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by: Hazel Stehr
Hazel Stehr
GPA 3.98


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Class Notes
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Popular in Biochemistry and Molecular Biology

This 8 page Class Notes was uploaded by Hazel Stehr on Saturday September 19, 2015. The Class Notes belongs to BMB 526 at Michigan State University taught by Staff in Fall. Since its upload, it has received 51 views. For similar materials see /class/207383/bmb-526-michigan-state-university in Biochemistry and Molecular Biology at Michigan State University.


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Date Created: 09/19/15
BMB 526 Molecular Biology and Genetics Overview The general objective of this course is to instruct students in the basic concepts principles and language of molecular biology and human genetics and to equip students to analyze diseases and the responses to diseases in molecular and genetic terms These principles will be illustrated using examples from clinical practice We anticipate that this training will enable students to recognize and solve genetic problems encountered in subsequent clinical training and experience Specific educational objectives for various sections of this course are included in the body of the coursepack These objectives represent a subset of the core competencies in genetics that are expected of all health professionals as put forth in guidelines from the American Society for Human Genetics and the National Coalition for Health Professional Education in Genetics DETAILED OBJECTIVES In this list the lecture session number 801 802 etc corresponds to the sessions listed in CurerT The letter after each session title indicates the CHM objectives that correspond to the session objectives Sservice CCare of Patients RRationality lntegration PProfessionalism TTransformation 01 Flow of Genetic Information T A Distinguish between gene as conceptual unit of information and DNA as the physical material in which that information is encoded Describe the central dogma of molecular biology including the informational roles of DNA RNA and protein Define the processes of replication transcription and translation Define genome and distinguish haploid and diploid organisms Describe the principal attributes of the genetic code Distinguish between degeneracy and unambiguity in the genetic code F Given a DNA or RNA sequence predict the corresponding protein sequence G Given a protein sequence identify one or more corresponding DNA or RNA sequences 01 ITIUO 802 Principles of Replication Prokaryotic Replication Mechanisms T DNA Structure A Describe the chemical bond that joins adjacent nucleotides in a nucleic acid polymer B Given a diagram of the chemical structure of a nucleic acid identify the 539 and 339 ends C Identify and describe the positions ofthe bases sugars and phosphates in the double helix model of DNA structure D Describe the forces that contribute to the stability of the double helix Explain the cooperativity of DNA denaturation and renaturation by reference to these forces Predict the relative melting temperatures of DNA molecules with various guanine cytosine contents E Given the sequence or composition of a single strand of DNA predict the sequence or composition of the complementary strand F Define the components and structure of a nucleosome and the role of histone H1 Describe the multiple levels of DNA packaging from 39 to 39 Define 39 39 and euchromatin DNA Replication Describe the roles of template and primer in DNA synthesis Define semiconservative replication Explain how semidiscontinuous replication leading and lagging strands arises from the 539 to 339 direction of polymerization Recognize or draw diagrams representing bidirectional replication from specific origins for linear and circular genomes l I 1 U OWgt E Identify the primary events in the following stages of replication prepriming priminginitiation elongation leading and lagging strands termination segregation F Define the roles and attributes of the following proteins primase DNA polymerase DNA ligase topoisomerase gyrase helicase SSB G Describe the fidelity mechanisms of DNA polymerases including the role of 339 to 539 exonuclease and 539 to 339 exonuclease activities H Describe the problem encountered by lagging strand synthesis at the ends of linear DNA molecules Identify the strategy including the novel features by which telomerase addresses that problem S03 Eukaryotic DNA Replication Mechanisms and Regulations T A Identify the phases of the eukaryotic cell cycle listing the principal events of each phase and the primary points at which the cycle is regulated S04 Mutations Genetic Diversity and Disease Recombination T A Define and apply the following terms allele locus haploid diploid homozygous and heterozygous wildtype and mutant alleles Recognize and provide examples of silent missense nonsense and frameshift mutations Distinguish between the effects of mutations in proteincoding regions and in regulatory regions of DNA Describe specific examples of each kind of mutation represented by various forms of hemoglobinopathies