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Biochemistry Test 1examination test
with correct marking scheme
biochemistry - Correct Answers a discipline in biochemistry; is the description of molecules in biology/chemistry of proteins molecular biology - Correct Answers a discipline in biochemistry; the manipulation of DNA, genetics cell biology - Correct Answers a discipline in biochemistry; larger scale, functions and mechanisms within a cell/cell energetics cellulose - Correct Answers a natural polymer; found in plants for storage glycogen - Correct Answers a natural polymer; found in animals for storage protein - Correct Answers a natural polymer; tightly linked bonds nucleotide - Correct Answers a natural polymer; covalent bonds C,H,N,O,S - Correct Answers chemical elements commonly found in biochemistry carbon - Correct Answers an element commonly found in biochemistry, creates strong single or double bonds with very little rotation covalent - Correct Answers 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 Answers a chemical bond in biology; weaker bonds, but additive, creates specificity, highly dynamic/transient bonds, required for molecular recognition electrostatic, hydrogen, van der wails, hydrophobic - Correct Answers 4 types of non-covalent interactions electrostatic - Correct Answers a non-covalent interaction; such as ionic bonds Na⁺ + Cl⁻ -> Nalco hydrogen - Correct Answers 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 Answers 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 Answers a non-covalent interaction; the interaction between molecules with temporary dipoles from fluctuating electrons, are weak but additive hydrophobic interaction - Correct Answers 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 Answers roles of water; many organic and biological materials are able to dissolve in water part of reaction - Correct Answers roles of water; water is a common substance in biochemical reactions such as the cleavage of bonds regulation - Correct Answers 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 Answers a substance found in nearly all biological reactions and organisms; has a bond angle between H's of 104.5°,
polypro tic - Correct Answers an acid is said to be this if it is capable of releasing more than 1 H⁺ ion HH equation - Correct Answers the name of the following equation(remember equation too): pH=pKa+log([base]/[acid]) buffer - Correct Answers a substance that significantly (to ±1 pH unit) can control molecular structure and activity acetate and citrate - Correct Answers two natural buffers 8.3 - Correct Answers a synthetic buffer; the Pak of TRIS 7.5 - Correct Answers a synthetic buffer; the Pak of HEPES(a zwitterion) phosphate, proteins, carbonate - Correct Answers 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 Answers the pH of blood lungs - Correct Answers an organ that regulates blood pH zwitterion - Correct Answers compounds that have both a positive and negative charge on the same molecule but are neutral overall side chain - Correct Answers also known as the R-group amino, carboxyl, alpha carbon, r-group - Correct Answers the 4 general constituents of an AA AA - Correct Answers short form for Amino Acid chiral - Correct Answers the ∝-carbon is said to be this (it has 4 groups attached) enantiomers - Correct Answers also known as stereo isomers, the only AA that is not is glycine, where R=H
+ - Correct Answers the charge of NH₃ (symbol) o - Correct Answers the charge of COO (symbol) D and L - Correct Answers 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 Answers a form of stereochemistry; used mainly in organic chemistry 20 - Correct Answers total number of AA's 2.3 - Correct Answers the carboxyl Pak 9.7 - Correct Answers the amino Pak 7 - Correct Answers the pH if the R-group has no net charge. i.e. charge is 0 equivalence - Correct Answers the point on a titration curve where the [zwitterion] concentration is the highest structure - Correct Answers during AA titrations, the ______ of the AA changes Isoelectric pH - Correct Answers defined as the pH were the structure of an AA or peptide has no net charge; the average of the Pak’s cysteine - Correct Answers oxidized S-S bonded aa usually outside the cell cysteine - Correct Answers reduced S, single cysteine usually found inside the cell histidine - Correct Answers an AA that usually regulates the active sites of an enzyme in response to pH
