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Biochemistry Final
UW-Platteville Buboltz's General Biochemistry Final Exam 2014 Fall
| Question | Answer |
|---|---|
| for amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have what charge | a net positive charge |
| titration of valine by a strong base, for example NaOH, reveals two pK's. The titration reaction occurring at pK2 (pK2=9.62) is: | -NH3 + OH- yields -NH2 + H2O |
| at the isoelectric pH of a tetrapeptide the total net charge is | Zero |
| an enzyme is found to have a narrow range of pH within which it can function effectively. This pH range is centered around pH=5.7, & its catalytic activity is actually difficult to even measure just 2.2 pH units higher than this optimal value. Why? | a conformational change occurs as the pH increases, which alters the protein's structure and therefore its function |
| for the amino acid lysine, the Henderson-Hasselbalch equation can be applied to how many ionization group(s) | three |
| the primary structure of a protein specifically describes the | linear sequence of its amino acids |
| the ionic charges associated with a protein molecule are | mostly contributed by the side chains of constituent amino acids |
| a mixture of 5 proteins (X, Y, Z, N & Q) is applied to a size-exclusion column. Given the information supplied, which will elute third? (X-35,000, Y-26,000, Z-146,000, N-26,000, Q-14,000 in g/mol) | Y and N elute together |
| the rate of migration for SDS-Page of polypeptides depends only on | size and not on conformation |
| which of the following undergoes an oxidation reaction to form a disulfide bond? | cysteine |
| a mutation that changes___________ would probably produce minimal effects on protein function, while a mutation that changes_________could produce dramatic effects | LLe to Leu; Asn to Ala |
| which residue can function as a "pH sensitive molecular switch": histidine, cysteine, proline, serine, and methionine | histidine |
| which of the following peptides would absorb light centered at 280 nm? ala-lys-his, his-pro-ala, ser-gly-asn, ala-ala-trp, or val-pro-leu | ala-ala-trp; the aromatic amino acids absorb light around 280 nm |
| in an aqueous solution, a globular protein's conformation will always reflect | the placement of hydrophobic residues within the interior of the protein |
| in the context of protein structure, which interactions are also known as "salt bridges" | ionic bonds |
| how are side chains in the alpha-helix oriented | radiate outward from the helical axis |
| amino acid residues commonly found in the middle of beta-turn are | pro and gly |
| in a globular protein its tertiary structure is likely stabilized by the interactions of | amino acid side chains in non-neighboring regions of the polypeptide chain |
| in a globular protein it could contain alpha helices that are stabilized by | hydrogen bonds |
| in a globular protein it could contain disulfide bonds that stabilize its | Tertiary structure |
| in a globular protein non-covalent forces are | the primary source of stability for its secondary and tertiary structure |
| a scientist observes that protein X will fold into its native conformation only when protein Y is also present in the same solution. Protein Y, however, can fold into its native conformation without protein X being present. Therefore protein Y may be a | molecular chaperone for protein X |
| in a protein the rotation about covalent bonds only can cause | conformational changes |
| NMR is a technique that can be used to analyze the 3D-structure of | proteins in solution |
| the polypeptide chains in the sheet are nearly fully extended in | Beta-sheets |
| structures in beta-sheets can occur in both | parallel and anti parallel forms |
| in anti parallel beta-sheets the hydrogen bonds between adjacent strands are | nearly perpendicular to the backbones of the strands |
| adjacent strands in beta-sheets form hydrogen bonds within | the plane of the sheet |
| Protein X can bind to either protein A or protein B to form a complex, with either association constant 10^8 M-1 (x with A) or 10^6 M-1 (X with B) which takes fewer molecules | in the presence of excess X, it takes fewer molecules of A than B to generate a given amount of complex |
| about how many residues per turn of the alpha-helices | 3.6 |
| a coenzyme is something that | is essential to the function of a protein, is not made up of amino acids, and is readily separated from the protein |
