Genetics Final Exam Review

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PKU
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autosomal recessive condition in which phenylalanine levels become excessive; developmental delays, cognitive impairment, small head, seizures, musty odor, fair skin, light colored eyes
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biomolecules
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have a carbon backbone
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covalent bonds
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atoms share electron, strong bond, nonpolar and polar based on electronegativities of atoms involved.
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nonpolar covalent bonds
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equal sharing of electrons, occurs between atoms with nearly identical electronegativities, hydrophobic.
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polar covalent bonds
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unequal sharing of electrons, occurs between atoms with different electronegativities, hydrophilic
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hydrogen bonds
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weak bonds, usually between N or O
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biological molecules
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have a hydrocarbon backbone, has functional groups, etc.
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Functional Groups
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important for proteins and amino acids; hydroxyl, phosphate, carboxyl, and amino
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hydroxyl
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-OH; nucleic acids
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carbonyl
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O=C; found in carbohydrates and nucleic acids
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carboxyl
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C=O=OH; important for proteins
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Amino
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N-HH; important for proteins
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sulfydryl
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-S-H; found in proteins
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Phosphate
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O-P-O=O; important for nucleic acids
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Methyl
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C-H-H-H; found in proteins
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macromolecules
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carbohydrates, lipids, proteins, nucleic acids
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carbohydrates
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CH2O; glucose, energy storage, structural (cellulose and chitin)
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lipids
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heterogeneous group; membranes, energy storage, hormones; hydrophobic
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nucleic acids
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store and transmit hereditary material; DNA contains genes and is passed from parent to offspring; RNA intermediate between DNA and protein.
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Nucleotides
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Nitrogenous base + phosphate group + sugar (OH in RNA and H in DNA)
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Nitrogenous Bases
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PUrines and Pyrimidines; adenine, guanine, cytosine, thymine, uracil
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Purines
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adenine and guanine
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pyrimidines
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cytosine, thymine, uracil
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polynucleotide chains
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synthesis by dehydration or condensation reaction and breakdown by hydrolysis reaction
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DNA
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double stranded, deoxyribose phosphate backbone, hydrogen bonding occurs between base pairs, AGTC
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RNA
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single stranded, ribose-phosphate backbone, AGUC
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Amino Acids
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polar or nonpolar; OH or H – H20 for dipeptide (important for PKU)
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antimitotic
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stops mitosis (nuclear division) cancer cells undergo mitosis at irregular fashion; hair loss, immunity, nausea because of no cell division in these areas.
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cell cycle
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cycle of duplication and division necessary for cells to reproduce, continuous, directional, DNA must be faithfully replicated and DNA accurately segregated between two daughter cells
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Interphase
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G1-replicate DNA nucleotides are building blocks and enzyme holds together, S- DNA synthesis copying, G2-separating DNA twice as much DNA than G1, G0- nondividing phase
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chromosome replication
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occurs in S phase; cohesin present one single chromosome with two identical chromatids
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M phase
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mitosis: nuclear division (karyokinesis), cytokinesis: cell division (cleavage); Prophase DNA coils, spindle going to nucleus, metaphase and anaphase results in accurate segregation; prophase, prometaphase, metaphase, anaphase, telophase
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prometaphase
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nuclear envelope is gone, spindles attach to chromosomes
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mitosis
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prometaphse spindles, metaphase line up, metaphase 4 chromosomes 8 DNA, anaphase 8 chromosomes 8 DNA
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Cell cycle checkpoints
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G1/S- checks for DNA damage to ensure faithful replication, G2/M- checks for proper replication, spindle- spindles are properly attached to chromosome to ensure accurate segregation; signals in cytoplasm
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kinase
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enzyme that regulates protein activity by adding phosphate group to protein; makes the structure and function different depending on the protein; MPF (mitosis promoting factor)
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Kinase activity
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kinase concentration constant for time vs. activity; kinase activity up and down; protein is always there, but not always active
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Cyclin
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concentration goes up and down; kinase only works if this active; peaks at mitosis to start the cell cycle
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tumor suppressor genes
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‘brakes’ inhibit cell division until conditions are right for progression; proteins produced by these genes are going to stop cell division
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proto-oncogenes
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‘gas pedal’ stuck; initiates controlled cell division; mutations convert them to oncogenes, which promote uncontrolled cell proliferation; growth factor receptor more per cell in cancer
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meiosis
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diploid-replication-reductional division Meiosis 1- haploid- equational division haploid; DNA content = 1/2x
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prophase 1
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formation of tetrads (bivalents); crossing over at chiasma between non-sister chromatids
