BSCI222 Dr. Kocher FINAL REVIEW
BSCI222 Dr. Kocher FINAL REVIEW BSCI222
Popular in Genetics
Popular in Biological Sciences
This 11 page Study Guide was uploaded by HannahJ on Friday December 11, 2015. The Study Guide belongs to BSCI222 at University of Maryland taught by Dr. Kocher in Fall 2015. Since its upload, it has received 150 views. For similar materials see Genetics in Biological Sciences at University of Maryland.
Reviews for BSCI222 Dr. Kocher FINAL REVIEW
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 12/11/15
BSCI222 Final Review Sheet ● dominant: an allele or phenotype that is expressed in homozygotes (AA) and heterozygotes (Aa) ● heterozygous: and individual organism that possesses two different alleles at a locus ● stages of mitosis: ○ interphase: chromosomes are relaxed and there is a nuclear membrane ○ prophase: chromosomes condense and the nuclear membrane disappears, spindle fibers begin to form ○ prometaphase: nuclear membrane is totally gone, spindle fibers and chromatids attach through the centromere ○ metaphase: homologous chromosomes line up on the metaphase plate ○ anaphase: spindle fibers begin to shorten, separating homologous chromosomes (one molecule of DNA pulled in each direction) ○ telophase: spindle fibers continue to shorten and the chromosomes are pulled to opposite ends of the cell ○ cytokinesis: the nuclear membrane begins to reform as the cell separates into two cells ● substages of prophase 1 of meiosis: ○ takes place during prophase one, dealing with sister chromosomes ○ leptotene: condense ○ zygotene: chromosomes pair up ○ pachytene: synaptonemal complex forms, recombination ○ diplotene: chiasmata, chromosomes linked at point of recombination (no more synaptonemal complex) ○ diakinesis: prepare for prometaphase ● types of chromosomes ○ acrocentric: centromere towards top ○ metacentric: centromere in middle ○ submetacentric: slightly off center ○ telocentric: centromere at very end ● stages of meiosis: ○ meiosis 1 ■ prophase 1: sister chromosomes pair (RECOMBINATION) ■ prometaphase 1: spindle fibers attach ■ metaphase 1: line up at metaphase plate ■ anaphase 1: sister chromosomes split apart ■ telophase 1: split into 2, diploid cells ○ meiosis 2 ■ prophase 2: sister chromatids pair (NO RECOMBINATION) ■ prometaphase 2: spindle fibers attach ■ metaphase 2: line up at metaphase plate ■ anaphase 2: sister chromatids split apart ■ telophase: split into 2, haploid cells ● punnett square basics: ○ mother’s alleles on top, father’s alleles on side ○ cross ○ make note of specific generation! (may be given P and told to cross F2) ○ homozygous: two of the same allele ○ heterozygous: one of each allele ○ for linked genes: ■ ex: AaBB with AaBb is set up with 4 on each side ● (AB AB aB aB/ AB Ab aB ab) ● branch diagram basics: ○ used with more than 2 alleles ○ start with one allele and find the fraction for showing dominant or recessive trait (phenotype) ○ start with 2 diagonals coming from each and continue for each individual gene ○ multiply fractions to get percent of each ● Chi Square Test ○ degrees of freedom: number of categories 1 ■ for hardy weinberg problems only: number of genotypes number of alleles ○ (OE)^2/E ● sex linked genes: ○ passed along through the X chromosome ○ males can’t be heterozygotes (only have one X) ○ females are often carries for recessive (have 2 X) ● punnett square for different phenotypes: ○ when the heterozygote has its own phenotype ○ punnett square is drawn in the same fashion, determine phenotypes based on genotype ● incomplete dominance: heterozygous falls in between the phenotypes of both homozygous ○ AA is red, aa is white, Aa is pink ● codominance: phenotypes of heterozygous shows phenotype of both homozygotes ○ ABO blood type ● epistasis: interaction of alleles from different genes alter phenotype ○ a gene at one locus masks or suppresses the effects of a gene at another locus ○ mutations in different genes complement each other's function ○ mutations at same locus can’t complement ○ if multiple genes are necessary for the production of a compound that results in a phenotype, multiple enzymes needed, lack of enzymes could prevent final form and cause multiple phenotypes ● pedigree for mode of inheritance: ○ autosomal recessive: equal in males and females, skips generations, closely related parents ○ autosomal dominant: equal in males and females, all affected have at least one parent that was affected ○ x linked recessive: