Genetics 3000: Final Exam Study Guide
Genetics 3000: Final Exam Study Guide 85033 - GEN 3000 - 002
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85033 - GEN 3000 - 002
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This 12 page Study Guide was uploaded by Lisa Blackburn on Monday April 25, 2016. The Study Guide belongs to 85033 - GEN 3000 - 002 at Clemson University taught by Kate Leanne Willingha Tsai in Fall 2015. Since its upload, it has received 109 views. For similar materials see Fundamental Genetics in Biomedical Sciences at Clemson University.
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Date Created: 04/25/16
Final Exam Study Guide: Chapters 17-19 and 21-22 Chapter 17: Recombinant Technology 1. Restriction Enzymes: recognizes specific nucleotide sequences, restriction sites, and makes a double stranded cut a. Restriction site: usually about 5-8 bases pair long b. We can use these enzymes to cut the DNA that we want to cut since it will recognizes bases and then cuts within the bases. They are powerful because RE doesn’t care what DNA it is cutting. c. They are palindromic, meaning that they are the same forward and back, the strands are complementary to each other i. Example: AGTGA ii. This strand reads the same forward and backward. Think of how the word racecar reads racecar backwards. d. When the restriction enzyme makes a cut, it is in a defined spot and will cut there every time i. Cohesive ends: this is a sticky/adhesive overhang cut ii. Blunt end: cuts straight down and is not sticky/adhesive e. Will not distinguish between type of DNA, if sees its recognition site, it will cut there i. Can cut DNA from two different organisms, and due to sticky ends, these DNA segments can stick together 2. Gene Cloning: amplification of a specific piece of DNA a. Cloning vector: stable, replicating DNA molecule which can be attached to foreign DNA and be then introduced into a cell i. The vector needs to be stable within a cell or the cell will degrade it ii. Vector properties: 1. Origin of replication: needs to be able to replicate itself inside the cell 2. Selectable Markers: to be able to see if the vector is inside the cell or not 3. Unique Reactive enzyme sites: so the vector will not get diced up by the cells own restrictive enzymes iii. Plasmids are often used as vectors. 1. Is put into the cell through transformation: DNA in the environment is taken up by the cell 3. DNA Libraries: collection of clones containing all of the DNA fragments from one source (this is what we create) a. Genomic library: consists of many overlapping fragments of the genome, with at least one copy of every DNA sequence in an organism’s genome b. cDNA library: contains DNA sequences only from genes that are transcribed c. Several clones may contain all or parts of your gene in interest, so how do you find the right clone? i. Screen the library to isolate only the clones that contain your gene of interest d. Probe: DNA or RNA complementary to sequence from a gene of interest, it is labeled 4. Polymerase Chain Reaction (PCR) a. What is needed: template, primer, nucleotides, polymerase i. Template: any nucleotide source ii. Primers: identifies target and provides a starting point iii. Nucleotides: for new strand synthesis iv. Polymerase: to synthesize DNA b. Stages/steps: denaturation, annealing, extension i. Denaturation: separate double stranded DNA template. Heat to 92-95° C ii. Annealing: primer binding. Cool to 45-75° C iii. Extension: DNA polymerase synthesize new DNA strands. Heat to 65- 75° C c. Gel Electrophoresis: DNA is placed in wells. Current is applied and the smaller pieces move faster through the gel than the larger ones. The farther down the piece, the smaller it is. 5. Southern Blot: the process of transferring DNA fragments from gel to membrane a. Northern Blot: RNA b. Western Blot: protein 6. In Situ Hybridization: probes are used to determine chromosomal location a. Visualized in the cell (in situ) b. Fluorescence ISH (FISH) c. Can be used to probe tissues for a particular mRNA d. Which cells are they being expressed in and what stage of development? 