| an increase in blood pH will cause hemoglobin to bind more tightly to oxygen is a result of | the effectors of hemoglobin-oxygen binding |
| conditions in the tissues which enhance the delivery of oxygen by hemoglobin are the presence of | CO2, 2,3-BPG, and protons |
| which reversible reaction of carbon dioxide explains how hemoglobin serves as a transporter of CO2 | reaction with the N-terminal amino groups to form a carbonate |
| a hyperbolic binding curve differs from a sigmoidal binding curve in that the hyperbolic curve | implies one affinity state only (single Kd) for oxygen binding |
| in order to drive shape changes from the oxy form of hemoglobin to the deoxy form, attractive interactions must arise between | oppositely charged groups on different subunits |
| an allosteric interaction between a ligand and a protein is one where | binding of a molecule to a binding site affects properties of another site on the protein |
| a good transition-state analog | binds to the enzyme more tightly than the substrate |
| which step in an enzyme-catalyzed reaction was assumed to be negligible by Michaelis and Menton in formulating their chemical model of enzyme action | formation of ES from E + P |
| to calculate the turnover number of an enzyme, you need to know | the enzyme concentration, and the initial velocity of the catalyzed reaction at [S]>>Km |
| what is the net charge on the peptide Gly-Ser-Arg-Lys-His-Asp-Val at pH 7.5? | +1 |
| what is the approximate molar mass of a protein containing 378 amino acids | ~37,800 |
| why do wool socks shrink when they are washed in hot water or heated in a dryer | processed wool is rich in beta-sheets, but returns to native alpha-helices upon heating |
| what is the formula for a carbohydrate | (CH2O)n |
| polysaccharide structure can be varied by differences in | chain length (number of sugars in each polysaccharide), the kind(s) of sugars in each polysaccharides, the presence of branching, and the types of linkages between sugar units |
| what type of bond links the monomers of a polysaccharide | glycosidic bond |
| sugar found in DNA | adopts a 5-membered cyclic structure, is a deoxy form of ribose, has a D-configuration, and is bonded to phosphate via the 3' and 5' carbons |
| anomers can be interconverted | via a linear intermediate |
| which does not apply to dihydroxyacetone: ketose, triose, chiral, water-soluble, or carbohydrate | chiral |
| what is the most generic nucleic acid form for storing genetic information | double-stranded DNA |
| in the Watson-Crick DNA model (i.e., "B-form" DNA), how many base pairs are found in one turn of the helix? | 10 |
| which base is at the 5' end of the molecule: ACCAGTCG | A is at 5' end, G is at 3' |
| what base is only found in DNA | thymine |
| what would be the effect of exposing both RNA and DNA to alkaline pH | RNA is hydrolyzed to nucleoside monophosphates |
| Histones are proteins around which DNA must be tightly wound chromosomes. Therefore, one may infer that all 5 histone proteins are rich in _____residues, whose charges allow binding to the sugar-phosphate backbone of DNA | lysine and arginine |
| it is easier to denature ("melt") DNA richer in AT than GC because | there is one fewer hydrogen bond in an AT base pair |
| in the Watson-Crick model for the DNA double helix the two strands run | anti-parallel to one another |
| in the Watson-Crick model for the DNA double helix the base-pairing occurs on the | inside of the double helix |
| in the Watson-Crick model for the DNA double helix the double helix is what handed | right-handed |
| in the Watson-Crick model for the DNA double helix the two strands have complementary | sequences |
| in the Watson-Crick model for the DNA double helix the grooves are | major and minor |
| storage fats that contain only saturated long chain fatty acids tend to form what at room temperature | solids |
| what would you expect for the fatty acyl chains of the membrane phospholipids of bacteria grown at high temperature | proportion of unsaturated fatty acyl groups decreases |
| the arrangement of lipid bilayers and other components is the basis for the currently widely accepted description which is called the | fluid mosaic model |
| when red-blood cells are treated w/ globular proteases most are broken down into peptides but a small fraction of the protein content is resistant. If peptide cleavage is the only effect, how can the protease-resistant fraction be explained? | it represents integral membrane proteins |
