GEN 3000: FINAL EXAM STUDY GUIDE
GEN 3000: FINAL EXAM STUDY GUIDE GEN 3000
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This 8 page Study Guide was uploaded by Jomary Arias on Wednesday April 27, 2016. The Study Guide belongs to GEN 3000 at Clemson University taught by Dr. Kate Tsai in Spring 2016. Since its upload, it has received 107 views. For similar materials see Genetics in Biomedical Sciences at Clemson University.
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Date Created: 04/27/16
GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai CHAPTER 17 [Key Terms]: Recombinant DNA technology- set of molecular techniques for locating, isolating, and altering and studying DNA segments. Recombinant DNA molecules- created by splicing different types of DNA Restriction Enzymes- first identified in 1971, recognize specific nucleotide sequence, restriction sites and makes double strand cut. Restriction site- about 4 to 8 bp long, Type II cut within recognition site which is usually palindromic reading 5’ to 3’ Cloning Vector- stable, replicating DNA molecules which can be attached to a piece of foreign DNA and introduced into a cell Plasmids- replicate independently of the bacterial chromosome, can be constructed Libraries- several clones may contain all or parts of your gene of interest Probe- DNA or RNA complementary to sequence from a gene or interest labeled Reverse- Transcription PCR- begin with RNA template Real time PCR- measure gene expression levels Northern Blot- RNA start source Western Blot- Protein start source, antibody probe DNA Libraries Genomic Libraries cDNA Library Collection of clones Many overlapping fragments Contains DNA sequences only containing ALL the DNA of the genome, w/ at least from genes that are fragments from one source one copy of every DNA transcribed sequence in an organism’s genome [Polymerase Chain Reaction PCR] 4 Requirements: 1) Template- of any nucleotide source 2) Primers- identifies target and provides a starting point 3) For new strand synthesis 4) Polymerase to synthesize DNA 3 Stages: This process is known as exponential amplification GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai 1) Denature- separates double stranded DNA template by heating it from 92 to 95ºC 2) Annealing- primer binding by cooling the double stranded DNA from 45 to 65ºC 3) Extension- DNA polymerase synthesizes new DNA strands by heating it from 65 to 75ºC [Limitations] Include: - Primer synthesis because you need to know something about the sequence - Contaminating DNA - Accuracy - Amplification size [Diagnostic Tools] Include: - Genetic Testing - Identification - Parentage [Sanger Sequence] - Uses dideoxyribonucleoside triphosphate which causes elongation to stop. This helps to identify bases and order by removing the 3’ OH group. - Use a template - Then a primer to allow annealing - DNA polymerase allows elongation CHAPTER 18 [Key Terms] Genomics- field of genetics that attempts to understand the content organization, function, and evolution of genetic information contained in whole genomes. Structural Genomics- studies the organization and sequence of genetic information contained with a genome. Genetic Maps- based on recombination frequencies Physical Maps- based on the direct DNA sequence GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai 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. Contig- overlapping fragments from a continuous DNA molecule Comparative Genomics- compares similarities and differences in a gene content, function, and organization among genomes of different organisms Gene Deserts- large area w/ no known genes Protein Diversity- modifications greatly increase number of proteins Functional Genomics- determining what the sequences do Transcriptome- all the RNA molecules transcribed from a genome Proteome- all the proteins encoded by the genome Microarrays- monitor gene expression in different tissues or under different conditions, similar to Northern. Proteomics- study of the proteome, complete set of proteins found in a given cell Mass Spectrometry- method for precisely determining the molecular mass of a molecule using a mass-to-charge ratio Systems Biology- influences bioinformatics by making connections b/w gene expressions in different locations Map- Based Approach Shot Gun Approach -Create a detailed genetics and physical maps -Maps are NOT needed of the genome -Separate chromosome out and sequence the -Provide known locations of genetic markers fragments