BIO 3100 Test Banks

BIO 3100 Test Banks BIO 3100 Lecture Exam I-A February 14, 2008 1. Universal features of all living cells include all of the following except: (a) nucleus or nucleoid (b) plasma membrane (c) cytoplasm (d) centrosome 2. An open system is one (a) that exchanges neither matter nor energy with its surroundings plasma membrane (b) that exchanges energy but not matter with its surroundings. (c) that exchanges both matter and energy with its surroundings. (d) that exchanges matter but not energy with its surroundings. 3. Which of the following is true about carbon bonding? (a) Carbon-carbon double bonds have freedom of rotation. (b) Carbon atoms can form covalent bonds with up to four other atoms. (c) Carbon can form double bonds with hydrogen. (d) Carbon-carbon single bonds cannot rotate. 4. Which of the following is true about the two molecules shown above? (a) They are the isomers formed due to freedom of rotation about C=C double bond. (b) The carbon double bonds in each are chiral centers. (c) They are the isomers formed due to rigidity of C=C double bond. (d) They can be interconverted without breaking any covalent bonds. 5. . Prokaryotic and eukaryotic cells possess which of the following? (a) Chloroplast (b) a nuclear envelope (c) mitochondria (d) a plasma membrane 6. If the free energy change DG for a reaction is -46.11 kJ/mol, the reaction is: (a) at equilibrium. (b) endergonic. (c) endothermic. (d) exergonic. (e) exothermic. 7. Exergonic and endergonic reactions differ in that (a) exergonic reactions have a positive free energy change (D G is positive) and endergonic reactions have a negative free energy change (D G is negative). (b) exergonic reactions require an input of energy and endergonic reactions release free energy. (c) exergonic reactions have a negative free energy change (D G is negative) and endergonic reactions have a positive free energy change (D G is positive). (d) exergonic reactions consume more free energy than is released and endergonic reactions release more free energy than is consumed. 8. Which of the following is true about stereoisomers? (a) They have different configurations. (b) They are indistinguishable by enzymes. (c) The have different chemical bonds. (d) They exist in equal amounts in living organisms. 9. Under what conditions is a carbon atom a chiral center? (a) if it has no stereoisomers (b) if it has only two different substituent groups (c) if it is symmetric (d) if it has four different substituent groups 10. Which of the following is true about hydrogen bonds? (a) Hydrogen bonds are longer and stronger than covalent bonds. (b) The geometry of a water molecule results in the equal sharing of electrons between the hydrogen and oxygen. (c) Hydrogen bonds must involve at least one water molecule. (d) Polar molecules are soluble in water because they can form hydrogen bonds with water molecules. 11. What is the concentration of H+ in a pH 0 solution of acid? (a) 0 M (b) 1 M (c) 1 X 10-7 M (d) 1 X 10-14 M 12. Hydrophobic interactions are formed due to: (a) the tendency of nonpolar groups to cluster together to avoid water molecules (b) the tendency of lipids to disperse in water. (c) the tendency of polar groups to interact with each other (d) all of the above 13. A buffer system consists of (a) a weak acid and its conjugate base. (b) a weak acid and a proton donor. (c) a weak acid and a proton. (d) a weak base and a proton acceptor. 14. Based on the Henderson-Hasselbalch equation (shown below), calculate the pH when the ratio of acetic acid to acetate is 10 to 1 (the pKa of acetic acid is 4.76). (a) 1.00 (b) 3.76 (c) 4.76 (d) 5.76 15. Which of the following properties of water is due to the tendency of water molecules to form H-bonds with each other: (a) High boiling point (b) High melting point (c) High heat of vaporization (d) All of the above 16. Which of the following is a weak interaction in aqueous systems: (a) Covalent bond (b) Van der Wall’s interaction (c) Hydrophobic interaction (d) H-bond (e) b, c and d 17. Van der Wall’s interactions are formed due to: (a) Polarity of covalent bond (b) Random, fluctuating distribution of electrons in an atom (c) Tendency of hydrophobic groups to avoid water (d) None of the above 18. Which of the following is true about pK: (a) pK is the pH at which an acid or base is half dissociated (b) pK is the pH at which a conjugate acid-base pair system exhibits maximum buffering capacity (c) All of the above (d) None of the above 19. The relationship between pK and strength of an acid is: (a) Higher the pK, stronger the acid (b) Higher the pK, weaker the acid (c) Lower the pK, weaker the acid (d) pK is not correlated to strength of an acid 20. Which isomer of amino acids is present in biological systems: (a) D-isomer (b) L-isomer (c) l-isomer (d) d-isomer 21. Which of the following amino acid groups is hydrophilic: (a) Alanine, proline, glycine (b) Aspartic acid, serine, cysteine (c) Leucine, proline, histidine (d) Phenylalanine, tyrosine, tryptophan 22. At the center of all 20 standard amino acids is what is termed the a- carbon that is covalently bonded with four other chemical groups. Which of these four chemical groups is not a normal component of all amino acids? (a) an amino group (b) a carboxyl group (c) a side chain (R group) (d) a methyl group 23. The isoelectric point, or pI, of an amino acid or a protein is (a) the pH at which the amino acid or protein has no net charge. (b) zero at pH 7.0. (c) the pH at which the amino acid or protein is neither hydrophobic nor hydrophilic. (d) the measure of the hydropathy of an amino acid or protein. 24. The formation of a peptide bond between two amino acids is an example of a(n) reaction. (a) cleavage (b) condensation (c) group transfer (d) isomerization (e) oxidation reduction 25. Which group or groups on a protein contribute most to its overall acid- base properties? (a) The a-amino groups of all non-terminal amino acids. (b) The N-terminal a-amino group on the protein. (c) The R groups on the protein. (d) The C-terminal a-carboxyl group on the protein. 26. Amino acids in a solution at near neutral pH exist in: (a) Acid form (b) Base form (c) Zwitterion form (d) All of the above 27. A non-protein amino acid has three ionizable groups. How many pK values do you expect for this amino acid? (a) 3 (b) 2 (c) 4 (d) 1 28. All polypeptides have same structure, but have different . (a) Backbone, main chain (b) Backbone, side chains. (c) Side chains, main chain (d) Side chains, backbone 29. Which of the following would best separate two proteins of distinct size but similar charge? (a) ion-exchange chromatography (b) affinity chromatography (c) Size exclusion chromatography (d) isoelectric focusing 30. The amino acid is likely found in the interior of the protein, while is likely found at the surface of a globular protein. (a) Valine, Serine (b) Glutamine, Leucine (c) Glycine, Phenylalanine (d) Arginine, Methionine (e) There is no preference for where an amino acid residue is likely to be found in a globular protein. 