Chem 464 Biochemistry

Transcription

1 Name: Chem 464 Biochemistry Multiple choice (4 points apiece): 1. Which of the following is not true of all naturally occurring DNA? A) Deoxyribose units are connected by 3',5'-phosphodiester bonds. B) The amount of A always equals the amount of T. C) The ratio A+T/G+C is constant for all natural DNAs. D) The two complementary strands are antiparallel. E) Two hydrogen bonds form between A and T. 2. Which of the following deoxyoligonucleotides will hybridize with a DNA containing the sequence (5')AGACTGGTC(3')? A) (5')CTCATTGAG(3') B) (5')GACCAGTCT(3') C) (5')GAGTCAACT(3') D) (5')TCTGACCAG(3') E) (5')TCTGGATCT(3') 3. Which of the following statements is true of lipids? A) Many contain fatty acids in ester or amide linkage. B) Most are simply polymers of isoprene. C) Testosterone is an important sphingolipid found in myelin. D) They are more soluble in water than in chloroform. E) They play only passive roles as energy-storage molecules. 4. Which of the following statements about membrane lipids is true? A) Glycerophospholipids are found only in the membranes of plant cells. B) Glycerophospholipids contain fatty acids linked to glycerol through amide bonds. C) Lecithin (phosphatidylcholine), which is used as an emulsifier in margarine and chocolate, is a sphingolipid. D) Some sphingolipids include oligosaccharides in their structure. E) Triacylglycerols are the principal components of erythrocyte membranes. 5. Which of these statements about the composition of biological membranes is false? A) In a given eukaryotic cell type (e.g., a hepatocyte), all intracellular membranes have essentially the same complement of lipids and proteins. B) The carbohydrate found in membranes is virtually all part of either glycolipids or glycoproteins. C) The plasma membranes of the cells of vertebrate animals contain more cholesterol than the mitochondrial membranes. D) The ratio of lipid to protein varies widely among cell types in a single organism. E) Triacylglycerols are not commonly found in membranes

2 6. Consider the transport of glucose into an erythrocyte by facilitated diffusion. When the glucose concentrations are 5 mm on the outside and 0.1 mm on the inside, the free-energy change for glucose uptake into the cell is: (These values may be of use to you: R = J/mol K; T = 298 K; 9 (Faraday constant) = 96,480 J/V; N = /mol.) A) less than 2 kj/mol. B) about 10 kj/mol. C) about 30 kj/mol. D) about -30 kjoule/mol. E) impossible to calculate without knowledge of the membrane potential. 7.The biological role of restriction enzymes is to: A) aid recombinant DNA research. B) degrade foreign DNA that enters a bacterium. C) make bacteria resistant to antibiotics. D) restrict the damage to DNA by ultraviolet light. E) restrict the size of DNA in certain bacteria. 2 Longer Problems 12 points each 9,12 8. In the space below draw the structure of sphingosine with an attached 18:2(Ä ) fatty acid. For the questions 9-15,YOU MAY SKIP TWO QUESTIONS 9 DNA Compare and contrast the structure of DNA and t-rna. DNA t-rna -2 Deoxyribose sugars Ribose Sugars -2 Thymine Uracil Several modified bases -2 Watson-Crick base pairs Watson-Crick + other base pairs -2 Linear B-form structure Clover-leaf with some A form plus hinge regions

3 3 10. Discuss the various reactions that occur spontaneously in any living cell that degrade DNA. If possible mention how frequently these reactions occur, and if there are any chemical agents that increase the rate of that reaction. Deamination - C to U about 100 events /cell/day A to G about 1 event /cell/day accelerated by nitrous acid and bisulfate Depurination (Purine base cleaved from sugar) 2 points each 10,000 lost /cell/day Pyrimidine dimerization by UV light (No rate) Ionizing radiation (X rays and ã rays) breaking bonds No rate Methylation (Alkylation) - no rate Oxidative damage peroxides and superoxides formed by UV or aerobic metabolism 11. Discuss the various types of phospholipids found in cell membranes. In this discussion include a rough structure of each kind of phospholipid and use the sketch to help focus on the differences between the different type of phospholipids. (Rough sketch means you can use a box for each major component, you don t have to know the details of the structure inside the box.) Glycerolphospholipids 2 points each sketch 6 point glycerol details 2 points Sphino details The upper fatty acid is usually a C 16 or C 18 saturated Fatty Acid, The lower is usually unsaturated. The XX group can be a variety of compounds including serine, ethanolamine, choline, inostitol, or even another glycerol. In some tissues the ester linkage at C-1 may be an ether linkage or an ether followed by a double bond on the C- 2 carbon of that fatty acid. Sphingomyelins X is usually Choline or ethanolamine. Usually found in the plasma membrane of animal cells and are prominent in myelin.