then put it all back together at regularly spaced intervals along each -Not helpful for repetitive regions chromosome. -Genomic DNA is cut into multiple overlapping -Allows them to order the clones along each fragments by restriction enzymes chromosome -Creates a series on contiguous fragments -Used to sequence the whole human genome known as “contigs” -Used for repetitive regions -Overlapping sequenced fragments are aligned based on the identical DNA sequence Prokaryotes Eukaryotes -Amount of DNA ranges b/w 490 kb- 9,105 kb -Genomes larger than prokaryotes -Number of genes- Avg 1 gene per 1000 bp -No relation between genome size and - 50% have assigned functions complexity Ex) E.coli- 4.6 Mb -No correlation b/w genome size and # of genes -Number & length of introns increases in more complex eukaryotes GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai [Microarrays] Similar to Northern but stronger Easy way to gain information for thousands of genes at one time point Insert a probe in a specific location for each gene DNA attached to the probe glows Compares which genes are expressed in at one point that may not be expressed in a different location Protein- microarrays can be used to analyze protein-protein interactions CHAPTER 19 [Key Terms] Biotechnology- use of living organisms to create a product of a process that helps improve the quality of like for humans and other organisms Genetic Engineering- altering an organisms genome (GMO’s) Biopharming- production of therapeutic proteins in GMOs Subunit Vaccine- utilizes a single or few proteins from a bacterium or virus to stimulate immune response ex) HPV vaccine Edible vaccine- utilized in food sources Transgenic- genome has been permanently changed by the addition of DNA Transgene- foreign DNA in a transgenic organism Microinjection- inject many copies of a transgene into pronucleus 10-30% of eggs survive, only a proton of those will contain integrated transgene Single nucleotide polymorphism (SNP)- a single base change Variable number of tandem repeats (VNTR)- differences in copy number Modified Genes Expression Microarrays- allow for DIRECT comparison of 2 samples Genome Wide Association Studies (GWAS)- utilize molecular markers that are spread throughout the genome [Biopharmaceuticals] - Insulin was the first gene product manufactured by recombinant DNA technology - Formerly known as Humulin approved by the FDA in 1982 - Prior to Humulin, insulin was obtained from pigs but it caused many health issues GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai Knock- Out Knock- In Cause a gene to be COMPLETELY disabled Sequence is inserted at a specific location Ex) Can replace mouse allele w/ human allele [RFLP] Restriction Fragment Length Polymorphism (RFLP)- changes in DNA sequence that modify restriction enzyme recognition sites Base changes b/w individuals will introduce or remove restriction enzyme sites Results in unique patterns in individuals Can trace within families [Modified Gene Expression Microarrays] Can detect host response to certain pathogens Allows faster diagnosis/ identification of pathogens Could provide target for treatment [SCID] X-linked Adenosine Deaminase Deficiency: Bone marrow stem cells, and leukemia No functional T and B lymphocytes Began by replacing missing enzymes Then genetically altering matures WBC Now targeted DNA in umbilical cord stem cells infused into newborns, 20 children affected have successfully undergone gene therapy CHAPTER 21 [Key Terms] Discontinuous Character(Qualitative)- possess only a few distinct phenotypes and can be measured in an individual Meristic Characters- NOT continuous but are determined by multiple genes/environment Threshold Characteristic- either present or absent Bell- Shape Normal Distribution- large number of factors contribute to a measurement Sample- must be taken at random and be large enough that chance do not influence Mean- average, center of distribution Positive #- genes that cause an INCREASE in 1 trait cause an INCREASE in the other trait GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai Negative #- genes that cause an INCREASE in one trait cause a DECREASE in the other trait Variance- indicates variability of group, GREATER variance, the more spread out the distribution is about the mean Standard Deviation- also measures spread, but defines it within “standard” variables Heritability- proportion of the total phenotypic variation that is due to genetic differences within a population (NOT