MBBE BIOL 402 study guide exam I PDF

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Notes from Dr.Nerukar class lecture/Lehninger Principles of Biochemistry 6th edition...

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MBBE/BIOL 402 Exam I study guide 2018 Instructor: Nerurkar, MBBE/CTAHR Note: The below information is only a study guide- mostly to strengthen your major concepts. To be successful in your exams you are still required to: Ø฀ Read textbook material (assigned pages given in the lecture slides) Ø฀ Study the slides Ø฀ Study back of the chapter questions if any. Ø฀ This will help you answer multiple-choice questions, true or false, fill in the blanks or match the pairs. Essay type questions generally appear as structures (amino acids), assigned figures and pathways or any questions uploaded on lecture notes, but are mostly from back of the chapter questions. Chapter # Section I Chapter 1 Chapter 3 Chapter 4 Chapter 5 Chapter 7 Chapter 10

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Back of chapter Questions

1-20 71-85, 92-93 115 – 133, 137-152 157 – 159, 162 – 166, 168 – 184 243 – 268 357 – 375

6, 11 None 5a, 5b, 7a, 7b, 9, 14a and 14b 3, 7, 9, 11 and 13 5, 9, 17, 23 3, 7, 9, 13, 15, 17

Chapter 1 1. 2. 3. 4. 5. 6. 7. 8. 9.

What are the three classes of cytoskeleton protein? What are the functions of cytoskeleton? What six characteristics distinguish living organisms from inanimate objects? What are the components of bacterial cell and their function? Distinguishing characteristics of eukaryotic cells Compare and contrast prokaryotic, animal and plant cells based on their organelles and their function. What are stereoisomers, enantiomers etc. Distinguish between gram positive and gram-negative bacteria. Why is an asymmetric carbon atom called a chiral center? All cells are surrounded by a plasma membrane composed of lipid and protein molecules. What is the function of the plasma membrane?

Chapter 3 1. 2. 3. 4. 5.

Review and memorize amino acid classifications, structures and their three letter abbreviations. Be able to recognize the amino acid structures. Review physical and chemical properties of amino acids. Briefly describe the five major groupings of amino acids. Which of the 20 amino acids is not chiral? Based on structure, which is a unique amino acid and why? 6. Which of the 20 standard amino acids are: a. cyclic; b. aromatic; c. sometimes charged at physiological pH; d. technically not hydrophobic, polar, or charged; e. basic; f. acidic; g. sulfurcontaining? 7. Name two uncommon amino acids that occur in proteins. By what route do they get into proteins? 8. Does the ability of some amino acids to absorb ultraviolet light translate into a useful technique for the detection of all proteins? Why or why not? !

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9. What structural property of amino acids permits the measurement of protein concentration by UV light absorption? Which amino acids have this property? 10. Proteins can contain nonstandard amino acids that are modified versions of the 20 amino acids discussed in this chapter. Do these modifications occur before or after the amino acids are incorporated into the protein molecule? Are amino acids always found incorporated into polypeptide chains in cells? 11. What is lost from amino acids in the formation of a peptide bond? 12. How do you write peptides or what are the rules of writing peptides? Or what is N-terminal and Cterminal in a peptide or protein? 13. List functions of small bioactive peptides with examples. 14. List functions of proteins with examples. 15. Name five or six different types of prosthetic groups that can be attached to proteins. Chapter 4 1. 2. 3. 4. 5. 6. 7.

Protein structure and function How are protein structure and function related? What are the four levels of protein structure? Fibrous and globular proteins. Which amino acids disrupt alpha helix and why? Which ones strengthen it? What noncovalent forces stabilize β-sheet structures? In silk fibrion, which amino acid residues have functional groups participating in interchain H bonds? Which have groups extending above and below the plane of the sheet? 8. What is unusual about peptide bonds involving the imino nitrogen of proline in β turns? 9. How many amino acid residues are typically found in a β turn and how is this structure stabilized? 10. What covalent bonds contribute strength in each of these fibrous proteins: α-keratin, collagen, elastin? 11. Wool and silk are both composed of fibrous proteins; wool can stretch and shrink but silk cannot. What is the molecular basis for the different characteristics of these two fibers? 12. How does vitamin C participate in collagen formation? 13. Describe the cellular responses to protein misfolding. 14. Protein folding 15. What does denaturation mean? Under what conditions are proteins denatured? 16. Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation? 17. How can changes in pH alter the conformation of a protein? 18. Compare and contrast myoglobin and hemoglobin. 19. Why are glycine and proline often found within a β-turn?

Chapter 5 1. 2. 3. 4. 5. 6. 7. !

Why is it important that iron is incorporated into the heme group, rather than free in the cell? Cooperative binding and allosteric effects Similarities and differences in fetal and adult hemoglobin Role of BPG and how it influences O2 affinity under different conditions Transport of molecules by hemoglobin other than O2 Conformations of hemoglobin Using hemoglobin as an example, discuss the effects the change of a single amino acid can have on the function of a protein. 2

8. Bohr Effect 9. Similarities and differences between the two immune systems. Types of immune cells and their functions. 10. Structure/function of antibody. 11. Muscle proteins and their functions. Chapter 7 1. 2. 3. 4. 5.

6. 7. 8. 9.

Is galactose an epimer of mannose? Why is phosphorylation of sugars beneficial to a cell? Why is the average blood glucose concentration a better way to monitor people with diabetes? What are the structural and functional differences between homopolysaccharides and heteropolysaccharides? Suppose you had three polysaccharides, amylose, amylopectin, and glycogen, each with the same number of monosaccharide subunits. Which would be degraded the fastest, assuming that the enzymes acting to degrade the polysaccharides all worked at the same rate? What are the similarities and differences between: a) cellulose and chitin, b) cellulose and glycogen; (c) D-glucose and D-fructose; (d) maltose and sucrose, (e) proteoglycans and glycol protein? What is the relationship among proteoglycans, fibrous proteins, integrins, and the extracellular matrix? How are the functions of glycoproteins different from those of glycosaminoglycans? How do glycolipids and lipopolysaccharides differ?

Chapter 10 1. 2. 3. 4. 5.

What are the structural similarities or differences among various lipids? What is the nonpolar portion of phosphatidylcholine? Compare sulpholipids and phospholipids. How are they similar? How are they different? What is the polar potion of sphingomyelin? Ceramides are structurally similar to diacylglycerols. Compare the attachment of head groups to diacylglycerol unit in glycerophospholipids with their attachments to ceramide in sphingolipids. 6. How does ibuprofen act to reduce inflammation and pain? 7. How does prednisone act to reduce inflammation? 8. Vegetable oil and solid shortening are both mixtures of triacylglycerols. Why is shortening a solid and vegetable oil a liquid at room temperature? 9. Although storage lipids are quite hydrophobic, membrane lipids are amphipathic and can have noncovalent interactions with polar molecules. For both types of lipids, function is dictated by structure. Why can’t storage lipids function as membrane lipids? 10. What is the polar portion of sphingomyelin? This portion of the lipid would face the aqueous surroundings. 11. Ceramides are structurally similar to diacylglycerols. Compare the attachment of head groups to the diacylglycerol unit in glycerophospholipids with their attachment to ceramide in sphingolipids. 12. What is the enzyme defect in individuals affected with Tay-Sachs disease? 13. How are steroid hormones able to be transported through the aqueous bloodstream? 14. What are the symptoms of deficiencies of vitamins A and D? 15. What are the symptoms of deficiencies of vitamins E and K? 16. How are steroid hormones, phosphatidylinositol, and eicosanoids similar and different in the locality of their effects? In their location in the cell? In their structure? !

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