1. Unit 5 – Molecular Genetics – Chapters 16, 17, 18, 19 & 20
Chapter 16 – The Molecular basis of Inheritance
Objective questions:
DNA as the Genetic Material
1. Explain why researchers originally thought protein was the genetic material.
2. Summarize the experiments performed by the following scientists that provided evidence that DNA is the genetic
material: a. Frederick Griffith
b. Oswald Avery, Maclyn McCarty and Colin MacLeod
c. Alfred Hershey and Martha Chase
d. Erwin Chargaff
3. Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain the
significance of the research of Rosalind Franklin.
4. Describe the structure of DNA. Explain the “base-paring rule” and describe its significance.
DNA Replication and Repair
5. Describe the semiconservative model of replication and the significance of the experiments by Matthew Meselson and
Franklin Stahl.
6. Describe the process of DNA replication. Note the structure of the many origins of replication and replication forks
and explain the role of DNA polymerase.
7. Explain what energy source drives the polymerization of DNA.
8. Define “antiparallel” and explain why continuous synthesis of both DNA strands is not possible.
9. Distinguish between the leading strand and the lagging strand.
10. Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3’ end.
11. Explain the roles of DNA ligase, primer, primase, helicase, and the single-strand binding protein.
12. Explain why an analogy can be made comparing DNA replication to a locomotive made of DNA polymerase moving
along a railroad track of DNA.
13. Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair.
14. Describe the structure and functions of telomeres. Explain the significance of telomerase to healthy and cancerous
cells.
Key terms:
transformation
semiconservative model
leading strand
primase
mismatch repair
telomere
bacteriophages
origins of replication
lagging strand
helicase
nuclease
telomerase
phage
double helix
replication fork
DNA polymerase
DNA ligase
primer
single-strand binding protein
nucleotide excision repair
Chapter 17 – From gene to Protein
Objective questions:
The Connection between genes and Proteins
2. Explain the reasoning that led Archibald Garrod to first suggest that genes dictate phenotypes through enzymes.
3. Describe beadle and Tatum’s experiments with Neurospora and explain the contributions they made to our
understanding of how genes control metabolism.
4. Distinguish between the “one gene – one enzyme” hypothesis and the “one gene – one polypeptide” hypothesis and
explain why the original hypothesis was changed.
5. Explain how RNA differs from DNA.
6. Briefly explain how information flows from gene to protein.
7. Distinguish between transcription and translation.
8. Compare where transcription and translation occur in prokaryotes and in eukaryotes.
9. Define “codon” and explain the relationship between the linear sequence of condons on mRNA and thelinear sequence
of amino acids in a polypeptide.
10. Explain the early techniques used to identify what amino acids are specified by triplets UUU, AAA, GGG and CCC.

2. 11. Explain why polypeptides begin with methionine when they are synthesized.
12. Explain in what way the genetic code is redundant and unambiguous.
13. Explain the significance of the reading frame during translation.
14. Explain the evolutionary significance of a nearly universal genetic code.
The Synthesis and Processing of RNA
15. Explain how RNA polymerase recognizes where transcription should begin.
16. Explain the general process of transcription, including the three major steps of initiation, elongation, and termination.
17. Explain how RNA is modified after transcription in eukaryotic cells.
18. Define and explain the role of ribozymes
19. Describe the functional and evolutionary significance of introns.
The Synthesis of Proteins
20. Describe the structure and functions of tRNA.
21. Describe the structure and functions of ribosomes.
22. Describe the process of translation (including initiation, elongation, and termination) and explain which enzymes,
protein factors and energy sources are needed for each stage.
23. Describe the significance of polyribosomes.
24. Explain what determines the primary structure of a protein and describe how a polypeptide must be modified before it
becomes fully functional.
25. Describe what determines whether a ribosome will be free in the cytosol or attached to the rough endoplasmic
reticulum.
26. Describe two properties of RNA that allow it to perform so many different functions.
27. Compare protein synthesis in prokaryotes and eukaryotes.
28. Define “point mutations.” Distinguish between base=pair substitutions and base-pair insertions. Give examples of
each and note the significance of such changes.
