Molecular Genetics Unit PDQ S 1-13

AP Biology Name______Korzeniewski 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:

 “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:

 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

 “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

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

 single-stranded binding proteins

 DNA polymerase  primase

 ligase

 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. the leading strand 2. the lagging strand 3. prime orientation of both parent strand and both daughter strands. 4. Replisome 5. Okazaki fragments

6. Why is telomerase necessary during the replication of eukaryotic chromosomes? Things you should make sure you understand:

 How to recognize the 5’ and 3’ ends of a DNA strand.  The structural differences between free nucleotides (nucleoside tri- phosphates), 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.

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#3 - Due Date: ___1-11-13_ Stamp: ______

Textbook Reading: Ch. 17.1-17.3

Part 2: Transcription

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.  initiation  elongation  termination

5. Explain what happens during each of the following post-transcriptional modifications of eukaryotic transcripts:

 splicing

 5’ capping

 poly adenylation

6. How do eukaryotic cells utilize alternative splicing to maximize variety of gene products that they can produce?

 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.

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#4 - Due Date: __1-11-13___ Stamp: ______

Part 3: Translation

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.

 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

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?

 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

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:

 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

 Videos By Paul Anderson: 1. “Viruses” 2. “Viral Replication”

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?

(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

 Videos By Paul Anderson:

 “Molecular Biology”

Part 1 – Genetic Engineering

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.

 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.

 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: ______

Part 2: Genetic Testing

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:

 How gel electrophoresis is used in genetic engineering.  How PCR is sued in genetic engineering.  The ethical considerations involved in genetic testing.

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#10 - Due Date: __1-28-13____ Stamp: ______

Part 3: Cloning & Sequencing

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).

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: ______

Part 4: Ethical Considerations

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

Part 1: Developmental Genetics

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?

 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.

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#13 - Due Date: ___1-30-13___ Stamp: ______

Presentation: Molecular Genetics 6: Genetics - Systems Perspectives **Note – This presentation is 2 parts

Part 2: Genomics

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:

 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.