Click on the items in the list below to access learning objectives
CHAPTER 25: BIOSYNTHESIS OF NUCLEOTIDES
1. Know the structures of the building blocks of nucleic acids:
3. Understand the biosynthesis of dTMP.
4. Know why nucleotide analogs and inhibitors of thymidylate synthase are used in drug therapy for diseases such as cancer, AIDS, herpes, etc.
CHAPTER 4, Part 1: DNA AND RNA, MOLECULES OF HEREDITY
1. Know the structures of the component nucleotides of DNA and RNA. Understand thephosphodiester bonds that join nucleosides together to form polynucleotides. Relate the direction of writing a DNA sequence to the polarityof the DNA chain. Know how to draw polynucleotides. [pp.75-77 and review Chapter 29]
2. Know how to apply nomenclature and shorthand conventions for DNA and RNA to draw polynucleotide structures.
3. Understand the experimental proofs that DNA and RNA contain genetic information.
4. Know the major structural features of the Watson-Crick DNA double helix. Relate the specificity of pairing of adenine with thymine and cytosine with guanine to the duplex (double-stranded) structure of DNA and to its replication.
5. Describe other features of DNA, such as: Occurrence in nature - strandedness, size, conformation (open vs supercoiled circles), physico-chemical properties (reversible helix-coil transition by temperature melting, buoyant density)
6. Compare the relative lengths of DNA molecules in viruses, bacteria, and eucaryotes.
b) What are the substrates
and reaction mechanism for synthesis of 3'-5' phosphodiester bonds by DNA
polymerase I (Pol I)?
What is the direction of DNA chain growth?
Discuss the accurracy of Pol I.
What are the functions of the template and primer?
CHAPTER 4, Part 2: FLOW OF GENETIC INFORMATION
1. Outline the flow of genetic information during gene expression.
2. Compare the sizes, relative amounts, structural features, and functions of the three major classes of RNA found in E. coli.
3. Describe the technique of nucleic acid hybridization. How can it be used to show the relationship of an RNA to its DNA template?
4. Know the substrates, products, and important enzymatic properties of DNA-dependent RNA polymerases. Explain the roles of the DNA template, the promoter, and the terminatorin transcription.
5. Compare DNA template conservation in RNA synthesis to that in DNA replication.
6. How does tRNA function as the adaptor molecule between mRNA and amino acids during protein synthesis? How are amino acids covalently attached to tRNA molecules? What is the codon/anticodon interaction between mRNA and tRNA. What is the role of the ribosome?
7. Describe the major characteristics of the genetic code. Define the terms degenerate, sequential, triplet, and nonoverlapping as they apply to the genetic code. What are the termination and initiation codons?
8. Be able to predict (using the genetic code) the sequence of amino acids encoded by any template DNA or mRNA sequence.
9. How universal is the genetic code? What are exceptions?
10. Describe the colinear relationship between the sequence of DNA in a bacterial gene and the sequence of the amino acids in the protein it encodes. Relate this concept to the intervening sequences (introns )that occur in eucaryotic genes.
11. How might exons be used in evolution of proteins with new functions?
CHAPTER 5: EXPLORING GENES AND GENOMES
1. Define recombinant DNA. Why do scientists work with it?
2. Describe the important features of restriction enzyme DNA substrates and the reactions catalyzed.
3. Gel electrophoresis is essential to the field of recombinant DNA technology. How can DNA molecules be detected in gels?
4. Know how DNA is sequenced by controlled interruption of DNA replication (the Sanger dideoxy chain-termination method). Know why this method works and how to predict the results and read DNA sequences. What are some other ways to sequence DNA? Know that DNA can be synthesized in the test tube for use in recombinant DNA technology.
5. What are some desired characteristics of a cloning vector? Outline the major steps in cloning a DNA molecule. Describe the reaction catalyzed by DNA ligase.
6. Compare the properties of cloning and expression vectors used in procaryotes vs eucaryotes. Why do introns in eucaryotic genes prevent their expression in procaryotes?
