BIOL 202 Final Exam Study Guide PDF

**What should I know for the final exam? (60-80 questions, 2 hours)** Know Amino acid structures, 1-letter abbreviations, chemical properties. Alanine Serine Aspartate Lysine Glycine Proline Cysteine Glutamine Arginine Glutamate Histidine Tryptophan Leucine Phenylalanine Tyrosine Me...

**What should I know for the final exam? (60-80 questions, 2 hours)** Know Amino acid structures, 1-letter abbreviations, chemical properties. Alanine Serine Aspartate Lysine Glycine Proline Cysteine Glutamine Arginine Glutamate Histidine Tryptophan Leucine Phenylalanine Tyrosine Methionine Know Functional groups (chemical properties, structure, where might you find them: in which biomolecules?) Methyl Phosphate Hydroxyl Amino Carboxyl Understand the overall principles of the central dogma. For each process: Which molecule acts as the template? Which molecule catalyzes the reaction? What molecule is generated from the reaction? Which sequence(s) is/are important for beginning the process? What regulates transcription? What happens after transcription but before translation to eukaryotic mRNAs (post-transcriptional modifications)? Which sequence(s) is/are important for stopping the process? How does it differ between prokaryotes and eukaryotes? Which two processes are coupled in prokaryotes? Use the sequence of one strand of DNA to figure out: The sequence of the opposite strand The given sequence is the template sequence: Find the mRNA sequence. Understand what it means when we say 2 nucleic acid strands are antiparallel & complementary. Use the mRNA sequence to determine the amino acid sequence that would be generated in translation. Use 3-point test cross data to find gene order. Given 2-point test cross data, determine gene distance based on recombinant and parental classes of offspring. Given a normal mRNA sequence and a mutant mRNA sequence, determine whether the mutation is silent/synonymous, missense, nonsense, or frameshift. Knowing genotypes of two parents for an autosomal recessive trait, be able to use a Punnett square to determine the probability of offspring getting the trait (or not). Knowing genotypes of two parents for an X-linked trait, be able to use a Punnett square to determine the probability of offspring getting the trait (or not) based on whether the offspring is male, female, or either. Knowing genotypes of two parents for an autosomal dominant or recessive trait, be able to use the probability rules to figure out the chance of offspring getting the trait and being a boy/girl. Know the difference between positive & negative control, and between repressible & inducible control when given an example of each. Use a provided pedigree diagram to determine phenotypes & genotypes of individuals and their chances of passing on the referenced trait. Contrast linkage with independent assortment & connect these ideas to chromosomes in meiosis. Compare and contrast sister chromatids and homologous chromosomes and know how they are involved in mitosis and meiosis. Be sure to recall how sister chromatids are formed. Know overall outcomes of mitosis & meiosis, and what happens in each phase. Pay special attention to: When does crossing over happen? When do chromosomes line up in the middle of the cell? When do they line up as tetrads vs. single chromosomes (with 2 sister chromatids)? When are sister chromatids separated? When are homologous chromosomes separated? Know the difference between the proteins involved in DNA replication. Helicase Ligase Gyrase/topoisomerase Single-stranded binding proteins Polymerase I Polymerase III Primase Compare DNA replication vs. PCR (test-tube replication, essentially). Understand the PCR steps: what happens in denaturation? Annealing? Elongation? Know what an operon is. What makes it an operon? Know the difference between diploid, haploid, triploid, tetraploid, aneuploid, polyploid, euploid, trisomic, monosomic. Know the difference between incomplete penetrance & variable expressivity Know the difference between incomplete dominance, complete dominance, co-dominance, & epistasis Understand the overall mechanism of trp attenuation (what happens to transcription of the operon) when trp is present (termination loop) vs. when there is no trp in the system (non-terminating loop). Explain each, & identify where you would find each of these bonds in a picture of DNA or protein interactions: Hydrogen bond Phosphodiester bond Covalent bond Van der Waals Hydrophobic interaction Peptide bond Know what happens at each site of the ribosome. Know the basic components of cell theory. Understand that DNA replication is not required for transcription to occur, and why that is the case. Understand