BCHM 2023 with verified questions and answers

scheme that describes the flow of information from one strand of DNA to a new strand of DNA central dogma filled with proteases and other digestive enzymes lysosomes the distance when two atoms no longer repulse each other yet have the strongest attraction is known as the __________ contact distance van der waals a molecule with both water-loving and water repelling properties amphipathic this chiral type of amino acids is found in proteins L-amino acids amino acid with imidazole side chain histidine when a peptide bond is formed between two amino acids, a ___ molecule is lost water sedimentation coefficients are expressed in ____ units Svedberg enzymes that do not have the required cofactor bound are called ____ apoenzymes ___ can be added prior to gel electrophoresis to denature the proteins SDS examples of cofactors include Zn+2, Mg+2, Ni+2 biotin, thiamine phyrophosphate pyridoxal phosphate, coenzyme A what structures did Pauling and Corey predict in 1951? alpha helix, beta sheet allosteric effectors alter the equilibria between R and T forms of a protein name two amino acids that are positively charged at a neutral pH lysine, arginine two-dimensional electrophoresis is a combination of what two techniques isoelectric focusing, SDS-PAGE list atoms commonly found in biological molecules that are often hydrogen bond acceptor oxygen, nitrogen proteins are chiefly composed of which of the following long, unbranched amino acid polymers the configuration of most alpha-carbon atoms of amino acids linked in a peptide bond is trans what is the advantage of adding SDS to gel eletrophoresis SDS allows proteins to be separated on the basis of approximate mass the rigid material that provides structural support to a plant cell is/are called the cell wall an acid ionizes to form a protein and its _____ conjugate base in the edman procedure for peptide sequence, phenyl isothiocyanate is used to selectively remove the ___________ residue as a PTH-derivative amino terminal reactions that have more than two reactants or substrates are considered _________ reactions second order ____ is the major fibrous protein present in skin, bone, tendon, cartilage and teeth collagen a reaction can occur spontaneously only if delta G is ___ negative ____ is an amino acid with a hydrophobic side chain containing a thioether methionine secretory vesicles fuse with the plasma membrane to release material outside of the cell via the process of exocytosis proteins can be separated from small molecules and ions through a semi-permeable membrane by the process of ____ dialysis an enzyme will be most sensitive to changes in cellular substrate concentration as well as show significant activity when the substrate is ____ near Km enzymes accelerate the rate of a chemical reaction by ___ the free energy of activation of the reaction lowering what are some features of active site of enzyme 1. active site is a 3-D cleft or crevice created by amino acids from different parts of the primary structure 2. the active site constitutes a small portion of the enzyme volume 3. active site creates unique microenvironments 4. the interaction of the enzyme and substrate at the active site involves multiple weak interactions 5. enzyme specificity depends on the molecular architecture at the active site. if noncovalent bonds are so much weaker than covalent bonds, how do they stabilize large biochemical structures? they are high in number. there are so many of them! how is lactate dehydrogenase assayed? Lactate + NAD -- pyruvate + NADH + H+ what are the four key classes of biomolecules proteins, lipids, carbohydrates, nucleotides define antigen and antibody antigen - foreign molecule exposed to a system antibody - protein produced in immunological response to the antigen three aromatic acids tyrosine, tryptophan, phenylalanine draw a sketch of a michaelis-mentin plot. write the equation. lol what is the pH of an aqueous solution with a protein concentration of 10-5 M pH = -log10 (H+) pH = -log10 (10-5) pH = 5 determine the turnover number of an enzyme having a concentration of 10-6 M and has a Vmax of a 0.6 M substrate per second? 