Medical Biochemistry: Answers to Experimental Techniques and Amino Acids Questions, Exams of Medical Biochemistry

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Medical Biochemistry, UCF Alanine - correct answers; Ala, A Arginine - correct answers; Arg, R Asparagine - correct answers; Asn, N Aspartic Acid - correct answers; Asp, D Experimental techniques: PCR - correct answers; -can amplify small amounts of DNA Experimental techniques: Western blot - correct answers; -measures protein levels in a sample using antibodies Experimental techniques: Southern blot - correct answers; -detects DNA levels Experimental techniques: Northern blot - correct answers; -detects RNA levels Experimental techniques: Gel electrophoresis - correct answers; -separates molecules on the basis of size Experimental techniques: SDS-PAGE/Reducing Gels vs Native Gels - correct answers; -SDS-PAGE/Reducing Gels: separates denatured proteins on the basis of size -Native gals: separates proteins in their native conformation that allows subunits to remain intact Experimental techniques: Molecular cloning - correct answers; -used to introduce genetic information into a plasmid for protein expression or genetic manipulation Experimental techniques: transformation/conjugation/transduction - correct answers; -used to transfer genetic information into into bacterial species Cysteine - correct answers; Cys, C Glutamic Acid - correct answers; Glu, E Glutamine - correct answers; Gln, Q Glycine - correct answers; Gly, G Histidine - correct answers; His, H Isoleucine - correct answers; Ile, I Leucine - correct answers; Leu, L Lysine - correct answers; Lys, K Methionine - correct answers; Met, M Phenylalanine - correct answers; Phe, F Proline - correct answers; Pro, P Serine - correct answers; Ser, S Threonine - correct answers; Thr, T Threonine, Thr, T - correct answers; -polar side chain Tryptophan, Trp, W - correct answers; -largest in size(bulky) -aromatic side chain Tyrosine, Tyr, Y - correct answers; -aromatic side chain -bulky -relatively polar Valine, Val, V - correct answers; -nonpolar -strongly hydrophobic (more likely to be found in the interior of a protein) Mechanical activation - correct answers; Tension can cause proteins to spring open Proteolytic cleavage - correct answers; Seen in biological process such as blood clotting, mitosis, apoptosis and complement SUMOylation - correct answers; Binds to lysine residues; plays a role in transcription & nuclear transport Ubiquitination - correct answers; Signal for protein degradation Glycosylation - correct answers; Seen in secretions; helps proteins fold properly in rough ER Acetylation - correct answers; Neutralizes positive charge Phosphorylation - correct answers; Transfer of high-energy group; changes charge; decreases hydrophobicity of regions; large structural movements ATP/ GTP hydrolysis - correct answers; Allows for conformational change; method for tRNA release from proteins 2,3- Bisphosphoglycerate - correct answers; Causes O2 release by stabilizing T state; negative heterotropic regulator Bohr effect - correct answers; pH difference between lungs and metabolic tissues increases efficiency of the O2 transport to tissues Cooperativity - correct answers; Multiple binding sites that interact with each other Relaxed State - correct answers; High O2 affinity; less interactions Tensed State - correct answers; Low O2 affinity; more interactions Carbon monoxide - correct answers; Blocks function of myoglobin, hemoglobin, and mitochondrial cytochromes Globins - correct answers; Proteins that bind free oxygen Hemoglobin structure - correct answers; Tetramer Myoglobin structure - correct answers; Monomer Induced Fit - correct answers; Conformational changes may occur upon ligand binding Lock and Key Model - correct answers; Assumes that complementary surfaces are pre-formed Weak binding - correct answers; Kd > 10 microM Strong binding - correct answers; Kd < 10 nM Negative ∆G - correct answers; Spontaneous reaction Prosthetic Group - correct answers; a coenzyme or metal ion that is tightly or even covalently bound to the enzyme protein Catalysts - correct answers; Increase reaction rate (velocity); lower activation energy Standard conditions - correct answers; T = 25 degrees C (298 K); 1 atm partial pressure; 1M concentration of reactants and products Formula for free energy change - correct answers; ∆G = ∆G'o + RTln [C]^c[D]^d /[A]^a[B]^b Lock and key model - correct answers; Enzyme active site and substrate have complementary shapes Induced fit model - correct answers; Brings specific functional groups on the enzyme into position to catalyze the reaction; also form more weak bonds in transition state. Electrostatic Catalysis - correct answers; Stabilization of TS intermediates through ionic interactions with metals or side chains Chymotrypsin cuts bonds adjacent to - correct answers; Aromatic amino acids Serine Proteases Triad - correct answers; Asp102, His57, Ser195 Enolase mechanism - correct answers; Metal ion and acid-base catalysis that utilizes lysine345 Transpeptidase - correct answers; Crosslinks peptidoglycan beta-Lactam - correct answers; Blocks peptidoglycan crosslinks Globular protein - correct answers; Soluble in water Quaternary Structure - correct answers; Multiple subunits forming a larger function structure Ribonuclease Experiment - correct answers; Amino acid sequence can determine native conformation Chaperones - correct answers; Macromolecules that assist in protein folding Parallel β sheet - correct answers; Has bent H-bonds (weaker); strands run in the same direction Alanine and Leucine - correct answers; Amino acids that are strong alpha helix formers Proline (cis) and glycine - correct answers; Amino acids common in beta turns Collagen - correct answers; 3 chains (left-handed) forming a superhelical right-handed triple helix Phi and Psi - correct answers; Angles around the alpha carbon Alpha keratin - correct answers; 2 parallel strands forming a left-handed coiled coil At acidic pH an amino acid's carboxyl group is - correct answers; Protonated (-COOH) At neutral pH an amino acid's carboxyl group is - correct answers; Deprotonated At alkaline pH an amino acid's amino group is - correct