Download Part 1: DNA Replication

AP Biology
Korzeniewski
Name___________________________
Date__________________Per_______
Molecular Genetics Unit – PDQ’s 1-13
#1 - Due Date: ____1-9-13___Stamp: ________________
Presentation: Molecular Genetics 1: DNA Introduction
Textbook Reading: Ch. 16.1
Supplementary Resources:
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
“Crash Course: Biology” Videos:
1. DNA Structure & Replication: Biology #10
Videos By Paul Anderson:
1. “DNA & RNA Part 1”
Questions to answer:
1. How did the work of TH Morgan and company contribute to the eventual
discovery that DNA was the genetic material in the cell?
2. Explain the transformation experiment conducted by Frederick Griffith.
What did the results of the experiment suggest?
3. Explain how the work of Avery, McCarty, and McLeod expanded on the
work done by Griffith. What did the results of their experiment suggest?
4. Explain the experiment conducted by Hershey and Chase. How did the
results of their experiment demonstrate that DNA was the genetic
material of bacteriophages?
5. What is important about the work done on DNA by Erwin Chargaff?
6. Explain how the work done by Rosalind Franklin and Maurice Wilkins
helped inform Watson and Crick’s model of the structure of DNA.
7. Briefly diagram the double helix structure of DNA. Include:
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At least one A,T,C,G per strand.
Labeled phosphates, deoxyribose, phosphodiester bonds, and the
correct number of hydrogen bonds per base pair.
Make sure to show the anti-parallel orientation of both strands.
Things you should make sure you understand:
(feel free to ask questions about them in class)
1. The specific details of the experiments discussed in this presentation.
2. How to identify all major features of the double helix.
#2 - Due Date: ___1-9-13___Stamp: _________________
Presentation: Molecular Genetics 2: The Central Dogma
***Note: This presentation includes 3 parts
Textbook Reading: Ch. 16.2
Supplementary Resources:


“Crash Course: Biology” Videos:
1. DNA Structure & Replication: Biology #10
2. DNA, Hot Pockets, & The Longest Word Ever: Biology #11
Videos By Paul Anderson:
1. DNA & RNA Part 2”
2. “DNA Replication”
3. “Transcription & Translation”
4. “The Central Dogma”
5. “Genotypes and Phenotypes”
Part 1: DNA Replication
Questions to answer:
1. Diagram the “Central Dogma” of molecular genetics. How does it allow for
DNA to serve as both the heritable molecule and code for protein
sequence?
2. Explain the experiment conducted by Meselson and Stahl. How did the
results of their experiment demonstrate the semi-conservative model of
DNA replication was the accurate model?
3. Explain how each of the following enzymes contributes to the process of
DNA replication:

Helicase
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single-stranded binding proteins
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DNA polymerase
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primase
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ligase
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Topisomerase/gyrase
4. How does replication of the leading strand differ from replication of the
lagging strand? Why can’t both strands of DNA be replicated in the same
fashion?
5. Diagram the replication fork. Include:
1.
2.
3.
4.
5.
the leading strand
the lagging strand
prime orientation of both parent strand and both daughter strands.
Replisome
Okazaki fragments
6. Why is telomerase necessary during the replication of eukaryotic
chromosomes?
Things you should make sure you understand:
(feel free to ask questions about them in class)
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How to recognize the 5’ and 3’ ends of a DNA strand.
The structural differences between free nucleotides (nucleoside triphosphates), and nucleotides in a nucleic acid.
Why replication is necessary for cells, where it happens, its inputs and
its outputs.
The specific details of the process of replication.
The mechanisms in replication that reduce the error rate.
The major differences in replication between prokaryotes and
eukaryotes.
________________________________________________________________
#3 - Due Date: ___1-11-13_
Stamp: ________________
Presentation: Molecular Genetics 2: The Central Dogma
***Note: This presentation includes 3 parts
Textbook Reading: Ch. 17.1-17.3
Part 2: Transcription
Questions to answer:
1. How did Beadle and Tatum’s work on auxotroph’s suggest that
metabolism was controlled by protein enzymes?
2. How does RNA polymerase identify where to begin transcription of a
gene?
3. Explain the relationship between the promoter, enhancers, and
transcription factors.
4. Diagram each of the following phases of transcription.
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

initiation
elongation
termination
5. Explain what happens during each of the following post-transcriptional
modifications of eukaryotic transcripts:
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splicing