fixed) Genetic Variance- different phenotypes in a population due to different genotypes Environmental Variance- due to environmental differences Genetic-Environmental Interaction Variance- effect of gene depends on environment Total phenotypic variance= V + V + P + VG E GE Phenotypic Correlation Genotypic Correlation Could be caused by genetic or environmental Often result of pleiotropy which is basically correlations one gene that affects multiple characteristics [Quantitative Characteristics] 1. Polygenic- result from the action of many genes, but a single phenotype 2. Environment- can impact phenotype through multifactorial complex and polygenic issues [Intensity of Wheat Kernels Red Pigmentation] Good Model Includes: 1. Genes affecting color segregate at 2 loci 2. Gene effect is additive 3. Environment plays NO ROLE! 4. Unlinked loci on different chromosomes [Calculating Number of Polygenes] n= # of loci that affect character n Usually 1/4 Ex) If 1/16 of F2, then n= 2 2n +1 = # of distinct phenotypic categories observed Ex) If 2 polygenes involved, n=2 Plant example below: GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai # Alleles 0 1 2 3 4 5 6 Height(in) 10 11 12 13 14 15 16 As the # of loci affecting a character INCREASES, the # of phenotypic classes also INCREASES CHAPTER 22 [Key Terms] Species- group of individuals able to reproduce Population- a group of individuals belonging to the same species that live an defined geographic area and actually or potentially interbreed Gene Pool- genetic information carried by member of a population, most have high degree of heterozygosity Goodness-of-fit chi square- # of alleles for the degrees of freedom Positive Assortative Mating- LIKE individuals mate ex) Tall mate with Tall Negative Assortative Mating- UNLIKE individuals mate Inbreeding- nonrandom mating, preferential mating b/w related individuals ( 0= random mating, 1= all alleles are identical by descent) Fitness (w)- relative reproductive success of a genotype, value ranges from 0 to 1 Reproductive Isolating Mechanisms- biological factor that prevents gene exchange Phylogenetic Tree- graphical representation of evolutionary relationships Molecular Clock- time of divergence from a common ancestor estimated based on changes in amino acid or nucleotide sequence [Hardy Weinberg Law] A mathematical model that evaluates the effect of reproduction on genotypic and allelic frequencies in a population Population must be large, contain random mating, and not affected by mutation/migration/natural selection Frequency of the alleles in the gene pool does NOT change over time and contributes equally to the next generation After one generation of random mating the genotypic frequencies for 2 alleles can be calculated using the following equation: 2 2 P + 2pq + q = 1 ( p = frequency of allele A) (q = frequency of allele a) GEN 3000: FINAL EXAM STUDY GUIDE CHAPTERS 17-22 Dr. Kate Tsai -p + q = 1 We are considering a SINGLE LOCUS! Purpose is to consider the impact of reproduction on the gene pool in order to look at migration and natural selection Genotypic frequency is determined by allelic frequency [What causes changes in allelic frequencies?] 1. Mutations- all genetic variants arise through mutation alleles which mutate via forward and reverse mutation 2. Migration- influx of genes from other populations - Prevents genetic divergence b/w populations - INCREASES genetic variation w/in populations - As migration ↑, the change in allelic frequency ↑ w/in a given population - Magnitude of change is affected by the differences in allelic frequencies of two populations [Genetic Drift] Deviation from expected allelic frequency due to sampling errors Population suffers severe size reduction known as “BOTTLE NECK” Founder Effect- when a small # of individuals start a population gene pool is limited A population may be reduced in size for a period of time b/c of limited resources [Reproductive Isolating Mechanisms] PRE-zygotic POST-zygotic Prevents zygote formation Zygote is formed but no gene flow occurs [How can speciation occur between different populations?] 1. Allopatric Speciation- occurs when there is a physical separation of the populations 2. Sympatric Speciation- NO external barrier; RIMS evolve within a single population Synonymous Substitutions NON-Synonymous Substitutions Nucleotide change that DO NOT alter amino Nucleotide change that DO alter amino acid acid sequence sequence
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