D Describe the principal features and genetic implications of homologous recombination E Use recombination frequencies among given sets of genes to establish relative distances between genes F Describe the role of sitespecific recombination in generating antibody diversity G Define the concept of transposition Distinguish the major mechanisms of transposition in prokaryotes and eukaryotes Describe the genetic effects of transposon insertions and of homologous recombination between two transposons 097 U 05 DNA Damage and Repair Molecular Basis of Mutations T Describe the process by which physical damage to DNA becomes fixed as a permanent mutation Recognize and provide examples of transitions transversions insertions and deletions Describe how deamination depurination and radiation damage results in mutations Distinguish between cellcycle arrest and apoptosis as cellular responses to DNA damage Describe the general features of the following DNA repair mechanisms and human genetic diseases associated with defects in these mechanisms direct repair of alkylation and UV photoproducts Base excision repair and DNA Nglycosylases Nucleotide excision repair pathway Mismatch repair Doublestrand break repair recombination repair moom gt U39PPN S06 RNA Structure and Synthesis Prokaryotic Transcription T RNA Structure and Synthesis A Recognize and describe the structures of the four common bases and the sugar found in RNA B Describe the primary structure of RNA and recognize the 539 and 339 ends of an RNA shown in a structure diagram C Describe the participation of RNA in doublestranded nucleic acids including GU basepairs D Describe general functions relative abundance and complexities of the following classes of RNA mRNA rRNA tRNA hnRNA snRNA Prokaryotic Transcription A List the essential components of a transcription reaction B Describe the subunit structure of E coli core polymerase and holoenzyme C Define promoter and describe the function of sigma factor D Describe the steps that occur within each of the three stages of transcription initiation elongation termination E Recognize transcription as a site of action for antibiotics 07 Eukaryotic Transcription T A List the essential components of a transcription reaction B Define promoter and describe the function of sigma factor C Describe the steps that occur within each of the three stages of transcription initiation elongation termination D Recognize transcription as a site of action for antibiotics 08 RNA Processing T A Define the roles relative activities and locations of the three eukaryotic RNA polymerases B Describe the organization of rRNA genes their location in the nucleus and the processing of the primary transcript into mature mRNA C Describe the general features of a promoterfor RNA polymerase II in contrast to a prokaryotic promoter D Describe the distinguishing features of a promoter for RNA polymerase III in contrast to a typical RNA pol ll promoter E Describe the events in processing of hnRNA into mRNA including 1 the structure and role of the 539 cap 2 the structure and role of the 339 polyadenylate tail 3 splicing including a define exon and intron b describe the general roles of snRNPs and the spliceosome c define what is meant by 539 and 339 or donor and acceptor splice sites and describe the importance of the sequences at those sites F Describe the events in processing of eukaryotic tRNAs Catalytic RNA A Define what is meant by the phrase quotcatalytic RNAquot and give two examples B Recognize or describe the putative role of RNA as the primordial informational molecule RNA Silencing A Define the general concept of RNAbased gene silencing B Distinguish between the origins of short interfering RNAs and microRNAs C Describe and distinguish between posttranscriptional and transcriptional effects of RNA silencing D List or rearrange biological phenomena in which RNA silencing occurs E Describe the technological and potentially therapeutic application of RNA silencing 809 Protein Synthesis Translation Mechanisms T Translation of Genetic Information A Describe the roles of mRNA tRNA rRNA codons and anticodons in the translation of genetic information from nucleic acid sequence to polypeptide sequence B Describe the quotwobblequot hypothesis distinguish the concepts of quotwobblequot and quotisoaccepting tRNAsquot recognize andor construct codonanticodon pairs including base pairs involving U or C Given a table of the genetic code apply the rules of genetic coding including wobble to the following situations 1 Given a codon identify the corresponding anticodons and amino acid 2 Given an anticodon identify the corresponding codons and amino acid 3 Given an amino acid identify the corresponding codons and anticodons Translational Machinery A Describe the ribosomes of bacteria and eukaryotes including their size subunits and the RNAs and approximate protein composition within each subunit B Describe the process of amino acid activation including 1 the role and specificity of amino acyltRNA synthetases 2 the position of the covalent bond formed with respect to both amino acid and tRNA 3 the role of ATP and the quotcostquot in highenergy