7. Sanger Sequencing: uses dideoxyribonucleoside triphosphate which causes elongation to stop a. Most popular b. Have to have a 3’OH group in order to connect and be useful c. Di-deoxy (missing both oxygens), if no 3’OH group it says it is done d. Keeps from extending to another piece of DNA Chapter 18: Genomics 1. Genomics: field of genetics that attempts to understand the content, organization, function, and evolution of genetic information contained in whole genomes a. Structural genomics: studies the organization and sequence of genetic info contained within a genome b. Genetic maps: based on recombination frequencies c. Physical maps: based on direct DNA sequence i. Map based sequencing ii. Whole genome shotgun sequencing d. Bioinformatics: emerging field consisting of molecular biology and computer science that centers on developing databases, computer-search algorithms, gene- prediction software, and other analytical tools i. at the point where data is created but is used without the use of computer programs ii. all from info from bioinformatics: sequencing the entire genome 2. Microarrays: monitors gene expression in different tissues or under different conditions a. Nucleic acid hybridization b. Microarray is looking into the transcriptome. The probes (dots) carry different amounts of expression. You can detect gene expression whether it is there or not for MANY genes with just one sample 3. Comparative Genetics: compares similarities and differences in gene content, function, and organization among genomes of different organisms a. Prokaryotes: amount of DNA ranges from 490 kb to 9,105 kb i. E. coli: approx.. 4.8 million base pairs ii. This makes the comparison between how big the genome is and how it relates to the base pairs iii. One gene is about 1,000 base pairs b. Eukaryotes: genome is larger than the prokaryotes i. No relation between genome size and complexity ii. No correlation between genome size and number of genes iii. Has move/larger genomes than most prokaryotes but there is no relationship to the genes c. Gene deserts: large area with no known genes d. Transposable elements: ~45% of DNA in human genome e. Protein diversity: modifications greatly increase number of proteins f. Number and length of introns increases in more complex eukaryotes g. Reference genome: several different pieces of genomes combined i. all humans are 99.9% the same ii. our genomes are the same, the difference is in the molecular markers of each individual 4. Functional Genomics: determining what the sequences do a. Transcriptome: all the RNA molecules transcribed from a genome i. All the transcripts, what is being expressed, just like the library, its unique to each tissue and each time point, very dynamic because it is being expressed b. Proteome: all the proteins encoded by the genome i. What has been translated into a protein, very dynamic, changes from one tissue to the next c. The biggest piece of the genome is unknown Chapter 19: Biotechnology 1. Biotechnology: use of living organisms to create a product or a process that improves the quality of life for humans and other organisms a. Genetic engineering: altering an organism’s genome i. Genetically modified organism (GMOs): an organism with a modified genome. b. Biopharmaceuticals: i. Insulin: first human gene product manufactured by recombinant DNA technology 1. Humulin: approved by FDA, genetically engineered bacteria a. Makes changes to make the exact insulin humans would make ii. Biopharming: production of therapeutic proteins in GMOs c. Subunit Vaccine: utilizes a single or few protein(s) from a bacterium or virus to stimulate an immune response i. Edible vaccine: use a food source for us, get the food source to express protein and then eating this food allows us to be safe from virus for different things d. Agricultural Biotechnology: modifying plants i. Selective breeding: humans use breeding to selectively develop particular phenotypic traits by choosing which mates with which to produce offspring 1. Artificial Selection: breeding of organisms to produce a certain desirable trait 2. Designed crosses 2. Transgenic Animals: made to study a gene, to figure out what impact a change of a gene has, what phenotype is this gene causing? a. not used as an agricultural benefit for the most part, animals are not looked at in the way plants are i. Transgenic plant: make this more agriculturally beneficial to us b. The genome is modified in the animals, we want it in the germ line c. Transgenic: genome has been permanently changed by the addition of DNA d. Transgene: foreign DNA in a transgenic organism e. Microinjection: injects many copies of a transgene into a pronucleus i. In the beginning, we used microinjection to create transgenic animals ii. Inefficient, super small percent will be germ line, meaning it is a small percentage that will be passed on in generations iii. Has been successfully used iv. Proved that SRY is the male determining factor through this method v. Knock out: target a specific gene. Removing/disabling the original gene 1. Tring to see what the gene is in charge of***** vi. Knock in: exchange a specific gene for a transgene 1. Usually looking at specific gene, like replacing a mouse allele with a human allele vii. A lot of reproductive