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meiosis 1
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chiasmats hold homologous together; kinetochores of sister chromatids fuse and function as one microtubules can attach to only one side of each centromere
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anaphase 1
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chiasmats add homologues together; kinetichores of sister chromatids fuse and function as one; microtubules can attach to only one side of each centromere; pull the homologous chromosomes apart and sister chromatids held together
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genetic variation
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independent assortment, crossing over, random fertilization
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transmission genetics
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the study of how traits are passed from one generation to another
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Gregor Mendel
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father of genetics; mid-late 1800s; independent assortment; used garden peas
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model organism
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easy to maintain, short lifespan, numerous offspring, genetic variation, known history
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true-breeding
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either AA or aa; removes confounding variables
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single-factor cross
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true breeding dominant x true breeding recessive; all tall
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monohybrid cross
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self-cross of F1 generation: 1:3 short
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Reciprocal Cross
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switch parental genotypes of true breeding to determine affects of gender; equal contributions
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alleles
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alternate versions of heritable factors (genes) exist
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Independent Segregation
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paired factors segregate randomly so that half of the gametes received one factor and half of the gametes received; alleles segregate during anaphase 1
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test cross
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heterozygous x recessive
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binomial expansion formula
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used when birth order is unknown: P = n!/A!a! (pA)A(Pa)a
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lethal alleles
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homozygous is lethal; mexican hairless dog and achondroplasia
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hierarchal dominance
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many alleles involved with one gene; dominance relationship
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incomplete dominance
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Rr = one allele doesn’t completely mask the trait; blending of the two traits
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ABO Blood Types
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IA IB dominant and i is recessive; IAIA type A; IAi type A; IBIB type B; IBi type B; IAIB type AB; ii type O; codominance
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codominance
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receive an intermediate phenotype; IAIB=AB
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lab coat colors
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9:3:4 when heterozygotes crossed; caused by epistasis; modification of 9:3:3:1 ratio; little e is masking the big B genotype; B gene determines color (black or brown) and E determines if pigment is deposited in hair: e-cannot deposit
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gene interactions
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genes at different loci contribute to the determination of a single phenotypic characteristic (2 genes contribute to one phenotype)
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epistasis
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one gene masks the effect of another gene at a different locus: epistatic-masking and hypostatic-being masked; results in a modified 9:3:3:1 ratio
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polydactyly
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autosomal dominant; incomplete penetrance example
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incomplete penetrance
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phenotype doesn’t always matter the genotype; % of individuals having a particular genotype that express the expected phenotype
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variable expressivity
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have same genotype but don’t all look the same; degree to which a penetrant gene or genotype is expressed; continuum of expression
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genetic heterogeneity
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genetic complementation; explains why none of children by affected parents have disease
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homogametic
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two of the same sex chromosome; females XX
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heterogametic
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half os gametes X and half Y; XY male
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karyotype
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used to determine chromosomes
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Turner Syndrome
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monosomy X; short stature, (45, X)
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Klinefelter Syndrome
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47, XXY; presence or absence of Y means male; male with female characteristics
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SRY
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gene on the Y-chromosome that determines male characteristics; can occasionally attach to X and cause phenotype male
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pseudoautosomal regions
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brackets on X and Y chromosomes that cause chromosomes to align during meiosis I
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Sutton and Boveri
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genes are located on chromosomes; chromosomes undergo segregation and independent assortment 1902
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Thomas Hunt Morgan
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embryologist who worked with drosophila mutants; reciprocal cross and eye color gene on x chromosome
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sex influenced trait
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trait expressed different in males and females; an allele is dominant in one sex and recessive in the other; autosomal; pattern baldness by too much DHT; different in heterozygotes
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sex limited trait
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trait appears in only one gender; autosomal; milk production example; add or subtract hormones to test
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dosage compensation
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to offset differences in the number of active sex chromosomes
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Barr and Bertram
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observed condensed structure in female cat cells but not in males
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Mary Lyon
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Barr body is an inactivated X chromosome
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X inactivation
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barr body turned off for proper function; normal has one, turner has zero
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mitochondrial inheritance