0.6/10^-6 = an acid with a pKa of 8.0 is present in a solution with a pH of 6.0. what is the ratio of protonated to deprotonated form of the acid? 6 = 8 + log (A)/(HA) log (A)/(HA) = -2 (A)/(HA) = antilog (-2) = 0.01 1/0.01 = 100 name three amino acids that form the catalytic triad of Chymotrypsin serine histidine aspartic acid three types of membrane proteins integral membrane proteins peripheral membrane proteins proteins associated with membranes by attachment to a hydrophobic moiety that is inserted into the membrane define anabolism and catabolism catabolism - combustion of carbon fuels to synthesize ATP anabolism - use ATP and reducing power to synthesize large biomoleculces name two activated carriers used for fuel oxidation NAD+, FAD complete the following steps of glycolysis..... etc phosphofructokinase fructose-1,6-biphosphate dihydroxyacetone phosphate glyceraldehyde-3-phosphate liposomes lipid vesicles, aqueous components surrounded by lipid membrnae used for drug transport why are fats considered a more efficient source of fuel than carbohydrates fats are more reduced than carbohydrates, hence release more energy on oxidation what is energy charge? how does energy charge affect phosphofructokinase in the skeletal muscle? ATP/AMP energy charge increase, phosphofructokinase decreases in mammals, the major site for triacylglycerol is adipose tissue ___ is a common steroid, that inserts into lipid bilayers, disrupting interactions between fatty acids, therby helping to maintain membrane fluidity cholesterol ___ is known as the "chemical currency" of metabolism ATP inactive chymotrypsiongen will be hydrolyzed to become an active enzyme called __ chymotrypsin glycolysis produces a net of ___ molecuels of ATP per one molecule of glucose 2 ___ is a drug that acts by inhibiting the enzyme glycopeptide transpeptidase, the enzyme required to make peptidoglycan, thus inhibiting the formation of cell wall in bacteria penicillin the binding of IP3 to the IP3 receptor results in the release of ___ ions from the ER calcium the hydrolysis of AP is an ___ reaction, hence it is used in couping with other unfavorable reactions that help them proceed exergonic the reactions that couple the loss of electrons by a donor with the gain of electrons by an acceptor molecule are known as ___ reactions redox _____ is an intestinal inflammatory disorder tha results because susceptible individuals are unable to digest certain proteins (rich in glutamine and proline) from wheat, rye, barley celiac disease ___ is a proteas released by the stomach for digestion of protein pepsin amylase digest carbs by cleaving the _____bonds of starch alpha-1,4 glycosidic Ras is a membrane of the ____ family of proteins small G proteins isomers that are non-superimposable mirror images of each other are called ___ enantiomers ____ - the type of amino acids found in the transmebrane helix of an integral protein hydrophobic ____ - this is a term applied to molecules that have both hydrophilic and hydrophobic moieties amphipathic __ is composed to two molecules of glucose linked together by a alpha-1,4-glycosidic bond maltose the _____ uses energy of ATP hydrolysis to simultaneously pump 3 Na+ ions out of the cell and two K+ ions into the cell Na-K pump ___ are passive transport systems that allow specific and rapid transport of ions down their concentration gradients ion channels ___ compound serves as an acyl carrier in metabolsim acetyl CoA pancreas releases ___ to buffer the pH of teh stomach juices as teh food moves from stomach to intestine NaHCO3 examples of second messengers include cAMP calcium ion diacylglycerol the reduced form of the flavin adenine dinucleotide is FADH2 what does the notation 18:2 for fatty acids imply? 18 carbons with 2 double bonds metabolic processes are regulated by regulation of the amount of enzyme allosteric control of enzyme activity accessibility of substrates by compartmentalization how does the binding of a hormone to a receptor activate a G protein? it causes an exchange of GTP for bound GDP lactose intolerance is caused by a deficiency of the enzyme lactase what forces stabilize the lipid bilayers van der waals interactions along with electrostatic and hydrogen bonding between the polar heads and surrounding water what type of enzyme catalyzes the intramolecular (within the molecule) shift of a chemical group mutase the process of converting atmospheric N2 to NH3 is called nitrogen fixation ___ is the process by