Pre-AP Biology DNA and Biotechnology Study Guide #1

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1 Last Name: First Name: Per. Pre-AP Biology DNA and Biotechnology Study Guide #1 Structure of DNA: Number of strands. Parallel or antiparallel?. Rosalind Franklin s x-ray crystallography image indicated that the 3-D shape of the molecule was a. Chargaff s ratios indicated that there is complementary base pairing: A with and C with. If the amount of A in a species DNA is 30%, the amount of T is, C is and G is. The bonds between the bases (A, T, C and G) are. While the bonds between nucleotides (between the sugar and phosphates of the backbone) are. and were the first to build and publish an accurate model of the DNA molecule. Add labels to the diagram: sugar, phosphate, A, T, C, G, H-bonds, covalent bonds. Structure of nucleotide: Describe the relationship of the nucleotide to DNA (include the vocabulary terms monomer and polymer) Label the three components (A, B, and C) that make up the nucleotide Meselson Stahl experiment: According the Meselson Stahl experiment, DNA replication is: Draw a picture model of the Meselson Stahl experiment findings. Include: light versus dark nucleotides (difference in shading), the initial DNA molecule and the two molecules that result after replication has been completed. What percentage of the original nucleotides would be remaining after 1 round of replication: after 2 rounds: after 3 rounds: after 4 rounds:. Describe and explain this pattern: DNA replication: Which enzyme is responsible for unwinding the double-helix? Which enzyme is responsible for building each complementary new strand using the original strands as a template? How does this enzyme know which bases to add to the growing new strands of DNA? Describe three times (reasons) that a cell would need to replicate its DNA: When, in the cell-cycle, is DNA replicated? Compare/contrast DNA and RNA: Comparison DNA RNA Name of sugar List of nucleotides Number of strands Where found in the cell Types of

2 Transcription and Translation: Describe the central dogma of biology (flow of genetic information): What is transcription? Where in the cell does it occur? What is translation? Where in the cell does it occur? Describe how different types of RNA interact during transcription: Sickle-cell Case-study: What is an allele? What is the mechanism whereby new alleles arise? How does the wild-type beta hemoglobin and the sickle-cell allele differ at the DNA level? What is the difference in the hemoglobin protein at the amino-acid level? Why do the sickle-cell type hemoglobin molecules stick together into long rods? What effect does this clumping have on the shape of red blood cells? What effect does this have on human health? Which of the following is the most accurate statement regarding the sickle-cell allele: this is an example of a negative mutation, this is an example of a positive mutation, whether the mutation is positive or negative depends on circumstances. Justify your choice of statement above: Mutations: What are mutations and how do they occur? What is the significance of mutations to evolution? What is a silent mutation? Explain why some mutations are silent. What is the significance of this? Describe what a frame-shift mutation is. Why is this type of mutation have a particularly large impact on the protein product? What is the difference between a frame-shift mutation at the start versus end of a gene?

3 Pre-AP Biology DNA and Biotechnology Study Guide Structure of DNA: Number of strands _2- double. Parallel or antiparallel? antiparallel. Rosalind Franklin s x-ray crystallography image indicated that the 3-D shape of the molecule was helical_. Chargaff s ratios indicated that there is complementary base pairing: A with _T_ and C with G_. If the amount of A in a species DNA is 30%, the amount of T is 30%, C is _20% and G is 20%_. The bonds between the bases (A, T, C and G) are _hydrogen_. While the bonds between nucleotides (between the sugar and phosphates of the backbone) are _covalent_. Watson and Crick were the first to build and publish an accurate model of the DNA molecule. Add labels to the diagram: sugar (5), phosphate (6), A (3), T (4), H-bonds (1), covalent bonds (2). Structure of nucleotide: Describe the relationship of the nucleotide to DNA (include the vocabulary terms monomer and polymer) nucleotides are the monomers of the polymer called DNA A is the phosphate group, B is the sugar (deoxyribose for DNA) and C is the nitrogenous base Meselson Stahl experiment: According the Meselson Stahl experiment, DNA replication is: semi-conservative Draw a picture model of the Meselson Stahl experiment findings. Include: light versus dark nucleotides (difference in shading), the initial DNA molecule and the two molecules that result after replication has been completed. Each side of the original DNA molecule serves as a template and new nucleotides are added based on base-pairing rules (A bonds with T and C bond with G). Half of each molecule is composed of the original nucleotides (dark) and half from new nucleotides (light). What percentage of the original nucleotides would be remaining after 1 round of replication: _1/2_ after 2 rounds: _1/4 after 3 rounds: _1/8_ after 4 rounds: _1/16_. Describe and explain this pattern: The pattern is exponential decay, reduced each round by ½ of the previous because of the semi-conservative nature of DNA replication. DNA replication: Which enzyme is responsible for unwinding the double-helix? helicase Which enzyme is responsible for building each complementary new strand using the original strands as a template? DNA polymerase How does this enzyme know which bases to add to the growing new strands of DNA? base-pair rules (A w. T and C w. G) Describe three times (reasons) that a cell would need to replicate its DNA: growth, replacement, reproduction When, in the cell-cycle is DNA replicated? S-phase (S stands for DNA synthesis) Compare/contrast DNA and RNA: Comparison DNA RNA Name of sugar deoxyribose Ribose List of nucleotides A, T, C, G A, U, C, G Number of strands 2 1 Where found in the cell Nucleus and mitochondria Nucleus, cytoplasm Types of Nuclear, mitochondrial mrna, trna, rrna Transcription and Translation:

4 Central dogma: DNA mrna protein. Transcription is the copying of the information stored in the DNA molecule of a gene into a mrna molecule and this occurs in the nucleus. Translation occurs in the cytoplasm or on the E.R. on a ribosome and involves trna molecules bringing amino acids in the correct order (because each trna anticodon corresponds to a mrna codon) to translate the code of mrna nucleotides into a polypeptide (protein). Sickle-cell Case-study: What is an allele? An allele is a version of a gene, i.e wild-type (normal) betaglobin or the sickle-cell variety What is the mechanism whereby new alleles arise? New alleles arise through mutation How does the wild-type beta hemoglobin and the sickle-cell allele differ at the DNA level? Only 1 nucleotide (A T) What is the difference in the hemoglobin protein at the amino-acid level? Only one amino acid difference Why do the sickle-cell type hemoglobin molecules stick together into long rods? The substituted amino acid is hyprophobic, therefore hemoglobin molecules clump together into long rods to shield that hydrophobic part. What effect does this clumping have on the shape of red blood cells? The clumping of hemoglobin into long rods distorts the shape of red blood cells, causing them to become sickle-shaped. What effect does this have on human health? The sickle-shaped red blood cells can get stuck in small capillaries, causing blood-clots that can result in a heart attack or stroke. Which of the following is the most accurate statement regarding the sickle-cell allele: this is an example of a negative mutation, this is an example of a positive mutation, whether the mutation is positive or negative depends on circumstances. Justify your choice of statement above: Having one copy of the sickle-cell allele (being a carrier) offers a survival and thus reproductive advantage in malarial zones because a carrier is partially resistant to potentially deadly malarial infections. However, being a carrier does not offer a survival advantage in areas without malaria, such as the U.S., in such locations the nutation would be considered negative. Mutations: A mutation is a random change in DNA code that occurs during DNA replication or through a failure in repair mechanisms. The significance is that mutation is the primary source of genetic diversity it is how we get brand new alleles. Genetic diversity is necessary for evolution through natural selection. Some mutations are silent (no change in amino acid) because of redundancy in the codons (64 codons for 20 amino acids) as a result many mutations do not affect the protein product. A frame-shift mutation results from the addition or deletion of one or two nucleotides, thereby shifting the reading-frame and changing all amino acids downstream. As a result, the earlier this occurs in a gene, the larger the impact. A simple substitution mutation (A T) resulted in the sickle-cell allele. The resulting hemoglobin protein clumps together into long rods, which distort the shape of red-blood cells. Being heterozygous is an advantage in malarial-zones because it confers partial resistance to malaria. No advantage where there is no malaria.

5 Last Name: First Name: Per. Pre-AP Biology DNA and Biotechnology Study Guide #2 Polymerase Chain Reaction (PCR): Why is PCR used by researchers? Describe how PCR works? Restriction enzymes: Where do restriction enzymes come from and what do they do? Describe two separate uses of restriction enzymes in biomedical research: Show how the DNA below is cut by EcoRI, which recognizes the sequence GAATTC and cuts between the G and A: How many cuts would be made? How many fragments of DNA would result? What would be the size (base-pairs)? Gel electrophoresis: Why is DNA loaded in the wells at the side of the gel box with the negative electrode? Draw the DNA fingerprint for the DNA sample to the left. What is recombinant DNA and how is it created and describe on use of this technology: Genetic Databases: What is a genome? What does it mean to sequence a genome? How can genetic databases (BLAST) be used? Recombinant DNA: What is recombinant DNA? Describe the steps for producing recombinant DNA: Give a specific example of how this technology as improved human health/welfare:

6 Polymerase Chain Reaction (PCR): Pre-AP Biology DNA and Biotechnology Study Guide #2 PCR quickly amplifies (makes many copies) of DNA. It uses a heat-stable DNA polymerase enzyme (taq polymerase) from a thermophilic bacterium and alternate heating and cooling cycles. Restriction enzymes: Restriction enzymes come from bacteria; bacteria use them protect themselves from viruses because the enzymes chop up viral DNA. Researchers use them to cut DNA into fragments to create DNA fingerprints in gel electrophoresis and to insert foreign genes when making recombinant DNA Two cuts by EcoRI (GAATTC), resulting in three fragments with the following sizes in base-pairs (from left to right): 11, 5, and 5. Gel electrophoresis: DNA is loaded at the negative side because DNA is negatively charged and would thus be repelled and travel through the gel towards the positive electrode. Recombinant DNA is DNA that is a combination of DNA from more than one organism. It is created by cutting both pieces of DNA with the same restriction enzyme. The sticky-ends will have complementary base-pairs, allowing the two pieces of DNA to connect together. DNA ligase solidifies the bonds. The human gene for insulin has been inserted into bacteria and today bacteria manufacture human insulin for those with diabetes. Genetic Databases: What is a genome? A genome is the complete set of genetic instructions (in the form of nucleotides) for an organism. What does it mean to sequence a genome? The sequence is the precise order from start to finish of the nucleotide bases (A, T, C, and Gs) in a genome. How can genetic databases (BLAST) be used? BLAST can be used to identify an unknown source of DNA, for example, it can tell you the species it belongs to. It can also be used to identify and research genetic disorders. Recombinant DNA: What is recombinant DNA? Recombinant DNA is DNA that is a combination of two or more sources. Describe the steps for producing recombinant DNA: Both sources of DNA are first cut with the same restriction enzyme, then the sticky ends are made stable by the enzyme DNA ligase. Give a specific example of how this technology as improved human health/welfare: The human insulin gene has been inserted into a bacterial plasmid (circular piece of DNA) and incorporated into live bacteria, which now transcribe the human gene and translate the resulting mrna into human insulin protein.