biology goes into making a transgenic animal 3. Molecular Markers: they are spread throughout the genome and are used as little road signs/markers a. Restriction fragment length polymorphism (RFLP): changes in DNA sequence that modify restriction enzyme recognition sites i. Base changes between individuals will introduce/remove RE sites ii. Results in a unique pattern in individuals iii. Can trace within a single family iv. If base changes and this causes a disease, then we can set up a quick PCR that amplifies this region of DNA. With each sample we will cut it, if cuts three times then the individual does not have the disease, if it only cuts once then we know that the individual has the disease b. Variable number of tandem repeats (VNTR): difference in copy number c. Single nucleotide polymorphism (SNP): a single base change d. Modified gene expression microarrays: allow for direct comparison of two samples i. Expression arrays: label normal RNA one color and the tumor another color 1. Put both on cell and see what color is present, the present color is the cell that only makes that RNA 2. Green: normal RNA is made 3. Red: tumor RNA is made 4. Yellow: equal expression of both RNA 5. Can be used to determine what genes are being expressed, types of tumor ii. Expression arrays can also detect host response to certain pathogens 1. Allows for faster diagnosis/identification of pathogen 2. Could provide a target for treatment 3. Can also be used for taking time points 4. A mouse is exposed to a pathogen: a unique array will show the response of the genes expressed a. Show what gene products are used to help fight off the pathogen, are we able to give this gene product to a patient for faster natural response? 4. Genome wide associate studies (GWAS): studies that look at the genome wide associate, used molecular markers that are spread throughout the genome, we know where these are located, we know that at this location, majority of people will have a certain base pair a. Goal: to find region of genome that seems to be inherited in the same way as your phenotype in question i. one group will have everyone with a disease ii. one group does not have the disease (control) iii. do we see one region of the genome in all diseased people that is not in the control? Or vice versa? iv. Determine genotypes for a large number of individuals, in general b. Does not require the use of a genomic library 5. Gene Therapy: if there is a gene that can be treated, but requires treatment over and over and over again, can we cure the disease and not just treat them? A technique that aims to transfer normal genes into the patient’s cells, to cure the disease a. Will only be somatic, not going to create a transgenic human, meaning that it will be in the germ line b. Limited only to the somatic line because… i. If you treat a patient with somatic genet therapy it will only affect the patient, if it is in the germ line, it will affect future generations ii. Fine line: what needs to be treated between what only one person things should be treated 1. One generation may want the treatment and a later generation may not (if in germ line this would be an issue) 2. This is starting to change in the future most likely, already pushing towards changing this Chapter 21: Quantitative Genetics 1. Quantitative genetics: genetic analysis of complex characters using math a. Discontinuous characters (qualitative): only a few distinct phenotypes, can be measure in an individual (either/or) i. Either you are tall or you are short (10 cm high or 3 cm short) b. Quantitative characters: continuous variations, many genes (polygenic) are involved and environment can influence these genes i. Can be 10 cm high 9 cm high 8 cm high 9.9 cm high and so forth, there is a wide range that an individual can fall anywhere in) c. Discontinuous characters: each genotype produces one phenotype d. Quantitative genetics: is more complex i. Polygenic characters can yield phenotypes that are similar even if genotypes are different ii. can vary continuously in a population, such as human height iii. Example: plant height 1. Will reach 10 cm, which is standard 2. Additional height is determined by extra alleles, every allele added is 1 cm added to height 3. additive allele: add something a. when look at phenotypes of different heights, the plant is 12 cm tall, but there are different genes where the 2 additional alleles are added b. (+) is added (-) is nonadditive meaning it is not helping to add height 2. Additive allele: Calculating the number of genes contributing to a quantitative trait, number of polygenes a. How many genes do we think are involved in this particular characteristic? b. 1/4 where