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BIOCH 200 Study Guide-Fall 2012.docx

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Department
Biochemistry
Course
BIOCH200
Professor
Nat Kavetal
Semester
Fall

Description
Learning Objectives for BIOCH 200 Introduction 1. Biomolecules You should be able to: Define each of the following terms: trace element, amino acid, carbohydrate, monosaccharide, nucleotide, lipid, monomer, polymer, residue, peptide bond, phosphodiester bond, glycosidic bond • List the most abundant elements in biological molecules. • List the major classes of biological molecules and biological polymers. • State the major functions of each type of biological polymer. 2. Water You should be able to: Define each of the following terms: polarity, hydrogen bond, electrostatic interaction, van der Waal’s radius, electronegativity, van der Waal’s interaction, dipole-dipole interaction, London dispersion forces, hydrophilic, hydrophobic, hydrophobic effect, amphiphilic, amphipathic, micelle • List the three major types of electrostatic force that act on biological molecules. • Compare the nature and relative strengths of bonds in biological molecules. • Explain the term "hydrophobic effect" and outline the role that entropy plays in the process. • Given their structures, identify molecules that are hydrophobic, hydrophilic, and both. 1 Department of Biochemistry University of Alberta Nucleotides and Nucleic Acids You should be able to: Define each of the following terms: nucleic acid, DNA, RNA, nucleotide, nucleoside, deoxynucleotide, base, purine, pyrimidine, antiparallel, bp, kb, oligonucleotide, B-DNA, stacking interactions, melting temperature, denaturation, renaturation, anneal 3. Nucleotides Distinguish between purine and pyrimidine bases. Name and distinguish between the two sugars that are incorporated into nucleotides. Number the carbon atoms in the sugar portion of a nucleotide. Name all nucleosides and nucleotides that contain the bases adenine, guanine, cytosine, thymine, and uracil. Compare the structure of nucleosides with the structure of nucleotides. Name, recognize and be able to draw the five major bases found in the nucleic acids. Number atoms in the purine and pyrimidine rings of the bases found in RNAand DNA. 4. The Primary Structure of Nucleic Acids Define the term nucleic acid. Recognize and identify a phosphodiester bond. Explain why nucleic acids are said to have a “sense of direction.” Write and read base sequences in nucleic acids. Identify the 5' and 3' ends of a nucleic acid base sequence. Describe and compare the primary structure of RNAand DNA. Use standard abbreviations for the primary structures of nucleic acids. Explain why RNAis susceptible to alkaline hydrolysis whereas DNAis resistant. Explain why the bases in a nucleic acid “stack” and identify the forces that favour stacking. Given the structure of a base, identify groups that are capable of forming H bonds. 5. Nucleotides as High Energy Molecules and Electron Carriers Identify a phosphoanhydride bond. State what is meant when nucleoside triphosphates are described as being “high energy” molecules. Explain why the h+drolysis of phosphoanhydride bonds is a highly favourable reaction. Recognize NAD and FAD as dinucleotides. Write equations to describe the reduction of NAD and FAD. 2 6. Secondary Structure of the Nucleic Acids State Chargaff’s rules and explain what they tell you about a nucleic acid. Describe the double helical structure of B-DNA. Given the sequence of a nucleic acid, write its complementary sequence. State how strands of DNAalign with one another specifically rather than randomly. Describe how the structure of double-stranded DNAis stabilized. State why it is important that the structure of DNAis stabilized by non-covalent forces only. State a role for the grooves in the structure of double-stranded DNA. List major differences between RNAand DNA3-D structures. 7. Denaturation of the Nucleic Acids • State why the denaturation of a double helix is favoured and identify the chemical conditions that cause denaturation. • Define “melting” of a double-stranded molecule of DNA. • Define the terms hypochromic and hyperchromic with respect to double-stranded nucleic acids. • Use a melting curve to determine the Tmof a double stranded nucleic acid. • Explain the term “renaturation.” • Describe and explain the relationship between the Tmof a double-stranded nucleic acid and its relative content of C and G. • State how and why the T of a nucleic acid is affected by pH and ionic strength. m • State whether or not RNAcan “melt” and justify your answer. 8. From Genes to Proteins: Transcription and Translation • Outline the central dogma of molecular biology. • Derive the sequence of an mRNAfrom the base sequence of a template or sense strand of DNA. • State the role of promoters and of general transcription factors, in transcription. • Identify the amino acid sequence encoded within an mRNA sequence. • Define the terms codon and anticodon. • Explain what is meant by the terms sense (coding) strand and template strand of a gene. • Sketch and label a diagram to illustrate the role of tRNAs in translation. • Define the term “reading frame” and state how a tRNA recognizes or “reads” a codon. • Define the term “genetic code,” use the genetic code table, and explain the term “degenerate.” • Define the terms promoter, general transcription factor, activator, repressor, enhancer, and silencer. • Define the term “gene expression.” 