31. The level of protein structure that describes all aspects of the three-dimensional folding of a polypeptide is referred to as the (a) quaternary structure. (b) secondary structure. (c) primary structure. (d) tertiary structure 32. The sequence of amino acid in a protein represents: (a) quaternary structure (b) primary structure (c) secondary structure (d) quaternary structure 33. The criteria of separation of protein in SDS-polyacrylamide gel electrophoresis is: (a) Mass of protein (b) Charge on protein (c) pI of protein (d) All of the above 34. The criteria of separation of proteins in affinity chromatography is: (a) Molecular weight of the protein (b) Net charge on the protein (c) Biological activity of the protein (d) pI of the protein 35. Hydrogen bonds between amino acids in the secondary structure of a polypeptide occur between which chemical groups? (a) the C=O and C-H groups (b) the C=O and C-R groups (c) the C=O groups (d) the C=O and N-H groups 36. Proline residues are most likely to occur in which of the following secondary structures? (a) an a-helix (b) a b-turn (c) a b-sheet (d) a coiled coil 37. Which of the following experiments provided the first evidence that the amino acid sequence of a polypeptide chain contains all the information required to fold the chain into its native, three-dimensional structure? (a) When ribonuclease is treated with urea, it loses its catalytic activity. (b) When denatured ribonuclease is allowed to renature, it regains its catalytic activity. (c) When renatured ribonuclease is allowed to denature, it regains its catalytic activity. (d) None of the above 38. Fibrous proteins differ from globular proteins in that (a) fibrous proteins tend to serve structural functions, and globular proteins are more likely to be enzymes. (b) globular proteins can often contain several types of secondary structure, whereas fibrous proteins usually consist largely of a single type of secondary structure. (c) globular proteins are soluble in water, and fibrous proteins are usually insoluble. (d) All of the above 39. In a region of polypeptide, every fourth residue is linked to each other by H- bond; there are 3.6 residues per turn of polypeptide and translational rise is 1.5 Ao. What is the secondary structure in this region of polypeptide: (a) The a-helix (b) The b-sheet (c) The b-turn (d) The collagen helix 40. Which of the following unusual amino acids are found in collagen helix: (a) Phosphoserine and phosphotyrosine (b) Hydroxylysine and hydroxyproline (c) Methyllysine and methylarginine (d) Carboxyglutamate and carboxyaspartate 41. The difference between a domain and a motif is that: (a) Motif maintains its structural and functional integrity when separated form its protein context while a domain does not (b) Domain maintains its structural and functional integrity when separated form its protein context while a motif does not (c) There is no difference between a domain and a motif (d) Domain has several secondary structure while motif does not 42. Which of the following statement is true about the tertiary structure of a protein in aqueous solution: (a) Hydrophilic residues are inside and hydrophobic residues are outside (b) Hydrophilic residues are outside and hydrophobic residues are inside (c) Both hydrophilic and hydrophobic residues are present on the surface as well as in the interior of protein (d) All of the above 43. According to which model, hydrophobic interactions are the driving force for protein folding: (a) Nucleation condensation model (b) Molten globule model (c) Both a and b (d) None of the above 44. What are the characteristics of prion: (a) It is a misfolded protein (b) It is rich in b-sheets (c) It is infectious (d) All of the above 45. If a protein has a sigmoidal ligand binding curve, this means: (a) Protein binds ligand tightly at the high ligand concentration and releases ligand rapidly at the low ligand concentration (b) Protein binds ligand loosely at the high ligand concentration and releases ligand slowly at the low ligand concentration (c) Protein does not bind ligand (d) Proteins affinity for ligand is not dependent on its concentration 46. Myoglobin oxygen-binding curve is a and hemoglobin oxygen- binding curve is . (a) sigmoidal, rectangular hyperbola (b) rectangular hyperbola, sigmoidal (c) sigmoidal, sigmoidal (d) rectangular hyperbola, rectangular hyperbola 47. Binding of oxygen to one subunit of hemoglobin enhances the affinity of other subunits for oxygen binding. This phenomenon is called: (a) Cooperativity (b) Allosterism (c) Activation (d) a and b 48. Kd of a protein for ligand X is 98 and for ligand Y is 8. Protein has higher binding affinity for: (a) Ligand X (b) Ligand Y (c) Equal affinity for both the ligands (d) None of the above 49. When binding of a ligand causes a protein to change from an inactive state to active state, the process is called: (a) Allostery (b) Induced fit (c) Cooperativity (d) Lock and key mechanism 50. Sickle cell anemia is because of: (a) Replacement of valine with glutamic acid at 6th position of b-chain (b) Replacement of glutamic acid with valine at 6th position of b- chain (c) Replacement of valine with glutamic acid at 6th position of a-chain (d) Replacement of glutamic acid with valine at 6th position of a-chain BIO 3100 Lecture Exam I-C February 17, 2009 1. Aspect of metabolism that deals with synthesis of biomolecules is called: (a) Catabolism (b) Monobolism (c) Anabolism (d) Sonobolism (e) Both A and C 2. Universal features of all living cells include all of the following except: (a) Mitochondria (b) plasma membrane (c) cytoplasm (d) Chloroplast (e) A and D 3. Which of the following is not true about carbon bonding? (a) Carbon-carbon double bonds do not have freedom of rotation (b) Carbon atoms can form covalent bonds with up to four other atoms (c) Carbon can form double bonds with hydrogen (d) Carbon-carbon single bonds can rotate freely 4. If the free energy change DG for a reaction is +1566.11 kJ/mol, the reaction is: (a) at equilibrium (b) endergonic (c) endothermic (d) exergonic (e) exothermic 5. Which of the following is true about Archae: (a) They are prokaryotes (b) They are eukaryotes (c) Their transcription and translation is eukaryote like (d) A and B (e) A and C 6. Under what conditions is a carbon atom a chiral center? (a) if it has no stereoisomers (b) if it has only two different substituent groups (c) if it is symmetric (d) if it has four different substituent groups 7. The difference between enantiomers and diasteromers is that: (a) Enantiomers have an achiral center while diasteromers have a chiral center (b) Enantiomers have a chiral center while diasteromers have an achiral center (c) Enantiomers are non-superimposable mirror images while diasteromers are superimposable mirror images (d) A and C (e) B and C 8. Conformation differ from configuration in that: (a) Conformation can be changed without breaking the bond while configuration cannot (b) Configuration can be changed without breaking the bond while conformation cannot (c) Conformation is conferred by free rotation of C-C single bond while configuration is conferred by lack of rotation about C=C double bond or the presence of a chiral center (d) All of the above (e) A and C 9. Which of the following is not true about H-bond (a) H-bond requires a H-atom in covalent bond with a highly electronegative atom (b) H-bond requires a H-bond acceptor (c) H-bond requires a H-bond donor (d) H-bond is longer and stronger than a covalent bond (e) A and D 10. How can thermodynamically unfavorable reactions, such as the synthesis of DNA and protein polymers, occur in cells? (a) Cells couple thermodynamically unfavorable reactions to reactions that result in a positive change in enthalpy (b) Cells couple thermodynamically unfavorable reactions to the hydrolysis of ATP (c) Cells couple thermodynamically unfavorable reactions to reactions that have a positive free energy (d) Cells couple thermodynamically unfavorable reactions to reactions that result in a decrease in entropy 11. In ice, each water molecule forms hydrogen bonds with four other water molecules, as compared to liquid water in which each water molecule forms hydrogen bonds with 3.4 other water molecules. A consequence of this is that : (a) ice is more dense than water (b) water has a relatively low boiling point (c) water has a relatively high melting point (d) water turning into ice is a spontaneous reaction because more 12. Hydrophobic interactions are formed due to: (a) Intrinsic attraction of nonpolar groups (b) the tendency of nonpolar groups to cluster together to avoid water molecules (c) thermodynamic stability of H-bonded water shield formed around the cluster of nonpolar groups (d) the tendency of polar