bonds S10 Translation and PostTranslational Protein Processing T Translation Mechanism A Compare and contrast the mechanisms used in E coliand eukaryotes for identifying start codons Identify the positions of ribosome binding sites for each open reading frame in a sketch of a polygenic mRNA B Describe the sequence of events leading to a translation initiation complex including small and large subunits mRNA initiator tRNA GTP and unspecified initiation factors C Summarize the three principal steps in elongation including the molecules that occupy the P and A sites within the ribosome and the role of GTP Describe the formation of peptide bonds including the implication for the direction of polypeptide chain growth D Sketch or recognize and label a diagram representing polysomes E Sketch or recognize and label a diagram representing the coupling of transcription and translation in bacteria F Briefly describe the mechanism by which stop codons are recognized and translation is terminated G Recognize or recall the steps in translation that may be sensitive to effects of antibiotics actions of specific antibiotics need not be memorized at this time Explain the potential effects that inhibitors of prokaryotic translation might have on mitochondrial translation Translation of MembraneBound and Secreted Proteins A List the sequence of events and cellular locations proposed by the quotsignal hypothesisquot for synthesis of membranebound and secreted proteins B Define and describe the roles of signal peptide signal recognition particle ER ribosome signal peptidase and stoptransfer sequence 811 Protein Processing T Posttranslational Processing A Describe the forces that drive polypeptides to fold into specific secondary and tertiary structures Review B Define chaperonins and describe their function C Describe the role of proteolysis in maturation of proteins as for insulin and digestive enzymes D Describe the structures and biological roles of the following chemical modifications of amino acids and give an example of a protein so modified 1 phosphorylation 2 acetylation 3 hydroxylation 4 ADPribosylation 5 acylation myristylation palmitoylation E Compare and contrast Olinked and Nlinked glycosylation with respect to 1 amino acids that are modified 2 structure of oligosaccharides 3 mechanism of sugar attachment F Describe the mechanisms used for targeting proteins to ysosomes nucleus and mitochondria G Describe the roles of secreted proteases and the ysosome in degrading extracellular proteins H Describe the roles of ubiquitin and proteasomes in degrading intracellular proteins 812 Regulation of Gene Expression Prokaryotes T A Explain the use of alternative sigma factors to regulate specific set of genes by recognition of specific promoter sequences B List and define the following components of an operon promoter operator repressor inducer corepressor polygenic mRNA C Describe the effects of high or low concentrations of lactose and glucose on expression of the lac operon 1 Describe the activity of the lac repressor under these conditions 2 Describe the activity of the CAP protein under these conditions 3 Apply the principles of a repressor or activator protein to a novel catabolic operon ie predict how regulation would be affected by relevant metabolites D Describe the effects of low or high concentrations of tryptophan on expression of the trp operon and contrast the behavior of the Trp repressor with that of the Lac repressor S13 Regulation of Gene Expression Eukaryotes T A Differentiate between polygenic mRNAs from prokaryotic operons and gene clusters in eukaryotes eg histone globin rRNA genes B Describe how DNA methylation and chromatin condensation affect gene expression Define euchromatin and heterochromatin C Define promoter enhancer and silencer with respect to gene expression Distinguish D between basal or general transcription factors and regulatory proteins such as E transcriptional activators Describe the functions or activities associated with most F regulatory proteins G Describe the distinguishing features of three classes of DNAbinding proteins helixturnhelix zincfinger and leucine zipper Sketch or recognize and label diagrams representing such proteins Using words or diagrams describe the potential of zipper proteins to combine as heterodimers and how such combinations might affect gene expression H Using words or diagrams explain how alternative splicing can result in synthesis of several different protein products from a single gene Give at least one example of alternative splicing and explain the physiological relevance Describe the concepts of mRNA turnover and mRNA transport and how these mechanisms might participate in gene regulation J List or recognize events in translation that can be targets for gene regulatory mechanisms Describe how iron regulates translation or stability of the mRNAs encoding ferritin and transferrin S14 Genomics and Proteomics T A Define genome and name or recognize the approximate sizes of viral bacterial yeast and human genomes B Describe the informational content of genomes including coding regions noncoding spacer regions repetitive DNAs dispersed