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affected individuals have an affected mother; trait never passed from father to offspring; can trace ancestry through mother
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x-linked recessive
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father must be affected for offspring to be affected; usually more males
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Y-linked
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affected father passes trait to all sons and no daughters; male-to-male transmission
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linked genes
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two or more genes can be located on the same chromosome; genes that are close together tend to be transmitted as a unit; if not independent assortment, linked genes present
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recombination
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crossing over that happens during prophase 1; sorting of alleles into new combinations; progeny exhibit mixing of maternal and paternal alleles
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independent assortment
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50% non-recombinant (parental) and 50% recombinant
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dependent assortment
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completely linked; no crossing over takes place between genes. 100% of gametes are nonrecombinant (parental)
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Between assortment
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some crossing over; 50%<parental gametes<100%; 0%<recombinant genes<50%; closer, crossing over less likely
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linkage maps
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gene map determining how far genes are from each other
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2 point test cross
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dihybrid (doubly heterozygous) x all recessive
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3 point test cross
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trihybrid (triply heterozygous) x all recessive
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cis configuration
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MD md
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trans configuration
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Md mD
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parental progeny
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greatest number in offspring after test cross
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recombinant progeny
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least number in offspring after test cross
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recombination frequency
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# of recombinant offspring/total X 100 = map units
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haplotype
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set of linked genetic markers that are generally inherited as a unit; used to detect crossover events
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LOD score > 3
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linked; data and number of recombinants 1000 times more likely chance they are linked verses not linked; log of odds score
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maternal effect gene
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genes exhibiting inheritance pattern in mother; cytoplasmic determination; mother’s genotype determines individual’s phenotype; products from nurse cells transferred to inside the egg
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genomic imprinting
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type of epigenetic inheritance; non-medelian grouping; expression of trait depends on whether it was inherited from the mother or the father
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monoallelic expression
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imprinted gene is expressed depending on how the genes are marked or methylated; either maternally inherited, paternally, but not both
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uniparental disomy
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one parent, two chromosomes, indiivduals inherit both chromosomes from each parent
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Angelman syndrome
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skinny, puppet-like; deleted region of chromosome 15 on the maternal chromosome
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Prader-Willi Syndrome
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obese, mental retardation; deleted region of 15 in father
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multifactorial inheritance
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due to an interactino between genes and the environment
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mendelian traits
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primarily due to a single gene
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polygenic traits
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due to multiple genes; variation is continuous, not discrete; individual genes follow Mendel’s laws; effect of genes is additive or synergistic
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monozygotic concordance
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comparison between identical twins
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dizygotic concordance
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comparison between fraternal twins
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concordance data
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if MZ concordance > DZ, it is assumed that trait is partly controlled by genetics, MZ should be 2x greater than DZ; MZ concordance <100% indicates that environment plays a role in expression
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adoption studies
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look at environment vs. adoptive parents to determine multifactorial traits
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association studies
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look for association between particular trait and a gene or a genetic marker and see if dfferent: SNP
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Single nucleotide polymorphism
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SNP; difference in single nucleotide
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purine
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has extra structure; adenine and guanine
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Fred Griffith
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studied mice; transferred R and S bacteria; S-virulent and R-no disease; mixed R and S; live R strains turned to S strains (bacterial transformation)
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Avery, Macleod, McCarty
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live S + various enzymes (destroying DNA, RNA, or protein) mixed with R strains; transformation occurred in DNAse
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Hershey and Chase
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bacteriophage experiments; tell difference between DNA and protein by phosphate; used radioactive isotypes to differentiate; proteins use sulfer-3s to label proteins but not DNA; P labels DNA; concluded DNA is the genetic material that viruses injected into bacteria
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Chargaff’s Rules
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ratios of nitrogenous bases; A%=%T (two hydrogen bonds) and G%=C% (three hydrogen bonds); %purine = %pyrimidine for double-stranded
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X Ray diffraction
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Franklin and Wilkins; DNA caused to scatter and detected by X-ray film; led to Watson and Crick
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Watson and Crick
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1953; hypothesized a double-helix and looked at spacing: 3.4 nm = one turn; width is 2nm ; 10bp per turn =.34 nm between base pairs
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phosphodiester bonds
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sugar phosphate backbone held together
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Hydrogen Bonding