groups to interact with each other (e) B and C 13. Which of the following properties of water are due to the tendency of water molecules to form H-bonds with each other: (a) High boiling point (b) High melting point (c) High heat of vaporization (d) All of the above (e) A and B 14. Which of the following is/are weak interaction(s) in aqueous systems: (a) Covalent bond (b) Van der Wall’s interaction (c) Hydrophobic interaction (d) H-bond (e) b, c and d 15. Which is a good solvent for polar solutes because: (a) Water molecules are able to form covalent bonds with polar solutes (b) Water molecules are able to form ionic bonds with polar solutes (c) Water molecules are able to form H-bond with polar solutes (d) Water molecules are able to form salt bridges with polar solutes (e) Polar solutes have a tendency to avoid water molecules 16. What is the concentration of H+ in a solution of pH 14? (a) 0 M (b) 1 M (c) 1 X 10-7 M (d) 1 X 10-14 M 17. Van der Waals interactions are formed between: (a) A hydrophobic group and a hydrophilic group (b) Two hydrophobic groups (c) Two hydrophilic groups (d) Any two atoms that are 5 Ao apart or less (e) None of the above 18. Based on the Henderson-Hasselbalch equation (shown below), calculate the pH when the ratio of acetic acid to acetate is 100 to 1 (the pKa of acetic acid is 4.76). (a) 1.00 (b) 2.76 (c) 4.76 (d) 6.76 19. Which of the following is true about pK: (a) pK is the pH at which an acid or base is half dissociated (b) pK reflects the proton donating tendency of an acid (c) pK is the pH at which a conjugate acid-base pair system exhibits maximum buffering capacity (d) All of the above (e) None of the above 20. Which buffer system is responsible for maintaining pH of the blood: (a) Acetic acid-acetate buffer system (b) Phosphate buffer system (c) Carbon dioxide-carbonate buffer system (d) Histidine based buffer system (e) All of the above 21. The difference between H-bond and salt bridge is that: (a) In H-bond, both donor and acceptor are partially negatively charged while in salt bridge they are partially positively charged (b) In H-bond, both donor and acceptor are partially negatively charged while in salt bridge they are completely positively charged (c) In H-bond, both donor and acceptor are partially negatively charged while in salt bridge they are completely negatively charged (d) In H-bond, both donor and acceptor are partially positively charged while in salt bridge they are completely positively charged 22. The relationship between pK and strength of an acid is: (a) Higher the pK, stronger the acid (b) Higher the pK, weaker the acid (c) Lower the pK, weaker the acid (d) pK is not correlated to strength of an acid 23. Acid base property of an amino acid is a function of ionization potential of its: (a) a-amino group (b) a -carboxyl group (c) R group if it is ionizable (d) All of the above (e) A and B only 24. Amino acids in a solution at near neutral pH exist in: (a) Acid form (b) Base form (c) Zwitterion form (d) All of the above 25. Which of the following amino acid groups is hydrophobic: (a) Alanine, proline, asparagine (b) Aspartic acid, serine, cysteine (c) Leucine, proline, histidine (d) Phenylalanine, Leucine, Valine 26. Which of the following amino acid groups have R-groups with strong H-bonding capacity: (a) Alanine, proline, asparagine (b) Asparagine, serine, cysteine (c) Leucine, proline, histidine (d) Phenylalanine, Leucine, Valine 27. During peptide bond formation: (a) a -amino group of one amino acid reacts with a -carboxyl group of another amino acid in a polymerization reaction (b) a -amino group of one amino acid reacts with a -carboxyl group of another amino acid in a condensation reaction (c) a -amino group of one amino acid reacts with R group of another amino acid in a polymerization reaction (d) a -amino group of one amino acid reacts with R group of another amino acid in a condensation reaction (e) None of the above 28. The criteria for separation of proteins during electrophoresis is: (a) Net charge on the protein (b) Molecular mass of protein (c) Differential affinities of proteins to stationary and mobile phases (d) Biological activity of protein (e) A and B 29. The criteria for separation of proteins during chromatography is: (a) Net charge on the protein (b) Molecular mass of protein (c) Differential affinities of proteins to stationary and mobile phases (d) Biological activity of protein (e) A and B 30. The isoelectric point, or pI, of an amino acid or a protein is (a) pH at which the amino acid or protein has no net charge. (b) Zero at pH 7.0. (c) pH at which the amino acid or protein is neither hydrophobic nor hydrophilic. (d) Measure of the hydropathy of an amino acid or protein. 31. Which group or groups on a protein contribute most to its overall acid-base properties? (a) The a-amino groups of all non-terminal amino acids. (b) The N-terminal a-amino group on the protein. (c) The R groups on the protein. (d) The C-terminal a-carboxyl group on the protein. 32. The amino acid is likely found in the interior of the protein, while is likely found at the surface of a globular protein. (a) Valine, Serine (b) Glutamine, Leucine (c) Glycine, Phenylalanine (d) Arginine, Methionine (e) There is no preference for where an amino acid residue is likely to be found in a globular protein. 33. Which of the following is not true about a polypeptide chain: (a) A polypeptide chain starts with N-terminus and ends with C-terminus (b) A polypeptide chain has a main chain and a number of side chains (c) A polypeptide chain has all peptide bonds in cis configuration (d) All of the above (e) None of the above 34. Which of the following experiments performed by Anfinsen provided the experimental evidence that the primary structure of a polypeptide chain contains all the information required to fold the chain into its native, three-dimensional structure? (a) When ribonuclease is treated with urea, it loses its catalytic activity (b) When denatured ribonuclease is allowed to renature by dialyzing off urea in the presence of traces of 2-ME, it regains its catalytic activity. (c) When renatured ribonuclease is allowed to denature, it regains its catalytic activity. (d) None of the above 35. X-ray diffraction and nuclear magnetic resonance (NMR), two techniques used to solve the three-dimensional structure of molecules, differ in that: (a) X-ray diffraction is limited to molecules that can be crystallized (b) NMR is better for analyzing large proteins (c) only molecules to be analyzed by NMR need to be labeled with isotopes (d) only x-ray diffraction is successful on all proteins (e) None of the above 36. In a region of polypeptide, every third residue is a glycine; there are 3 residues per turn of polypeptide and helicity is left handed. What is the secondary structure in this region of polypeptide: (a) a-helix (b) b-sheet (c) b-turn (d) Collagen helix 37. Antiparallel b-sheets are more stable than parallel b-sheets because: (a) Antiparallel b-sheets have polypeptide segments running in the opposite direction while parallel b-sheets have polypeptide segments running in same direction (b) Antiparallel b-sheets are stabilized by linear H-bonds while parallel b-sheets are stabilized by angular H-bonds (c) Both A and B (d) None of the above 38. Hydrogen bonds between amino acids in the secondary structure of a polypeptide occur between which chemical groups? (a) the C=O and C-H groups (b) the C=O and C-R groups (c) the C=O groups (d) the C=O and N-H groups 39. The regions of the protein without any secondary structure are called: (a) a-helix (b) b-turn (c) b-sheet (d) Coiled coil (e) Loop 40. A segment of the polypeptide folds independently into a globular structure; is associated with DNA binding activity; and maintains its characteristic globular structure and DNA binding activity when separated form the remainder of the polypeptide chain. This