repetitive elements such as SlNEs and LlNEs and satellite DNA Name or recognize the relative proportions of the human genomic represented by these sequence classes C Describe the applications of the information from the Human Genome Project HGP D microarrays pharmacogenomics toxicogenomics S A B C D S m0 003 n S List the implications of the HGP in terms of understanding human biology research health care and some of the ethical issues Define proteomics List the limits of sequencing the genome in terms of understanding the proteome List the modifications that add to the variety of proteins Describe some applications of proteomics 15 Chromosome Dynamics Meiosis Mitosis Gametogenesis T List in correct sequence the stages of mitosis somatic cell division and the chromosomal events that occur in each stage List in correct sequence the stages of meiosis germ cell division and the chromosomal events that occur in each stage Correlate chromosomal events in meiosis with the Mendelian concepts of independent assortment and segregation of alleles Describe the phenomenon of crossingover and explain how it affects segregation of alleles Identify haploid and diploid stages of gametogenesis describe each stage with respect to mitosis and meiosis 16817 Basics of Cytogenetics T Identify clinical conditions for which a chromosomal analysis is appropriate as well as those for which a chromosomal analysis would be uninformative or inappropriate Correct use of terms that relate to chromosome structure and identification Review chromosome behavior during both somatic cell division and germ line cell division especially in regards to chromosome condensation and crossing over Become familiar with the application of various types of FISH techniques 18S19 Modes of Inheritance Pedigrees and Simple risk calculations probabilities T Given a descriptive family history draw a corresponding pedigree Given a pedigree describe the degree of relatedness between any two individuals Given a pedigree infer possible or probable modes of inheritance or rule out unlikely modes of inheritance Construct a fictional pedigree that corresponds to any given mode of inheritance Identify general pedigree characteristics that distinguish autosomal dominant autosomal recessive Xlinked dominant Xlinked recessive and mitochondrial modes of inheritance Given a pedigree for any of the aforementioned modes of inheritance predict the probability of affected offspring Given partial pedigree information and any of the modes of inheritance identify expected genotypes or phenotypes of members of the pedigree Calculate the probability that any given individual has a specific genotype or phenotype Given parental genotypes for a gene with two alleles construct and use a Punnett square to predict the number of offspring with various genotypes or phenotypes Describe the modes of inheritance for each of the following genetic conditions or diseases cystic fibrosis Duchenne muscular dystrophy familial hypercholesterolemia hemophilia A Huntington disease incontinentia pigmenti l Leber hereditary optic quot MELAS quot39 39 type 1 Phenylketonuria Rett syndrome sicklecell anemia Note You will NOT be expected to learn the clinical symptoms or population frequencies of these diseases Describe the conditions for appropriate use of the sum rule the product rule and the binomial distribution function of probability and apply those rules to simple questions of genetic predictions 2021 Factors that Modulate Inheritance PatternsT A Define the terms below and describe or recognize in a pedigree the effect that each might have on the pattern of inherited characteristics 1 Phenotypic Expression Reduced penetrance Variable expressivity Pleiotropy Allelic heterogeneity Locus heterogeneity Delayed age of onset Anticipation 2 Interaction of Genes Codominance Incomplete dominance or recessiveness Epistasis Sexlimited diseases Sexinfluenced diseases 3 Mosaicism Xinactivation Somatic mosaicism Germline mosaicism 4 Miscellaneous Interaction of Genes and Environment De novo mutations Nonpaternity nonmaternity Phenocopies Multifactorial inheritance Genomic imprinting and uniparental disomy 5 Determining Recurrence Risks with Bayesian Analysis B Recognize the tools counselors have to estimate separate recurrence risks When are Mendelian risks applicable when can they be modified by Bayesian analysis 822 Multifactorial Inheritance T gt quot39 B C D Understand the definition of multifactorial diseases as opposed to polygenic diseases or diseases with locus heterogeneity Understand the definition and distribution of quantitative traits Describe the threshold model of mutifactorial diseases Explain how differences in gender thresholds affect recurrence risks in families Describe how the family history will affect an individual s recurrence risk for a multifactorial disease Explain how twin studies help to distinguish the effects of genes vs environment Define concordant discordant and heritability For the following examples of mutifactorial diseases identify or recognize genetic and environmental influences if known congenital malformations coronary heart disease hypertension cancer