skips generations, males don’t give to sons, females often carriers ○ x linked dominant: every generation, males pass to all girls but not boys ○ y linked: only in males, every generation ● frequency of recombination: ○ take 2 smallest and combine ○ divide by the total number to get frequency of recombination ● mapping gene with distances ○ start with smallest and work up ● gene order, map distance, interferences (3 point cross) ○ parental: biggest number ○ gene order: compare parental to double crossovers (smallest) ■ whichever is different is in the middle ■ ++cn/bw+ ■ +++/bwcn ■ first 2 are the same, last is in different orientation (cn+/+cn) so cn is in middle ○ distance between: ■ rewrite in gene order and put slashes for crossovers ■ count up slashes in each area and divide by total ○ interference: 1 (observed DCO/ expected DCO) ■ expected: multiply two distances found prior together (decimals) ■ O/E = coefficient of coincidence ● phenotypes can “go missing” due to chromosome variations causing them to be unable to survive (deletion, insertion, inversion, duplication, translocation) ● Down Syndrome causes: ○ possible gametes for the 1421 translocation include: ■ normal VIABLE ■ balanced carrier (1421 translocation and 1 14 and 1 21) VIABLE ■ translocation trisomy 14 (translocation, 2 14 and one 21) ■ monosomy 14 (one 14 and 2 21) ■ monosomy 21 (one 21 and 2 14) ■ down syndrome (2 21, one translocation, 1 14) VIABLE ● interrupted mating mapping: ○ use data to piece together order of bacteria ● complementation: two different mutations in the heterozygous condition are exhibited as the wild type phenotype, indicates that the mutations are at different loci ● complementation test: ○ if it doesn’t grow/shows no complementation, then they are on the same gene ○ if it does grow/shows complementation, different gene ● 2 nucleotides per base pair ● 10 base pairs per turn of DNA ● one base pair is 3.4 A ● structure of DNA/RNA ○ 3’ OH connects to O coming off of PO4 group ● DNA to RNA bases ○ A goes to U instead of T ● around 200 bp make up a nucleosome and linker DNA ● replication fork: ○ replication occurs in 5’ to 3’ direction ○ gyrase: unwinds DNA, relieves tension ○ helicase: moves 5’3’, binds to lagging strand, breaks H bonds ○ singlestrand binding proteins: keep two strands separated ○ origin: where replication starts ○ RNA polymerase: lays down RNA primer ○ DNA polymerase III: adds complementary DNA bases ○ ligase: joins breaks in lagging strand ○ okazaki fragment: short newly synthesized DNA fragments on lagging strand ○ leading strand: continues easily in 5’ to 3’ direction ○ lagging strand: RNA primers added continually, working in reverse, RNA bases replaced with DNA bases by DNA polymerase I, joined together by ligase ● tree diagram of transcription: ○ initiation (5’) at end with smallest branch, termination (3’) after biggest branch ○ DNA is “trunk” RNA is “branches” ○ branch tip closest to DNA is 3’ and furthest is 5’ ● 5’3’ exonuclease activity: allows it go backwards and fix mistakes ● 3’5’ exonuclease activity: allows it to remove RNA primer ● eukaryotic protein coding gene ○ TATA box at 25 ○ poly A tail at end ○ introns start with GT and end with AG ○ corresponding RNA transcript will have ■ AUAU box at 25 ■ GU and AG at intron ● need 32 tRNAs to read genetic code because of wobble rules ○ wobble: base pairing between codon and anticodon in which there is nonstandard pairing, usually at the third position of the codon ○ allows more than one codon to pair with the same anticodon ● introns are cut out of RNA, hold no coding information ● E. Coli partial diploids ○ lacI (repressor) ■ I is dominant over all, always bound, no activity ■ I does not allow it to bind, always open ■ only need one to work properly ○ lacP (promoter) ■ P does not allow production, only impacts same gene ○ lacO (operator) ■ Oc is dominant, repressor cannot bind, always produces, only impacts gene its on ○ lacZ (beta galactosidase) ■ Z will not work ■ only need one to work properly ○ lacY (permease) ■ Y will not work ■ only need one work properly ● enhancer: sequence of DNA that stimulates maximum transcription of a nearby gene, only effective on the same DNA molecule, not fixed in relation to transcription start site ● response element: short sequences of DNA that can regulate transcription ● insulator: limits the interactions of enhancers with other genes as long as it is placed in between the enhancer and