that each of our cells has the same genome because they all came from the same zygote through mitosis, and be able to determine why the transcriptome and proteome are different for different cell types. Know the difference between transition and transversion mutations. Know what it means for DNA replication to be semiconservative (always, in all organisms) & bidirectional (always bidirectional - unless rolling circle replication occurs for some phages or F-factor plasmids). For the Lac operon, be able to determine: Under which condition would the repressor be bound to the DNA? Under which conditions would there be low-level transcription? Under which conditions would there be high-level transcription? Under which conditions would there be no transcription? Under which condition would CAP/CRP bind to DNA? Know how to figure out the degrees of freedom for a chi-square test. Know the overall purpose of a chi-square test in genetics. Understand what it means for a mutation to be somatic vs. germline, & spontaneous vs. induced. Know what epigenetics is, especially how it impacts phenotype. Know what a gene is. Understand the structure of a gene: Which part(s) of a gene code for the mRNA molecule? Which part(s) of a gene code for the final protein molecule? Know how chromatin remodeling complex impact gene expression. Contrast purines vs. pyrimidines & know which nucleotides fit into which category. Understand the difference between protein primary, secondary, tertiary, & quaternary structures Explain what snRNPs are and what do they do in cells. Identify the difference between ribose, deoxyribose, and dideoxyribose structures, and know what each of these is used for/where it would be found. Contrast inversion, duplication, deletion, translocation & the overall outcome of each on meiosis Given a sex chromosome genotype, determine how many Barr bodies would be in the cell. Know the difference between the leading strand and lagging strand. Explain how ddNTPs are used in sequencing. Interpret Microarray data like that shown in your notes (what does each color mean? What molecule are we measuring the presence of?) Know how blue/white screening works -- what does it mean if the cells are blue? White? How is transcription impacted by methylation of CpG islands on DNA? Know how dosage compensation works in mammals. Relate the concepts of gene silencing and gene imprinting to DNA methylation. Know the difference between an alkylating agent, intercalating agent, base analog: what does each of these do to DNA sequence? Know what it means when we say that mutation is random. Understand the difference between a promoter, an operator, an enhancer, and a silencer. Know how the Trp repressor controls Trp operon expression. Understand how transposons and retrotransposons can result in mutations. Know how you could use the following in biotechnology at a basic level (what does each do?): PCR Restriction enzymes Ligase Electrophoresis Crispr Plasmid antibiotic resistance gene Plasmid LacZ gene Plasmid multiple cloning site (polylinker site) RT-PCR Microarray DNA Sequencing RNA-seq Understand how mRNA codons interact with tRNA anticodons, based on principles of complementary/antiparallel interactions and the wobble hypothesis. How does this determine which amino acid is added next in the protein sequence? How does this fit with the redundancy of the genetic code? Understand how alleles segregate into gametes. Understand the difference between heterochromatin and euchromatin. Understand the role of telomerase in extending the ends of chromosomes. Be familiar with the outcomes of each of these mechanisms of eukaryotic gene regulation: alternative splicing, alternative promoters, histone modifications (epigenetics), cytosine methylation Explain how crossover rates relate to physical distance between markers. Explain the difference between a coupling (cis) and a repulsion (trans) heterozygote and be able to identify whether a heterozygote is coupling or repulsion given a chromosome configuration. Understand the differences between structural genomics, functional genomics, comparative genomics, and metagenomics. Recognize that complex traits are influenced by multiple genes (polygenic inheritance). Contrast the genetic and environmental influences on phenotypic variation and understand how this relates to broad sense and narrow sense heritabilities. **Population genetics problems: Given the Hardy-Weinberg equations and a genotype or allele frequency, be able to find another genotype or allele frequency for that population, assuming that the population meets all Hardy-Weinberg requirements.** **Know the requirements for a population to be in Hardy-Weinberg equilibrium.**