4 4 12. What are the main fat soluble vitamins? What are what is their role in your body, and what conditions occur if you have a deficiency of each vitamin. The fat soluble vitamins are D, A, E, and K 3 points each based on level of detail D - also called cholecalciferol normally formed in skin from the reaction of 7- dehydrocholesterol and UV light. The further reactions in liver and kidney take it to the active form. This vitamin is involved with calcium uptake, and a deficiency leads to rickets A. - also called retinol. Is a visual pigment but its derivative, retinoic acid also acts a a hormone controlling development of epithelial cells. First isolated from fish oils (Hence the drinking of Cod liver oil in old movies) whole milk, eggs and butter, are also good sources. Also sweet potatoes and other yellow vegetables. A deficiency leads to dry skin slow development and growth and night blindness. E. - a group of lipids call tocopherols that contain an aromatic ring and long isoprenoid tail. Act as membrane bound anti-oxidants. Found in eggs and vegetable oils. A deficiency leads to dry scaly skin muscular weakness and wasting. K. - Undergoes oxidation and reduction during the formation of prothrombin, one of the early steps in blood clotting. Vitamin K 1 is found in green plant leaves. A deficiency leads to slower blood clotting 13. Membrane fusion is a key element in many different biological processes. Name at least 4 different processes that depend on membrane fusion, and then describe how at least one of these processes takes place at the molecular level. Processes that involve membrane fusion include: budding of vesicles from the Golgi apparatus, Exocytosis, endocytosis, Viral infection, the fusion of sperm and egg, fusion of vacuoles, and the separation of membranes during cell division. 4 points for 4 processes, 8 points of describing mechanism The one mechanism described in the book was the fusion of a vesicle containing neurotransmitters with the plasma membrane at the synapse of a neuron, an exocytosis type event. A sketch like figure helps. In this process the vesicle has v-snare at its surface and the inside of the plasma membrane where it is supposed to fuse has t-snare protein and SNAP 25 protein. During fusion the two SNARE protein bind to each other and the SNAP25 and intertwine to make long fibers. This intertwining bring the two membranes close together and initiates the fusion process in which first the outer leaflets of two membranes fuse, and then the inner leaflets fuse to connect the vesicle membrane with the plasma membrane.

5 5 14. In our discussion of proteins that move small molecules across membranes, how are channel type proteins different than transporter type proteins. How do these proteins differ in both kinetics and in mechanism. Transporter proteins must bind to the substance to be transported and carry it across the membrane. Kinetically this gives it enzyme like behavior with a hyperbolic rate vs concentration curve in which there is a V MAX showing that this mechanism can be saturated, and K M representing how well the substance binds to the transporter. Channel proteins, on the other hand, essentially make a hole in the membrane through which ions can pass. The ions can move at near the diffusion limit, and the channel cannot be saturated and does not have a K. 6 points each M 15. Explain how DNA fingerprinting works. What I was trying to ask with this question was a discussion of DNA genotyping as presented in Box 9-1 of your text. In the US the FBI and local law enforcement use the CODIS database of loci that identify 13 regions on 12 of your chromosomes that are prone to sequence length polymorphisms. These polymorphism occur when short, ~4 residues sequences are repeated in a tandem linear manner, making the DNA at this locus longer. A DNA sample is first amplified using a slightly modified method in which the primers for different loci are labeled with different fluorescent dyes. The amplified DNA is then denatured and separated using capillary electrophoresis. As the electrophoresis separates the DNA fragments based on the length, the fluorescent dyes are used to identify each fragment, and the length of the fragment recorded. An exact match at all loci uniquely identifies an individual, and close matches can be used to identify individuals in a family group.

6 1 C, 2B, 3A 4D 5A 6B 7B 6