the promoter site by limiting spread of changes in chromatin structure ● DNAse I hypersensitivity: area of DNA that is very sensitive to DNAse I, cuts DNA ● alternative splicing: post transcriptional regulation, ability of RNA to splice at different sites to create different proteins from the same gene ● CpG island: areas with a lot of C and G bases, found near transcription start sites, methylation of C’s represses transcription ● substitution: changing one nucleotide for another ○ transversion: purine to pyrimidine or viceversa ■ AG/TC ○ transition: purine to purine or pyrimidine to pyrimidine ■ A/G or T/C ○ missense: changes amino acid ○ nonsense: changes to stop codon ○ silent: encodes for same amino acid ○ forward: wildtype to mutant ○ backward: mutant to wild type ● restriction site map: ○ piece together like a puzzle ○ ex: A is 200, B is 300, AB is 100 (must go B and then A with B 200 in front) ● find space between restriction sites ○ ex: 40% GC and 60% TA ○ find sequence and multiply each letter in sequence by percent and then do reciprocal ○ ex: GGATCC = (.2 x .2 .3 x .3 x .2 x .2) = .000144……...6944 bp ● read DNA sequence from gel from bottom up (5’ to 3’) ● hunchback is involved in the anterior structures ● positive regulation will increase, negative will decrease ● environment, epigenetics and genetic differences contribute to cancer rates around the world being different ● response to quantitative selection is RS h ○ R is response to selection: difference between mean trait in parents and mean trait in offspring ○ h is narrow sense heritability ○ S is selection differential: difference between mean trait in general population and mean trait in population selected for breeding ● can use mono and dizygotic twins to compare impact of genetics versus environment ○ mono: same egg ○ di: two eggs ● heritability is equal to m in mx+b ● calculate frequencies in a population ○ (homozygotes x 2) + heterozygotes / (total number of people x 2) ● UPGMA tree: ○ start with smallest in chart and draw branch, each stem is half the distance ○ then make cluster between what you already did use averages ● closest relative: ○ if it stems directly with another it is that ○ if it stems with a whole group, it is equally related to the entire group ● dosage compensation: ○ mechanism to ensure that proper expression occurs whether an individual has one or two copies of a chromosome ○ needed because the amount of gene expression is important and the Y (W) chromosome gradually loses genes during evolution, resulting in X (Z) genes being present in different amounts in males and females ● modified mendelian cross ○ recessive epistasis: ■ (9:3:4), 2 recessive alleles inhibit expression of an allele at another locus ○ dominant epistasis ■ (12:3:1) 1 dominant allele inhibits expression of an allele at another locus ○ duplicative recessive epistasis: ■ (9:7) 2 recessive alleles at either of 2 loci can suppress a phenotype ○ duplicative interaction ■ (9:6:1) 1 dominant allele at both loci gives a different phenotype than 1 dominant allele at either locus ○ duplicative dominant epistasis: ■ (15:1) 1 dominant allele at either locus can suppress a phenotype ○ dominant and recessive epistasis: ■ (13:3) 1 dominant allele of one gene gives the same phenotype as 2 copies of the recessive alle for another gene ● ABO Blood System: ○ three alleles, A B and O, at the H and I locus ○ can modify a previous carbohydrate compound by adding the A/B sugar or none at all ○ have two alleles, any combination ○ O has no antigens and anti A and B antibodies ○ A has A antigens and anti B antibodies ○ B has B antigens and anti A antibodies ○ AB has A and B antigens and no antibodies ● allopolyploidy: condition in which two sets of chromosomes of a polyploid individual possessing more than two haploid sets are derived from two or more species ● RISC: RNAinduced silencing complex, combination of small interfering RNA or microRNA and proteins that cleave mRNA and lead to degradation of mRNA, impact transcription and translation ● nucleosome: basic repeating unit of chromatin, core of eight histone proteins and around 147 bp of DNA that wraps 2 times ● sigma factor is the prokaryotic transcription factor ● GpppNpNp is the 5’ cap structure ● types of inversions: ○ crossing over in inversion loops causes nonviable gametes, results in reduced recombination rates ○ pericentric inversion: ■ includes the centromere ○ paracentric inversion: ■ does not