Biology 30

Morinville Community High School

Unit 4: Molecular Genetics

Name: ______________

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Chapter 18 text p. 622-671 Key Concept A: DNA structure and the historical events that lead to it’s discovery A1. Isolating DNA as the hereditary material: Avery, MacLeod, McCarty & Hershey and Chase A2. Chemical Components of DNA & Chargaff’s Rule A3. 3D Structure of DNA: Franklin, Watson, and Crick Key Concept B: DNA Replication B1. Semi-Conservative Replication of DNA Key Concept C: Protein Synthesis C1. Genes and the Genetic Code C2. The nature of RNA & Amino Acids C3. Transcription C4. Translation C5. Control of Gene Expression Key Concept D: Mutations D1. Causes & Severity of Mutations D2. Types of Mutations

• Same-, Non-, and Mis-Sense • Point Mutations • Chromosome Mutations • Chromosome Number Mutations & Karyotypes

Key Concept E: Genetic Technlogoy E1. Restriction Enzyme s and Ligases E2. Gel Electrophoresis and DNA Fingerprinting E3. PCR Key Concept F: Biotechnology Products F1. Transgenic Bacteria (Gene Cloning) F2. Transgenic Plants & Animals

Key Concept G: Diagnosis and Treatment of Genetic Disorders G1. Genetic Counseling G2. Prenatal Diagnosis G3. Genetic Screening G4. Treating Human Genetic Disorders

Molecular Genetics Unit Outline

MOLECULAR GENETICS UNIT EXAM

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A1. Isolating DNA structure and the historical events that lead to it’s discovery p. 622-625 Complete the following table to identify the contribution that each of the following made to the discovery of DNA as the hereditary material:

Scientist Discovery Year

Friedrich Miescher

Frederick Griffith

Oswald Avery, Colin MacLeod,

and Maclyn McCarty

Alfred Hershey and

Martha Chase

Introductory Activity: Extracting DNA

Purpose The purpose of this activity is to develop an understanding for the structure of DNA at a molecule level and to observe DNA that has been extracted from fruit. It is important therefore to follow the instructions carefully & ask questions where necessary.

DNA Extraction

1. Put a ¼ strawberry or slice of banana into a sandwich bag and close.

2. Thoroughly mush up the fruit, getting rid of all the big chunks,

leaving only liquid pulp.

3. While the fruit is being mixed, measure out 10 ml of lysis solution. MEASUREMENTS NEED TO BE EXACT USING GRADUATED CYLINDER.

4. Add 10 ml of lysis solution to the fruit in the bag, close and mix

by gentle inversion and squishing. Mix for 5 minutes. Note: try to avoid creating too much foam.

5. Place cheesecloth into a funnel and pour the fruit solution

through the cheesecloth, collecting the fruit liquid solution in the large test tube. The cheesecloth should filter out the chunks.

6. Tilt the test tube and slowly add 10 ml of 95% ethanol along the

surface of the fruit solution and watch the DNA extract! After a minute, plug the test tube with a stopper and mix by inversion a few times to collect the remaining DNA from the fruits solution. The DNA will look like a white bubbly glob!

7. Discard solid waste products into garbage, and liquids down the

drain.

Key Concept A: DNA Structure and the historical events that lead to it’s discovery (p. 622-630)

Notes

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A2. Chemical Components of DNA and Chargaff’s Rule p. 626-628 DNA is composed of individual units called ______________________________ Each nucleotide consists of the following three molecules: 1. 2. 3. Draw a DNA Nucleotide: Complete the following table: Type of Nitrogen

Base Examples Number of Rings

Purines 1. ____________

2. ____________

Pyramidines 3. ____________

4. ____________

DNA is two long strands of nucleotides that are bound together in a spiral

shape called a ___________________________________________.

Explain in your own words the contribution each of the following scientists made in the discovery of the Double Helix: Edwin Chargaff:

Rosalind Franklin:

James Watson and Francis Crick:

• The two DNA strands are anti-parallel • Sugar-phosphate backbones on the outside with the paired

nucleotide bases on the inside • The phosphate end of the chain is referred to as the 5’ end. The

opposite end is the 3’ end.

Vocabulary

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Thought Lab: DNA Deductions Edwin Chargaff discovered that the nucleotide composition of DNA varies from one species to another. However, the nucleotide composition always follows certain rules. This constant relationship became known as Chargaff's rule: the amount of adenine is equal to the amount of thymine, and the amount of cytosine is equal to that of guanine. Pre-lab questions Use the molecule to the right to answer the following questions. a) What is the number of base pairs illustrated in the molecule to the right? b) How many base pairs long is this DNA molecule? c) What is the number of nucleotides shown in the diagram? d) How many different nucleotides are there in the diagram? e) What percentage of the nitrogen bases are adenine? Without calculating, what percent must be thymine? f) If a DNA molecule contains 17.5% cytosine molecules, then what percentage must be thymine molecules? Show your work. g) How many hydrogen bonds hold together adenine and thymine? h) How many hydrogen bonds hold together cytosine and guanine?

i) Label a hydrogen bond on the diagram. j) Label a phosphate group on the diagram. k) Label a deoxyribose sugar on the diagram.