segment of the polypeptide represents a: (a) A motif (b) A domain (c) A supersecondary structure (d) A and C (e) B and C 41. According to molten globule model of protein folding: (a) Hydrophobic interactions are the driving force of protein folding (b) Ionic interactions are the driving force of protein folding (c) Interaction of nonpolar residues located far apart in primary structure is the driving force of protein folding (d) All of the above (e) A and C 42. In what way do the DnaK-DnaJ class and the chaperonin class of proteins differ from each other? (a) Only the chaperonin class requires ATP hydrolysis (b) In chaperonin, protein fold in a small chamber or microenvironment (c) In chaperonin, protein folds on the surface with the help of ATP (d) All of the above 43. What are the characteristics of prion: (a) It is a misfolded protein (b) It is resistant to degradation (c) It is infectious (d) All of the above 44. Proline residues are most likely to occur in which of the following secondary structures? (a) an a-helix (b) a b-turn (c) a b-sheet (d) a loop 45. Which of the following statement is true about the tertiary structure of a protein in aqueous solution: (a) Hydrophilic residues are inside and hydrophobic residues are outside (b) Hydrophilic residues are outside and hydrophobic residues are inside (c) Both hydrophilic and hydrophobic residues are present on the surface as well as in the interior of protein (d) All of the above 46. Kd of a protein for ligand Z is 1X10-10and for ligand X is 5X10-10. Protein has a higher binding affinity for: (a) Ligand X (b) Ligand Z (c) Equal affinity for both the ligands (d) None of the above 47. The transition of hemoglobin between R-state and T-state is dependent on: (a) Concentration of dissolved O2 in the blood (b) pH of the blood (c) Concentration of dissolved CO2 in the blood (d) All of the above (e) A and B only 48. What does the slope of the Hill plot tells us about ligand-protein interaction: (a) Number of ligand-binding sites on the protein (b) Degree of interaction between different ligand-binding sites on the protein (c) Cooperativity of ligand binding sites on protein (d) All of the above (e) B and C 49. Iron in heme ring of myoglobin and hemoglobin is prevented from being oxidized from ferrous to ferric state because: (a) Of the electron donating effect of four nitrogen atoms of heme in coordinate linkage with iron (b) Iron in heme forms a coordinate bond with imidazole group of histidine (c) Heme is buried deep in a pocket of the folded protein (d) All of the above 50. Hemoglobin has a sigmoidal ligand binding curve, this means: (a) Hemoglobin binds O2 tightly when O2 concentration is high and releases O2 rapidly when O2 concentration is low (b) Hemoglobin binds O2 loosely at the high O2 concentration and releases O2 slowly at the low O2 concentration (c) Hemoglobin does not bind O2 (d) Hemoglobin affinity for O2is not dependent on its concentration BIO 3100 Lecture Exam I-A February 11, 2010 1. Prokaryotic and eukaryotic cells possess which of the following? (a) Ribosomes (b) Mitochondria (c) Plasma membrane (d) A and C (e) A and B 2. Which of the following is true about carbon bonding? (a) Carbon-carbon double bonds have freedom of rotation (b) Carbon atoms can form covalent bonds with up to four other atoms (c) Carbon-carbon single bonds cannot rotate (d) B and C (e) A and B 3. Aspect of metabolism that deals with the breakdown of biomolecules with the release of energy is called: (a) Catabolism (b) Monobolism (c) Anabolism (d) Sonobolism (e) Both A and C 4. Universal features of all living cells include all of the following except: (a) nucleus or nucleoid (b) plasma membrane (c) cytoplasm (d) mitochondria 5. An open system is one (a) that exchanges neither matter nor energy with its surroundings plasma membrane (b) that exchanges energy but not matter with its surroundings. (c) that exchanges both matter and energy with its surroundings. (d) that exchanges matter but not energy with its surroundings. 6. Which of the following is true about Archae: (a) They are prokaryotes (b) They are eukaryotes (c) They are plants (d) A and B (e) A and C 7. L- and D-forms of an amino acid are: (a) Different configurations of an amino acid (b) Different conformations of an amino acid (c) Enantiomers of an amino acid (d) Diasteromers of an amino acid (e) A and C 8. Different conformations of a compound are possible due to: (a) Presence of a chiral center (b) Free rotation about C-C single bond (c) Lack of free rotation about C=C double bond (d) All of the above (e) A and C 9. How can thermodynamically unfavorable reactions, such as the synthesis of DNA and protein polymers, occur in cells? (a) Cells couple thermodynamically unfavorable reactions to reactions that result in a positive change in free energy (b) Cells couple thermodynamically unfavorable reactions to an exergonic reaction like hydrolysis of ATP (c) Cells couple thermodynamically unfavorable reactions to reactions that exothermic (d) Cells couple thermodynamically unfavorable reactions to reactions that result in a decrease in entropy 10. Stereospecific configurations are conferred by: (a) Presence of a chiral center (b) Free rotation about C-C single bond (c) Lack of free rotation about C=C double bond (d) All of the above (e) A and C 11. Which of the following element combinations make up about 99% of a living cell? (a) C, N, P and S (b) C, N. H and O (c) C, H, N and Na (d) C, O, P and H 12. If the free energy change DG for a reaction is -1560.11 kJ/mol, the reaction is: (a) at equilibrium (b) endergonic (c) endothermic (d) exergonic (e) exothermic 13. The concentration of H+ ions in an aqueous solution is 1X10-10 M. What will be the concentration of OH- ions in this solution: (a) 1X10-10 M (b) 1X10-4 M (c) 1X10-14 M (d) 1X10-1 M 14. Based on the Henderson-Hasselbalch equation (shown below), calculate the pH when the ratio of acetic acid to acetate is 10 to 1 (the pKa of acetic acid is 4.76). (a) 1.00 (b) 3.76 (c) 4.76 (d) 5.76 15. Hydrophobic interactions are formed due to: (a) Tendency of nonpolar groups to cluster together to avoid water molecules (b) Thermodynamic stability of H-bonded water shield formed around the cluster of nonpolar groups (c) All of the above (d) None of the above 16. Exergonic and endergonic reactions differ in that (a) exergonic reactions have a positive free energy change (D G is positive) and endergonic reactions have a negative free energy change (D G is negative). (b) exergonic reactions require an input of energy and endergonic reactions release free energy. (c) exergonic reactions have a negative free energy change (D G is negative) and endergonic reactions have a positive free energy change (D G is positive). (d) exergonic reactions consume more free energy than is released and endergonic reactions release more free energy than is consumed. 