BIO 348: Cell Biology
Review Sheet - Exam #2
Dr. Azad Gucwa
Chapter 5: DNA Structure
Concept questions
1. Understand the purpose and results of each of the pioneering experiments we discussed in class that helped confirm
DNA (not proteins) as the genetic material (i.e. Griffith’s experiment, Avery, and Hershey-Chase “Blender” experiment).
2. What are the components of a DNA nucleotide? What are the differences between DNA and RNA nucleotides?
3. Describe and be able to identify all the parts of the the double helix structure of DNA. What are the sides of the DNA
double helix composed of? What is in the middle of the strands? How are the strands held together? What does it
mean that the DNA is antiparallel? Explain the 5’ and 3’ ends of the DNA strands.
4. What is meant by complementary base pairing? Who binds with whom? Know this! Very well.
5. Define and understand the differences between genes, genomes and chromosomes.
6. Describe the properties of the human genome (size, composition (coding vs. noncoding areas), # of genes, and
composition of “junk DNA”).
7. What is the purpose of chromosomes? Describe the chromosome profile found in humans. What is a karyotype? What
would that karyotype look like for a male or female human?
8. What is the difference between chromatin and a mitotic chromosome? What is the purpose of condensing the
chromosomes? Describe the structure of a mitotic chromosome and identify the various components (centromere,
telomere, chromatids, etc.)
9. Describe the levels of chromosome organization in euchromatin as well as a mitotic chromosome.
10. What is the purpose of histones? How many are there and how are they organized? Why are histones composed
largely of positively charged amino acids?
11. What are nucleosomes? What is the composition of an individual nucleosome?
12. How does the linker histone (H1) help create chromatin fibers?
13. What are the different levels of chromatin organization? How does this organization assist in compacting the DNA?
14. What processes does DNA tightly bound to chromatin interfere with?
15. What is chromatin remodeling? Which modification(s) can positively or negatively affect transcription?
16. What is the purpose of X inactivation? How is it accomplished?
Chapter 6: DNA Replication and Repair
Vocabulary

DNA Replication
o Semiconservative
o Conservative
o Dispersive
o Origin of replication
o Replication bubble
o Replication fork
o Template
o Leading strand
o Lagging strand
o Single strand binding protein
o Semidiscontinuous
o Okazaki fragments
o Enzymes of replication:
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
o
o

DNA Polymerase
Primase

RNA Primer

Helicase

Gyrase (topoisomerase)

Prevents supercoiling

Ligase
Exonuclease
Telomeres/telomerase
DNA Repair
o Mismatch repair
o DNA Damage

Ultraviolet (UV) Radiation
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
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Gamma & X-Rays
Thymine Dimers
Deamination
Depurination
Excision repair
Double Strand Breaks
Nonhomologous end joining
Homologous recombination
Nuclease digestion
Strand invasion
DNA synthesis
Ligation
Concept Questions
1. Understand and be able to explain the Meselson-Stahl experiment. How does DNA replication occur
(semiconservative, conservative, dispersive)?
2. Describe the overall process of DNA replication. How does the parent DNA molecule serve as templates for new strand
synthesis? What is the purpose of base-pairing in DNA replication?
3. Describe the events at the replication bubble. How do they form? How do they “grow”?
4. How does DNA polymerase catalyze the synthesis of a new stand of DNA? Where does it get the energy to build the
new strand? In which direction does DNA pol add new nucleotides?
5. Describe the process of DNA replication in both the leading strand and the (dreaded) lagging strand. What is the
purpose of each of the enzymes used in DNA replication? What are Okazaki fragments and how do they end up getting
made into seamless new strands of DNA?
6. Describe the action of topoisomerase (DNA gyrase) in relieving supercoiling of DNA.
7. What is the function of the exonuclease activity found in DNA polymerases?
8. What is the purpose of the telomeres? What does telomerase do?
9. How does mismatch occur? How does DNA polymerase prevent mismatch repair? What mechanisms do cells have to
repair mismatch damage if DNA pol doesn’t catch it? How does the mismatch repair machinery know which strand to
repair?
10. List some agents that may damage DNA. List and describe the different types of DNA damage discussed in class.
11. What are the strategies to repair double strand breaks? NHEJ vs. Homologous recombination
12. Describe the process of homologous recombination.
Chapter 7: Genes to Proteins
Vocabulary
 Prokaryotic Transcription
o RNA polymerase
o Sigma factor
o Initiation
 Promoter
o Elongation
o Termination
 Terminator sequence
o Eukaryotic transcription
initiation
 General transcription

factors
 TATA box

 TATA Binding Protein (TBP)
 TFIID
 Transcription initiation
complex
 TFIIH
 Helicase
 Kinase
 Holoenzyme
 RNA Processing
o Pre-mRNA