n=number of loci that affect character i. Use the most extreme phenotypes for these equations ii. If 1/16 is for the extreme phenotype then there n=2 c. Alternatively for low number of polygenes: 2n+1=number of phenotypic categories observed i. If 2 polygenes are involved, n=2. Then 2n+1=5 and each phenotype is the result of 4, 3, 2, 1, or 0 additive alleles 3. Frequency distributions: a. Qualitative (discontinuous) characteristic: falls distinctly in one category b. Quantitative (continuous) characteristic: can fall anywhere in a range c. Sometimes a population is too large to measure so a sample is uses i. Samples must be taken at random and must be large enough so chance differences do not interfere ii. Mean: is the average, or center of distribution 1. Where the majority should fall iii. Variance: how spread out from the mean the population is 1. Greater the variance: the farther spread out from the mean iv. Standard deviation: if you go 1 standard deviation out you get about 68% of the population 1. This means that we can start to convert to probabilities 2. Randomly pulled out, you will fall in 95% of the time in X range 4. Correlations a. Phenotypic correlation: could be caused by genetic or environmental correlations i. Genes are not causing correlation b. Genetic correlation: result of pleiotropy, one gene that affects multiple characteristics i. Positive: as one increases, the other increases. As one decreases, the other decreases. Moves in the same direction ii. Negative: as one increases the other decreases. As on decreases, the other increases. Moves in opposite directions 5. Environment can also affect phenotype a. Heritability: looks at the portion of actual phenotypic variation. How much is based on genotypes of population and how much is based on the impact of the environment? i. Can only be used in specific population at a specific time. It changes all the time ii. High number: genetic factors are causing the range iii. Low number: more environmental factors are causing the range iv. Not fixed for a trait, is always changing 1. Can get different heritability for the same traits of different populations v. Specific to a single populations at a specific point of time. vi. High heritability does not mean that the environment is not playing a role, it just means that all individuals have a similar environment 1. If the population moved to a different environment, then the heritability may change and the environment may impact it more than genetics 6. Phenotypic Variance: differences between members of a group a. Phenotypic variance (V ) iP the quantitative measure of phenotype b. Genetic variance (V ) Gs different phenotypes in a population due to different genotypes i. V Gas sub components ii. Additive genetic variance (V )Ais the additive effect genes have on phenotype iii. Dominance genetic variance (V ) iD not additive, some genes can have a dominant influence iv. Genetic interaction variance (V ) Ienes at different loci may interact like alleles at the same locus, also not additive v. V GV +VA+V D i c. Environmental variance (V ) isEdue to environmental differences d. Genetic-environmental variance (V ) isGEhe effect gene depends on environment i. Example: Plant A (AA) is 5 cm tall, plant B (aa) is 3 cm tall. When moved to a more wet environment, plant B becomes 10 cm tall while plant A becomes 8 cm tall ii. The environment impacted both plants by allowing them to grow taller in the wet area, but they grew at a different rate, this means that the genes and the environment played a roll iii. If the environment was only the factor, then both plants would grow at the same rate e. Total phenotypic variance=V =V +P +VG E GE or = V AV +D+ Vi+V E GE f. do not need to know how to calculate, but need to know the parts 7. Test for heritability a. Types of heritability: i. Broad sense: how much phenotypic variation is controlled genetically? 1. Looking at all genetic components. Includes all subparts 2. Will get a number 0-1 3. Closer to 0: less genetic variation, environment plays a role a. Does not mean genes do not impact the phenotype, saying that there is no genetic variation between the tested individuals at that point of time, the environment just has a major impact 4. Closer to 1: more genetic variation, genes play a role a. does not mean environment does not play a role, just means that the environment for the individuals is constant, if put in a different environment, they may have a different heritability 5. all genetic impact is included ii. HERITABILITY IS ALWAYS CHANGING iii. Narrow sense: focuses on the additive component, how much is determining phenotypic variation? 