17. Water is liquid at room temperature because of the: (a) Ability of water molecules to interact by H-bonds (b) Ability of water molecules to serve as a good solvent for polar solutes (c) Ability of water molecules to interact by van der Waal’s interaction (d) Ability of water molecules to facilitate hydrophobic interactions 18. Formation of H-bond requires: (a) a H-atom in covalent bond with a highly electronegative atom (b) a H-bond acceptor (c) a H-bond donor (d) All of the above (e) A and C 19. Which of the following is true about Van der Waals interactions: (a) They are formed due to random, fluctuating distribution of electrons in an atom (b) They are formed between any two adjacent uncharged, non-bonded atoms that are 5 Ao apart or less (c) All of the above (d) None of the above 20. Which of the following is true about pK: (a) pK is the pH at which an acid or base is half dissociated (b) pK is the negative log of dissociation constant (Ka) (c) pK is the pH at which a conjugate acid-base pair system exhibits maximum buffering capacity (d) All of the above (e) A and C only 21. Why water is considered the molecule of life: (a) Because it is a good solvent for many biomolecules (b) Because it supports weak interactions that are crucial for maintaining the biologically active conformation of a number of macromolecules (c) Because it is chemical participant in many biological reactions (d) All of the above (e) A and B only 22. Which of the following is not a weak interaction in aqueous systems: (a) Covalent bond (b) Van der Wall’s interaction (c) Hydrophobic interaction (d) H-bond (e) Ionic interaction 23. Which is the predominant ionic form of an amino acid at its isoelectric point (pI): (a) Zwitter ion form (b) Acid form (c) Base form (d) All of the above 24. Which of the following amino acid groups is amphipathic: (a) Alanine, proline, glycine (b) Aspartic acid, serine, cysteine (c) Leucine, proline, histidine (d) Lysine, tyrosine, tryptophan 25. At the center of all 20 standard amino acids is what is termed the a- carbon that is covalently bonded with four other chemical groups. Which of these four chemical groups is not a normal component of all amino acids? (a) an amino group (b) a carboxyl group (c) a side chain (R group) (d) a methyl group 26. The isoelectric point, or pI, of an amino acid or a protein is (a) the pH at which the amino acid or protein has no net charge. (b) zero at pH 7.0. (c) the pH at which the amino acid or protein is neither hydrophobic nor hydrophilic. (d) the measure of the hydropathy of an amino acid or protein. 27. The formation of a peptide bond between two amino acids is an example of: (a) Polymerization reaction (b) Condensation reaction (c) Endergonic reaction (d) A and C only (e) B and C only 28. Which group or groups on a protein contribute most to its overall acid- base properties? (a) The a-amino groups of all non-terminal amino acids. (b) The N-terminal a-amino group on the protein. (c) The R groups on the protein. (d) The C-terminal a-carboxyl group on the protein. 29. A 25 residue long polypeptide has 7 hydrophobic R groups, 4 polar hydrophilic R groups, 10 negatively charged R groups and 4 positively charged R groups. What is the net charge on the polypeptide? (a) -6 (b) +6 (c) -4 (d) +10 30. The secondary structural conformation of a-helix is stabilized by: (a) Van der Waals interaction between the backbone C=O and N-H groups of every fourth residue (b) H-bonding between the backbone C=O and R groups of every fourth residue (c) H-bonding between the backbone C=O and N-H groups of every fourth residue (d) H-bonding between the backbone C=O and N-H groups of every third residue 31. A region of polypeptide is in the form of an imperfect helix, with 2 residues per turn of the helix, and translational rise of 3.4 Ao. What is the secondary structure in this region of polypeptide: (a) a-helix (b) b-conformation (c) b-turn (d) Collagen helix 32. Proline residues are most likely to occur in which of the following secondary structures? (a) an a-helix (b) a b-turn (c) a b-sheet (d) a coiled coil 33. Isoelectric focusing is an electrophoretic technique that is used to determine: (a) Mass of the protein (b) Isoelectric point (pI) of the protein (c) Biological activity of the protein (d) Purity of the protein 34. The criteria of separation of proteins in affinity chromatography is: (a) Molecular weight of the protein (b) Net charge on the protein (c) Biological activity of the protein (d) pI of the protein 35. Acid base property of an amino acid is a function of ionization potential of its: (a) a-amino group (b) a -carboxyl group (c) R group if it is ionizable (d) All of the above (e) A and B only 36. During size exclusion chromatography, protein A gets excluded from the beads and elutes first, while protein B gets included into the beads and elutes later. This observation suggest that: (a) Protein A is heavier in size that protein B (b) Protein B is heavier in size that protein A (c) Both protein A and B are of the same size (d) We cannot conclude anything about the size of the protein from this observation 37. The criteria for separation of proteins during electrophoresis is: (a) Net charge on the protein (b) Charge/mass ratio of the protein (c) Differential affinities of proteins to stationary and mobile phases (d) Biological activity of protein 38. Which of the following is not true about a polypeptide chain: (a) A polypeptide chain starts with N-terminus and ends with C-terminus (b) A polypeptide chain has a main chain and a number of side chains (c) A polypeptide chain is made up of residues (d) The sequence of amino acids in a polypeptide chain reflects its secondary structure 39. Which of the following statements is true about the tertiary structure of a protein in aqueous solution: (a) Hydrophilic residues are inside and hydrophobic residues are outside (b) Hydrophilic residues are outside and hydrophobic residues are inside (c) Both hydrophilic and hydrophobic residues are present on the surface as well as in the interior of protein (d) All of the above 40. Fibrous proteins differ from globular proteins in that (a) fibrous proteins tend to serve structural functions, and globular proteins are more likely to be enzymes. (b) globular proteins can often contain several types of secondary structure, whereas fibrous proteins usually consist largely of a single type of secondary structure. (c) globular proteins are soluble in water, and fibrous proteins are usually insoluble. (d) All of the above 41. The amino acid is likely found in the interior of the protein, while is likely found at the surface of a globular protein. (a) Valine, Serine (b) Glutamine, Leucine (c) Glycine, Phenylalanine (d) Arginine, Methionine (e) There is no preference for where an amino acid residue is likely to be found in a globular protein. 42. Which of the following properties of peptide bond are conferred by resonance? (a) Rigidity (b) Polarity (c) Planarity (d) All of the above (e) None of the above 43. Hydroxylysine is found in collagen protein. Which of the following statement is true about hydroxylysine? (a) Hydroxylysine is a non-standard amino acid (b) Hydroxylysine has a hydroxyl group attached to the lysine residues (c) Hydroxyl group is added to the lysine after it is incorporated into collagen protein (d) All of the above (e) None of the above 44. Which of the following statements are true about a-keratin? (a) It has two right handed a-helices, oriented in parallel and wrapped around each other is (b) It is a structural protein (c) A defect in a-keratin causes scurvy (d) All of the above (e) A and B only 45. The level of protein structure that describes all aspects of the three-dimensional folding of a polypeptide is referred to as the (a) tertiary structure (b) quaternary structure (c) secondary structure (d) primary structure 46. Myoglobin is a conjugated protein because: (a) It is made up of a single polypeptide of 153 residues (b) It has a heme prosthetic group (c) It was the first protein whose 3D structure was determined (d) It has more than 70% residues in a-helical region 47. Which of the following is the only covalent interaction that stabilizes the tertiary structure of a protein: (a) Disulfide bond (b) Van der Wall’s interaction (c) Hydrophobic interaction (d) H-bond (e) Ionic interaction 48. The difference between H-bond and salt bridge is that: (a) In H-bond, both donor and acceptor are partially negatively charged while in salt bridge they are partially positively charged (b) In H-bond, both donor and acceptor are partially negatively charged while in salt bridge they are completely positively charged (c) In H-bond, both donor and acceptor are partially negatively charged while in salt bridge they are completely negatively charged (d) In H-bond, both donor and acceptor are partially positively charged while in salt bridge they are completely positively charged 49. Tertiary