Biochemistry Test 1 with correct answers 2023-24

Biochemistry Test 1 biochemistry - correct answer a discipline in biochemistry; is the description of molecules in biology/chemistry of proteins molecular biology - correct answer a discipline in biochemistry; the manipulation of DNA, genetics cell biology - correct answer a discipline in biochemistry; larger scale, functions and mechanisms within a cell/cell energetics cellulose - correct answer a natural polymer; found in plants for storage glycogen - correct answer a natural polymer; found in animals for storage protein - correct answer a natural polymer; tightly linked bonds nucleotide - correct answer a natural polymer; covalent bonds C,H,N,O,S - correct answer chemical elements commonly found in biochemistry carbon - correct answer an element commonly found in biochemistry, creates strong single or double bonds with very little rotation covalent - correct answer a chemical bond in biology; a pair of shared electrons, very strong, bonds between polymers, >1 bond per atom, flexible and alternate re-arrangement non-covalent - correct answer a chemical bond in biology; weaker bonds, but additive, creates specificity, highly dynamic/transient bonds, required for molecular recognition electrostatic, hydrogen, van der waals, hydrophobic - correct answer 4 types of non-covalent interactions electrostatic - correct answer a non-covalent interaction; such as ionic bonds Na⁺ + Cl⁻ -> NaCl hydrogen - correct answer a non-covalent interaction; a H is shared between two electronegative atoms such as F,O, or N; the more electronegative atom pulls the electron closer, creating a dipole donor acceptor - correct answer the H bond _____ becomes more tightly linked, the H bond_____becomes less tightly linked (two answers separated by a space please) Van Der Waals - correct answer a non-covalent interaction; the interaction between molecules with temporary dipoles from fluctuating electrons, are weak but additive hydrophobic interaction - correct answer a non-covalent interaction; the clustering of these molecules in polar substances i.e. water interacts with itself and causes other non-polar residues to cluster biological solvent - correct answer roles of water; many organic and biological materials are able to dissolve in water part of reaction - correct answer roles of water; water is a common substance in biochemical reactions such as the cleavage of bonds regulation - correct answer roles of water; water is essential in regulating temperature and pH (the ideal temperature of water with the highest heat capacity is 37°C) water - correct answer a substance found in nearly all biological reactions and organisms; has a bond angle between H's of 104.5°, has a dipole, H-bonds with itself, cohesive and dissolves polar or charged compounds hydrophilic - correct answer water as a solvent; types of bonding in water "loving" compounds are dipole-dipole, H-bonding, and dipole-ion hydrophobic aliphatic - correct answer water as a solvent; types of bonds formed with water "fearing" compounds are called______. Non-polar/apolar compounds that usually fall in this category are long chained molecules composed of C and H called______molecules (two answers separated by a space please) amphiphilic - correct answer water as a solvent; water "loving and fearing" compounds that contain both polar and non polar regions micelle - correct answer a conformation formed by amphiphilic substances in water that usually serve to sequester different regions in the cell 55.5 - correct answer the concentration of water (molar) pH - correct answer the power of hydrogen (acidity) of a solution, = -log[H⁺] acid - correct answer relating to pH; a substance that releases a proton base - correct answer relating to pH; a substance that accepts a proton Ka - correct answer relating to pH; = ([H⁺][A⁻])/[HA] pKa - correct answer relating to pH; = -log[Ka] monoprotic - correct answer an acid is said to be this if it is capable of releasing 1 H⁺ ion inflection point - correct answer the point on a titration curve that is ½ the way to neutralization, where pH=pKa polyprotic - correct answer an acid is said to be this if it is capable of releasing more than 1 H⁺ ion HH equation - correct answer the name of the following equation(remember equation too): pH=pKa+log([base]/[acid]) buffer - correct answer a substance that significantly (to ±1 pH unit) can control molecular structure and activity acetate and citrate - correct answer two natural buffers 8.3 - correct answer a synthetic buffer; the pKa of TRIS 7.5 - correct