5’ capping

poly adenylation
6. How do eukaryotic cells utilize alternative splicing to maximize variety of
gene products that they can produce?
Things you should make sure you understand:
(feel free to ask questions about them in class)
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The relationship between DNA, RNA, Protein, Cells and the Organism.
Why transcription is necessary for cells, where it happens, its inputs
and its outputs.
The major structural differences between RNA and DNA.
The specific details of the process of transcription.
The major differences in transcription between prokaryotes and
eukaryotes.
________________________________________________________________
#4 - Due Date: __1-11-13___
Stamp: _______________
Presentation: Molecular Genetics 2: The Central Dogma
***Note: This presentation includes 3 parts
Textbook Reading: Ch. 17.4
Part 3: Translation
Questions to answer:
1. Explain the meaning of this statment: “The genetic code is punctuated,
unambiguous, and redundant.”
2. How does the structure of a tRNA molecules enable its function?
3. How does the structure of a ribosome enable its function?
4. Diagram what happens during each of the following phases of translation.
Include the location (A, P, or E site) of incoming tRNA molecules,
incoming amino acids, the growing polypeptide chain, uncharged tRNA
molecules and release factors as appropriate:



initiation
elongation
termination
5. Diagram a complete eukaryotic transcription unit. Define each part.
6. Explain the effect that point mutations and frameshift mutations can have
on gene products. Make sure to differentiate between:
1. neutral (silent) mutation
2. missense mutations
3. nonsense mutations
4. Why insertion/deletion of three bases is less deleterious than
insertion/deletion of one or two bases.
Things you should make sure you understand:
(feel free to ask questions about them in class)
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

How mRNA sequence dictates protein sequence.
Why translation is necessary for cells, where it happens, its inputs and
its outputs.
How amino acids are associated and disassociated from tRNA
molecules.
The major differences in translation between prokaryotes and
eukaryotes.
How and why the meaning of the term “gene” has changed over the
past 100 years.
#5 - Due Date: ___1-15-13____ Stamp: _____________
Presentation: Molecular Genetics 3: Regulation of Gene Expression
*Note – This presentation has 2 parts.
Textbook Reading: Ch. 17.6, 18.3, 18.4
Part 1: Prokaryotic Regulation
Questions to answer:
1. Why do prokaryotes need to be able to regulate their metabolism quickly?
2. What is the advantage to prokaryotes grouping related metabolic gene
products into a single operon?
3. Diagram a typical operon. Include and label structural genes, promoter,
RNA polymerase, and repressor protein.
4. What determines if the repressor protein for an operon will be attached or
detached from the operator?
5. Compare a repressible operon with an inducible operon. How are they
similar? How are they different? What determines if an operon will be
repressible or inducible? Give an example of each type of operon in a
typical prokaryotic cell.
6. Explain the function of the CAP/cAMP system. Why is it necessary?
Things you should make sure you understand:
(feel free to ask questions about them in class)


How operons specifically, and gene regulation in general is used in
prokaryotes to modulate their metabolism.
The major similarities and difference of repressible and inducible operons.
#6 - Due Date: ___1-15-13___
Stamp: _____________
Presentation: Molecular Genetics 3: Regulation of Gene Expression
*Note – This presentation has 2 parts.
Textbook Reading: Ch. 19
Part 2: Eukaryotic Regulation
Questions to answer:
1. Why do eukaryotic cells need to be able to turn genes on and off as
necessary?
2. How does the control of gene expression lead to differentiation of cell
function in multicellular eukaryotes?
3. Define each of the following terms and explain how each provides a
eukaryotic cell with the ability to regulate gene expression:
1. nucleosomes
2. DNA methylation
3. Transcription factors/enhancers
4. alternative splicing
5. mRNA degradation
6. RNA interference (RNAi)
7. Protein processing and degradation.
4. Explain the following statement: "Generally speaking, the faster a
eukaryotic cell needs to regulate gene expression, the more downstream
from transcription that regulation will occur."
5. How is it possible that only 1.5% of the human genome can code for gene
products, but humans can be so complex in their physiology?
Things you should make sure you understand:
(feel free to ask questions about them in class)