1. will get a number 0-1 2. closer to 1: the offspring will look more like their parents 3. closer to 0: not always resembling parents 8. Selection: a. Natural selection: exists currently, helps to determine who gets to contribute to the next generation b. Keys: i. More individuals are produced than the amount that will reproduce ii. Lots of phenotypic variation iii. Some phenotypic variation is heritable, due to genetic variance 1. Variations give adaption to environment c. Artificial selection: is used all the time to determine how much heritability there is for a trait of interest. i. Will be limited at some point, competition between natural selection and artificial selection 1. Organisms are becoming more and more genetically similar, the individuals are very similar causing the heritability to go down due to the little variation. 2. Natural selection can kick in to stop artificial selection from getting all the way to additive or all the way down to no additive a. Example: at some point a plant may have too many additive alleles, causing it to be too tall. The plant cannot support itself and will fall over and die. Therefore, unable to reproduce Chapter 22: Population Genetics 1. Species: group of individuals that are able to reproduce a. Population: a group of individuals that belong to the same species that live in a defined geographic area and interbreed b. Gene pool: the genetic info carried by members of a population c. Heterozygosity: most populations have a high degree 2. Hardy-Weinberg Law: a. Forms the basis of what is done for population genetics b. Allows us to look at different loci and see how it is changing in time, what reproduction will do on the gene pool c. Makes BIG assumptions i. Population is infinite ii. Random mating iii. Not affected by mutation/migration/natural selection d. Predictions that can be made: i. Which allelic frequencies of a population that will not change ii. Genotypic frequencies that will not change after one generation e. Most populations, these assumptions will not be true for the most part f. This gives us a place to start, too many things to consider without this as a starting point g. Plug in variables for our alleles i. Frequency of A allele = p ii. Frequency of a allele = q iii. p+q=1 (100% of population) iv. for genot2pic equa2ions… 1. p +2pq+q =1 2. p= A 3. q=a 4. pq=Aa 5. use punnett squares to find the frequencies 6. can address multiple alleles with this equation, we only will do two h. when looking at Hardy-Weinberg, we are considering one locus at a time i. we can look at populations, even if nonrandom mating, because there is some gene that is doing what we expect it to do ii. the entire population may not hold assumptions, but the locus in question could still work with the assumptions iii. can use this as a starting point, even if assumptions are wrong i. how we use this in a real population i. figure out the freq. for AA, Aa, and aa ii. what freq. are we seeing for p and q? iii. those with AA are counted twice for q (A) and those with Aa are counted once for q (A) 1. example: a. AA=135 b. Aa=44 c. aa=11 d. total = 190 e. p=(2*135+44)/2*190=.826 f. q=1-p=.174 2 2 iv. determine what we would expect in next generation by doing p +2pq+q v. instead of looking at the next generation, we can multiple the freq. by the total population then use a chi-square to determine based on the freq. if the population is in Hardy-Weinberg 1. example: a. AA=p =(.826) =.636 * 190 = 129.8 individuals b. Aa=2p2=2(.826)2.174)=.287 * 190=54.4 individuals c. aa=q =(.174) =.03 * 5.7 individuals 2. will not be tested on chi-square, just know it is used with Hardy- Weinberg j. if Hard-Weinberg is met, then the genome and allele freq. will not change over time, meaning evolution will not happen i. evolution needs genome and allele freq. to change ii. any change in genome or allele freq. can influence the other 3. Nonrandom mating a. Positive assortative mating (Pam): like individuals will mate i. If tall humans are AA or Aa and small humans are aa and only tall humans mate, it will take out the tendency for small humans, but there is still a small percentage (if Aa mates with Aa there is chance for aa) b. Negative assortative mating: is more random mating, move away from same genome c. Inbreeding: extreme form of positive assortative mating i. Everyone is genetically the same ii. Will not need to calculate inbreeding coefficient, but know that.. 1. 1: all alleles are identical by descent 2. 