults is to reproduce, only pass on 50% of your genes
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Genes make proteins
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chromosomes contain genes, genes transcribed into RNA, RNA directs protein synthesis
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How genes make protein ***know this***
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1) synthesis of mRNA in the nucleus
2) movement of mRNA into cytoplasm via nuclear pore 3) synthesis of protein |
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medical cytogenetics
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study of chromosomes and abnormailities
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Constitutional abnormalities
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are present from birth – inherited or induced early in utero
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Acquired abnormalities
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occur later in life, often associated with cancer
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Deletion:
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loss of material from single chromosome
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Inversion:
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2 breaks in chromosome followed by 180° flip and re-attachment
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Translocation:
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exchange of material between 2 or more chromosomes (instead of re-attaching the piece that broke they swap with another chromosome)
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Nondisjunction:
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failure to separate; results in extra chromosomes or absent chromosomes.
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Immortalized cell:
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a cell that continues to divide and lives ‘forever’
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Down’s syndrome:
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3 normal copies of chromosome 21,
proteins are 1/3 overproduced |
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Klinefelters syndrome
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a syndrome affecting males in which the cells have an extra X chromosome (in addition to the normal XY), characterized by a tall thin physique, small infertile testes, and enlarged breasts.
Nondisjunction happens in meiosis I, the whole set of the chromosomes went into one gamete |
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Leukemia
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Translocation – common between chromosome 9 and chromosome 22
Translocation happens in the stem cells in the bone marrow during development |
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Amniocentisis
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commonly done during pregnancy to get a sample of fetal DNA from amniotic fluid
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Transcervical chorionic villus sampling
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Metal probe in vaginal canal and scrape cells off the fetal side of the placenta
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Maternal blood test
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Free floating fetal DNA in the serum of mothers
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Pre-implantation Screening
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1. Test tube fertilization
2. Many 8-cell embryos 3. Test single cell from each 4. Implant healthy embryo |
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Recombination:
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The production of new allele combinations that differ from that of parental types.
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expected ratio in a testcross of unlinked genes
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1:1:1:1
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Linkage:
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association of genes on the same chromosome. linked genes inherited together
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Cis conformation:
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(coupling) both dominant or wild type alleles on one homologue
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Trans conformation:
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(repulsion) dominant or wildtype alleles on different homologues
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Crossing over:
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(recombination) precise breakage and union of DNA resulting in genetic exchange between non-sister chromatids of homologous chromosomes
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crossing over occurs during
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prophase I in meiosis
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Chismata:
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points of intersection where 2 chromosomes exchange genetic material during crossover
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Linkage maps
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conceptual diagram of relative distance between linked loci based on recombination frequency
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Why are linkage maps important? (3)
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1) understanding gene function: correlating phenotype with chromosome position
2) genome evolution: comparing relative position of same genes in different organisms 3) Facilitate strain building: catalogue of markers aids crosses to produce high P of recombination |
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neighbourhood effect
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clustered genes often transcribe as one unit
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Genes cannot produce phenotypes because
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1) interactions with other genes
2) internal environment (cell) 3) external environment (organism) |
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What are the 4 major interactions to produce a phenotype from a gene
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1) Transcription- turned on or off by regulatory proteins
2) protein interactions- several proteins from different genes may be required to form molecular machine 3) Protein activation- protein from gene 1 may need modification by protein from gene 2 4) environment- enzymes require substrates, gene expression requires raw material |
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signal transduction
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environmental cue triggers consecutive gene controlled steps in pathway
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One gene- one enzyme hypothesis
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idea that genes act through the production of enzymes, with each gene responsible for producing a single enzyme that in turn affects a single step in a metabolic pathway.
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who proposed the one gene one enzyme hypothesis
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Beadle and Tatum
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Auxotrophic mutants
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individuals that grow in culture only when supplemented with substance not required by wildtype
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one gene- one polypeptide
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most genes encode for one polypeptide; some encode for specialized RNAs
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Complete Dominance
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dominant phenotype expressed when only one copy of the allele is present
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phenylketonuria
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PKU, Autosomal recessive, haplosufficient
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PKU
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caused by deficiency in phenylalanine hydroxylase (PAH)
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absence of PAH
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causes a build up of phenylalanine causes disorders in homozygous recessives
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Incomplete dominance
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heterozygote intermediate between two homozygous phenotypes
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Haplosufficiency:
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heterozygote has enough normal gene product to be phenotypically normal
ie. aa= affected, Aa= carrier but phenotypically normal |
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haploinsufficient
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heterozygote does not have enough of the normal gene product to be phenotypically normal
ie. aa & Aa=affected AA= normal |
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gene dosage
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each allele yields certain amount of protein production- finite amount towards phenotype
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co-dominance
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expression in heterozygote of both phenotypes normally shown by either allele
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Population genetics
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is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow.
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Hardy-Weinberg formula
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p^2+2pq+q^2=1
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Hardy-Weinberg Equilibrium:
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allele and genotype frequencies are at equilibrium after one round of random mating and do not change in the absence of other influences
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Assumptions of H-W equilibrium:
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1. Large, closed population
2. Completely random mating 3. Equal survival of all genotypes 4. Equal fertility of all genotypes 5. No mutation |
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What does Deviation from HWE tell us?