answer a synthetic buffer; the pKa of HEPES(a zwitterion) phosphate, proteins, carbonate - correct answer 3 cellular buffers (hint: first can be found at 1mM in blood, examples of the second are hemoglobin and albumen, the third is the most common) 7.4 - correct answer the pH of blood lungs - correct answer an organ that regulates blood pH zwitterion - correct answer compounds that have both a positive and negative charge on the same molecule but are neutral overall side chain - correct answer also known as the R-group amino, carboxyl, alpha carbon, r-group - correct answer the 4 general constituents of an AA AA - correct answer short form for Amino Acid chiral - correct answer the ∝-carbon is said to be this (it has 4 groups attached) enantiomers - correct answer also known as stereo isomers, the only AA that is not is glycine, where R=H + - correct answer the charge of NH₃ (symbol) - - correct answer the charge of COO (symbol) D and L - correct answer a form of stereochemistry; polarization of light; nearly all biological AA's are in the "L" form when produced, "D" is rare R and S - correct answer a form of stereochemistry; used mainly in organic chemistry 20 - correct answer total number of AA's 2.3 - correct answer the carboxyl pKa 9.7 - correct answer the amino pKa 7 - correct answer the pH if the R-group has no net charge. ie. charge is 0 equivalence - correct answer the point on a titration curve where the [zwitterion] concentration is the highest structure - correct answer during AA titrations, the ______ of the AA changes Isoelectric pH - correct answer defined as the pH were the structure of an AA or peptide has no net charge; the average of the pKa's cystine - correct answer oxidized S-S bonded aa usually outside the cell cysteine - correct answer reduced S, single cysteine usually found inside the cell histidine - correct answer an AA that usually regulates the active sites of an enzyme in response to pH condensation - correct answer the name of the reaction when 2 AA's join their amino and carboxyl terminus (water is removed) multiple - correct answer 1 to 10 AA's together polypeptide - correct answer 10 to 100 AA's together protein - correct answer greater than 100 AA's together residue - correct answer another name for the side chain of an AA left right - correct answer directionality of drawn peptides; ______side is the N terminus, ______side is the C terminus (two answers please, separated by a space) hydrolysis - correct answer the name of the reaction when 2 AA's break their amino and carboxyl terminus (water, 6M HCl and heat are added) peptidases - correct answer specialized proteins that break peptide bonds (trypsin and chymotrypsin are examples) 1 AMU - correct answer equivalent mass of 1 Da (Dalton) 110 DA - correct answer the average mass of an AA monomeric - correct answer protein composition; protein consists of a single polypeptide chain multisubunit - correct answer protein composition; same as oligiomeric; protein consists of two or more polypeptide chains (chains can be identical or different) oligiomeric - correct answer protein composition; 2 or more polypeptide chains together subunit - correct answer protein composition; single pieces of a multisubunit protein simple - correct answer protein composition; a protein is said to be this if it is only composed of AA's (no other groups) conjugated - correct answer protein composition; a protein is said to be this if it contains AA's and other chemical groups (such as organics or metal ions) prosthetic group - correct answer protein composition; names of non AA groups found on conjugated proteins, cofactors/coenzymes covalently linked to protein globular - correct answer protein composition; a protein is said to be this if it is water soluble and found in the cytoplasm of cells fibrous - correct answer protein composition; a protein is said to be this if it is water soluble and found in the cell structure assay development - correct answer first step in protein isolation and purification source and lyse - correct answer second step step in protein isolation and purification fractional centrifugation - correct answer a protein isolation technique that separates the supernatant from the pellet supernatant - correct answer the liquid component left from a fractional centrifugation pellet - correct answer the more solid component separated from a fractional centrifugation chromatography - correct answer a protein isolation technique that separates proteins based on many characteristics gel filtration or molecular exclusion - correct