which noncarbohdyrate precursor molecules are converted into glucose gluconeogenesis cholesterol and triacylglycerols are transported in body fluids in the form of ___ lipoproteins in the urea cycle, the hydrolysis of arginine by arginase produces ornithine and ___ urea the function of the ___ cycle is to harvest high-energy electrons TCA ___ is an enzyme in the inner mitochondrial membrane that carries out the synthesis of ATP ATP synthase triacylglycerols are stored in ___ tissue in animals adipose ____ - the process that takes place with the help of the enzyme complex known as fatty acid synthase fatty acid synthesis the major tissue in which gluconeogensis takes place is __ liver this complex of the ETC does not pump protons complex II how are fatty acids larger than the 16 carbons formed? by elongation reactions catalyzed by enzymes on the ER which amino acids can be directly deaminated to produce NH4+? serine and threonine ___ is a component of the myelin sheath sphinogomyelin ___ is a cofactor for transamination reactions pyridoxine odd-numbered unsaturated fatty acids are metabolized by which of the following enzymes? isomerase when glucose is totally oxidized to CO2 and H2O, how many ATP molecules are yielded? 30 in the TCA cycle, the oxidative decarboxylation of alpha-ketoglutarate is calazyed by alpha-ketoglutarate dehydrogenase this is a large multi-subunit enzyme complex that links glycolysis and the citric acid cycle pyruvate dehydrogenase in the cori cycle, lactate produced in muscle tissue is converted to glucose in the cel, the ETC occurs in the _ mitochondria ____ is caused by a deficiency in vitamin B1 (thiamine) beri beri organisms that can convert fat into sugar use the ___ cycle glyoxylate the protein involved with thermogenesis by uncoupling electron transport from oxidative phosphorylation is uncoupling protein 1 a strong oxidizing agent has a tendency to ___ accept the enzyme __ is activated by hormones and is rsponsible for the degradation of triacylglycerol lipase the process of conversion of NH4+ to NO3- nitrification ___ is an example of an essential w-fatty acid tha tneeds to be supplied by diet linoleate ketogenic amino acids are degraded to form ___ acetyl CoA the active form of vitamin ___ is derived from cholesterol D how many ATP molecules are generated by the complete oxidation of one molecule of palmitate 106 name the four steps of beta-oxidatoin of fatty acids 1. oxidaton 2. hydration 3. oxidation 4. thiolysis how does energy charge afefct pyruvate dehydrogenase energy charge: ATP/AMP high energy charge inhibits PDH complex low energy charge stimulates it how many high energy electrons and ATP are generated by the citric acid cycle. in what form are these electrons obtained from the cycle? 8 electrons and 1 ATP. NADH and FADH2 what are the two components tha tmake up ATP synthase? F0 and F1 what is the main characteristic that distinguishes essential amino acids from essential amino acids amino acids that can be synthesized by humans are called nonessential; usually synthesized by simple reactions amino acids that are required in the diet are essential amino acids. these amino acids usually have complex synthetic pathways and cannot be synthesized by humans how does the presence of AMP and glucose affect gluconeogenesis? in gluconeogenesis where does the final step of the converstion of glucose 6-phosphate to glucose take place? AMP and glucose inhibit gluconeogenesis the final step occurs in the ER membrane what are lipoproteins? what are the two main types of lipoproteins? lipoprotein: consist of a protein component and various lipids, depending on type of particle. serve to solubilize the lipids and direct the particles to specific targets classified according to density: the greater the proportion of lipid, the less dense the particle LDL (low density) = major carrier of cholesterol HDL (high density) = carries cholesterol released into the blood back to the liver; reverse cholesterol transport what is proton motive force? what process proceed due to the presence of this force? proton translocation generates a gradient; the protons cannot diffuse back into the matrix because the membrane is impermeable to ions. imbalance of protons serves as a source of free energy, known as "proton motive force" can be used to drive ATP synthesis