simple - Correct Answers protein composition; a protein is said to be this if it is only composed of AA's (no other groups) conjugated - Correct Answers 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 Answers protein composition; names of non AA groups found on conjugated proteins, cofactors/coenzymes covalently linked to protein globular - Correct Answers protein composition; a protein is said to be this if it is water soluble and found in the cytoplasm of cells fibrous - Correct Answers protein composition; a protein is said to be this if it is water soluble and found in the cell structure assay development - Correct Answers first step in protein isolation and purification source and lyse - Correct Answers second step step in protein isolation and purification fractional centrifugation - Correct Answers a protein isolation technique that separates the supernatant from the pellet supernatant - Correct Answers the liquid component left from a fractional centrifugation pellet - Correct Answers the more solid component separated from a fractional centrifugation chromatography - Correct Answers a protein isolation technique that separates proteins based on many characteristics gel filtration or molecular exclusion - Correct Answers a method of chromatography; separation based on size, large proteins elute first, small proteins elute later,
ionic exchange - Correct Answers a method of chromatography; separates proteins based on charge (PI); gel is usually agarose or cellulose affinity chromatography - Correct Answers 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 entropic processes) HPLC - Correct Answers a method of chromatography; separation based on hydrophobic interactions, works well with peptides, resin is small, slow flow, high pressure specific activity - Correct Answers total activity/total protein Yield - Correct Answers total activity(current)/total activity(original) purification level - Correct Answers specific activity(current)/specific activity(original) SDS-PAGE - Correct Answers 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 Answers sodium dodecyl sulfate, a negatively charged detergent used to coat proteins in molecular size and weight assay (used with PAGE) PAGE - Correct Answers polyacrylamide gel electrophoresis, gel used in molecular size and weight assay (used with SDS) beta-mercaptoethanol - Correct Answers reducing agent for cysteine that breaks S-S bonds acrylamide - Correct Answers a neurotoxic component of PAGE gel, it forms a 3-D mesh/pores in the gel bus-acrylamide - Correct Answers causes acrylamide to crosslink in PAGE gel, the higher the concentration, the more crosslinking and the smaller the pores
alpha helix - Correct Answers 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- residues per turn is average, proline disrupts steric interactions and is usually found at the ends to prevent bonding beta sheet - Correct Answers a secondary structure; sheet-like, 2 or more interactions, small AA's are favored anti-parallel - Correct Answers the configuration of the more common beta sheets which form tighter H-bonds, which leads to smaller loops bends or loops - Correct Answers a secondary structure; reverses in the direction of the main chain, usually connects an alpha helix and beta sheet common bend - Correct Answers a secondary structure; known as a beta turn, connects different anti parallel sheets bend - Correct Answers a secondary structure; 4 residues with H- bonding between AA 1 and AA 4 loop - Correct Answers a secondary structure; longer bends which are usually >6 AAs alpha alpha motif - Correct Answers a super secondary structure; usually deals with DNA beta beta motif - Correct Answers a super secondary structure; a more common structure Greek key - Correct Answers a super secondary structure; 4 adjacent beta strands beta barrel - Correct Answers a super secondary structure; parallel beta strands connected with an alpha helix
collagen - Correct Answers a super secondary structure; a fibrous protein that contains a triple helix(super helix) high in proline and hydroxyproline, a non-conventional helix early events - Correct Answers first part of the protein folding pathway; the formation of secondary structure intermediate - Correct Answers second part of the protein folding pathway; formation of ionic bonds final - Correct Answers last part of the protein folding pathway; compaction of the protein in vivo - Correct Answers a biological process that occurs in its natural environment molecular chaperone - Correct Answers a folding accessory protein; binds unfolded proteins by "sheltering" exposed non-polar regions heat shock protein - Correct Answers a folding accessory protein; ensures that proteins do not de-nature at high temperatures heat, organic solvents, SDS, urea - Correct Answers the 4 causes of protein unfolding denaturation - Correct Answers the loss of protein function (as well as structure), can be renatured "in vitro" homotypic - Correct Answers a protein in which all the subunits are the same heterotypic - Correct Answers a protein in which the subunits are different 141 - Correct Answers the number of AA's on one alpha chain in hemoglobin 144 - Correct Answers the number of AA's on one beta chain in hemoglobin