include the centromere ● gene transfer in bacteria ○ conjugation: transferred from one bacteria to another via a conjugation bridge, happens in continuous direction, stop at different points to see position ○ transformation: picking up from the environment, observe rate at which two or more genes are co transformed, closer together more likely to be transferred together, frequency can be used to map genes ○ transduction: transfer through bacterial phage, rates of cotransduction tell relative distance between genes, recombination frequencies calculated as ratio of recombinant plaques to total plaques ● CoT curve: ○ line that takes up more space (wider) is the larger organism ○ size of humps represent repetitive frequency (more shallow is less repetitive) ● Meselson and Stahl and DNA replication ○ grown on N15 medium and transferred to N14 to replicate ○ centrifuged in a cesium chloride density gradient centrifuge ○ conservative: both replicated but not separated (HH and LL) , expect 2 bands (one heavy one light) ○ semiconservative: both strands separated and replicated (HL HL), expect 1 band ( in between) ■ after second round expect 2 bands (one light and one in between) ○ dispersive: random parts replicated, expect 1 band ( in between) ■ after second round expect 1 band (in between but closer to light) ● Seymour Benzer and rII locus of T4 ○ T4 phage produces small plaques with rough edges on both B and K E.Coli ○ mutant T4 grows larger with defined edges only on B E.Coli ○ collected 2400 rII mutants and coinfected E.Coli with two mutants ■ if mutation at separate bases, recombination can occur and restore wild type and allow to grow on K ○ used deletion mapping to minimize pairwise comparisons ■ large collection of deletion mutants of different sizes ■ if mutation was inside deletion, no recombination and wildtype wouldn’t restore ■ could narrow mutants down to smaller bins to carry out between two specific mutants ○ major conclusions: 450 sites in the gnee, able to map down to the nucleotide level ● DNA glycosylase: set of enzymes that recognizes and removes a specific type of modified base during base excision repair ● southern blot: process by which denatured, single stranded DNA fragments are transferred from agel to a solid support such as a nitrocellulose or nylon filter ● attenuation: type of gene regulation in some bacterial operon in which transcription is initiated but terminates prematurely before the transcription of the structural genes ● paramutation: epigenetic change in which one allele of a genotype alters the expression of another allele, the altered expression persists for several generations ● EtBr/ ethidium bromide is used for intercalation, inserts in grooves of DNA ● Knudson studied retinoblastoma ● erbB is an oncogene ● eukaryotic gene expression ○ chromatin remodeling: moving nucleosomes down to expose new DNA ○ transcription: GAL4, proteins binding to sequences in the promoter region can increase or decrease transcription (GAL80 binds to GAL4 with no galactose, with galactose GAL3 binds to GAL80 and release GAL4 and transcription starts) ○ mRNA processing and stability: removal of introns and unnecessary exons, degrade from 5’ cap or poly A tail ○ mRNA localization: transported by molecular motors on microtubules to parts of cytoplasm where they are translated into proteins ○ translation: increase of initiation factors increases the assembly of ribosomes and rate of translation (T cells) ○ post translational processing/localization: transported to golgi complex for packaging ○ phosphorylation: add phosphate to p53 to stop it from working, remove with kinase to allow it to work and control growth ● key elements of a plasmid cloning vector ○ origin of replication ○ selectable marker (amp) ○ lacZ gene with restriction sites inside ○ circular ● 4^n = how far apart an enzyme cuts (n= # base recognition) 9 ● human genome = 3 x 10 ● 2 = copies of DNA made in PCR (n = # of cycles) ● expected proportion of double recombinants = decimal distances multiplied ● Ames Test ○ evaluates potential of chemicals to cause cancer ○ mutagenesis in bacteria can serve as an indicator of carcinogenesis in humans ○ auxotrophic strains of Salmonella with his ○ add rat liver to improve potency of mutagen ○ test different concentrations of mutagen to see if they grow on a medium lacking histidine (will be converted to his+ if it grows) ○ HERP (human exposure rodent potency) tells what percent of rodent