answer a method of chromatography; separation based on size, large proteins elute first, small proteins elute later, ionic exchange - correct answer a method of chromatography; separates proteins based on charge (PI); gel is usually agarose or cellulose affinity chromatography - correct answer a method of chromatography; separation based on ligand attachment; protein attaches to ligand in gel; excess ligand is then poured in, eluting the protein (due to entriopic processes) HPLC - correct answer a method of chromatography; separation based on hydrophobic interactions, works well with peptides, resin is small, slow flow, high pressure specific activity - correct answer total activity/total protein Yield - correct answer total activity(current)/total activity(original) purification level - correct answer specific activity(current)/specific activity(original) SDS-PAGE - correct answer a gel used to determine the molecular size and purity of a protein, smaller proteins migrate faster, charge does not matter, blue dye stains basic residues SDS - correct answer sodium dodecyl sulfate, a negatively charged detergent used to coat proteins in molecular size and weight assay (used with PAGE) PAGE - correct answer polyacrylamide gel electrophoresis, gel used in molecular size and weight assay (used with SDS) beta-mercaptoethanol - correct answer reducing agent for cistiene that breaks S-S bonds acrylamide - correct answer a neurotoxic component of PAGE gel, it forms a 3-D mesh/pores in the gel bis-acrylamide - correct answer causes acrylamide to crosslink in PAGE gel, the higher the concentration, the more crosslinking and the smaller the pores isoelectric focusing - correct answer used to determine the size for unknown proteins, separation based purely on charge (pH gradient) ampholytes - correct answer the name of the group of compounds that create the pH gradient in isoelectric focusing 2-d electrophoresis - correct answer a handy molecular technique that first employs IEF in one direction and SDS-PAGE in the other primary - correct answer a level of protein structure; the AA sequence of the protein secondary - correct answer a level of protein structure; how AA sequences form small structures such as ∝-helices or þ-sheets tertiary - correct answer a level of protein structure; the interaction of ∝-helices or þ-sheets, globular forlds quaternary - correct answer a level of protein structure; interactions between 2 protein chains Edman degeneration - correct answer method to determine primary structure; reagent binds to first N terminus stripping of AA, AA then identified by HPLC, cycle repeated and good for proteins up to 50AA's long two enzymatic digestions - correct answer method to determine primary structure; first, trypsin recognizes ARG and LYS and cleaves after the bond, second chymotrypsin recognises PHE, TRP and TYR, cleaving after each DNA sequencing - correct answer method to determine primary structure; low quantities of sample required, high speed, examples are the Human Genome Project native conformation - correct answer this refers to a protein that is properly folded (functional) in structure and is in its natural environment alpha helix - correct answer a secondary structure; rod-like, with R-chains branching out, stabilized by H bonds between N-H and C=O groups. 3.6 residues per turn with H bonding every 4 aa. 10-20 residues per turn is average, proline disrupts steric interactions and is usually found at the ends to prevent bonding beta sheet - correct answer a secondary structure; sheet-like, 2 or more interactions, small AA's are favored anti parallel - correct answer the configuration of the more common beta sheets which form tighter H-bonds, which leads to smaller loops bends or loops - correct answer a secondary structure; reverses in the direction of the main chain, usually connects an alpha helix and beta sheet common bend - correct answer a secondary structure; known as a beta turn, connects different anti parallel sheets bend - correct answer a secondary structure; 4 residues with H-bonding between AA 1 and AA 4 loop - correct answer a secondary structure; longer bends which are usually >6 AAs alpha alpha motif - correct answer a supersecondary structure; usually deals with DNA beta beta motif - correct answer a supersecondary structure; a more common structure greek key - correct answer a supersecondary structure; 4 adjacent beta strands beta barrel - correct answer a supersecondary structure; parallel beta strands connected with an alpha helix collagen - correct answer a supersecondary