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strands held together
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antiparallel
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complimentary and 5’3′
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B Form
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the most common form of DNA in living cells
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Semiconservative Method of Replication
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proposed by Watson and Crick; Meselson and Stahl tested; labeled DNA with radioactive nitrogen; two rounds of separation
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Conservative Method
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Dispersive Method
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Kornberg and Ochoa
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made own nucleotides; added to intact DNA and got long strands of radioactive DNA; added to fragmented DNA and got no long strands of DNA
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okazaki fragments
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short molecules of single-stranded DNA that are formed on the lagging strand during DNA replication; discontinuous; together by DNA ligase enzyme
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telomeres
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DNA synthesis occurs here; telomerase makes telomeres shorter; as adults age, telomeres shorter and shorter, allowing more issues
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DNA
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genetic material for inheritance that stores information and is passed on; storage molecule; double stranded; stable and cannot function as enzyme
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gene expression
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the process of ‘reading’ the instructions in DNA to produce a RNA molecule or protein
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central dogma
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DNA to RNA to protein; Francis and Crick; if RnA not final product, translation occurs
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introns
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spliced and usually do not code for proteins
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exons
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spliced together and are coding regions
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RNA
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carries protein-encoding information and helps to make proteins; has two hydroxyl groups on 3′ and 2′ whereas DNA has one OH; unstable and functions as enzyme
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mRNA
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encodes amino acid sequence
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tRNA
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transports specific amino acids to the ribosome for protein synthesis
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rRNA
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associates with proteins to form ribosomes, which structurally support and catalyze protein synthesis
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RNA polymerase
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joins enzymes together; induces transcription
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helicase
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enzyme that helps separate DNA strands at origin of replication
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primase
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primer made of RNA for syntheiss
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lagging strand
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goes from 3′ to 5′ end; small fragments called okazaki
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leading strand
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goes from 5′ to 3′ end; continuous in one piece
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DNA ligase
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seals and forms new phosphodiester bond to join okazaki fragments
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transcription components
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building blocks (three phosphates for energy) template strand, and enzymes (rna polymerase and transcription factors)
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nontemplate strand
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sense strand or coding strand
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template strand
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nonsense strand or noncoding strand; RNA polymerase reads template strand (origin of replication) at promotor (specific to RNA pol); coding region transcribed where codons are; terminator part of RNA
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initiation
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RNA pol and TF recognize promotor and separates DNA strands (Helicase not needed)
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elongation
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RNA reads DNA template strand and adds complementary nucleotides in 5′ 3′ direction (U instead of T); different in prokaryotic and eukaryotic by number of polymerases
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termination
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RNA reaches terminator, dissociates from DNA and release RNA
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TATA box
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only has hydrogen bonds and easier to pull apart; promoter region in prokaryotes
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AUG
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start codon
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Initiation eukaryotes
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require may need Transcription factors, RNA pol II
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regulatory elements
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elements (have an affect) located far from the gene; enhancers and silencers
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enhancer
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rate of transcription increases when activator binds to enhancer
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silencer
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rate of transcription decreases when repressor binds to silencer
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termination
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pro- mediated by specific sequences in RNA and DNA and by specific proteins: UGA UAA UAG eukaryotic- do not know sequences
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UGA UAA UAG
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stop codons
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Complimentary to Template strand
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antiparallel; result of transcription
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ribosomes
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E P A site; small subunit added then large subunit added; tRNA anticodon enters slots; cap important for ribosome to bind to prokaryote; when translation done exits through E
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Shine-dalgarno sequence
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leader sequence in ribosome SSU binding
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initiator tRNA
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small ribosomal subunit binds followed by binding of this
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peptidyl transferase
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formation of peptide; catalyzed by ribozyme that recognizes start and makes peptide bonds for protein; NH+3 amino group and N- terminus (carboxyl) N on left, C on right
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translocation
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to reuse empty tRNA; shifts over and recharged EPA goes to EPA site; continues until stop codon
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germline mutation
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passed on to future generations
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somatic cell mutation
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size of patch depend on timing of mutation, genetic mosaic, mutation not transmitted to offspring