7. What are nucleic acid and antibody probes? Explain the biochemical basis of their specificities. How are they used to screen for cells harboring recombinant DNA?
8. Explain how to design a nucleic acid probe by reverse translating (using the genetic code) an amino acid sequence of a protein into a nucleotide sequence.
9. What kind of information is obtained by chromosome walking? How is it done?
10. Distinguish between genomic and cDNA libraries. How is each type of library constructed - note similarities and differences? Why are yeast artificial chromosomes (YACs) used?
11. Know how foreign DNA can be incorporated into plant and animal cells to engineer transgenic organisms.
12. List some actual and potential uses of recombinant DNA technology. What are some implications of recombinant DNA technology with respect to moral and social values?
13. How can RFLPs (restriction fragment length polymorphisms) and PCR (the polymerase chain reaction) be used to provide evidence that a suspect might or might not have committed a crime?
CHAPTER 28: DNA STRUCTURE, REPLICATION AND REPAIR
KNOW THE FOLLOWING:
A. DNA STRUCTURE1) Deviations from Watson-Crick structure in real B-DNA as deduced from x-ray structure. Dynamic nature of structure of biologically-active DNA.
B. DNA-PROTEIN
INTERACTIONS:
- nature of non-specific
vs. specificinteractions.
- basic features
of the DNA and proteins which bind to it
- conformational changes
of DNA due to interactions with DNA-binding proteins.
1) Topology of DNA (state of supercoiling), biological importance.
2) functions of DNA topoisomerases. (topoisomerase I, DNA gyrase)
C. DNA REPLICATION
1) DNA Polymerases: Pol I, Pol II, Pol III (properties, substrates, enzyme activities, biological roles).
2) Initiation of replication (requirements, proteins involved and steps in the process).
3) Models of leading and lagging strand DNA synthesis by Pol III.
4) RNA primer removal and termination of replication.
1) Mutations (types and how introduced in a gene).
2) Properties of mutagens and how they work to cause mutation.E. DNA REPAIR
1) How post-replicational DNA repair systems work
2) Examples: (T-T dimers, uracil in DNA, mismatched bases).F. IS A MUTAGEN ALSO A CARCINOGEN? The Ames test
G. HOW IS THE FIDELITY OF GENETIC INFORMATION IN DNA MAINTAINED DURING DNA REPLICATION?
2) The role of DNA repair in keeping genes from accumulating mutations.
Know the essential features/processes/mechanisms of:
A. PROCARYOTES
3. Mode of action of the antibiotic transcription inhibitors rifamycin and actinomycin D
b) transcriptional factors,
roles, enhancer sequencesand
functions
4. RNA editing - posttranscriptional codon editing
5. mRNA splicing signals (sequence elements), mechanisms, and transesterifications.
6. spliceosomes, composition and function.
Know the important features/processes of -
1. Amino acid activation- enzymes, reactions, and fidelity (proofreading) mechanisms.
2. tRNA structure and function.
3. Codon-anticodon recognition, wobble base pairing for recognition of multiple codons by one anticodon
4. Structure and function
of ribosomes, participation of rRNA and ribosomal proteins in the 3-dimensional
structure
of ribosomes, coupled transcription
and translation, polyribosomes.
5. Direction of polypeptide chain elongation and direction of mRNA reading.
6. Sequence of events
in protein synthesis
- required components, etc. (initiation,
elongation, termination,
protein folding and processing).
- Procaryotic details and eucaryotic
comparisons.
- Know about error
correction by Ef-Tu in binding of amino-acyl tRNA to ribosome during
translation.
7. Understand how antibiotic inhibitors of translation work.
CHAPTER 35 [Stryer 4th Edition]: PROTEIN TARGETING
Understand several selected examples which illustrate some basic principles of protein transport across membranes.