| fatty acids have an even number of carbon atoms between | 16-24 in total |
| there are two types of lipids: non-polar lipids and "polar" lipids. Polar lipids are really just what | amphiphatic |
| the shortest alpha helix segment in a protein that will span a membrane bilayer has about how many amino acid residues | 20 |
| individual lipid bilayer molecules are free to diffuse in what direction of the bilayer | laterally in the surface of the bilayer |
| the fluidity of a lipid bilayer will be increased by | increasing the temperature |
| G proteins act as signaling proteins but have a mechanism that does what that involves the hydrolysis of a nucleoside triphsphate | intrinsic shut-off |
| which does not contribute to the regulation of enzymatic activity: protein phosphorylation, allosteric effectors, protein stability, mRNA stability, and DNA stability | DNA stability |
| in the signal-cascade pathway that causes glucose to be released from glycogen in response to the hormone epinephrine, what is the immediate product of adenyl cyclase? | cAMP |
| What are some similarities between transporters and enzymes | undergo conformational changes upon binding their substrates, interact w/ their substrates stoichiometrically, reach a saturation limit when supplied w/ excess of substrate,& show structural complementarity in binding very specifically w/ their substrates |
| what is not a similarity between transporters and enzymes | enzymes cause a chemical modification to their substrates; transporters just move them |
| in mitochondria, phosphate ion and H+ are transported together from the intermembrane space into the matrix. This means that the transport protein must | be a symporter |
| citrate synthase is a key regulatory enzyme of the citric acid cycle. What are some inhibitors | ATP, NADH |
| pyruvate kinase is allosterically inhibited by | a high concentration of ATP |
| reaction steps that are far from equilibrium are good control points in metabolic pathways because | these reactions are highly exergonig |
| F26BP does what to PFK-1 | activates |
| F26BP does what to fructose-1,6-bisphosphate | inhibits |
| is fructose-1,6-bisphosphatase reaction is exergonic or endergonic | exergonic |
| why is it important for proper cll function that proteins turn over rather than persisting indefinately after being synthesized | this would allow changes in enzyme activity levels. if proteins were never degraded, all enzymes wuld remain present indefinately |
| what happens to FBPase-2 when FBPase-2 is phosphorylated | activated |
| what happens to PFK-2 when FBPase-2 is phosphorylated | inactivated |
| what happens to [F26BP] when FBPase-2 is phosphorylated | decrease |
| what happens to PFK-1 when FBPase-2 is phosphorylated | inhibited |
| what happens to FBPase-1 when FBPase-2 is phosphorylated | activated |
| what happens to glycolysis when FBPase-2 is phosphorylated | slow down |
| what happens to gluconeogensis when FBPase-2 is phosphorylated | will accelerate |
| which of these cofactors participates directly in most of the oxidation-reduction reactions in the fermentation of glucose to lactate?: ADP, ATP, FAD/FADH2, glyceraldehyde 3-phoosphate, or NAD+/NADH | NAD+/NADH |
| the anerobic conversion of 1 mol of glucose to 2 mol of lactate (i.e., no citric acid cycle, no ox-phos) is accompnaied by a net production of how much ATP | 2 mol of ATP |
| the conversion of 1 mol of pyruvate to 3 mol of CO2 via pyruvate dehydrogenase and the citric acid cycle also yields | 4 mol of NADH, 1 mol of FADH2, and 1 mol of ATP (or GTP) |
| the rate of entry of acetyl-CoA into the citric acid cycle is decreased when the ratio of [ATP]/[ADP] is | high |
| citrate synthase and the NAD+-specific isocitrate dehydrogenase are two key regulatory enzymes of the citric acid cycle. These enzymes are inhibited by: | ATP and/or NADH |
| reducd QH2 is not formed by which complex | complex III and cytochrome c |
| almost all of the xygen (O2) one consumes in breathing is converted to | water |
| Vitamin B2 (riboflavin) | FAD |
| Vitamin B1 | TPP; thiamine pyrophosphate |
| Vitamin B3 | NAD+ |
| Vitamin B5 | Coenzyme A |
| complex I is | NADH: ubiquinone oxido reductase |
| Complex II is | succinate dehydrogenase |
| Complex III is | cytochrome bc1 complex |
| Complex IV is | cytochrome oxidase |
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