0: mating is random 4. Mutations: all genetic variants arise through mutations a. There is a large amount of generations before we see the mutation shift allele freq. b. Mutations have little impact on allelic freq. but it is necessary for mutations to occur 5. Migration: influx of genes from other populations, gene flow a. Within populations, migration can impact the population change i. How much migration takes place? ii. If one person leaves one populations for another, then there will not be much on an impact on the second population iii. If 100 people leave one population from another, then there will be an impact iv. Also depends on size of population v. If they are similar, migration does not have a great impact vi. If the populations differ a lot, migration will have a big impact vii. As migration increases, the change in allelic freq. increases b. Through time, migration causes freq. of two populations to become similar i. Gene pools of populations become similar c. Adds genetic variation to population 6. Genetic Drift: deviation from expected allelic freq. due to chance a. Is completely random b. The larger the population, the closer you will get to the actual freq. c. Flip a coin 5 times vs flipping a coin 1000 times i. Will get more to a 50% for 1000 times d. Effective populations size: this population looks like it is very big (the population) i. But with humans, there is an age that you are no longer or not able to reproduce ii. Only a subset of population that can contribute with reproduction at a certain time iii. Also, if the ratio of the males vs. females differs 1. If 20 males and 20 females all will reproduce 2. If 75 males and 25 females, only 25 males and all females will reproduce e. Allelic freq. can be drastically different before and after a bottleneck effect i. Bottlenecks occur when a significant percentage of the population is removed or prevented from breeding ii. Who made it through? iii. Humans: wars, famines, etc. f. Founder effect: individuals leave one population to start a new one i. Small number that starts new populations: the gene pool is limited ii. Those who start the new population will determine the freq. not going to be the same as the original population they came from 1. Small number that starts new populations: huge genetic drift g. Genetic drift causes… i. Changes of allelic freq. in population, increase or decrease ii. Reduces genetic variation in a population 1. Can be 0 where an allele is lost 2. Can be 1 where an allele is fixed h. Different populations diverge differently 7. Natural selection at work a. Individuals with adaptive traits produce more offspring i. Variations gives ability to adapt ii. Natural selection can have a big impact b. Fitness (W): relative reproductive success of a genotype i. How well is the population fit to survive ii. If fitness is 1, not 100% of offspring with this genotype will survive to reproduce 1. When compared to other genotypes, it is more fit 2. There is selection when there is one more fit then the other c. Selection coefficient (s): relative selection against a genotype, s=1-W i. When looking a fitness and selection, it is specific to a population at one point and time 1. Most fit in this environment 2. Same phenotypes can be beneficial in one environment and detrimental in another d. Directional selection: benefiting one allele or another i. W =11>W m12ns 22at AA and Aa result the same phenotype ii. W >11>W m12ns 22at AA and Aa result in different phenotypes e. Stabilizing selection: heterozygous is favored over the homozygous i. Will keep both alleles and if environment changes, this variation is still there ii. Better and stable f. Disruptive selection: homozygous is favored over the heterozygous i. Is disruptive, because the variation is gone. If the environment changes, then there will be a drastic shift ii. Unstable 8. Biological Evolution: now that we see different forces that are changing populations, brings up how are populations changing through time a. Genetic change taking place in a group of two organisms b. Changes in the gene pool, genetic changes in groups c. Biological species concept: members of the same species have the potential to exchange genes; different species cannot d. Reproductive isolating mechanisms: biological factor that prevents gene exchange i. Prezygotic: prevents formation of a zygote ii. Postzygotic: zygote is formed, but something prevents the gene flow e. Alllopatric speciation: occurs when there is a physical separation of populations i. Mutation occurs and the populations interbreed resulting in a complete different population ii. When brought back, they cannot breed together f. Sympatric speciation: no external barrier; certain ones breed with like ones, after a certain point, they can no longer breed together i. Green breeds with green and blue breeds with blue ii. After a point, green can no longer breed with blue
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