structure of proteins differ from quaternary structure in that: (a) Tertiary structure is due to interaction of residues far apart on the same polypeptide while quaternary structure is due to interaction of residues on different polypeptides (b) Tertiary structure is present in all proteins while quaternary structure is present in only multi-subunit proteins (c) All of the above (d) None of the above 50. Which technique are you going to use for proteomic analysis of total cellular proteins : (a) SDS-PAGE (b) Two dimensional gel electrophoresis (c) Isoelectric focusing (d) Size exclusion chromatography BIO 3100 Lecture Exam I-A February 15, 2011 1. Universal features of all living cells include: (a) A well defined nucleus (b) plasma membrane (c) cytoplasm (d) centrosome (e) B and C 2. Under what conditions is a carbon atom a chiral center? (a) if it has no stereoisomers (b) if it has only two different substituent groups (c) if it is symmetric (d) if it has four different substituent groups 3. Which of the following is not true about carbon bonding? (a) Carbon-carbon double bonds do not have freedom of rotation (b) Carbon atoms can form covalent bonds with up to four other atoms (c) Carbon can form ionic bonds with hydrogen (d) Carbon-carbon single bonds can rotate freely 4. Which of the following is true about the two molecules shown above? (a) They are the isomers formed due to freedom of rotation about C=C double bond (b) The carbon double bonds in each are chiral centers. (c) They are the isomers formed due to rigidity of C=C double bond (d) They can be interconverted without breaking any covalent bonds 5. Conformation differs from configuration in that: (a) Conformation can be changed without breaking the bond while configuration cannot (b) Configuration can be changed without breaking the bond while conformation cannot (c) Conformation is conferred by free rotation of C-C single bond while configuration is conferred by lack of rotation about C=C double bond or the presence of a chiral center (d) All of the above (e) A and C 6. Exergonic and endergonic reactions differ in that (a) Exergonic reactions have a positive free energy change (D G is positive) and endergonic reactions have a negative free energy change (D G is negative). (b) Exergonic reactions require an input of energy and endergonic reactions release free energy. (c) Exergonic reactions have a negative free energy change (D G is negative) and endergonic reactions have a positive free energy change (D G is positive). (d) Exergonic reactions consume more free energy than is released and endergonic reactions release more free energy than is consumed. 7. If change in entropy of a reaction (DS) has a large positive value and change in enthalpy (DH) of the reaction has a small positive value, it is likely that the reaction is: (Hint DG = DH – TDS) (a) exergonic (b) endergonic (c) exothermic (d) endothermic (e) Both A and C 8. Which of the following is true about D- and L-isomers of all protein amino acids except glycine: (a) They are enantiomers (b) They are diasteromers (c) They represent absolute configurations comparable to D- and L- glyceraldehyde (d) A and C (e) B and C 9. Which of the following is true of metabolism? (a) Degradative reactions require an input of energy (b) Synthetic pathways are anabolic (c) Catabolism and anabolism are linked by O2 (d) Catabolic reactions require the breakdown of ATP, and anabolic reactions generate ATP 10. The concentration of OH- ions in an aqueous solution is 1X10-10 M. What is the pH of the solution: (a) 10 (b) 4 (c) 0 (d) 14 11. Which of the following is true about condensation reactions? (a) Condensation reactions are invariably exergonic. (b) Condensation reactions involve the loss of the elements of water. (c) Formation of peptide bond is a condensation reaction (d) A and C (e) B and C 12. Water molecules exhibit maximum capacity to interact with each other by H- bonds in: (a) Gaseous state (b) Liquid state (c) Solid state (d) A solution of polar solutes 13. Which of the following is not true about H-bond (a) H-bond requires a H-bond acceptor (b) H-bond requires a H-bond donor (c) H-bond is stronger when the three atom system (the donor, the acceptor and H-atom) are in a straight line (d) H-bond is stronger than a covalent bond (e) A and D 14. Which of the following is true about how crystalline salts, such as NaCl, behave in water? (a) Water can form hydrogen bonds with NaCl (b) NaCl does not spontaneously dissolve in water because the Na+ and Cl- ions are in the form of a stable crystalline lattice (c) Crystalline salts dissolve in water because it results in an increase in entropy (d) Crystalline salts dissolve in water because water adds to the electrostatic attractions of Na+ and Cl- ions 15. Which of the following is true about hydrophobic interactions: (a) They are formed due to the tendency of nonpolar groups to cluster together to avoid water molecules (b) Their driving force is the thermodynamic stability of the water lattice that is formed around a cluster of nonpolar groups (c) They provide stability to the bilayered structure of biological membranes (d) All of the above (e) A and B only 16. Van der Waals interactions are formed between: (a) A hydrophobic group and a hydrophilic group (b) Two hydrophobic groups (c) Two hydrophilic groups (d) Any two uncharged atoms that are 5 Ao apart or less (e) None of the above 17. Based on the Henderson-Hasselbalch equation (shown below), calculate the pH when the ratio of acetic acid to acetate is 1 to 10 (the pKa of acetic acid is 4.76). (a) 1.00 (b) 3.76 (c) 4.76 (d) 5.76 18. Cells need to be buffered because: (a) They need to be able to increase or decrease their cytosolic pH to adapt to various environmental conditions (b) Their proteins work best at low pH (c) They need to maintain a specific cytosolic pH to keep biomolecules from being ionized (d) They need to maintain a specific cytosolic pH to keep biomolecules at their optimal ionic state 19. Which of the following is true about the titration curves of solutions of weak acids? (a) The pH for optimal buffering power of a weak acid is 7.00. (b) You can calculate the pKa of an acid, given the pH and the molar ratio of the acid and its conjugate base. (c) The pKa of a weak acid is the pH at which the acid is completely dissociated. (d) At a pH below the pKa of a weak acid, its conjugate base will predominate. 20. A and B are two weak acids with pKa of 3.3 and 5.3 respectively. Based on this information, which of the following statements is true: (a) A is a stronger acid than B and its capacity to donate proton is 10 times more than B (b) A is a stronger acid than B and its capacity to donate proton is 100 times more than B (c) A is a stronger acid than B and its capacity to donate proton is 2 times more than B (d) B is a stronger acid than A and its capacity to donate proton is 10 times more than A (e) B is a stronger acid than A and its capacity to donate proton is 100 times more than A 21. Acid base property of an amino acid is a function of ionization potential of its: (a) a-amino group (b) a -carboxyl group (c) R group if it is ionizable (d) All of the above (e) A and B only 22. The criteria for separation of proteins during chromatography is: (a) Net charge on the protein (b) Molecular mass of protein (c) Differential affinities of proteins to stationary and mobile phases (d) Biological activity of protein (e) A and B 23. The criteria for separation of proteins during electrophoresis is: (a) Net charge on the protein (b) Molecular mass of protein (c) Differential affinities of proteins to stationary and mobile phases (d) Biological activity of protein (e) A and B 24. Which of the following would best separate two proteins of distinct size but similar charge? (a) ion-exchange chromatography (b) SDS-PAGE (c) Size exclusion chromatography (d) A and B (e) B and C 25. An amino acid has an