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spontaneous mutations
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occur randomly due to errors in cellular/biological process
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induced mutations
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due to exposure to a mutagen
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directed mutation theory
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selected conditions could promote the formation of specific mutaitons
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random mutation theory
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environmental factors simply select for the survival of those individuals that happen to possess beneficial mutations
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mutation rate
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commonly expressed as the number of new mutations in a given gene per generation; increased by presence of mutagens; implies time
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hot spots
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locations within the chromosome that make them more susceptible to mutation
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mutation frequency
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the number of mutant genes divided by the total number of genes in a population # of cases / 2(# of individuals)
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ionizing radiation
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shorter wavelength and high energy; free radicals by dislodging e- from atoms; includes X rays and gamma rays; severe damage to DNA
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ultraviolet radiation
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longer wavelength and lower energy
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base modifiers
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changes functional groups on the bases; incorrect base pairing
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intercalating agents
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goes between DNA messes up splicing, makes smaller or longer with addition or deletion; frameshift mutation
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base analogue
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structures similar to regular nucleotides and cause incorrect or incomplete DNA replication
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transition
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DNA level base substitutions; purine to purine/pyrimidine to pyrimidine
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transversion
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DNA level base substitution purine to pyrimidine
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phenotypic mutations
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missense, nonsense, silent mutations
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missense
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codes for a different amino acid
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nonsense
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incorporates a stop codon
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silent mutation
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synonymous mutation codes for same thing
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frameshift mutations
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DNA level base insertion and base deletion
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In-Frame Insertions and Deletions
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insertion or deletion of nucleotides in multiples of three; Trinucleotide repeat expansion has sequence of 3 nucleotides can increase from one generation to the next, Fragile X and Huntings has them repeated
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anticipation
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symptoms worsen from one generation to the next
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DNA repair pathway
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detection-excision-polymerization-ligation
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nucleotide excision
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repairs UV, chemical, etc. replaces up to 30 nucleotides
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base excision
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from oxidative damage and free radicals, replaces 1-5 nucleotides
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Xeroderma Pigmentosum
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autosomal recessive; 7 genes involved; skin disease
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cokayne syndrome
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mutation in ERCC6 (involved in excision repair) on chrosome ten; progeria
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mismatch repair
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original strand methylated and new strand is not, detected and removed wrong areas by enzymes
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cytogenetics
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subdiscipline in which scientists study chromosome structure and link variations of structure with specific traits or disorders
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chromatin
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DNA and associated proteins that give shape
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euchromatin
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less condensed; majority of chromosome; stains lightly; active DNA
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heterochromatin
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condensed at telomeres and centromeres; not transcribed b/c used to hold together; repeated DNA in regions; sometimes barr body is example
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centromere
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specific repeated blocks of DNA that facilitate binding of specific proteins i.e. kinetochore; important for proper segregation
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telomere
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area for t-loop that prevents degradation; prevent attachment of chromosomes to others
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origin of replication
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A-T rich sequences facilitate melting of DNA template
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histones
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subunits occurred at different distances; core of histone proteins and DNA wrapped around them; 200 pieces of DnA per each nucleosome; protected DNA from degradation by nuclease
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nucleosome
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beads on a string goes to 30 nm fiber to radial loops attached to scaffold in interphase chromosome
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chromosome nomenclature
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chromosome #, short arm=p long arm=q
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radial loops
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compaction level in interphase
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telocentric
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centromere at end
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acrocentric
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centromere near end
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submetacentric
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p arm and a q arm
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metacentric
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centromere in center
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euploid variations
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multiple of n chromosomes
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aneuploid variations
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extra, not a multiple of n chromosomes
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FISH
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usually two red and two green; yellow means fused
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hybridization