diabetes bipolar affective disorder 23 Biochemical Genetics Inborn Errors of Metabolisim T A B C D E S Describe and distinguish the biochemical and genetic effects of loss of function and gain of function mutations Recognize or describe how mutations representing allelic heterogeneity and locus heterogeneity might affect a metabolic pathway Recognize or describe the effects that regulatory or processing mutations might have on a metabolic pathway Recognize or name examples of specific genetic diseases within each of the following categories Metabolic enzymes Enzyme cofactors Hormones and receptors Structural proteins Transport proteins Recognize or apply the principles dominantrecessive 39 a a diseases or pathways described in lecture textbook course pack 0 of biochemical genetics gainloss of function quot quot 39 39 5 mutations to uations u I39 n 7 l39 r In new sIt 24 Population Genetics HardyWeinberg Equilibrium T A Summarize the principle and its mathematical basis that describes the maintenance of low 07 0 0 frequency and recessive alleles within a population Recognize or describe the conditions or assumptions under which the HardyWeinberg equilibrium principle holds Recognize or describe how each of the following conditions might affect prediction from the HardyWeinberg equilibrium principle migration new mutations natural selection nonrandom mating consanguinity genetic drift founder effects bias of ascertainment Given the frequency in a population of a particular phenotype use the HardyWeinberg equation to calculate the corresponding allele frequencies and genotype frequencies E Given the frequency of an allele for a particular trait autosomal or Xlinked recessive or dominant calculate the corresponding phenotype and genotype frequencies 25 Recombinant DNA T A Describe the features of DNA sequences recognized by restriction endonucleases sketch or recognize a DNA sequence that has dyad symmetry Describe the products of digestion cleavage by restriction enzymes sketch or a 39 5N t d 4 3N t d d and bluntended fragments Given a DNA sequence and a list of recognition and cleavage sites for restriction enzymes identify the positions and products of digestion B Describe in words or diagrams the general concept of recombinant DNA Describe the function of DNA ligase Describe the essential features of a cloning vector List five types of cloning vectors and their distinguishing features C Define genomic and cDNA inserts Compare the informational content of genomic and cDNA clones Describe the synthesis of cDNA including the role of reverse transcriptase Explain using words or diagrams how expression vectors are used to direct the synthesis of a human protein in E coli List the unique features of an expression vector D Describe the concept of clone libraries and how such libraries are constructed Distinguish between the concepts of selection and screening Describe how molecular probes DNA RNA oligonucleotide antibody can be used to identify specific recombinant DNA clones E Using words or diagrams explain in concept but not in technical detail how recombinant DNA techniques can be used to 1 obtain a cloned gene fragment given a protein sample or antibody 2 obtain a specific protein if given a gene fragment or probe F Identify the kinds of information revealed by Southern Northern and Western blots Summarize these procedures identifying the molecules being detected and the probes used G Describe the process and products of the polymerase chain reaction PCR 2627 Molecular Analysis of Genes Detection Methods PCR Diagnostic Applications of Molecular Analysis T A Define the following types of DNA polymorphisms restricted fragment length polymorphisms RFLP variable number of tandem repeats VNTR simple tandem repeats STR and simple DNA sequence differences B Demonstrate the effects of the above polymorphisms using simple schematic diagrams or by interpreting Southern Blot or PCR results depicting these polymorphisms Distinguish between informative and noninformative data for pedigree analysis Use DNA polymorphisms as markers of distinct chromosomes and as alleles of specific loci for calculating recombination frequencies and fortracking chromosomes through pedigrees From simple informative pedigree data for any two markers estimate recombination frequency E Predict the phenotype or genotype for individuals in a pedigree based on informative polymorphism data 00 28 Gene Mapping and Linkage Analysis T Draw or recognize and label diagrams describing meiotic crossover recombination between homologous chromosomes Describe the implication of meiotic crossover for the segregation of alleles of different genes on the same chromosome C Describe the role of recombination in genetic linkage mapping Given recombination frequencies D gt n 07 between three or four genes on a given chromosome construct an approximate genetIc map Recognize the statistical information denoted by a LOD score Z and by 9 max in gene mapping Identify LOD scores that either support or refute the hypothesis that two genes or markers are linked Relate 9 max values to genetic distance


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