CHAPTER 31: CONTROL OF GENE EXPRESSION IN PROKARYOTES
Know the principles involved/mechanisms/important features of the following:
1. Lactose operon - structure, function and regulation (repressor, activation and cAMP - CAP protein, regulatory elements of gene, promoter, operator)
2. Bacteriophage
lambda - regulation of gene transcription [Genetic " Switch" Mechanism]
a) lambda
gene functions
b) lambda
repressor (cI gene product) and maintenance of lysogenic
state
c) 0L
and 0R sites and function
d) relation
of repressor
and cro protein to lysogenic
- lytic state changes
3. Helix-turn-helix motifs of regulatory proteins which bind to DNA.
4. Tryptophan operon and attenuation(regulatory model - how does it work)
5. Mechanism of translational control of ribosomal protein synthesis.
CHAPTER 31: CONTROL OF GENE EXPRESSION IN EUKARYOTES
1. How does the number of DNA molecules relate to the number of chromosomes in a haploid cell.
2. Describe the composition and structure of nucleosomes and chromatin
3. Compare procaryotic and eucarotic DNA replication. Contrast the rates of movement of the replication fork in procaryotes and eucaryotes, and explain how multiple origins allow for rapid duplication of genomes in eucaryotes. Where are parental and newly synthesized histones located after chromosome replication
4. Describe telomere (chromosome ends) replication.
5. What is the role of cyclin in triggering cell division.
6. Know the properties of plant chloroplast and human mitochondrial genomes, relative to nuclear genomes.
7. What are some types of repeated DNA elements of eucaryotic and what proportion of the nuclear genome do they represent?
8. How are eucaryotic rRNAgenes arranged and expressed?
9. Explain how a single-copy gene can give rise to an abundant protein (ex: silkworm fibroin gene expression).
10. What is the percent of mammalian DNA that is likely to encode proteins? What are some examples of repeated and unique protein coding genes in eucaryotes?
11. How do chromosomal puffs, nuclease susceptibility and the degree of methylation of the chromosome relate to transcriptional activity (gene expression) in mammals?
12. How do transcriptional activators work? Consider the classes of regulators which have zinc fingers, and zinc clusters and leucine zippers. Know the role of these elements in DNA-binding.
13. What are functions of homeotic genes and how does the homeo domain of polypeptides relate to regulation of gene expression.
1. What are major structural and functional features of viruses.
2. Define virion,compare virions which have a capsid and those with a membrane envelope.
3. Compare the complexity of genomes and assembly processes of the viruses discussed in class.
4. Know the variety of mechanisms of replication of RNA viruses. Note the roles of:
5. Describe replication of poliovirus RNA and know the role of polyproteins in the virus life cycle.RNA-directed RNA polymerases (RNA replicases) and
RNA-directed DNA polymerases (reverse transcriptases).
6. Why does influenza virus continue to be a problem even though vaccines are available?
9. Define oncogene and know some major classes of oncogenes. How do these genes relate to their normal cellular counterparts- the proto-oncogenes.
10. Know how a tyrosine kinase type oncogene functions to cause unregulated cell proliferation (cancer).
Know the important features of the following:
1. Review retroviruses (genome structure, replication strategy and mechanisms, integration as DNA into the host genome) [See also virus lectures].
2. Structure of AIDS virus (HIV), its genome, and function of gene products.
3. Evidence that HIV causes AIDS.
4. HIV Infection cycle, from cell infection to new virus assembly and budding from infected cell.
5. Regulation of HIV gene expression (functions of nef, tat, rev genes).
6. Relation of HIV to other human and monkey retroviruses, geographic occurrence.
7. T4 lymphocyte (and other cells containing CD4 cell
surface receptors) as infection
targets, infection mechanism,
susceptible tissues. Understand
the roles during disease progression of receptors [CD4
and CCR5]on macrophage
cells infected early and the receptor
protein CXCR4 of T-cells infected and destroyed later in the process.
8. Possible AIDS therapies - molecular strategies (nucleotide analogs, protease inhibitors, vaccines, antisense RNA, etc.).
9. Problems with vaccine development resulting from virus mutations which change antigenic determinants.
10. Improved chances of sucessful treatment with multiple drug therapies
Last Updated on 8/25/2010 By
Dr. Don P. Bourque
Email: dbourque@u.arizona.edu