29. Describe several examples of mutagens and they cause mutations.
30. Describe the historical evolution of the concept of a gene.
Key terms
one gene-one polypeptide hypothesis
translation
template strand
promoter
transcription initiation complex
RNA splicing
alternative RNA splicing
anticodon
ribosomal RNA (rRNA)
polyribosome
mutation
nonsense mutation
mutagen
RNA processing
codon
terminator
TATA box
intron
ribozymes
wobble
P site
signal peptide
point mutation
insertion
transcription
messenger RNQA (mRNA)
primary transcript
triplet code
reading frame
RNA polymerase
transcription unit
transcription factor
5’ cap
poly (A) tail
exon
spliceosome
domain
transfer RNA (tRNA)
aminoacyl-tRNA synthesis
A site
E site
signal-recognition particle (SRP)
base-pair substitution missense mutation
deletion
frameshift mutation

3. Chapter 18 – Microbial Models: The Genetics of Viruses and Bacteria
Objective questions:
The Genetics of Viruses
1. Recount the history leading up to the discovery of viruses. Include the contributions of Adolf Mayer, D. Ivanowsky,
Martinus Beijerinck, and Wendell Stanley.
2. List and describe the structural components of viruses.
3. Explain why viruses are obligate parasites.
4. Distinguish between the lytic and lysogenic reproductive cycles, using phage T4 and phage lambda as examples.
5. Describe the reproductive cycle of an enveloped virus. Explain how the reproductive cycle of herpes viruses is
different.
6. Describe the reproductive cycle of retroviruses.
7. Explain how viral infections in animals cause disease.
8. Define “vaccine’ and describe the research of Jenner that led to the development of the smallpox vaccine.
9. Describe the best current medical defenses against viruses. Explain how AZT helps to fight HIV infectons.
10. Describe the mechanisms by which new viral diseases emerge.
11. List some viruses that have been implicated in human cancers and explain how tumor viruses transform cells.
12. Distinguish between the horizontal and vertical routes of viral transmissions in plants.
13. Describe the st5uctures and replication cycles of viroids and prions.
14. List some characteristics that viruses share with living organisms and explain why viruses do not fit our usual
definition of life.
15. Describe the evidence that viruses probably evolved from fragments of cellular nucleic acid.
The genetics of bacteria
16. Describe the structure of a bacterial chromosome.
17. Describe the process of binary fission in bacteria.
18. Compare the sources of genetic variation in bacteria and humans.
19. Compare the processes of transformation, transduction, and conjugation.
20. Distinguish between plasmids and viruses. Define episome.
21. Explain how the F plasmid controls conjugation in bacteria.
22. Describe the significance of R plasmids. Explain how the widespread use of antibiotics contributes to R-plasmid
related disease.
23. Define transposon and describe two types of transposition.
24. Distinguish between an insertion sequence and a complex transposon.
25. Describe the role of transposase and DNA polymerase in the process of transposition.
26. Briefly describe two main strategies that cells use to control metabolism.
27. Explain the adaptive advantages of genes grouped into an operon.
28. using the trp operon as an example, explain the concept of an operon and the function of the operator, repressor and
co-repressor.
29. Distinguish between structural and regulatory genes.
30. Describe how the lac operon functions and explain the role of the inducer, allolactose.
31. Explain how repressible and inducible enzymes differ and how those differences reflect differences in the pathways
they control.
32. Distinguish between positive and negative control and give examples of each from the lac operon.
33. Explain how cyclic AMP and the cyclic AMP receptor protein are affected by glucose concentration.
Key terms:
capsid
viral envelopes
bacteriophages
phages
host range
lytic cycle
virulent phage
lysogenic cycle
temperate phages
prophage
provirus
retrovirus
reverse transcriptase
HIV (human immunodeficiency virus)
AIDS (acquired immunodeficiency syndrome)
vaccine
viroid
prions
nucleoid
transformation
transduction
generalized transduction
specialized transduction
conjugation
F factor
plasmid
episome
F plasmid
R plasmid
transposon
insertion sequence
operator
operon
repressor
regulatory gene
corepressor
inducer

4. cyclic AMP (cAMP)
cAMP receptor protein (CRP)
Chapter 19- The Organization and Control of Eukaryotic Genomes
Objective questions:
Eukaryotic Chromatin Structure
1.Compare the structure and organization of prokaryotic and eukaryotic genomes.
2. Describe the current model for progressive levels of DNA packing.
3. Explain how histones influence folding in eukaryotic DNA.
4. Distinguish between heterochromatin and euchromatin.
Genome Organization at the DNA Level
5. Describe the structure and functions of the portions of eukaryotic DNA that do not encode protein or RNA.
6. Define and distinguish between the three types of satellite DNA.
7. Explain how tandemly repeated nucleotide triplets can lead to human disease.
8. Describe the role of telomeres and centromeres.
9. Describe the structure and proportion of interspersed repetitive DNA.
10. Using the genes for rRNA as an example, explain how multigene families of identical genes can be
advantageous for a cell.