better release of all oxygen molecules, is an allosteric effector, negatively charged gamma - Correct Answers found in fetal Hob, 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 Hob sickle cell anemia - Correct Answers a Hob mutation; a mutation from Glu6-->Val in the beta subunit decreases the solubility, causing fibrous aggregations thalassemia - Correct Answers a Hob mutation; the loss or substantial reduction of a single Hob chain alpha thalassemia - Correct Answers a Hob mutation; no alpha subunits in Hob, 4 beta subunits (Hahn) beta thalassemia - Correct Answers a Hob mutation; no beta subunits, 4 alpha subunits; this condition is more common immunoglobulin - Correct Answers structures involved in immune response IgG - Correct Answers an immunoglobulin that is most common IgA - Correct Answers an immunoglobulin that is usually found in secretions (such as saliva) Inge - Correct Answers an immunoglobulin that is usually related to allergenic responses 12 - Correct Answers the number of domains in IgG variable region - Correct Answers a region on an antibody that changes, allowing the recognition of different antigens constant region - Correct Answers a region on an antibody that does not change
hypervariable loop - Correct Answers a structure found in the beta chains of immunoglobulin folds that allows for the recognition of different antigens hydrogen peroxide - Correct Answers a waste product which is detrimental to cells, it degrades on its own slowly and requires a high activation energy transition state - Correct Answers an unflavored state at the peak of the activation energy between reactants and products cofactor - Correct Answers enzymes; a second chemical entity (organic or inorganic) coenzyme - Correct Answers enzymes; usually organic or organometallic, does not a form a permanent part of the enzyme holoenzyme - Correct Answers enzymes; a complete complex of protein and cofactor Apo enzyme - Correct Answers enzymes; just the protein component in a holoenzyme Vo - Correct Answers enzyme kinetics; initial velocity, ([P]/time) at start of reaction, =(Vmax[S])/(Km+[S]) Vmax - Correct Answers enzyme kinetics; the maximum velocity for an enzyme Km - Correct Answers enzyme kinetics; Michalis constant Km=[S] - Correct Answers when Vo=KAMAX/ Vo=KAMAX/2 - Correct Answers when Km=[S] high Km - Correct Answers enzyme kinetics; is an uptight bond between enzyme and substrate, low affinity low Km - Correct Answers enzyme kinetics; is a tight bond between enzyme and substrate, high affinity
inhibition - Correct Answers an enzymatic process where an effector shuts down or reduces an enzymes activity; drugs and toxins exert their effects through this mechanism irreversible - Correct Answers enzymatic inhibition; covalent bonds permanently change an enzyme reversible - Correct Answers enzymatic inhibition; non-covalent bonding effectors stop enzymatic processes, the three general forms are competitive, non-competitive (pure and mixed), and uncompetitive competitive - Correct Answers 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-competitive - Correct Answers enzymatic inhibition; inhibitor and substrate bind to different sites; Km stays the same, Vmax changes mixed non-competitive - Correct Answers enzymatic inhibition; inhibitor and substrate bind to different sites; Vmax and Km changes uncompetitive - Correct Answers enzymatic inhibition; inhibitor binds to the ES complex, Km decreases and Vmax increases, locks the substrate in position allosteric - Correct Answers 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 allosteric - Correct Answers in enzymes, binding or catalytic changes cause a conformational change elsewhere homotopic - Correct Answers enzymatic allosteric; where the substrate and the effector molecule are identical heterotrophic - Correct Answers enzymatic allosteric; where the substrate and the effector are different
MWC concerted model - Correct Answers 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 Answers allosteric regulation; enzymes can either be found going from TT->TR->RR, the TR hybrid is possible covalent modification - Correct Answers cellular enzyme regulation; modification via phosphorylation of Seer, Thru, Tyr or ubiquitination of Lys proteolytic cleavage - Correct Answers cellular enzyme regulation; some enzymes are synthesized in the inactive form, the zymogen is cleaved into the active state, this is an irreversible process isoenzyme - Correct Answers cellular enzyme regulation; enzymes that carry out the same reaction but have different kinetics, regulatory properties, forms of coenzymes, and distribution zymogen - Correct Answers cellular enzyme regulation; the term used to describe an enzyme formed in an inactive state that has to be cleaved in order to work
