Foundations of biology final exam review PDF

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Complete final exam review with a summary of the entire course. Labeled clearly and divided into all aspects the course announced would be on the exam. BIOL:1411:0AAA, Fall 2017, Alan Kay, John Logsdon, Brenda Leicht...

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Lecture 29- chapter 15 ● Mutations change the sequence of DNA and may alter or eliminate encoded proteins with or without phenotypic consequences ○ Distinguish among different types of mutations in coding regions of genes ■ Somatic mutations ● Occur in body cells ● Passed on by mitosis but not to sexually produced offspring ■ Germ-line mutations ● Occur in germ line cells ○ Cells that give rise to gametes ● A gamete passes the mutation on at fertilization ■ Genetic mutation ● Change in the nucleotide sequence of DNA transmitted to the next generation ○ Evaluate whether a change in coding sequence influences the resulting protein ■ Loss of function mutation ● Codes for a nonfunctional protein ● Affects protein function and may lead to structural proteins or enzymes that no longer work ● Almost always recessive ● Ex. cystic fibrosis ■ Gain of function mutation ● Codes for a protein with new function ● Lead to a protein with altered function ● Ex. insecticide resistance ■ Silent mutation ● Codes for a functional protein ● Do not change polypeptide sequence ● Do not affect protein function ■ Conditional mutations ● Cause phenotypes under restrictive conditions but are not detectable under permissive conditions ○ Contrast between point mutations and different chromosomal mutations ■ May or may not be phenotypically apparent ■ Point mutation ● Results from the gain, loss, or substitution of a single base pair of DNA ● Can either alter or not alter the polypeptide sequence ○ Silent point mutation ■ Redundant site of codon ○ Missense point mutation ■ Nonsynonymous site changes a single amino acid ○ Nonsense point mutation

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Shortens polypeptide by causing premature termination of translation ○ Frame shift point mutation ■ Changes reading frame ■ Chromosomal mutations ● More extensive ● May change the position of genes or cause multiple genes in a DNA segment to be duplicated or lost ● Deletion ○ Missing the intervening region ○ Often have severe phenotypic consequences (especially when homozygous and genes missing in deleted region) ● Inversions ○ Flipping the intervening region ○ Excluding the breakpoints ○ No change in DNA sequence ● Duplication ○ Homologous chromosomes can break in different places and repair incorrectly ○ Increases copy number of genes can cause phenotypic effects ● Translocations ○ Non homologous chromosomes can break and repair with wrong fragments ○ Sterility can result due to problems with meiotic segregation Mutations occur spontaneously at low rates, but can also be induced by mutagens ○ Illustrate the stepwise changes in a DNA base leading to a mutation ■ ○ Contrast spontaneous sources of mutation with the impacts of mutagens ■ Spontaneous mutations ● Bases can have different structures ● May form tautomers ○ Rare tautomers can pair with the wrong bases ● Chemical reactions may change bases ○ Recognize that mutation is the source of new genetic variation ■ Semiconservative replication maintains an old copy of each base sequence in each newly replicated molecule ● Produces one daughter molecule with changed basepair ■ Changes in DNA sequence occur spontaneously and due to external factors ■ Cause induced mutations ● Chemicals can alter bases