11. Using alpha-globin and beta-globin genes as examples, describe how multigene families of nonidentical
genes
probably evolve; include the role of transposition in your description.
12. Define pseudogenes.
13. Describe the process and significance of gene amplification.
14. Define and explain the significance of transposons and retrotransposons.
15. Explain how genetic recombination during development results in millions of different kinds of antibody
molecules.
The Control of Gene Expression
16. Define differentiation and describe at what level gene expression is generally controlled.
17. Explain how DNA methylation and histone acetylation affects chromatin structure and he regulation of
transcription.
18. Describe the eukaryotic processing of pre-mRNA.
19. Define control elements and explain how they influence transcription.
20. Explain the potential role that promoters, enhancers, activators, and repressors play in transcriptional
control.
21. Describe the two basic structural domains of transcription factors.
22. Explain how eukaryotic genes can be coordinately expressed and give some examples of coordinate gene
expression in eukaryotes.
23. Describe the process of alternative splicing.
24. Describe factors that influence the lifetime of mRNA in the cytoplasm. Compare the longevity of mRNA in
prokaryotes and eukaryotes.
25. Explain how gene expression may be controlled at the translational and posttranslational level.
Key terms:
histone
nucleosome
repetitive DNA
satellite DNA
pseudogenes
gene amplification
cellular differentiation
DNA methylation
control elements
enhancer
alternative RNA splicing
proteasome
tumor-suppressor gene ras gene
heterochromatin
Alu element
retrotransposons
genomic imprinting
activator
oncogene
p53 gene
euchromatin(“true chromatin”)
multigene family
immunoglobulins
histone acetylation
DNA-binding domain
proto-oncogene
Chapter 20 – DNA Technology and Genomics
Objective questions
DNA Cloning
1. Explain how advances in recombinant DNA technology have helped scientists study the eukaryotic genome.
2. Describe the natural function of restriction enzymes.
3. Explain how the creation of sticky ends by restriction enzymes is useful in producing a recombinant DNA

5. molecule.
4. Outline the procedures for cloning a eukaryotic gene in a bacterial plasmid.
5. Describe the role of an expression vector.
6. Explain how eukaryotic genes are cloned to avoid the problems associated with introns.
7. Describe two advantages of using yeast cells instead of bacteria as hosts for cloning or expressing eukaryotic genes.
8. Describe three techniques to aggressively introduce recombinant DNA into eukaryotic cells.
9. Define and distinguish between genomic libraries using plasmids, phages, and cDNA.
10. Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure.
DNA Analysis and Genomics
11. Explain how gel electrophoresis is used to analyze nucleic acids and proteins and to distinguish between two
alleles of a gene.
12. describe the process of nucleic acid hybridization.
13. Describe the Southern blotting procedure and explain how it can be used to detect and analyze instances of
restriction fragment length polymorphism (RFLP)
14. Explain how RFLP analysis facilitated the process of genomic mapping.
15. List the goals of the Human Genome Project.
16. Explain how linkage mapping, physical mapping and DNA sequencing each contributed to the genome mapping
project.
17. Describe the alternate approach to whole-genome sequencing pursued by J. Craig Venter and the Celera
Genomics company. Describe the advantages and disadvantages of public and private efforts.
18. Describe the surprising results of the Human Genome Project.
19. Explain how the vertebrate genome, including that of human, generates greater diversity than the genomes
of invertebrate organisms.
20. Describe what we have learned by comparing the human genome to that of other organisms.
21. Explain the purposes of gene expression studies. Describe the use of DNA microarray assays and explain
how they facilitate such studies.
22. Explain how in vitro mutagenesis and RNA interference help to discover the functions of some genes.
23. Define and compare the fields of proteomics and genomics.
24. Explain the significance of single nucleotide polymorphisms in the study of the human genome.
Practical Applications of DNA technology
25. Describe how DNA technology can have medical applications in such areas as the diagnosis of genetic
disease, the development of gene therapy, vaccine production, and the development of pharmaceutical products.