o
5’ cap
 Reverse guanosine
o 3’ Poly-A tail
o RNA Splicing
 Introns
 Exons
 snRNPs
 Spliceosome
 Lariat
 Alternative splicing
Nuclear Export
o Nuclear pore complex
Translation
o Genetic code
o Codons
o Reading frame
o tRNA
 anticodon
 tRNA charging
 aminoacyl tRNA
synthetase
o ribosomes
o Translation initiation
o
o
o
o
o
o
Eukaryotic (translation)
initiation factors (eIFs)
 initiator tRNAiMet
Translation Elongation
 Peptidyltransferase
(ribozyme)
 Peptide bond
Translation termination
 Stop codons
 Release factor
Polycistronic mRNA
Polysomes
Protein modification
 Cleavage
 Glycosylation
 Phosphorylation
 Cofactor/coenzyme
addition
 Binding to other protein
subunits
Proteasome
 ubiquitin
Concept Question
1. What is the central dogma of molecular biology? How does information flow?
2. Describe the differences in the overall process of gene expression in eukaryotes vs. prokaryotes.
3. How is RNA different that DNA? List and describe the functions of the different types of RNA found in a cell.
4. Describe the process of Transcription initiation, elongation, and termination in prokaryotes.
5. What are the functions of the 3 different eukaryotic RNA polymerases?
6.
7.
8.
9.
10.
11.
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21.
Describe the process of eukaryotic transcription initiation. What are the roles of transcription factors in this process?
Describe the roles of TBP (TFIID) and TFIIH.
Why doesn’t prokaryotic mRNA go through RNA processing?
What occurs during eukaryotic RNA processing? Understand how each modification is done and why.
What is the purpose of alternative splicing?
How does the nuclear pore complex recognize mRNA and allow it to leave the nucleus?
How does mRNA stability affect gene expression? (i.e. level of protein synthesis)
Describe the features of the genetic code (# of codons, types of codons, etc.). Why is it said to be degenerate? Is the
genetic code truly universal? Why or why not?
Describe the structure and function of tRNA. What is tRNA charging?
What is the composition and structure of ribosomes? Where do ribosomes get made?
What are the three sites within a ribosome?
Describe the process of translation initiation. What components have to come together in order to initiate translation?
Describe the process of translation elongation. What are the functions of each of the different sites in the ribosome (A,
P, E)? What is the function of peptidyltransferase during elongation?
Describe the process of translation termination.
What is polycistronic mRNA? What types of organisms utilize polycistronic mRNA?
What types of modifications may be necessary to activate a protein once it has been synthesized?
How can proteins get degraded once the cell no longer needs them?
Chapter 8: Control of Gene Expression
Vocabulary
 Gene Expression
 Differentiation
 Differential gene expression
 Housekeeping genes
 Regulatory proteins
 Transcription factors
 Control sequences
 Negative vs. positive control
 Prokaryotic gene expression
o Components of Operons
 Structural genes
 Promoter
 Operator
 Repressor
 Regulatory gene
 Polycistronic mRNA
o

Inducible vs. repressible
operons
 Trp operon
 Corepressor
 Lac operon
 Inducer
 CAP protein
 cAMP
Eukaryotic Gene Expression
o General transcription factors
o Specific transcription factors
o Upstream
o Promotor
 Core promoter
 TATA Box
 Proximal promoter
o Enhancers
o
o
o
o
o
o
o
Transcription activators
Transcription repressors
Mediators
Transcription factors
 DNA-binding domain
 Transactivation domain
 ligand-binding domain
 Dimerization
 homodimers
 heterodimers
Combinatorial control
Differential Development
Chromatin remodeling
 Histone Acetylases
 Histone deacetylases
 DNA Methylation
 Epigenetic inheritance
Concepts
1. What is gene expression? Why do cells need regulate and control their gene expression?
2. Describe the process of prokaryotic gene expression. What is the purpose of operons? What are the components of
the operon and what is the purpose of each?
3. What is the difference between an inducible and repressible operon? Describe what happens in the presence or
absence of tryptophan in the trp operon. Describe what happens in the presence or absence of lactose and in the
presence and absence of glucose in the lac operon.
4. Describe the different levels of control of gene expression found in eukaryotes.
5. Describe the function of transcription factors, both general and specific. Describe the upstream sequences before a
gene (i.e. proximal promoter, distal promoter, enhancer sequences).
6. How can enhancer sequences influence a gene from far away? What is the function of mediators?
7. How does combinatorial control of gene expression work? What are the benefits?
8. Describe the general components of transcription factors. How does dimerization increase the flexibility of
transcription factors
9. What is differential development and how do transcription factors contribute?
10. How does chromatin remodeling affect gene expression? What is the purpose of Histone acetylation? Histone
deacetylation? DNA Methylation? How are Histone and DNA modifications inherited by subsequent generations
(epigenetic inheritance)?