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1. The 5 major assumptions are not valid for study population.
2. Some external force is acting on genotype frequencies 3. Evolutionary change may be happening via altered genotype and eventually allele frequencies |
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Inbreeding's effect on population genetics
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Inbreeding introduces possibility of homozygosity by descent above and beyond that predicted by frequency of alleles (p2+q2). causes homozygotes ie. loss of diversity
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Inbreeding coefficient(F):
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probability that both alleles in an individual are identical by descent
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For a completely outbred population (F=0), genotype frequency determined by H-W equation ...
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p^2+2pq+q^2=1
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For a completely inbred population (F=1), genotype frequencies determined by the equation...
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p+q=1, there are no heterozygotes
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Assortative mating:
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non-random mating pattern where individuals choose mates based on phenotype (and thus genotype)
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Enforced outbreeding:
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when mating between related individuals occur less often than expected by chance.
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HIV
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retrovirus, 9 major genes, ~10,000 bases, 2 single stranded copies, inserts into host cell via reverse transcriptase
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How HIV inserts itself into the host cell (7)
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1. fusion of HIV to the host cell surface
2. HIV RNA, reverse transcriptase, integrase and other viral proteins enter the host cell 3. viral DNA is formed by reverse transcriptase 4. Viral DNA is transported across the nucleus and integrates into the host DNA 5. New viral RNA is used as genomic RNA and to make viral proteins 6. New viral RNA and proteins move to the cell surface and a new immature HIV forms 7. the virus matures by protease releasing individual HIV proteins |
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Escherichia coli
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E-coli, Bacterium, DNA based genome haploid, ~4200 genes, 4 million bp genome, carries plasmids, ~2um long
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plasmid
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an independent small circle of DNA
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2 major types of chromosome changes that can affect cell/organisms function
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1. change in chromosome number
2. change in chromosome structure |
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double strand breaks are..
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detrimental
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population
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group of individuals of same species in same place and same time: an evolutionary unit within common gene pool
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gene pool
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the total extent of genetic variation within a group (population, species) all the alleles
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2 types of genetic variation
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1. Discontinuous (Qualitative)
2. Continuous (Quantitative) |
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Discontinuous genetic variation
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Qualitative. character found in 2 or more distinct forms, easy to categorize. E.g. Brown and blue eyes.
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Continuous genetic variation
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Quantitative. unbroken range of phenotypes, can be measured but difficult to categorize. E.g. height, mass.
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population genetics is based on which type of genetic variation
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discontinuous
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Genetic composition
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collective frequencies of different genotypes
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6 major factors affecting allele frequency:
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1. Effect of mating patterns
2. Migration 3. Mutation 4. Recombination 6. Genetic Drift |
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Genetic drift
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random changes in allele frequencies due to sampling error
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2 major sides to population genetics
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1. Measuring genetic variation
2. Predicting changes |
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measuring variation
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simple relationship between presence of allele and trait
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Genotype Frequency
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observed proportion of individuals with particular allele combination in the population.
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Allele Frequency:
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the proportion of specific allele present in a population based on all copies of alleles present for that gene.
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Polymorphism:
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more than one allele and associated phenotypes in a population.
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Polymorphism can be characterized at 3 levels
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1. Visible phenotype
2. Protein composition 3. DNA sequence variance |
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2 types of change in chromosome number
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1. abberant euploidy
2. anueploidy |
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Aberrant euploidy
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change in chromosome number by multiples of whole set
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Aneuploidy
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changes in number of parts of chromosome sets. Caused primarily by parental nondisjunction during meiosis
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Polyploids
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organisms that have 2+ full chromosome sets ie. 3n, 4n, 5n etc.
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monoploid
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Individuals that are normally diploid but become haploid aberrantly
o Not well tolerated o Expresses everything o Unmask harmful mutations |
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Genetic load
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accumulation of harmful recessive mutations in the genome of an individual or populations
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Autopolyploid
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multiple chromosome sets derived from within a single species
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2 examples of autopolyploids
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bananas-sterile autotriploids (3n)
Grapes – autotetraploids |
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Allopolyploids
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multiple chromosome sets in one organism derived from 2 separate species(from of hybridization)
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Changes in chromosome structure happen due to
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breakage and repair
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2 type of arrangments
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1. balanced - no net DNA change
2. unbalanced- changed DNA dosage |
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Balanced rearrangements
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inversion and reciprocal translocation
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Inversion
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chromosome segment broken in 2 places, flipped 180 degrees and rejoined
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Reciprocal translocation
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2 non-homologous chromosomes each broken once, resulting in chromosome fragments switch places
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breaks are fixed by
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1. non homologous end joining (inversion)
2. recombination (translocation) |
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Unbalanced rearrangements
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deletion and duplication.
both types result in gain/loss of DNA therefore changes in the gene dosage |
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Deletion
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segment of chromosome broken 2x and fragments lost- ends of remaining pieces join together
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Duplication
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segment of chromosome arm is repeated can be tandem duplication of DNA sequence or in different location
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speciation
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chromosome changes cause new phenotype, present barrier to reproduction with ancestral type
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3 differences between humans and chimps
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1. Fusion of chromosome 2 (ape 2+3) with small deletion
2. Pericentric inversion at chromosome 5 3. small telemetric deletion at chromosome 6 |