26. Explain how DNA technology is used in forensic sciences.
27. Describe how gene manipulation has practical applications for environmental and agricultural work.
28. Describe how plant genes can be manipulated using the Ti plasmid carried by Agrobacterium as a vector.
29. Explain how DNA technology can be used to improve the nutritional value of crops and to develop plants that can
produce pharmaceutical products.
30. Describe the safety and ethical questions related to recombinant DNA studies and the biotechnology industry.
Key terms:
recombinant DNA
genetic engineering
restriction enzyme
restriction site
DNA ligase
cloning vector
expression vector
complementary DNA (cDNA)
electroporation
genomic library
polymerase chain reaction (PCR)
restriction fragment length
polymorphisms (RFLPs)
bacterial artificial chromosome (BAC)
RNA interference (RNAi)
proteomics
single nucleotide polymorphisms (SNPs)
genetically modified (GM) organisms
biotechnology
gene cloning
restriction fragments
sticky ends
nucleic acid probe
denaturation
yeast artificial chromosomes (YACs)
cDNA library
genomics
gel electrophoresis
Southern blotting
Human Genome Project
chromosome walking
DNA microarray assays
in vitro mutagenesis
bioinformatics
gene therapy
transgenic organisms
Ti plasmid

6. molecule.
4. Outline the procedures for cloning a eukaryotic gene in a bacterial plasmid.
5. Describe the role of an expression vector.
6. Explain how eukaryotic genes are cloned to avoid the problems associated with introns.
7. Describe two advantages of using yeast cells instead of bacteria as hosts for cloning or expressing eukaryotic genes.
8. Describe three techniques to aggressively introduce recombinant DNA into eukaryotic cells.
9. Define and distinguish between genomic libraries using plasmids, phages, and cDNA.
10. Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure.
DNA Analysis and Genomics
11. Explain how gel electrophoresis is used to analyze nucleic acids and proteins and to distinguish between two
alleles of a gene.
12. describe the process of nucleic acid hybridization.
13. Describe the Southern blotting procedure and explain how it can be used to detect and analyze instances of
restriction fragment length polymorphism (RFLP)
14. Explain how RFLP analysis facilitated the process of genomic mapping.
15. List the goals of the Human Genome Project.
16. Explain how linkage mapping, physical mapping and DNA sequencing each contributed to the genome mapping
project.
17. Describe the alternate approach to whole-genome sequencing pursued by J. Craig Venter and the Celera
Genomics company. Describe the advantages and disadvantages of public and private efforts.
18. Describe the surprising results of the Human Genome Project.
19. Explain how the vertebrate genome, including that of human, generates greater diversity than the genomes
of invertebrate organisms.
20. Describe what we have learned by comparing the human genome to that of other organisms.
21. Explain the purposes of gene expression studies. Describe the use of DNA microarray assays and explain
how they facilitate such studies.
22. Explain how in vitro mutagenesis and RNA interference help to discover the functions of some genes.
23. Define and compare the fields of proteomics and genomics.
24. Explain the significance of single nucleotide polymorphisms in the study of the human genome.
Practical Applications of DNA technology
25. Describe how DNA technology can have medical applications in such areas as the diagnosis of genetic
disease, the development of gene therapy, vaccine production, and the development of pharmaceutical products.
26. Explain how DNA technology is used in forensic sciences.
27. Describe how gene manipulation has practical applications for environmental and agricultural work.
28. Describe how plant genes can be manipulated using the Ti plasmid carried by Agrobacterium as a vector.
29. Explain how DNA technology can be used to improve the nutritional value of crops and to develop plants that can
produce pharmaceutical products.
30. Describe the safety and ethical questions related to recombinant DNA studies and the biotechnology industry.
Key terms:
recombinant DNA
genetic engineering
restriction enzyme
restriction site
DNA ligase
cloning vector
expression vector
complementary DNA (cDNA)
electroporation
genomic library
polymerase chain reaction (PCR)
restriction fragment length
polymorphisms (RFLPs)
bacterial artificial chromosome (BAC)
RNA interference (RNAi)
proteomics
single nucleotide polymorphisms (SNPs)
genetically modified (GM) organisms
biotechnology
gene cloning
restriction fragments
sticky ends
nucleic acid probe
denaturation
yeast artificial chromosomes (YACs)
cDNA library
genomics
gel electrophoresis
Southern blotting
Human Genome Project
chromosome walking
DNA microarray assays
in vitro mutagenesis
bioinformatics
gene therapy
transgenic organisms
Ti plasmid