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different pieces of single-stranded DNA bind to one another
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Down Syndrome
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trisomy 21
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Edward Syndrome
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trisomy 18; mental and physical deficiences, early death, clenched fist
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Patau syndrome
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trisomy 13; mental and physical deficiencies, triangular nose, cleft lip
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nondisjunction
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failure of homologous chromosomes or sister chromatids to separate during mitosis or meiosis
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mosaicism
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part of organism carries cells genetically different from other parts; have cells with different numbers of chromosomes due to mitotic nondisjunction
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Cri-du-Chat
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high pitched cry, low birth weight, small head; 46, XX del5
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terminal deletion
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deletion at end of chromosome
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interstitial deletion
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deletion in middle of chromosome
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Comparative Genomic Hybridization
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label DNA with dye and label test with green; hybridize; test>reference >1= duplication; <1=deletion
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duplication
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duplication causes paralogs
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pericentric inversion
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inverted region around the centromere; position affect
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paracentric inversion
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inverted region on one arm; position affect
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translocation
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cross location exchange in material between nonhomologous chromosomes
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simple translocation
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stays on one arm
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reciprocal translocation
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takes around centromere on another chromosome
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balanced translocation
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no loss or gain of genetic material
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unbalanced translocation
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loss or gain of genetic material
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robertsonian translocation
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breakage of acrocentric chromosome leaving sticky ends; long arms join to form one large metacentric chromosome and short arms are lost
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housekeeping genes
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essential genes that are constitutively expressed
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regulated genes
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genes that are turned on or turned off depending on environment conditions
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structural genes
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encode proteins that have a catalytic function or a structural function as opposed to regulatory function
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repressor
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decrease transcription by preventing RNA pol binding to promotor
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activator
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increase transcription by facilitating RNA pol binding at promotor
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homeodomain
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important motif proteins that regulate development of multicellular organisms
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lactose
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lactose converted by beta galactosidase and side product is allolactase; induces production of lactose utilizying enzymes
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lacY
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mutation prevents lactose from entering cell
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lacZ
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mutated lactose doesn’t get broken down by beta-galac
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lacI
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transcribed when lactose present and absent (codes for repressor)
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lacp
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mutation results in no transcription
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operator
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regulatory proteins like repressor bind
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allolactose
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lactose converted to this and is an inducer that binds to repressor to prevent binding to operator
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cortisol
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glucocorticoid hormone known as stress hormone modulates activity of regulatory transcription factors; can increase or decrease transcription whether binds to enhancer or repressor
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core promoter
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proteins bind to this located close to +1 site and recruit RNA pol; facilitates basal level of transcription
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control elements
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activators bind to enhancers to increase transcription and repressors bind to silence to decrease transcription; often located far from gene
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methylation
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modification involved in epigenetic regulation; blocks binding of activator to enhancer because near enhancer
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epigenetic changes
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changes in gene expression without changes to the DNA sequence
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Rett Syndrome
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distinct hand movements, mental retardation, lethal in males, mutation in MECP2 gene; recognizes methylated cytosines and alters expression; Rett syndrome cannot regulate expression; No MECp2 can’t have closed conformation and expressed too much
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Regulation by methylation
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MECP2 recruits Histone deacetylate and converts chromatin to closed conformation (w/o genes will be expressed too much)
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closed conformation
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chromatin very tightly packed and transcription may be difficult or impossible
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open conformation
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chromatin is highly extended and transcription can take place
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acetylation
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HAT allows open conformation; dissociated DnA is hypersensitive to DNAse and is available for transcription
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deacetylation
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open to closed conformation by HDAC
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alternative splicing
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splicing of pre-mRNA in multiple ways resulting in different mature mRNA molecules produced from a single gene; cutting and joining what is left
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RNA interference