structure; a fibrous protein that contains a triple helix(superhelix) high in proline and hydroxyproline, a non-conventional helix early events - correct answer first part of the protein folding pathway; the formation of secondary structure intermediate - correct answer second part of the protein folding pathway; formation of ionic bonds final - correct answer last part of the protein folding pathway; compaction of the protein in vivo - correct answer a biological process that occurs in it's natural environment molecular chaperone - correct answer a folding accessory protein; binds unfolded proteins by "sheltering" exposed non-polar regions heat shock protein - correct answer a folding accessory protein; ensures that proteins do not de-nature at high temperatures heat, organic solvents, SDS, urea - correct answer the 4 causes of protein unfolding denaturization - correct answer the loss of protein function (as well as structure), can be renatured "in vitro" homotypic - correct answer a protein in which all the subunits are the same heterotypic - correct answer a protein in which the subunits are different 141 - correct answer the number of AA's on one alpha chain in hemoglobin 144 - correct answer the number of AA's on one beta chain in hemoglobin protoporphyrin - correct answer a prosthetic group (polypyrole ring) that binds Fe, has 4 bonding points 6 - correct answer the number of bonding points that Fe requires Histidine F8 - correct answer interacts with Fe in hemoglobin Histidine E7 - correct answer shields the Fe in hemoglobin in the +2 state of oxygen uptake hemoglobin - correct answer an oxygen carrying molecule, forms a sigmoidal oxygen binding curve, found in the vascular system, 50% saturation @ 3kPa myoglobin - correct answer an oxygen carrying molecule, forms a hyperbolic oxygen binding curve, found in the musculature for uptake, 50% saturation @ .2kPa allosteric interaction - correct answer the binding of one site affects binding at another site the bohr effect - correct answer the co-operative binding of hemoglobin and its dependency on protons and carbon dioxide concentrations (allosteric effectors) deoxy - correct answer the T(tense) state of hemoglobin, central cavity is larger oxy - correct answer the R(relaxed) state of hemoglobin, central cavity is smaller tent - correct answer the physical form hemoglobin helix assumes when in the unbound state linear - correct answer the physical form hemoglobin helix assumes when in the bound state 2,3-BPG - correct answer a molecule present in high concentrations in RBC, binds to the T state of Hb, and allows for the better release of all oxygen molecules, is an allosteric effector, negatively charged gamma - correct answer found in fetal Hb, replaces the two beta subunits, difference between the beta is that it has a serine at 143 instead of a histidine, higher affinity for oxygen than maternal Hb sickle cell anemia - correct answer a Hb mutation; a mutation from Glu6-->Val in the beta subunit decreases the solubility, causing fibrous aggregations thalassemia - correct answer a Hb mutation; the loss or substantial reduction of a single Hb chain alpha thalassemia - correct answer a Hb mutation; no alpha subunits in Hb, 4 beta subunits (HbH) beta thalassemia - correct answer a Hb mutation; no beta subunits, 4 alpha subunits; this condition is more common immunoglobulin - correct answer structures involved in immune response IgG - correct answer an immunoglobulin that is most common IgA - correct answer an immunoglobulin that is usually found in secretions (such as saliva) IgE - correct answer an immunoglobulin that is usually related to allergenic responses 12 - correct answer the number of domains in IgG variable region - correct answer a region on an antibody that changes, allowing the recognition of different antigens constant region - correct answer a region on an antibody that does not change hypervariable loop - correct answer a structure found in the beta chains of immunoglobulin folds that allows for the recognition of different antigens hydrogen peroxide - correct answer a waste product which is detrimental to cells, it degrades on its own slowly and requires a high activation energy transition state - correct answer an unfavored state at the peak of the activation energy between reactants and products cofactor - correct answer enzymes; a second chemical entity (organic or inorganic) coenzyme - correct answer enzymes; usually organic or organometallic, does not a form a permanent part of the enzyme holoenzyme - correct answer enzymes; a complete