ionizable R-group with a pKa of 6.0. This amino acid helps in buffering the pH of cytoplasm. Identify the amino acid: (a) Lysine (b) Arginine (c) Serine (d) Glycine (e) Histidine 26. Which of the following amino acid R-group is hydrophobic: (a) Phenylalanine, isoleucine, valine (b) Alanine, proline, asparagine (c) Aspartic acid, serine, methionine (d) Leucine, proline, histidine 27. Which of the following amino acids has a net positive charge at pH 7.0 (a) Arginine (b) Cysteine (c) Lysine (d) All of the above (e) A and C 28. Which of the following methods are you going to use to determine the primary structure of a protein: (a) Edman degradation (b) Size exclusion chromatography (c) Nuclear magnetic resonance (d) Isoelectric focusing 29. Which of the following is true about conjugated proteins: (a) They are composed of only amino acids (b) They have a non-amino acid component called prosthetic group (c) They have a heme group (d) All of the above (e) A and C only 30. When an enzymatic protein is purified from a complex mixture of proteins what usually happens to total protein amount and specific activity during the purification process? (a) Total protein amount and specific activity both increase (b) Total protein amount and specific activity both decrease (c) Total protein amount increases and specific activity decreases (d) Total protein amount decreases and specific activity increases 31. X-ray diffraction and nuclear magnetic resonance (NMR), two techniques used to solve the three-dimensional structure of proteins, differ in that: (a) X-ray diffraction is limited to proteins that can be crystallized (b) NMR gives a higher resolution image (c) NMR is limited to proteins that can be crystallized (d) Only X-ray diffraction is successful on all proteins (e) None of the above 32. In a region of polypeptide, every third residue is a glycine; there are 3 residues per turn of polypeptide and helicity is left handed. What is the secondary structure in this region of polypeptide: (a) a-helix (b) b-sheet (c) b-turn (d) Collagen helix 33. The regions of the protein without any secondary structure are called: (a) a-helix (b) b-turn (c) b-sheet (d) Loop 34. Hydrogen bonds between amino acids in the secondary structure of a polypeptide occur between which chemical groups? (a) the C=O and C-H groups (b) the C=O and C-R groups (c) the C=O groups (d) the C=O and N-H groups 35. A segment of the polypeptide folds independently into a globular structure; is associated with DNA binding activity; and maintains its characteristic globular structure and DNA binding activity when separated from the remainder of the polypeptide chain. This segment of the polypeptide represents a: (a) A motif (b) A domain (c) A loop (d) A and B 36. According to molten globule model of protein folding: (a) Hydrophobic interactions are the driving force of protein folding (b) Ionic interactions are the driving force of protein folding (c) Interaction of nonpolar residues located far apart in primary structure is the driving force of protein folding (d) All of the above (e) A and C 37. What are the characteristics of prion: (a) It is a misfolded protein (b) It is resistant to degradation (c) It is infectious (d) All of the above 38. Which of the following bonds in the main chain of a polypeptide are pure single bonds: (a) N-Ca bonds (b) Ca-C bonds (c) C-N peptide bonds (d) All of the above (e) A and B only 39. A 35 residue long polypeptide has 17 hydrophobic R groups, 3 polar hydrophilic R groups, 10 negatively charged R groups and 5 positively charged R groups. What is the net charge on the polypeptide? (a) -6 (b) +6 (c) -5 (d) +10 40. Which of the following experiments provided the first evidence that the amino acid sequence of a polypeptide chain contains all the information required to fold the chain into its native, three-dimensional structure? (a) When ribonuclease is treated with urea, it loses its catalytic activity. (b) When denatured ribonuclease is allowed to renature, it regains its catalytic activity. (c) When renatured ribonuclease is allowed to denature, it regains its catalytic activity. (d) None of the above 41. A protein is in its native conformation when (a) it is thermodynamically least stable (b) it has the highest Gibbs free energy (c) it is in any of its functional, folded states (d) it is unfolded 42. . Why is the a-helix conformation in polypeptides such a stable form? (a) The a-helix structure is stabilized by hydrophobic interactions (b) The a-helix structure is stabilized by hydrogen bonds (c) The a-helix structure is stabilized by disulfide bonds (d) The a-helix structure is stabilized by proline residues. 43. Antiparallel b-sheets are more stable than parallel b-sheets because: (a) They have polypeptide chains linked by loops or turns (b) They have a different H-bonding pattern (c) They have peptide bonds in cis configuration (d) They are not present in myoglobin 44. Which of the following statements are not true about proline: (a) It is an imino acid (b) It is not compatible with a-helical secondary conformation (c) The peptide bonds involving proline have a higher tendency to be in cis configuration (d) It is never present in b-turn (e) A and C only 45. Which of the following statements is true about the tertiary structure of a protein in aqueous solution: (a) It is stabilized by disulfide bonds and a number of weak interactions like H-bonds, hydrophobic interactions, ionic interactions and van der Waals interactions (b) Hydrophilic residues are outside and hydrophobic residues are inside (c) Loops and turns are present wherever polypeptide chain makes a turn (d) All of the above (e) A and B only 46. Scurvy is caused by: (a) Deficiency of ascorbic acid (b) Lack of hydroxylation of lysine and proline (c) Deficiency of collagen polypeptide (d) A and B (e) B and C 47. During size exclusion chromatography, protein A gets included into the beads while protein B gets excluded from the beads. This observation suggest that: (a) Protein A is heavier in size that protein B (b) Protein B is heavier in size that protein A (c) Both protein A and B are of the same size (d) We cannot conclude anything about the size of the protein from this observation 48. The isoelectric point, or pI, of a protein: (a) is the pH at which the protein has no net charge (b) can be determined by isoelectric focusing (c) is the pH at which the amino acid or protein is neither hydrophobic nor hydrophilic. (d) A and B (e) B and C 49. Which group or groups on a protein contribute most to its overall acid- base properties? (a) The a-amino groups of all non-terminal amino acids (b) The N-terminal a-amino group on the protein (c) The R groups on the protein (d) The C-terminal a-carboxyl group on the protein 50. The mammalian RNA polymerase II is composed of 12 subunits. All the 12 subunits are globular and without any prosthetic group. Based on this information, which of the following statements is true about mammalian RNA polymerase II: (a) It is a conjugated protein (b) It is not an oligomeric protein (c) It has a quaternary structure (d) It is a fibrous protein (e) All of the above BIO 3100 Lecture Exam I-A February 14, 2012 1. According to which of the following laws/theories, an increase in entropy of a system leads to a greater thermodynamic stability: (a) First law of thermodynamics (b) Second law of thermodynamics (c) Darwin’s theory of organic evolution (d) Stoke’s law 2. Which of the following is true about the two molecules shown below? (a) They have the same configuration (b) They are cis-trans isomers (c) They are enantiomers of each other (d) They are diastereomers of each other. 