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Some chemicals add other groups to bases ○ During replication, DNA polymerase incorporates any base opposite the modification ■ Deamination ● Loss of an amino group ● Many human genetic diseases are caused by mutations that affect the functions of protein Lecture 30 chapter 15 ● Mutations occur spontaneously at low rates, but can also be induced by mutagens ○ Illustrate the stepwise changes in a DNA base leading to a mutation ■ Ex. UV radiation ● Absorbed by thymine ● Formed covalent bonds with adjacent nucleotides ● Disrupts DNA replication ○ Contrast spontaneous sources of mutation with the impacts of mutagens ○ Recognize that mutation is the course of new genetic variation ● Many human genetic diseases are caused by mutations that affect the functions of proteins ○ Relate a well characterized genetic disease with the known mutations(s), that causality of the disease phenotype, and the availability of screens ■ Ex. sickle cell anemia ● One of the beta globin chains in the hemoglobin in blood cells is replaced by valine and causes the shape of the cell to change ● Causes anemia ○ Recognize the existence of protein variants that maintain similar function ■ Polymorphism ■ Numerous normal alleles of a genes that produce the same functioning proteins ○ Genetic markers ■ Provide reference loci for associating genotype with phenotype ● Two mutations needed : influences disease phenotype and marker mutation ● Co-inheritance of the marker and the disease-causing allele occurs due to genetic linkage - loci are closely linked ● The polymerase chain reaction (PCR) generates a large number of copies of a targeted genome region through cycles of DNA replication ○ Describe the components and cycling strategy of PCR ● Copies of DNA sequences are made by this technique ○ amplification of the sequence ○ Copies of the target region double every cycle ● Cycle of PCR: ○ DNA fragments denatured (separate 2 strands of DNA) at ~95°C

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Primer bases pair (anneal) to the target sites ~50°C-60°C Heat tolerant polymerase synthesizes DNA from 3’-OH of DNA primer ○ Repeated 30-35 times ○ Illustrate the polarity of primers annealed to complementary sites of a genomic DNA template during PCR Mutation generates variation in single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) that can be assayed ○ Identify methods that are appropriate for the detection of either SNP or STR alleles ○ SNPs ■ Single nucleotide polymorphisms ■ Inherited variations involving a single base originating by point mutations ○ STRs ■ Short repetitive sequences occurring side by side on chromosomes ■ Usually in noncoding regions ○ Justify the use of PCR, restriction enzymes, gel electrophoresis, and/or hybridization in the analysis of genetic markers ■ PCR ● Sequence differences in genetic markers must be identifiable by current DNA analysis methods ○ Codominance is best ● Restriction enzymes can be used to identify SNPs in restriction sites ○ SNPs can be directly assayed ● STRs vary in length and there are multiple alleles at each marker locus ■ Gel electrophoresis ● Separate DNA fragments by size ● Negatively charged DNA fragments move towards the positive end ● Smaller fragments move through the gel faster than larger ones ■ RFLPs ● Restriction fragment length polymorphisms ● Restriction enzymes cut DNA at specific sequences generating smaller fragments ● Mutations at restriction sites that change the ability of the enzyme to cut ● Observed as bands on an electrophoresis gel following digestion of PCR amplified target or hybridization of digested DNA with a probe ■ Hybridization methods ● SNPs are detected using the allele-specific oligonucleotide hybridization method

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Short synthetic DNA strands called oligonucleotide probes hybridize with denatured PCR products ○ Hybridization to the DNA containing the complementary SNP is detected by a radioactive or fluorescent label on the probe ■ Strand of genomic DNA is paired with a probe through complementary base pairing ● Incorporation of base complementary to genomic template monitored by dye Lecture 31 chapters 15 & 17 ● Genetic markers linked to a mendelian trait are used to localize and screen for causative mutations ○ Explain the role of meiotic recombination in finding a gene of interest ■ Mendelian traits segregate as single autosomal or sex linked loci ■ Most human traits are multifactorial ● Caused by interactions of many genes and the environment ○ Interpret inheritance patterns of phenotypes and genetic markers to measure associations Lecture 32 chapters 17 & 18 ● The Human Genome Project initiated in 1986, and in parallel with Celera Genomics released a draft sequence in 2003 ○ Recognize the difference in proportion of protein-coding and non-coding regions ○ List different features of the human genome and relate these to other organisms ■ Protein coding genes make up less than 2% ■ A gene can code several proteins ■ Average gene has ~27,000 base pairs ■ Human genes have many introns ● Average intron size ~3500 base pairs ■ Genes are not even distributed over the genome ■ Over 50% of the genome is transposons and other repetitive sequences ■ 97% of the genome is the same in all people ● Large scale analysis of SNPs between case- control populations identifies genomic regions that influence multifactorial traits ○ Contrast the genetic basis of mendelian and multifactorial traits ■ Multifactorial traits ● Rapid genotyping technologies are understanding genetic basis for many diseases ● Technologies to analyze SNPs include rapid sequencing and other direct detection methods ○ Identify similarities and differences among methods used to connect genotype with phenotype ■ Functional analysis in model organisms also informs studies of variation in humans by revealing candidate genes in regions associated with traits