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lin4 interferes with translation of lin14; mutant lin4 results in lin14 expressed at wrong time
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microRnA
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cause RNA interference; encoded by genes that produce small RNA molecules; silence expression of specific mRNAs; produce relatively large RNA that is self-complementary; dice RNA to small fragments
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RISC
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RNA induced silencing complex; bind protein first and protein silences gene; translation of mRnA won’t happen
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post-translational regulation
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phosphorylation or other chemial modifications can alter the activity of a protein after it is produced on polypeptide chain (acetylation, methylation, phosphorylation)
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adrenaline
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causes activation of phosphorylase enzyme to break down glycogen to produce glucose for quick energy source
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transgenic organism
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introduction of new gene into an organism; rice: started with pathogen agrobacterium and incorporated into plant cell and cloned; treat with various hormones and result in new plant
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recombinant DNA
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combination of fragments of DNA from different sources (cutting and pasting)
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restriction enzymes
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restriction endonucleases cut at specific sequences (gives control over which fragments of DNA we get) and causes sticky ends; most palindromic; hydrogen bonds and the phosphodiester bond (ligase) for separating and cutting and sealing back together
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sticky ends
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complimentary to each other and single stranded DNA
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isolate DnA
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physically cut desired DNA fragment from gel and extract DNA; run on gel
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gene cloning
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isolation of and copying a particular gene; gene of interest in foreign DNA + cloning vector = place recombinant DNA on bacteria and replicate DNA; reproduce to make new DNA molecules
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Cloning Vectors
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origin of replication, selectable marker (antibiotic resistance and auxotrophic marker for specific nutrient) and unique restriction sites where gene of interest is inserted (multiple cloning site or polylinker)
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plasmid
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15 kb; bacterial transformation but can only clone small pieces of DNA and inefficient
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lambda phage
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phage infection up to 23 kb; virus good at getting DNA in cell efficient, but not big enough
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BAC
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bacterial transformation up to 500 kb bacterial artificial chromosome
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YAC
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yeast artificial chromosome in yeast transformation up to 600 kb
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plasmid vector
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polylinker in middle of lacZ gene; + restriction endonuclease enzyme cuts within lacZ+ foreign DnA and ligase added: plasmid not taken, empty plasmid taken by cell, recombinant taken up by cell; change color in search of beta-galac
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blue/white color screening
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tests for functional beta-galactosidase product to determine result; white contain vector harboring insert; blue colonies contain empty bector
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lambda phage vector
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specific to E. coli, must package DNA, cuts down on empty vectors b/c won’t take up DnA if not right size
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DNA library
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collection of clones containing all the DNA fragments from one source; isolate DnA and then cut with restriction enzymes; organize by cloning them in a vector
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genomic library
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contains a copy of every fragment of genome, including introns if DnA is from a eukaryote
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cDNA
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complementary DnA contains only those DNA sequences that are transcribed into mRNA; contains only exons: ONLY genes expressed
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formation of cDNA
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isolate mature mRNA from cells-reverse transcriptase-RNADNA hybrid-degrade RNA+DNA polymerase and primer and get double stranded cDNA
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plasmid library
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DnA fragments from source-inserted into plasmid vector-transformation-each cell contains a single fragment and all cells in library
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phage library
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fragments from source-inserted into phage vector-phages infect e. coli- each phage contains a single fragment and together in library
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Screening DNA Library
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colony-replica-filter-hybridization with two different sources that will stick together and probed only to spots containing ssDNA-x ray film exposes and colonies containing the gene present
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disease diagnosis
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restriction site isn’t normal in diseased; isolate DNA, cut with restrictions, run digested on gel, if different then affected
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RFLP
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restriction fragment length polymorphisms; use PCR to make copies of desired region, cut DNA with restriction enzyme and analyze on gel
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biopharming
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transgenic animals/plants cross of a gene from one species to another to amek protein secreted from milk; lysozyme and antithrombin in goat’s milk
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VNTR
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variable number of tandem repeats; use PCR to amplify region, run gel to separate PCR products based on size, several set must be used to ensure fingerprinting
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bioremediation
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use genetically engineered microbes to degrade toxic substances in environment
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northern blot
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when, where, and how much RnA transcribed; tagged probe to detect specific; present in varying amounts in each tissue and alternatively spliced in each tissue
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western blot
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detects specific proteins; antibodies to be complementary to proteins; only in one lane = only in red blood cells
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microarrays
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gene chips; used to monitor gene expression of many genes at one time; isolated and fragmented and tagged with hybridization; red- has and more transcription so affected by cancer cells green-doens’t have and gene was now turned off; yellow-both clear-nothing
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pharmacogenomics
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the study of how one’s genome influences his/her reaction to drugs; analyze genome and find which side affects to a drug