The major similarities and differences in how eukaryotes regulate their
gene expression compared to how prokaryotes regulate their gene
expression.
Why eukaryotes have more levels of regulation of their genome than
prokaryoes do.
#7 - Due Date: ____1-15-13_____
Stamp: ___________
Presentation: Molecular Genetics 4: Viruses
Textbook Reading: Ch. 18.1, 18.2
Supplementary Resources:

Videos By Paul Anderson:
1. “Viruses”
2. “Viral Replication”
Questions to answer:
1. Why are viruses classified as "obligate intracellular parasites"?
2. What are the minimum parts required for a functional virus?
3. Diagram the lytic and lysogenic cycles of bacteriophages and give
examples of viruses who follow each.
4. What is the evolutionary advantage of an RNA genome in eukaryotic cell
virus?
5. Why is permanent immunity to the flu impossible to acquire?
6. What cell type does HIV infect? How does this lead to AIDS?
Things you should make sure you understand:
(feel free to ask questions about them in class)





Why viruses are not considered to be alive in the classical sense of the
term.
The similarities and difference between prokaryotic and eukaryotic
viruses.
Multiple examples of human diseases caused by viruses.
The relationship between certain viral infections and increased risk of
some forms of cancer.
The similarities and differences between viruses, viroids, and prions.
#8 - Due Date: __1-17-13____
Stamp: ______________
Presentation: Molecular Genetics 5: Biotechnology
**Note - This presentation has 4 parts
Textbook Reading: Ch. 20
Supplementary Resources:

Videos By Paul Anderson:

“Molecular Biology”
Part 1 – Genetic Engineering
Questions to answer:
Restriction Enzymes:
1. How do restriction enzymes work?
2. Explain the significance of “sticky ends” and why they were given that
name.
Vectors:
3. Diagram a typical designed plasmid vector. Label and define each of the
following parts:



The ori
The multiple cloning sequence (you might need the internet)
Selectable markers--give two examples of genes used as
selectable markers.
Genetic Engineering:
4. How does bacterial transformation work? What do bacteria use it for?
What do genetic engineers use it for?
5. What is cDNA? How is it made? Why is it necessary?
6. Diagram the process of genetic engineering a bacterium.
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
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
Begin with a plasmid and the gene of interest.
Show how the gene is inserted in the plasmid.
Show how the plasmid is incorporated into a bacterial cell.
Show how the cell copies the plasmid.
Show how the cell expresses the gene of interest.
7. Explain how reporter genes (selectable markers) can be used to separate
bacteria who have taken up the transformed plasmid from those who
have taken up the non-transformed plasmid.
Things you should make sure you understand:
(feel free to ask questions about them in class)




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

How restriction enzymes evolved.
The use of restriction enzymes in genetic engineering.
The use of vectors in genetic engineering.
Why bacterial cells are comparatively easy to genetically engineer.
How ligase is used in genetic engineering.
How reporter genes like LacZ and Green Flourescent Protein are used in
genetic engineering.
How genetically engineering eukaryotes differs from genetically
engineering prokaryotes.
How genetically engineering complex (multi-gene) traits differs from
genetically engineering simple (single-gene) traits.
#9 - Due Date: __1-17-13_____
Stamp: _____________
Presentation: Molecular Genetics 5: Biotechnology
**Note - This presentation has 4 parts
Textbook Reading: Ch. 20
Part 2: Genetic Testing
Questions to answer:
Gel Electrophoresis & Labeling:
1. How does gel electrophoresis work? What properties of the DNA does it
utilize?
2. Where will the smallest fragments of DNA be found on a gel after it runs?
Where will the largest fragments be found? How is the size of a
particular fragment determined?
3. Why is it necessary to utilize probes for labeling particular DNA
sequences? How is this process accomplished?
The Polymerase Chain Reaction:
4. Explain the purpose of the Polymerase Chain Reaction. Why is it useful?
5. Explain the function of the following in PCR
1. Taq polymerase
2. primers.
3. thermal cycler.
6. Explain what happens during each phase of a PCR cycle, and the
temperature at which each phase occurs:
1. Denaturation.
2. Annealing.
3. Elongation.
Genetic Testing:
7. Explain the relationship between single nucleotide polymorphisms
(“SNPs”) and restriction fragment length polymorphisms (“RFLPs”)? How
are they caused and why do they matter?
8. Pick one real-world application that uses PCR and gel electrophoresis and
specifically explain how each process is used in that application
Things you should make sure you understand:
(feel free to ask questions about them in class)