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Sequencing DNA template is accomplished by assessing the incorporation of individual bases ○ Interpret the base sequence and polarity from products of a sequencing reaction on a single template ■ Rely on measuring the sequential incorporation of bases as DNA is synthesized ■ Components ● DNA polymerase ● Short primer complementary to template strand ● All 2’ deoxynucleoside triphosphates (dATP, dCTP, dGTP, dTTP) ● All 2’, 3’ dideoxynucleoside triphosphates (ddATP, dCTP, ddGTP, ddTTP) ○ Labeled uniquely so that each can be detected ● Template DNA, sequencing reaction reliably read only 100-700 bases of the template ○ Recognize the components and processes used in Sanger sequencing using dye terminators ■ Uses ddNTPs in combination with normal dNTPs ■ Synthesis stops when a ddNTP is added by DNA polymerase to polynucleotide chain because ddNTP has no hydroxyl group at the 3’ position ■ The sequence is determined by detecting the terminal 3’ base at each position in the DNA PCR or cloning is used to generate large quantities of identical template DNA for sequencing ○ Relate between different methods for amplifying a sequence template and the uses of the sequence data ■ PCR ● Polymerase chain reaction ● Each primer used for PCR amplification can be used to sequence one strand of PCR product ■ Isolate recombinant DNA clone from bacteria ■ DNA Barcode Project ● Uses DNA sequences from mitochondrial genome to identify species ● Works under the assumption that differences in gene sequences are generally greater between species than among individuals within a species ○ Compare primer template orientation in PCR and sequencing reactions ■ Template ● Recombinant DNA clones are often used as sequencing template ○ Genomic library

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Collection of DNA fragments that comprise genome of an organism ○ cDNA library ■ Collection of DNA copies of mRNA molecules from a cell, tissue, or organism ● Plasmids are good for amplification ○ Many have genes for antibiotic resistance which can be selectable markers ○ Have a bacterial origin of replication (ori) and can replicate independently of the host chromosome ○ Contrast sequencing reactions on a single template to massively parallel methods ■ High throughput sequencing ● Each template is fixed in 2D and base incorporation is read sequentially ● Used to simultaneously sequence many different template molecules ● Involved physical binding of the template DNA to a solid surface or to microbeads and amplification of NDA templates by PCR ■ Massively parallel methods ● Thousands or millions of sequencing reactions are run at once Lecture 33 chapters 18 & 21 ● Darwin outlines basic principles, and supporting evidence, that provide a foundation for modern evolutionary theory ○ Recognize Darwin’s and Wallace’s contributions in the establishment of a scientific theory of evolution ■ Evolution is the genetic/phenotypic change in populations from generation to generation ■ Evolutionary theory is the understanding of application of the mechanisms of evolutionary change to biological problems ■ Darwin’s proposal of evolution depended on ● Species change over time ● Divergent species share a common ancestor ● Natural selection causes this change ○ Relate between artificial selection and natural selection ■ Natural selection ● Slight variations among individuals affect the chances of surviving and producing offspring ■ Artificial selection ● Selective breeding of animals and plants by humans produced changes in characteristics of these breeds ● Populations evolve through differential survival and reproduction of individuals

Lecture 34 chapter 21 ● Bacterial enzymes and plasmid vectors are used to create and clone recombinant DNA molecules ○ Identify restriction enzyme cut sites and the recombinant products generated following ligation ○ List the characteristics of vectors that facilitate their selection, replication, and expression in a host cell ■ Vector can generate clones by incorporating DNA ● Natural selection influences a population through individual differences in fitness expressed through survival and reproduction...