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Procedure – Complete the following on a separate sheet of paper 1. Copy the following table. Imagine that you are analyzing a DNA sample from the liver tissue of newly discovered species of mouse. Use the information in the table below to complete the nucleotide composition of your sample that will be 10 base pairs long.

Nucleotide Bases

Percentage in DNA sample

Number present in a molecule 10 bp long

Number present along one side of the double helix

adenine 31 cytosine guanine thymine

2. Draw a linear stretch of double stranded DNA molecule 10 base pairs long, with a nucleotide sequence that corresponds to the nucleotide composition of your sample.

Start by building the left side first; then build the

complementary right side. Use solid lines to show covalent bonds and dotted lines to show hydrogen bonds. (see diagram on the first page)

Make sure your purines, adenine and guanine, have a double-ring structure. Make sure your pyrimidines, cytosine and thymine, have a single-ring structure.

Label the 5' and 3' ends.

Analysis 1. Would the nucleotide composition of mouse liver tissue be different from a second DNA sample from the muscle tissue of the same mouse. Explain your answer. 2. Would the nucleotide composition of your original DNA sample be different from the nucleotide composition of a tissue sample from your gametes? Explain you answer. 3. Would the nucleotide composition of your liver tissue DNA sample be different from the nucleotide composition of a tissue sample from the liver of a deer? Explain your answer. Hand in the Procedure and Analysis Questions

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B1. Semi-Conservative Replication of DNA p.630-633 Semi-Conservative Replication: Draw a model of Semi-Conservative Replication:

DNA Replication happens in the following three stages: SEPARATING THE STRANDS

1. DNA helicase unzips the double helix by breaking the hydrogen bonds between the complimentary bases in the two strands

BUILDING THE COMPLEMENTARY STRAND

2. DNA polymerase III adds complementary nucleotides to the growing strands, adenine pairs with thymine and cytosine pairs with guanine, using the exposed strands of the parent DNA molecule as a template. DNA polymerase can only synthesize new DNA in a 5’ to 3’ direction

3. The leading strand is formed continuously

4. The lagging strand is formed in short fragments, starting from an

RNA primer.

5. DNA polymerase I cuts out the RNA primers and replaces them with the appropriate DNA nucleotides.

6. DNA ligase joins the fragments

DNA REPAIR 7. Trailing DNA polymerase enzymes “check” the base pairs to ensure that correct pairing has occurred.

Key Concept B: DNA Replication (p. 630-633)

Vocabulary

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DNA Replication

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C1. Genes and the Genetic Code p.629-630 & p.637-637 Gene: Cenral Dogma of Protein Synthesis (p.636): The genetic code is much like a book, where the arrangement of letters (in this case nucleotides) will result in different meanings (in this case different amino acids) How many nucleotides code for one amino acid? How many different types of amino acids are there? Describe how the genetic code is….

a) redundant:

b) continuous:

c) universal:

C2. The Nature of RNA & Amino Acids p.636-637 There are three different types of RNA involved in protein synthesis. What does RNA stand for: ______________________________________________ List three ways in which RNA is different than DNA: 1. 2. 3. In RNA, the nucleotide thymine is replaced by ________________. Types of RNA: What does the “m” stand for in mRNA? What does the “r” stand for in rRNA? What does the “t” stand for in tRNA?

Key Concept C: Protein Synthesis (p. 636-642)

Vocabulary

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C3. Transcription p.637-638 What does the word Transcription mean? Where does mRNA transcription take place in the cell?

Steps in DNA Transcription

1. The two strands of a DNA molecule, sense and antisense, separate along the length of a gene

2. The antisense strand forms the template for transcription; the sense strand is transcribed

3. RNA polymerase binds at a site called the promoter region: this determines where transcription starts.

4. RNA nucleotides form hydrogen bonds with the complementary nucleotide sequence of the DNA strand, however the base thymine is replaced with uracil.