3 Department of Biochemistry University of Alberta Protein Structure and Function 9. The Amino Acids and the Properties of Their Side Chains Draw the structure of a generic amino acid. Name and draw the 20 amino acids incorporated into proteins and use their 3-letter designations. State why all isolated amino acids bear at least one positive and one negative charge. Explain why all of the amino acids except for glycine are chiral. Classify the 20 amino acid side chains according to their properties (hydrophobic, polar, or charged). Assign other properties to “special” individual side chains (Ser, Thr, Tyr, Cys, His, Gly, Pro). State why it is important to know the properties of the amino acid side chains. 10. Peptide Bonds and Protein Primary Structure Explain why peptides are described as having a “sense of direction.” Define the term “primary structure” for a polypeptide. Use 3-letter designations for the amino acids to write the sequence of a polypeptide. Explain why the amino acids in a polypeptide are called residues. Explain why peptide bonds are planar and rigid. Draw a dipeptide, if given the structures of two amino acids. Define the term “polypeptide backbone.” 11. The Secondary Structure of Polypeptides Define the four major levels of protein structure. State how the properties of peptide bonds limit the possible conformations a polypeptide can adopt. Describe the structural features of an α-helix. Describe the structural features of parallel and antiparallel β-sheets. Distinguish regular and irregular secondary structure. Recognize the elements of secondary structure represented in a ribbon diagram. State how secondary structure is stabilized. 4 12. The Tertiary and Quaternary Structure of Proteins Define tertiary and quaternary levels of protein structure. State how the surface and core regions of soluble globular proteins differ. Identify amino acids that are most likely to be found at the core of a soluble globular protein. Explain why irregular secondary structure is more likely to be found at the surface of a globular protein than are α-helices and β-sheets. State how the tertiary and quaternary levels of protein structure are stabilized. Describe the terms ion pair, H bond, and disulphide bridge, and state their roles in protein tertiary structure. Define the term “prosthetic group” and state why proteins need them. 13. The Structure and Function of Myoglobin and Hemoglobin Describe and compare the structures of myoglobin and hemoglobin. State the physiological functions of myoglobin and hemoglobin. Sketch oxygen binding curves for myoglobin and hemoglobin and use the curves to explain how these proteins meet physiological requirements. Describe the oxygen binding site in myoglobin. State the functions of the proximal and distal histidine residues in myoglobin and hemoglobin. Sketch a binding curve to illustrate cooperative binding behaviour. Outline the general molecular mechanism behind cooperative binding. Describe the general mechanism of action of an allosteric effector. Describe the molecular mechanism by which oxygen causes hemoglobin to switch states. Sketch oxygen binding curves to illustrate the Bohr effect. + Describe the mechanism by which H ions stabilize the T state of hemoglobin. Sketch binding curves to illustrate the effect of BPG on the oxygen binding behaviour of hemoglobin. Outline the mechanism by which BPG exerts its effect on hemoglobin. Identify three specific roles for histidine residues in hemoglobin function. Differentiate between conservative and critical amino acid substitutions. Sketch binding curves to illustrate the difference in the oxygen binding behaviour of fetal and adult hemoglobins. State how fetal hemoglobin differs structurally from adult hemoglobin. Explain how the structural difference between fetal and adult hemoglobin results in their different oxygen binding behaviours. 5 Department of Biochemistry University of Alberta Enzymes 14. What are Enzymes? Define the term “enzyme.” Describe the structure of enzymes and state how it is stabilized. State what is meant when we describe enzymes as “specific.” Define the term “substrate.” State why the regulation of enzymes is possible. 15. How Do Enzymes Work? Sketch a free energy diagram to compare thermodynamically favourable and non-favourable reactions. State what is meant by the term “spontaneous” when used to describe a biological reaction. State what determines the speed of an uncatalyzed biological reaction and illustrate your answer with a free energy diagram. Explain how increasing the temperature might increase the speed of an uncatalyzed reaction. State how enzymes increase the speed of a reaction and use a free energy diagram to illustrate this. List four mechanisms which contribute to an enzyme’s ability to reduce the activation energy barrier of a reaction. Define the term “active site.” Describe how substrates bind in the active site with specificity and relatively high affinity. Define the term induced fit. Explain what is meant by the “proximity and orientation” effect. State two ways in which enzymes may participate in a chemical reaction. Define the terms cofactor, cosubstrate, and prosthetic group. State why enzymes need cofactors. Explain what is meant by the term “preferential transition state stabilization.” 6 16. Regulating Enzyme Activity Sketch a graph to illustrate the relationship between reaction velocity and substrate concentration for allosteric and non-allosteric enzymes. Identify six processes by which enzyme activity can be regulated, in vivo. Explain how competitive inhibitors slow down an enzyme catalyzed reaction. Explain why competitive inhibition can be overcome by increasing the substrate concentration. Sketch a graph to illustrate the effect of a competitive inhibitor on the rate of an enzyme catalyzed reaction (non-allosteric). State why transition state analogs often make better competitive inhibitors than substrate analogs. Sketch a graph to illustrate the effect of allosteric inhibitors and activato
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