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Answer all questions  Genetic.docx BIOL-2416 Baggett - Unit 04 – Study Tips Study Suggestions for Exam #4 over Chapters 14-16 & 18 General Exam Format and Information What to bring: knowledge and understanding, your signed 4x6 notecard, at least 2 sharpened pencils and a calculator if you have one (can borrow from me if needed during exam, but no phones allowed) The exam will be administered from 6:00 p.m. to 8:00 p.m. No need to return after the exam this time. Question breakdown (test total is 100 points) · 40 regular multiple-choice questions (2 pts each x 40 = 80 pts) · 4 chapters is ~8-12 questions per chapter for Ch. 14, 15, 16 and 18 · you should go back and review the cell cycle (Ch. 2), chromosome mapping (Ch.5), chromosome structure and variation (Ch.6) and bacterial plasmids, transformation and immune-like defense (Ch. 7) as you study this unit since must of this content builds on topics from those chapters. · 2 or 3 of the multiple-choice questions will be from Genetics in Practice openers · 3 short essay questions (5-8 pts each) plus 1 bonus short essay question – *For this exam, I have noted the concept most likely to show up in the short essay questions for you (see chapter headings) Topics and Key Terms by Chapter – What to Study for Chapter 14 – expect a short essay on combined: #5, #6 and #10 1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint. 2. Terms from chapter to review (in addition to those directly mentioned in specific topics below): recombinant DNA, transgenic organism, nuclease, agarose, methylene blue, ethidium bromide (EtBr), SYBR Green, anneal / annealing, primer, antibiotic, antibiotic resistance 3. Describe the normal cellular origin and role of restriction enzymes, what types of sequences they recognize, how they cut DNA and what scientists use them for in the laboratory 3.1. Distinguish between the type of cut that makes a cohesive (sticky) end versus a blunt end. 3.2. Identify which restriction enzymes will produce larger fragments (cut less often) based on length of the recognition sequence. **You will NOT be tested on the engineered nuclease section (no questions on this). 4. For CRISPR-Cas systems: 4.1. Describe the normal cellular origin and role of CRISPR-Cas systems, how they know which sequences to recognize ( crRNA), which part has nuclease activity to cut the DNA 4.2. Explain how scientists have engineered this system to cut and modify any specific sequence they desire, including what sgRNA is and how Non-Homologous End-Joining (NHEJ) and Homology Directed Repair ( HDR) enzymes are involved. 5. Explain what gel electrophoresis is, what creates the gel matrix for DNA gels and how we use it to separate and visualize DNA. 6. Describe the three steps of Polymerase Chain Reaction (PCR), including why they are repeated, how primers are involved, where they bind (why just outside the region you want to amplify?) & the key role of Taq polymerase. 7. Define “ gene cloning” and describe the 3 requirements for any cloning vector to work 7.1. Identify key characteristics of plasmid vectors, the basic transformation process and the two common hosts scientists use by the scientific names (which specific bacteria and yeast from Ch. 1) 7.2. Describe the unique characteristics of expression vectors and how scientists obtain eukaryotic DNA that can be used with them (see next item) 8. Describe how a DNA library is made, stored and the differences between making and using a genomic library versus a cDNA library 9. Describe how Sanger sequencing ( dideoxy sequencing) works and what is special about dideoxy nucleotides ( ddNTPs) that allows them to be used in this method. 10. Describe microsatellites ( short tandem repeats, STRs) in DNA and explain how they are used in DNA fingerprinting or profiling to identify DNA samples. Be able to relate this to #5 and #6 in a complete crime scene analysis procedure. 11. Define or recognize examples of forward genetics versus reverse genetics methodologies. What to Study for Chapter 15 – likely no short essay on this chapter since Ch. 18 has two 1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint. 2. Differentiate between genomics and proteomics. 2.1. Describe the differences between the Human Genome Project (HGP) and the Human Proteome Project (HPP) in both their purpose and who they are examining humans (HGP focused on humans as whole organisms, while HPP is looking at different cell types within humans) 2.2. Define structural genomics and functional genomics in relation to these two terms. 3. Describe the approach to sequencing a complex genome that ended up working for the HGP, including the role of genetic linkage mapping, physical mapping, map-based sequencing and whole genome shotgun sequencing. **You will NOT be tested on NextGen or newer sequencing methods (no questions on this). 4. Describe what a Single Nucleotide Polymorphism (SNP) is and why a single SNP does not provide much information about a person or group of people, but a haplotype can. 4.1. Explain how a Genome-Wide Association Study (GWAS) uses genome sequence and SNP information to being to analyze possible causes of a genetic condition, including the limitations of these studies. 5. Identify the interdisciplinary fields involved in bioinformatics and why. 6. Describe what metagenomics is and that it primarily focuses on microbial communities (and why helpful there) **You will NOT be tested on using BLAST to analyze homologues or orthologs or RNA-seq (no questions on this). 