complex of protein and cofactor apoenzyme - correct answer enzymes; just the protein component in a holoenzyme Vo - correct answer enzyme kinetics; initial velocity, ([P]/time) at start of reaction, =(Vmax[S])/(Km+[S]) Vmax - correct answer enzyme kinetics; the maximum velocity for an enzyme Km - correct answer enzyme kinetics; Michaelis constant Km=[S] - correct answer when Vo=Kmax/2 Vo=Kmax/2 - correct answer when Km=[S] high Km - correct answer enzyme kinetics; is an utight bond between enzyme and substrate, low affinity low Km - correct answer enzyme kinetics; is a tight bond between enzyme and substrate, high affinity turnover number - correct answer Vmax/[E] allosteric enzymes - correct answer enzymes mediated by a modulator or effector, or substrate active site - correct answer a region on an enzyme where the substrate binds specific, small, weak - correct answer the 3 characteristics of active sites lock and key - correct answer ES complex theory; the enzyme and substrate are rigid structures induced fit - correct answer ES complex theory; enzyme active site is similar to substrate, the enzyme "stretches" a conformational change occurs and the substrate binds TS model - correct answer ES complex theory; enzyme stabilizes the substrate, which can lead to products general acid/base catalysis - correct answer mechanisms of enzyme activity; assists in proton transfer reactions, functional groups act as acids or bases metal ion catalysis - correct answer mechanisms of enzyme activity; (30% of all enzymes) hold a substrate properly, stabilizes negative intermediates to polarize scissile bonds, participate in redox reactions covalent catalysis - correct answer mechanisms of enzyme activity; nucleophilic groups on enzyme reacts and forms covalent bonds with substrate, usually interacts with carbonyl in serine scissile - correct answer a bond in a substrate that is to be broken nucleophilic - correct answer substances high in electrons/lone pairs inhibition - correct answer an enzymatic process where an effector shuts down or reduces an enzymes activity; drugs and toxins exert their effects through this mechanism irreversible - correct answer enzymatic inhibition; covalent bonds permanantly change an enzyme reversible - correct answer enzymatic inhibition; non-covalent bonding effectors stop enzymatic processes, the three general forms are competative, non-competative (pure and mixed), and uncompetative competative - correct answer enzymatic inhibition; where the effector resembles the substrate, binds to the active site, high [S] lessens the effect of the inhibitor, Vmax stays the same, Km is altered pure non-competative - correct answer enzymatic inhibition; inhibitor and substrate bind to different sites; Km stays the same, Vmax changes mixed non-competative - correct answer enzymatic inhibition; inhibitor and substrate bind to different sites; Vmax and Km changes uncompetative - correct answer enzymatic inhibition; inhibitor binds to the ES complex, Km decreases and Vmax increases, locks the substrate in position allosteric - correct answer regulatory pathways are usually controlled by these class of enzymes; in addition, the first enzyme in the pathway is usually the regulatory one and of this type allosterism - correct answer in enzymes, binding or catalytic changes cause a conformational change elsewhere homotropic - correct answer enzymatic allosterism; where the substrate and the effector molecule are identical heterotropic - correct answer enzymatic allosterism; where the substrate and the effector are different MWC concerted model - correct answer allosteric regulation; enzymes can either be found in the TT or RR state, the effector molecule shifts the enzyme to one state (hybrid TR not possible) sequential model - correct answer allosteric regulation; enzymes can either be found going from TT->TR->RR, the TR hybrid is possible covalent modification - correct answer cellular enzyme regulation; modification via phosphorylation of Ser, Thr, Tyr or ubiquitination of Lys proteolytic cleavage - correct answer cellular enzyme regulation; some enzymes are synthesized in the inactive form, the zymogen is cleaved into the active state, this is a irreversible process isoenzyme - correct answer cellular enzyme regulation; enzymes that carry out the same reaction but have different kinetics, regulatory properties, forms of coenzymes, and distribution zymogen - correct answer cellular enzyme regulation; the term used to describle an enzyme formed in an inactive state that has to be cleaved in order to work