Biochem Exam 1: Water Properties, Buffers, Amino Acids, Proteins & Plasma Analysis, Exams of Medical Biochemistry

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Medical Biochemistry Exam 1 Describe the physical and chemical properties of water - ANSWERS;- Abnormally high boiling point (100 degrees Celsius) Abnormally high freezing point (0 degrees Celsius) Abnormally high melting point Solid is less dense than liquid (ice floats in liquid water) Heat capacity H bonding Dipolar character Dissociation into charged particles Describe the effects of hydrogen bonding in physiological solutions - ANSWERS;- Rates of enzyme reactions Permeabiliyy of membranes to many molecules Stability and conformation of proteins, etc. Rates of transport through membranes Absorption, etc. of drugs Hydrophobicity or hydrophilicity of a compound Explain the Henderson-Hasselbach equation - ANSWERS;- pH = pKa + log ([A-]/[HA]) When log = 0, pH = pKa and amount of acid/base is equal Describe the role of buffers in physiology and chemistry - ANSWERS;- Buffers maintain the pH, to allow reactions to occur without upsetting the balance of the system. Phosphate and bicarbonate: bicarbonate buffer system is more important because there is more of it (carbonic anhydrase is important for the body) Buffers keep pH within 1 pH unit (either side) Describe the differences in metabolic and respiratory acidosis and alkalosis - ANSWERS;- Metabolic acidosis - usage of "fuels" increase in lactic acid in body, kidney excretes sulfuric acid, lactic acid, ammonia, and phosphoric acid Respiratory acidosis - carbonic acid to be excreted by lungs, too much CO2 in body Respiratory alkalosis - decreased in metabolism of fuels, too much O2 due to hyperventilation, decrease pressure of CO2 Describe the categories of the 20 amino acids found in proteins - ANSWERS;- Simple Aliphatic Aliphatic with hydroxyl or sulfur side chains Aromatic Basic Acidic with amides Describe properties of the simple aliphatic amino acids - ANSWERS;- Hydrophobic character increases with chain size. Glycine - precursor for hemes and purines Alanine - precursor for glucose in glyconeogensis Valine Isoleucine Leucine Proline - secondary amine, constraints on shape *Maple syrup disease - Valine, Isoleucine, Leucine Describe properties of the aliphatic amino acids containing hydroxyl groups or sulfur - ANSWERS;- Hydroxyl - modified by phosphorylation, weakly polar and hydrophilic Serine - precursor for purines, pyrimidines, and sphingosine Threonine Sulfur: Cysteine - ionize own side chain, 2 cysteines can form disulfide linkages = cystine Methionine - source of methyl groups in biochemical pathways Describe the different levels of structure in proteins and their importance - ANSWERS;- Primary - amino acid sequence. Important to elucidate the mechanism of an action of an enzyme, undertaking the relationship between sequence and folding, and studying molecular pathology to determine if alterations are causing dysfunction or disease (example sickle cell anemia, 1 AA change in hemoglobin) Secondary - folded into alpha helices, beta pleated sheets, beta turns - more organized and adds hydrogen bonding Tertiary - 3D structure, more compact, bring hydrophobic regions to core and hydrophilic to exterior. Quaternary - 2 or more polypeptide chains, non covalent forces (electrostatic attraction/salt bridges, internal hydrogen bonding, van der waals and London dispersion forces, and entropy-driven hydrophobic effect) - form oligomeric proteins Describe how proteins are denatured by heat, pH changes, organic solvents, and chaotropic agents - ANSWERS;- Chaotropic - strip water from protein, disrupt H bonds Detergents - makes peptide rodlike Organic solvents - break bonds and like dissolves like Drastic pH changes - affect the bonds, especially electrostatic attractions High temperatures cause vibration to break molecules apart, basis for Tag polymerase used in PCR Describe how some proteins require chaperonin and complexes for folding, and how mis-folded proteins are involved in diseases such as those caused by prions - ANSWERS;- Peptide chains are initially too short for secondary structure is to form, chaperones help the correct structures take place- heat shock proteins such as chaperonin Prions - beta pleated sheet, water insoluble, and protease resistant. When prions (incorrect form instead of alpha helices) come in contact with same sequence, change to wrong form - Creutzfeldt-Jakob disease, bovine spongiform encephalopathy, kuru, and fatal familial insomnia) Commonly occurring modifications of proteins - ANSWERS;- Acetylation Carboxylation Hydroxyl action Glycosylation Phosphorylation Disulfide linkages Which AA get phosphorylation? - ANSWERS;- Serine Threonine Tyrosine Alpha helix - ANSWERS;- -tightly coiled formation that is stabilized by H bonding between imido N-H groups and the oxygen atom of carbonyl groups of the main chain ex. Alpha-keratin Beta pleated sheers - ANSWERS;- Formed by hydrogen bonds between neighboring polypeptide chains or long regions of the same chain Most stable is antiparallel Beta turns - ANSWERS;- Structure that accomplish reversals in direction of peptide chains Also have hydrogen bonds which allow abrupt changes in direction Leucine zippers, zinc fingers, and Kringle domains - ANSWERS;- Zinc fingers - 4 AA complex with zinc, forms 12 AA protrusion, occur in repeating motifs Kringle domains - large loops stabilized by disulfide linkages, important in blood coagulation Leucine zippers - leucines along alpha helices, form protein dimers, allow basic AA to bind DNA Describe the difference between blood serum and plasma - ANSWERS;- Plasma - cell-free blood plus anticoagulant Serum - cell-free blood lacking fibrinogen Both are clear, yellowish due to bilirubin (degradation product from heme/hemoglobin) Describe the general method for clinical analysis of plasma proteins - ANSWERS;- Electrophoretogram pH 6.8 Cellulose acid strips/sheets used Separates into 5 major groups using positive and negative poles Staining allows bands to be visualized Describe the general appearance of an electrophoretogram showing separation of albumin, alpha-1, alpha-2, beta-, and gamma globulins - ANSWERS;- From positive pole to negative pole: albumin (most), alpha 1, alpha 2, beta, then gamma Describe the structure and properties of albumin - ANSWERS;- 580 amino acids, single polypeptide chain No carbohydrate (unusual) Compact and globular due to 17 disulfide linkages between cysteines Low viscosity Contributes most to osmotic pressure in plasma 18 negative charges per molecule Describe the role of albumin in the body and where it is produced - ANSWERS;- Produced in the liver Transports bilirubin, fatty acids, other non-specific binding compounds. Translocates sulfa drugs, penicillin, and aspirin Found in skin, muscle, GI, and circulation Contributed to osmotic pressure Concentration in serum is 4g/dL List typical proteins found in the various factions and the roles, for example several proteins involved in iron homeostasis - ANSWERS;- Describe appearance of acute phase response proteins such as C-reactive protein in pathological conditions - ANSWERS;- Describe an example of abnormal concentrations of plasma proteins associated with pathology - ANSWERS;- Describe in general terms by use of a Gibbs free energy plot how an enzyme can affect a biochemical reaction - ANSWERS;-