5. The enzyme RNA polymerase will attach individual RNA nucleotides together to extend the growing mRNA molecule.

6. When the RNA polymerase reaches the terminator sequence, it detaches from the DNA and the newly formed mRNA strand is released

7. The DNA double helix reforms

Vocabulary

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C4. Translation Steps in Translation: On the series of diagrams to the right, identify the following:

• mRNA • rRNA (ribosome) • tRNA • A codon • An anti-codon

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C5. Control of Gene Expression As a zygote divides, groups of cells take on different shapes and functions. This process is called ____________________ Each different cell has all the genes, but different genes are active in different kinds of cells. A sophisticated regulatory system of control genes switches protein synthesis genes on and off, responding to environmental changes and shaping the differentiation of various cell lineages.

in the boxes below to show which genes you think would be active in each of the cell types. Write switched "on" or switched "off"

Pancreas Cells

Blood Cells Muscle Cell

alpha cells

beta cells

WBC R BC

Genes for…. glycolysis enzymes

Muscle contraction Proteins (actin & myosin)

glucagon

insulin

hemoglobin

Specialized cells may retain all of their genetic potential. Because of this

ability, it is possible to switch on genes from a single specialized cell and

manipulate the cell to reactivate and recognize that it is a single zygote

cell. This zygote will then begin the embryological process, resulting in a

cloned organism.

Stem cells are undifferentiated cells that can be transformed into

specialized tissues. Stem cell research is attempting:

Indicate

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D1. Causes of Mutations p.644-645 List three examples of physical mutagens: 1. 2. 3. List three examples of chemical mutagens: 1. 2. 3. Mutations generally result in a protein that does not function as well or does not function at all. In some rare cases, mutations can provide an advantage and be beneficial. These changes may give that organism a competitive advantage.

D2. Types of Mutations Same-Sense Mutations: Mutations that do not affect the final gene product. The mutated DNA sequence produces the same protein as the original DNA sequence. Level of Severity: _________________ Mis-Sense Mutations: Mutations change the DNA sequence, and the resulting protein, but the protein is still functional in some capacity. Level of Severity: _________________ Non-Sense Mutations: Mutation changes the DNA sequence and the protein such that the protein no longer functions. Level of Severity: _________________ Mutations come in 3 main varieties: Point Mutation: A change in the DNA sequence at one specific location. These include:

• base substitutions • addition and deletions of bases (resulting in a reading frame shift

unless they occur in multiples of three) • tautomerism (incorrect base pairing)

Chromosome Mutation: Whole sections of chromosome are rearranged. This often leads to promoters being placed before genes that control the cell cycle. These types of mutations generally lead to cancer. Chromosome Number Mutations: incorrect number of chromosomes resulting from an error in spermatogenesis or oogenesis.

Key Concept D: Mutations (p.644-645)

Vocabulary

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Point Mutations. Using the following DNA sequence, write a new DNA sequence that would result from each type of point mutation. Show the corresponding polypeptide and indicate whether you think it will be nonsense, missense, or samesense. DNA: AAT CGG CTC AAC GGT AAA

Polypeptide:

Substitution New DNA Sequence: Polypeptide: Severity: Addition New DNA Sequence: Polypeptide: Severity: Deletion New DNA Sequence: Polypeptide: Severity:

Chromosome Mutations

Practice

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Chromosome Number Mutations Karyotope: Identify the chromosome mutation for each of the following syndromes: Down syndrome: Patau Syndrome: Edward Syndrome: Turner Syndrome: Klinefelter Syndrome: Jacobs Syndrome: Triple X Syndrom (yes, this is a real disorder):

Vocabulary

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E1. Restriction Enzymes and Ligases p.648 Restriction Enzymes: are like molecular scissors that can cut double-stranded DNA at a specific base pair sequence. Example: The restriction enzyme called EcoR1 cuts the DNA at a specific recognition site: GAATTC . Each DNA strand is cut, leaving overhanging ends called sticky ends. Ligase: an enzyme that is used to join complementary DNA fragments together. Recombinant DNA. DNA molecule that includes genetic material from different sources.

Origin of Restriction Endonucleases Restriction enzymes, such as endonucleases, have been isolated from many bacteria. Restriction enzymes are named according to the bacterial species from which they were first isolated. There are now hundreds of restriction enzymes used by genetic engineers.

Recognition Sites for Selected Restriction Enzymes

Enzyme Source Recognition Site

EcoR1 Escherichia coli G A A T T C BamH1 BAcillus

amyloliquefaciens G G A T C C

Hae III Haemophilus aegyptius

G G C C

Hind III Haemophilus influenzae

A A G C T T

Hpa1 Haemophilus parainfluenzae

G T T A A C

Hpa II Haemophilus parainfluenzae

C C G G

Mbo 1 Moraxella bovis G A T C Not 1 Norcardia otitdis-

caviarum G C G G C C G C

Taq 1 Thermus aquaticus T C G A

Key Concept E: Genetic Technologies (p.648-651)