answers; Neutral (-NH2) Anion exchange chromatography is used to - correct answers; Purify negatively-charged proteins Cation exchange chromatography is used to - correct answers; Purify positively-charged proteins Size exclusion chromatography is used to - correct answers; Separate proteins based on size Affinity chromatography is used to - correct answers; Seperate proteins based on their affinity for a ligand Electrophoresis - correct answers; Electric field pulls proteins according to their charge SDS-PAGE - correct answers; Proteins separated based on size alone Western Blotting - correct answers; Uses antibody to tag specific protein on a membrane Water's dipoles - correct answers; O bears a partial negative charge and each H a partial positive charge Hydrogen bonding - correct answers; Strong dipole-dipole or charge-dipole interaction that arises between an acid (proton donor) and a base (proton acceptor) Water is a good solvent for what? - correct answers; Charged and polar molecules Water is a poor solvent for what? - correct answers; Nonpolar molecules Buffers - correct answers; Solutions that resist change in pH Ionic interactions - correct answers; Electrostatic interactions between permanently charged species, or between the ion and a permanent dipole Dipole interactions - correct answers; Electrostatic interactions between uncharged polar molecules van der Waals interactions - correct answers; Weak interactions between all atoms, regardless of polarity, attractive (dispersion) and repulsive (steric) component Hydrophobic effect - correct answers; The ordering of water molecules around nonpolar substances pH - correct answers; Negative logarithm of the hydrogen ion concentration pKa - correct answers; Negative logarithm of Ka; measurement of acidity Chemoautotroph - correct answers; Chemical energy source & CO2 carbon source Chemoheterotroph - correct answers; Chemical energy source & organic compounds' carbon source Photoautotroph - correct answers; Light energy source & CO2 carbon source Photoheterotroph - correct answers; Light energy source, organic compounds' carbon source Endergonic reaction - correct answers; Anabolic, thermodynamically unfavorable Exergonic Reaction - correct answers; Catabolic, thermodynamically favorable Relationship between G and Keq - correct answers; Inverse Structural isomers - correct answers; Same atoms but different order of bonding, different properties Enantiomers - correct answers; Stereoisomers that are mirror images Diastereomers - correct answers; Stereoisomers that are not mirror images The pH scale is logarithmic. - correct answers; true 2,3-bisphosphoglycerate - correct answers; stabilizes R state leading to oxygen release. stabilizes T state leading to oxygen binding. is a positive heterotropic regulator. decreases at higher altitudes. Correct: helps prevent hypoxia. Enzymatic catalysis - correct answers; has high specificity. A large Keq value is associated with which of the following values in a chemical reaction? - correct answers; Negative ΔG A chiral carbon - correct answers; has four different substituents. All molecules are able to form - correct answers; van der Waals interactions. Proteins are used for - correct answers; transport. catalysis. structure. regulation. Correct: All of the answer choices are correct. Which of the following mutations is related to sickle cell anemia? - correct answers; glutamate >> valine. Which of the following is NOT true? - correct answers; Hydrogen bonds are strongest when the bonded molecules are oriented to maximize electrostatic interaction (ideally in a line, not bent). Hydrogen bonds are the source of water's unique properties. Hydrogen bonding in water is cooperative. Hydrogen bonds take part in enzyme/substrate interactions. Correct: Hydrogen bonds are stronger than covalent bonds. Which of the following is true about Hydrogen bonds? - correct answers; Hydrogen bonds are strongest when the bonded molecules are oriented to maximize electrostatic interaction (ideally in a line, not bent). Hydrogen bonds are the source of water's unique properties. Hydrogen bonding in water is cooperative. Hydrogen bonds take part in enzyme/substrate interactions. Correct: All of the above are true A racemic drug is sometimes not prescribed because it - correct answers; contains the other isomer, which may have negative side effects. Hemoglobin is a __________ that when treated with urea becomes a __________. - correct answers; tetramer, pair of heterodimers. When hydrophobic molecules aggregate - correct answers; fewer water molecules are ordered; water entropy is increased. The __________ state of hemoglobin has __________ interactions, and has a __________ affinity for oxygen. - correct answers; T, more, lower. Which of the following is NOT a reversible covalent modification? - correct answers; Zymogen Reversible covalent modifications include: - correct answers; Phosphorylation. Methylation. Acetylation. Adenylylation. Plants use light as an energy source and CO2 as a carbon source; therefore, they are __________. - correct answers; photoautotrophs At what point will an amino acid have a net charge of zero? - correct answers; pH = pI In an SDS-PAGE gel - correct answers; small proteins move faster. The RNA World Hypothesis states that - correct answers; RNA most likely preceded DNA and proteins. All of the following are benefits of NMR - correct answers; it can detect many hydrogens. it can be carried out in solution. the protein does not need to be crystallized. All of the following are benefits of NMR, EXCEPT - correct answers; it works well with small and large proteins. In water, protons exist free in solution. - correct answers; false Hemoglobin binding is cooperative; it undergoes - correct answers; positive homotropic regulation. Bacteria that have been treated by lysozyme and is put into a hypotonic solution - correct answers; will lyse due to water entering the bacteria. Which of the following modifications does NOT occur typically on lysine residues? - correct answers; Phosphorylation. All of the following modifications occur typically on lysine residues: - correct answers; Biotinylation. Acetylation. SUMOylation. Ubiquitination.