carcinogenic potency a person receives from a given average daily exposure over a lifetime, more quantitative than Ames test, computed in eukaryotic system ● using positional cloning to find mutation ○ linkage between phenotype and molecular marker in families with several members who have the disease, compare inheritance of disease with that molecular marker, give info about chromosome ○ chromosome walking/jumping. overlapping clones covering the region isolated from genomic library, starting with cloned gene marker closest to the gene of interest walk towards gene one clone at a time. genomic library consists of a set of overlapping DNA fragments, one end of clone of neighboring marker used to make complementary probe, continue process ○ after candidate genes identified, additional linkage patterns and expression patterns ○ causative mutations can be identified by sequencing a healthy and an affected person ● 7 types of cancer causing genes: ○ telomerase ■ In most somatic cells this is repressed, which limits the amount of replications each cell can undergo (its Hayflick limit). Telomerase is often upregulated in cancer cells and thus allows the cell to undergo multiple divisions while keeping its chromatin intact. ○ cell cycle regulators ■ mitosis promoting factor and cyclindependent kinase are involved. A RB protein will bind to E2F to keep in inactive, which thus increases concentrations of CDK. As these levels increase, eventually RB will be inactive and E2F will be released, allowing it to bind to DNA and stimulate the transcription of genes needed for DNA replication. ○ signal transduction pathways ■ this has to do with Ras protein. the growth factor binds to the receptor which causes a conformational change (adding of phosphate groups), which allows adaptor molecules to bind and link to Ras. activated Ras activated MEK and thus MAP kinase, which moves into the nucleus and activates transcription factors. When there is a mutation in Ras, it is always on. ○ DNA repair systems ■ DNA repair systems are supposed to check the DNA after it has been replicated in order to make sure that no mistakes were made, and to fix them if they were. If the systems do not work properly mutations will go unchanged and can cause cancers. ○ angiogenesis factors ■ angiogenesis is the ability to create new blood vessels. cancer cells need a lot more nutrients and oxygen in order to grow at the rate they do. overexpression of angiogenesis promoting factors allow cells to have these nutrients and grow. ○ metastasis ■ this is the ability of cells to move around the body. this occurs often through a palladin mutation which disrupts actin cytoskeletal network of mesenchymal cells which allows increased mobility around the body. ○ miRNA ■ this is a level of post transcriptional expression. low levels can contribute to cancer by allowing oncogenes that are usually controlled by miRNAs to be expressed at high levels (let7 miRNA controls Ras, lung cancer has low levels of let7 which allows for STP to be on) ● nondisjunction: meiosis messes up, both X and Y go into same gamete, one has none ● lethal genes: mice body color, Y is dominant for yellow color, recessive for lethality ● F plasmid transfers to bacterial cell without it ● high frequency recombination: F factor combines with other genes, leads to high frequency of recombination ● F’ is when a F plasmid recombines back out and takes a small piece of bacterial chromosome, next will have 2 copies ● Griffith: chemical substance from one cell is capable of genetically transforming another cell ● Avery, Macleod, McCarty: found that DNA is hereditary material New Information: ● Vp = Vg + Ve ○ Vp = total phenotypic variance ○ Vg = genetic variance ○ Ve = environmental variance ● IQ narrow sense heritability around 34% ● 4 forces of change ○ random genetic drift ■ sample error of populations ■ includes bottleneck ■ big influence ○ mutation ■ very small influence ○ migration ■ continentisland model ○ selection ■ balancing selection: heterozygotes most fit and homozygous lost ● selective deaths to substitute one allele for another ○ D = 2pq (s) + q^2 (2s) ■ s is selection coefficient ○ D = 2log (base e) p is total number of deaths to achieve fixation ● observed rate of evolution is only slightly lower than the observed rate of mutation (molecular clock) ● easy to use mitochondrial DNA for studying evolutionary history
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'