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Practice Question: A genetic engineer wants to use the restriction enzyme BamH1 which cuts each DNA sequence after its first guanine nucleotide. a) Consult table on the previous page and write out the recognition site for this enzyme:_________ b) Circle every recognition site on the DNA sequence below that would be cut by BamH1. AATGGGTACG CACAGTGGAT CCACGTAGTA TGCGATGCGT AGTGTTTATG GAGAGAAGAA AACGCGTCGC CTTTTATCGA TGCTGTACGG ATGCGGAAGT GGCGATGAGG ATCCATGCAA TCGCGGCCGA TCGXGTAATA TATCGTGGCT GCGTTTATTA TCGTGACTAG TAGCAGTATG CGATGTGACT GATGCTATGC TGACTATGCT ATGTTTTTAT GCTGGATCCA GCGTAAGCAT TTCGCTGCGT GGATCCCATA TCCTTATATG CATATATTCT TATACGGATC GCGCACGTTT c) State how many fragments of DNA were created by this action.___________ E2. Gel electrophoresis and DNA fingerprinting p.649-650 Gel Electrophoresis is a method that separates large molecules ( DNA or proteins) on the basis of mass and electric charge. text p. 649-650 To prepare DNA for gel electrophoresis a DNA sample is cut

up into fragments with ______________________________________.

This pattern is called a DNA fingerprint DNA fingerprinting: a technique used to distinguish between individuals of the same species using samples of their DNA Example: DNA from a section of chromosome 4 of two different individuals

What would the DNA fingerprint look like of each individual?

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E3. PCR PCR is a technique for amplifying a DNA sequence by repeated cycles of strand separation and replication

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genetic engineering: transgenic organisms: F1. Transgenic Bacteria / Gene Cloning Transformation of bacteria: Bacteria are the most common

organisms that are transformed by genetic engineers.

Transgenic bacteria may be used to study gene expression or

gene function, to create and maintain a stock of particular DNA

fragment, or to synthesize a useful gene product.

For example, transgenic bacteria have been engineered to

produce human insulin for diabetics and human growth

hormone, used in treatment of pituitary dwarfism.

Steps in Cloning hGH , using a bacterial plasmid

The use of recombinant DNA hGH raises ethical questions:

Key Concept F: Biotechnology products (p. 654-658)

Vocabulary

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F2. Transgenic Plants & Animals

Transgenic plants:

Summarize the role of golden rice as a transgenic plant. Explain how this transgenic plant helps achieves a social, economic or environmental goal.

Transgenic animals:

Give an example of a transgenic animal that helps achieve a social, economic, or environmental goal. Explain how the transgenic animal achieves this.

There are organizations that have opposed the use of transgenic organisms. Some risks cited by these groups: -Environmental threats -Health effects -Social and economic issues Use text p. 657 to expand upon each of the above risks

Notes

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G1. Genetic Counseling: Prior to having children, parents can seek out a genetic councilor to inform them of the risks of having a child with a genetic disorder. The councilor takes a full family history and based on genetic inheritance patterns can predict certain probabilities. The parents can then decide whether or not it is worth the risk. Genetic counseling is not common and is generally only done when there is a significant family history of genetic disorders and parents are concerned about their own children. G2. Prenatal Diagnosis

Explain how the following procedures can contribute to the diagnosis of genetic conditions.

ultrasound: amniocentesis: chorionic villi sampling:

G3. Genetic Screening Genetic material from fetal tissue, a child or an adult can be screened for genetic markers. genetic markers : a characteristic that provides information about the genotype of the individual DNA probe: How is a DNA probe used to screen for genetic conditions? G4. Treating human disorders gene therapy: DNA vector: Differentiate between somatic gene therapy and germ-line gene therapy:

Key Concept G: Diagnosis and treatment of genetic disorders (p. 658-661)

Vocabulary

Vocabulary

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Example of gene therapy

Issues Related to Gene Therapy Technological issues: How can scientists be sure that the gene’s insertion does not harm some other necessary cell function? Societal issues: Should gene therapy be reserved for treating serious diseases or should we explore the potential use for enhancing athletic ability, physical appearance, or even intelligence? Should we try to eliminate genetic defects in our children and their descendants? Should we interfere with evolution in this way? From a biological perspective, the elimination of unwanted genes from the gene pool could backfire. Genetic variety is a necessary ingredient for the survival of a species as environmental conditions change with time. Genes that are damaging under some conditions may be advantageous under others. (one example is the sickle-cell gene) Are we willing to risk making genetic changes that could be detrimental to our species in the future? Should we use gene therapy on those who can afford it, or should we have unlimited access by all , thereby increasing taxes to cover health costs? The procedures now being tested are expensive and require expertise and equipment found only in major medical centers. Should we use gene therapy to such an extent that we support the eugenics movement? Largely because of the events of Nazi Germany, our society rejects the notion of eugenics— the effort to control the genetic makeup of human populations. The possibility of gene therapy raises fears in this regard. Ethical issues:

Provide two ethical issues associated with genetic screening and gene therapy. text p. 661