How gel electrophoresis is used in genetic engineering.
How PCR is sued in genetic engineering.
The ethical considerations involved in genetic testing.
________________________________________________________________
#10 - Due Date: __1-28-13____
Stamp: _____________
Presentation: Molecular Genetics 5: Biotechnology
**Note - This presentation has 4 parts
Textbook Reading: Ch. 20
Part 3: Cloning & Sequencing
Questions to answer:
Cloning:
1. Compare and contrast therapeutic cloning with reproductive cloning.
DNA Libraries:
2. What is the purpose of a DNA “library”? How can specific genes be
retrieved from a DNA library?
DNA Sequencing:
3. What are dideoxynucleotides? Why are they used in DNA sequencing?
4. Explain how the Sanger sequencing method works.
5. How has sequencing technology advanced since the development of the
process by Fred Sanger? Give three examples.
Microarrays:
6. What is the purpose of a microarray? Give an example of a real-world
application of microarray analysis (you probably need to use the internet).
Things you should make sure you understand:
(feel free to ask questions about them in class)
1. The ethical considerations involved in reproductive and therapeutic
cloning.
2. How DNA sequencing is used in genetic engineering.
#11 - Due Date: ___1-28-13___
Stamp: _____________
Presentation: Molecular Genetics 5: Biotechnology
**Note - This presentation has 4 parts
Textbook Reading: Ch. 20
Part 4: Ethical Considerations
Questions to answer:
1. Give three examples of things that the biotechnology revolution has
allowed us to do that couldn’t have been done at a prior point in human
history.
You will most likely need to do a bit of research to answer these questions:
2. From a legal standpoint, how much information do you have a right to
know about the genetically engineered nature of the food you eat and the
products that you consume?
3. From a legal standpoint, how much information do other people and
entities have the right to know about your genome?
4. From a legal standpoint, what sorts of genetically engineered technologies
are individuals allowed to copyright?
5. From a legal standpoint, what constraints are placed on the scientific
establishment with regard to altering the genetic material of organisms?
This one is for your own consideration:
6. Consider the answers to the last five questions. From a personal
moral/ethical standpoint, how do you feel about those answers?
#12 - Due Date: __1-30-13___
Stamp: ______________
Presentation: Molecular Genetics 6: Genetics - Systems Perspectives
**Note – This presentation is 2 parts
Textbook Reading: Ch. 21
Part 1: Developmental Genetics
Questions to answer:
1. Define the term “differentiation.”
2. Explain the function of each of the following as relates to the process of
differentiation:
1. cytoplasmic determinants
2. cellular induction
3. cellular determination
3. Why does determination have to precede differentiation?
4. How do cells acquire positional information about their location in a
developing embryo?
5. Explain the function of bicoid.
6. What are the homeobox genes? What do they do in a developing animal?
Things you should make sure you understand:
(feel free to ask questions about them in class)
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


How mutations in developmental genes can lead to relatively rapid
evolutionary change.
The evolutionary significance of the universality of developmental genes
across all animal phyla.
The relationship between development, gene expression, and cell
signalling.
The role of genetic switches in development.
________________________________________________________________
#13 - Due Date: ___1-30-13___
Stamp: ____________
Presentation: Molecular Genetics 6: Genetics - Systems Perspectives
**Note – This presentation is 2 parts
Textbook Reading: Ch. 21
Part 2: Genomics
Questions to answer:
1. Explain the purpose of the Human Genome Project (HGP).
2. What is bioinformatics and why is it a necessary and important field of
study?
3. Is there any particular pattern among genomes and the organisms who
have them?
4. Explain what transposable elements are and give an overview of their
function.
5. On a percentage basis, what type of sequence comprises the most of the
human genome? What type of sequence comprises the least?
6. Explain the types of signatures that have been left in the human genome
when looking at our split from rodents and from chimpanzees.
Things you should make sure you understand:
(feel free to ask questions about them in class)

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


The difference in genome sequencing taken by the public human genome
project, and the private initiative helmed by Craig Venter.
Why the human genome project finished sequencing four years ahead of
schedule.
The roles of all major categories of DNA sequences in the human
genome.
The differences between different kinds of gene families found in
genomes.
The relationship between gene duplication and genome evolution.