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genomics
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development and application of new mapping, sequencing, and computational procedures to analyze the entire genomes of organisms
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Human Genome Project
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to discuss longterm exposure to low-level radiation; launched 1990 and completed 2001/2004; did not have appropriate technology and were looking for other energy sources; to map sequence and to develop new technology and sequence model organisms: genetic maps physical maps and complete genome sequence
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HGP linkage maps
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maps showing relative location of genes/markers based on recominbination frequency throughout world; used genetic markers
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genetic markers
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not in coding regions b/c this DNA shows much more variation; Restriction fragment length polymorphisms restriction at + or -, microsatellite markers b/c many distinct individuals, and SNPs
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microsatellite markers
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use PCR to amplify alleles in genomic DNA samples, denature PCR products and size-fractionate by gel electrophoresis
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haplotype
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set of linked genetic markers that are generally inherited as a unit to track transmission of disease causing alleles; pinpoint where located
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restriction map
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determines the relative positions of and distances between restriction sites on a piece of DNA: digest DNA with restriction enzymes, show smaller fragments produced by cuts; gel to determine order
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STS mapping
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marker is a short unique sequence of DNA whose location in the genome is unknown; goal to identify and sequence overlapping clones
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clone-by-clone sequencing
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map based sequencing clean; fragments in order then sequenced
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shotgun sequencing
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messy and scatters lots of DNA and deals with afterwards; fragments sequenced then put in order based on overlapping sequence
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HGP
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sequencing DNA-assembled-annotation for protein encoding genes from other databases- gene expression proteome
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proteome
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study of the proteome (complete set of proteins present in a cell); begin by characterizing complete set of mRNAs present in a cell transcriptosome
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proteomics
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discover all proteins produced and determine functions
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comparative genomics
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sequence the genomes of other organisms, in order to compare similar genes between species; multifactorial?
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Haplotype map
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individual SNPs found by comparing individuals; look for blocks of SNPs inherited together; tightly linked SNPs constitute haplotype; only portion of SNPs in a haplotype need to be determined to identify; if linked to disease then identifying can be diagnostic
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population genetics
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study of variation and inheritance within populations; use mathematical models and experimental techniques to answer questions: prevention of extinction and variation and adaptation
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genetic variation
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amount determines a population’s potential to adapt to its environment
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Hardy-Weinberg Law
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population is large, randomly mating, and not affected by migration, mutation, or natural selection, then allelic frequences and genotypic frequencies will not change; if in eqiulibrium, reproduction alone will not alter
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genotypic frequency
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proportion of a population that has a particular genotype: #individuals with genotype/total # individuals (sum of all =1)
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allelic frequency
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proportion of the gene pool represented by a particular allele frequency of big T allele: in a apopulation #/total: alleles are what is passed on
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P
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dominant allele for Hardy-weinberg
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Q
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recessive allele for hardy-weinberg
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Hardy-weinberg equilibrium
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allelic frequencies: p+q=1; genotypic frequencies: p2 q2 and 2pq with assumption it is at equilibrium
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Allelic Frequency from Genotype Number
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2(#homozygousdominant)+#heterozygotes/2(total number of individuals); for q use recessive
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Chi Square Hardy-Weinberg
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df= # genotypes -# alleles
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H-W to estimate allelic frequencies
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q2 = .0005; q= sq. root = .02; p=.98; f(carriers) =2pq = .0392
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nonrandom mating
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inbreeding; self fertilization
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gene flow
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migration; individuals or gametes move from one population to another; reduces genetic divergence among populations; m=population of migrants; (qdonor-qrecessive)m=Qnew
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genetic drift
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statistical accidents; random fluctuation in allele frequencies increases as population size decreases; random change due to change; sampling error due to small population, founder effect, bottleneck effect
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mutation
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ultimate source of variation; so rarely that not alone changes frequency
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selection
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only agent that produces adaptive evolutionary changes
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assortative mating
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tendency for like individuals to mate
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disassortive mating
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tendency for unlike individuals to mate
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heterozygote advantage (balanced polymorphism)
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heterozygotes appear to be protected against fungal infections in PKU and not enough to cause symptoms but enough to inactive fungal toxin that is lethal
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sarkosyl
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breaks membrane in lab for lac operon
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ONPG
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phosphate that changes color when reacts with b-galac
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nucleotide excision repair
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fixes UV light repair, etc.

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