3. Which of the following is true about the two molecules shown below? (a) They are the isomers formed due to freedom of rotation about C=C double bond (b) The carbon double bonds in each are chiral centers. (c) They are the isomers formed due to rigidity of C=C double bond (d) They can be interconverted without breaking any covalent bonds 4. The synthesis of peptide bond during protein synthesis is: (a) An endergonic reaction (b) An anabolic reaction (c) A condensation reaction (d) All of the above (e) A and C only 5. How can thermodynamically unfavorable reactions, such as the synthesis of DNA, RNA and proteins, occur in cells? (a) Cells couple thermodynamically unfavorable reactions to reactions that result in a positive change in enthalpy (b) Cells couple thermodynamically unfavorable reactions to an exergonic reaction like hydrolysis of ATP (c) Cells couple thermodynamically unfavorable reactions to reactions that have a positive free energy (d) Cells couple thermodynamically unfavorable reactions to reactions that result in a decrease in entropy 6. Different configurations of a carbon containing biomolecule are conferred by: (a) Presence of a chiral center (b) Free rotation about C-C single bond (c) Lack of free rotation about C=C double bond (d) All of the above (e) A and C 7. Which of the following is true about iodine: (a) It is a major constituent of biomolecules (b) It is a trace element (c) It is a constituent of thyroxin (d) All of the above (e) B and C 8. Cysteine residues play an important role in the structure of many proteins by: (a) providing covalent links between parts of a polypeptide chain or between two different polypeptide chains (b) forming disulfide bonds with another amino acid (c) linking two protein chains through hydrophobic interactions (d) reducing two cysteine residues 9. Which of the following is true about hydrogen bonds? (a) Hydrogen bonds are longer and stronger than covalent bonds (b) The geometry of a water molecule results in the equal sharing of electrons between the hydrogen and oxygen (c) Hydrogen bonds must involve at least one water molecule (d) Polar molecules are soluble in water because they can form hydrogen bonds with water molecules 10. What is the concentration of H+ in a solution of 0.1M NaOH? (a) 0.01M (b) 2 M (c) 10-13 M (d) 10-1 M 11. Hydrophobic interactions account for (a) why biomolecules are amphipathic (b) why the nonpolar regions of molecules cluster together in water (c) the tendency of lipids to disperse in water (d) why the polar regions of molecules are associated with water. 12. Water is essential for formation of biological membranes because: (a) Biological membranes are stabilized by ionic interactions which are possible only in an aqueous solution (b) Biological membranes are stabilized by Van der Waals interactions which are possible only in an aqueous solution (c) Biological membranes are stabilized by hydrophobic interactions which are possible only in an aqueous solution (d) Biological membranes are stabilized by H-bonds which are possible only in an aqueous solution (e) All of the above 13. On the basis of the structural diagram given below, where H-bond is indicated by a dotted line between H and N, which of the following statements is true: (a) Oxygen is the H-bond acceptor and nitrogen is the H-bond donor (b) Oxygen is the H-bond donor and nitrogen is the H-bond acceptor (c) Neither oxygen nor nitrogen are H-bond donors (d) Neither oxygen nor nitrogen are H-bond acceptors 14. Which of the following is true about pK: (a) pK is the pH at which an acid or base is half dissociated (b) pK is the negative log of hydrogen ion concentration (c) pK is the pH at which a conjugate acid-base pair system exhibits maximum buffering capacity (d) All of the above (e) A and C only 15. The properties that make water the molecule of life include: (a) It is a good solvent for many biomolecules (b) It supports weak interactions that are crucial for maintaining the biologically active conformation of a number of macromolecules (c) It has a bond angle of 104.5o (d) All of the above (e) A and B only 16. Van der Waals interactions are possible: (a) Between any two hydrophobic groups that are 5 Ao apart or less (b) Between any two uncharged hydrophilic groups that are 5 Ao apart or less (c) Between a hydrophobic group and an uncharged hydrophilic group that are 5 Ao apart or less (d) All of the above (e) None of the above 17. Which of the following statements is true about an amino acid and a residue? (a) Amino acid is the form present in proteins while residue is the free form (b) Residue is present in proteins while amino acid is the free form (c) Residue is derived from an amino acid by the loss of an –OH gp from the carboxy end and a hydrogen atom from the amino end (d) A and B (e) B and C 18. Which of the following amino acids has no net charge at pH 7.0? (a) Lysine (b) Isoleucine (c) Aspartic acid (d) Arginine 19. Which of the following led Linus Pauling and Robert Corey to conclude that peptide bond has a partial double bond character? (a) Bond length of C-N peptide bond (b) Electron delocalization (c) Resonance (d) Rigidity of peptide bond (e) B, C and D 20. The principal form of an amino acid under physiological conditions is: (a) Acid form (b) Base form (c) Zwitter ion form (d) Unionized form 21. Which of the following statement are true about the amino acid shown below: (a) It is one of the 20 standard amino acids in proteins (b) The hydroxyl group is added to this amino acid at 4-C position after its incorporation into the polypeptide chain (c) It is a constituent of collagen (d) A and B only (e) B and C only 22. A protein retained on an ion-exchange chromatography column is usually eluted off the column by: (a) gradually increasing the salt concentration of the elution buffer (b) adding the protein's free ligand (c) applying electric field to the column (d) allowing the retained protein to naturally come off the column after the non-specifically bound proteins have first passed through the resin. 23. Topoisomerase is an enzyme composed of 6 different polypeptides. It has a globular structure. The active site of the enzyme has a permanently attached Mg2+ion. Based on this information, which of the following statements are true: (a) Topoisomerase is a fibrous protein (b) Topoisomerase is a simple protein (c) Topoisomerase is a multisubunit protein (d) All of the above (e) B and C only 24. What is the highest level of structural organization in collagen? (a) Primary (b) Secondary (c) Tertiary (d) Quaternary 25. Which group or groups on a protein contribute most to its overall acid-base properties? (a) Aromatic R groups (b) Polar R groups (c) Ionizable R groups (d) Hydrophobic R groups 26. The titration curve of a non-protein amino acid is shown below. How many ionizable functional groups are there in this amino acid? (a) 0 (b) 5 (c) 3 (d) 4 27. In size exclusion chromatography, small proteins are able to enter the pores of the beads and therefore move down slowly through the beads. Such proteins are said to be: (a) excluded from the beads (b) included into the beads (c) crosslinked to the beads (d) immobilized on the beads 28. The R group of which of the following amino acids has a strong tendency to form H-bonds? (a) Valine (b) Isoleucine (c) Glutamine (d) Phenylalanine 29. Which of the following is not true about SDS polyacrylamide gel electrophoresis of proteins? (a) Polyacrylamide acts as a molecular sieve (b) It separates charged proteins by using an electric field (c) Larger proteins move faster in the gel than smaller proteins (d) It separates proteins that differ in molecular weight. 30. Which of the following types of electrophoresis are you going to use to analyze total proteins in a cell? (a) Isoelectric focusing (b) SDS-PAGE (c) Two-dimensional-PAGE (d) A and B (e) B and C 31. Which of the following is true about glycine? (a) It is an imino acid (b) It frequently occurs in b-turns (c) It exists in L- and D- configurations (d) All of the above (e) A and B only 32. A protein binds very tightly to a cation exchanger and can be eluted from the column only at extremely high ionic stren