7. Describe what a microarray is and how it is used by scientists to analyze gene expression differences between cell types or groups of individuals to identify genes involved in a process (such as cancer patients or developmental changes) 8. For comparative genomics, review and be able to discuss basic features of prokaryotic versus eukaryotic genomes (general size of genome, # of genes and gene “density”) and the impact of transposons in repetitive DNA in eukaryotic genomes. What to Study for Chapter 16 – expect a short essay on combined #3, #4 and #6 1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint. 2. Terms from chapter to review (in addition to those directly mentioned in specific topics below): cell cycle checkpoints, contact inhibition, density dependent inhibition, metastasis / metastasize / metastatic, benign, malignant 3. Describe the primary characteristics of cancer (differentiating it from normal cells) and explain why it is a group of genetic diseases, not just one. 4. Explain why cancer is not typically inherited and why most non-inherited cancer arises later in life rather than in young people 5. Identify the environmental factor that contributes most to the development of cancer ( tobacco) as well as the relative overall impact of environmental factors on cancer development ( around 40% of cancer cases). 6. Describe how cancer develops, including what clonal evolution means and the genetic changes involved in developing a tumor, how it becomes malignant and how metastasis occurs. 7. Identify what the proteins encoded by proto-oncogenes normally do in the cell and why mutations in these genes are often dominant alleles (why are most oncogenes dominant?) 7.1. Recognize the proto-oncogene example ras has an oncogene mutant version present in 1/3 of all tumors 8. Identify what roles the proteins encoded by tumor suppressor genes normally play in the cell and why mutations in these genes are often recessive 8.1. Recognize the key examples of tumor suppressor genes discussed and their normal functions: p53, RB, BRCA1 (and not listed in chart, but there is also a BRCA2 with similar function) 8.2. Explain what haploinsuffiency is and how it might affect a heterozygote who inherited one knock-out allele for a tumor suppressor gene 8.3. Describe how inheriting one knock-out allele for a tumor suppressor gene might lead to increased development of cancer even though the allele is recessive (i.e. explain loss of heterozygosity cause & effect) **You will NOT be tested on cyclins and cdks, though I may mention them in a question, so recognize that they are involved in checkpoints and forward/stop signals so you aren’t confused by the mention. 9. Describe how retinoblastoma (Rb) cancer develops, including which cell cycle checkpoint fails (G1-to-S) and what the 2-hit hypothesis explains about inherited versus sporadic (non-inherited) retinoblastoma tumors (which are almost always unilateral and which are often bilateral and why). 10. Recognize and identify the role of secondary mutations in genes for telomerase, angiogenesis and cytoskeletal and ECM structure as well as aneuploidy and large chromosomal mutations on tumor development and cancer progression. 11. Identify the 2 key ways that viruses, especially retroviruses like HPV, can cause cancer after infection. What to Study for Chapter 18 – expect a short essay on #3 or #5 AND also on #7, including 7.1 1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint. 2. Terms from chapter to review (in addition to those directly mentioned in specific topics below): evolution, gene pool, genotypic frequency, allelic frequency, pre-zygotic, post-zygotic, speciation 3. Calculate genotypic and allelic frequencies for an autosomal locus with two alleles given population information (total number of individuals and number of individuals with each phenotype). 4. Describe the Hardy-Weinberg law (i.e. equations) and the conditions required for genetic equilibrium to exist in a population. 5. Apply the predictions of the Hardy-Weinberg law to calculate genotypic and allelic frequencies for populations in HW equilibrium given one piece of information (such as q2) 6. Describe the forces that drive evolution ( genetic drift, nonrandom mating, mutation, migration, and natural selection) and their effects on allelic frequencies of a population. 6.1. For genetic drift, also explain the causes of genetic drift ( sampling error, randomness), what factors influence the magnitude of drift and what bottleneck effect and founder effect are. 6.2. For natural selection, explain how evolutionary change of this type differs from the others 6.3. Identify which forces increase diversity and which decrease diversity WITHIN a population 6.4. Identify which forces increase diversity and which decrease diversity BETWEEN SEPARATE populations 7. Recite the biological species definition and describe its limitations. 7.1. Be ready to define Reproductive Isolating Mechanism (RIM) and describe at least two examples. 8. Explain the difference between allopatric and sympatric speciation 8.1. Identify the forces that drive evolution in each type of speciation. 9. Explain how phylogenetic trees are used to show evolutionary relationships and the difference between anagenesis and cladogenesis in evolutionary relationships and appearance on the tree. 10. Explain why rates of nucleotide substitutions vary among different parts of the genome and within a gene. 11. Define the molecular clock, including the key assumption it makes and how scientists apply it to evolutionary studies. Page 2 of 2