Amino Acids and Protein Structure: Definition and Properties, Quizzes of Biology

Download Amino Acids and Protein Structure: Definition and Properties and more Quizzes Biology in PDF only on Docsity! TERM 1 vitalism DEFINITION 1 1800s animate world obeys different chemical laws than the inanimate world "organic" compounds could only be made by living things TERM 2 Friedrich Wohler DEFINITION 2 1828 synthesized urea from ammonium cyanate refutation ofvitalism - made an organic compound from an inorganic one TERM 3 Lewis Pasteur DEFINITION 3 1862 disproved spontaneous generation showed that sterilized solutions did not spontaneously form life air required to produce microbes living organisms arise from living organisms still a vitalist; "ferments" in yeast viewed inseparable from life TERM 4 Edward & Hans Buchner DEFINITION 4 1897: DEATH OF VITALISM fermented sucrose to alcohol using yeast extract -> chemical reactions can occur outside of cells! death of vitalism: enzymes are cell derived catalysts TERM 5 Emil Fisher DEFINITION 5 1890 - lock and key model to visualize the substrate and enzyme interaction Fischer esterification, Fischer projection 1891 configuration of D-glucose TERM 6 First biochemistry departments established DEFINITION 6 early 1900s isolation of biomolecules, study of structure, functions and role in metabolism TERM 7 James B. Sumner DEFINITION 7 1926: crystallized the first enzyme (urease) and showed it was a protein TERM 8 Linus Pauling & Robert Corey DEFINITION 8 1930s: X-ray crystallography of amino acids and peptides (gets structure) TERM 9 3D structure of 1st proteins DEFINITION 9 done by x-ray crystallography Max Perutz - hemoglobin John Kendrew - myoglobin TERM 10 James Watson & Frances Crick DEFINITION 10 1953: 3D structure of DNA showed that molecular biology as part of biochemistry TERM 21 Hydrogen bonds in water DEFINITION 21 water is cohesive water h-bonds: ~20kJ/mol, relatively strong attraction between slightly negative O and slightly positive H bonds are directional - more stable when linear TERM 22 How many hydrogen bonds can a single water molecule form? DEFINITION 22 up to 4 but they continually form and break, average is 3.4 per molecule TERM 23 Why is water an excellent solvent for polar molecules and molecules that ionize? DEFINITION 23 It weakens electrostatic forces & H-bonds by competing for their attraction forms oriented solvation shells around ions TERM 24 hydrophilic DEFINITION 24 polar or charged molecules that dissolve readily in water TERM 25 hydrophobic DEFINITION 25 nonpolar molecules (like hydrocarbons) that do not dissolve in water TERM 26 Hydrophobic effect DEFINITION 26 nonpolar solute molecules are driven together in water NOT because they have a high affinity for each other because water bonds strongly to itself water that surrounds nonpolar molecules is more restricted in its interaction with other water molecules MAJOR driving force in protein folding TERM 27 Amphipathic DEFINITION 27 molecules that are bothhydrophilic and hydrophobic TERM 28 4 types of noncovalent bonds DEFINITION 28 Charge-charge (electrostatic) hydrogen bonds Van der Waals interactions hydrophobic interactions these are all reversible molecular interactions TERM 29 Charge-charge interactions DEFINITION 29 AKA ionic bond, salt linkage, salt bride, ion pair, electrostatic interaction optimal distance: 2.8 angstroms potentially strongest noncovalent interaction: ~40-200 TERM 30 Hydrogen bonds DEFINITION 30 a hydrogen atom is shared between two other atoms can form between charged or uncharged molecules H-donor: atom to which H is more tightly associated H-acceptor: atom to which H is less tightly associated, has partial negative charge to attract H Bond distance: ~2.6 - 3.1 angstroms bond energy: ~2-20 kJ/mol highly directional, strongest in straight line TERM 31 Van der Waals bonds DEFINITION 31 non-specific attractive force important when any two atoms are 3-4 angstroms apart. Most important when numerous atoms in one molecule come close to atoms in another molecule weaker and less specific than electrostatic & H-bonds distribution of electric charge around an atomchanges w/ time - > asymmetry leads to attractions Attraction is distance dependent: most strong atVan der Waals contact distance, 2.4 - 4 angstroms energy: 0.4-4 kJ/mol TERM 32 Hydrophobic attractions DEFINITION 32 weak interations: 3-10 kJ/mol Interactions between nonpolar molecules due to tendency of water to bond strongly to itself major driving force for folding of macromolecules, binding of substrates to enzymes, and formation of membranes TERM 33 nucleophile DEFINITION 33 electronsrich group due to a negative charge or to unshared pairs of electrons tend to donateelectrons to positively charged orelectron defiecient groups known as electrophiles most common biological nucleophiles contain O, N, S, or C water is a weak nucleophile TERM 34 how is non-beneficial hydrolysis in organisms prevented? DEFINITION 34 biopolymer stability at physiological pH inactive or inaccessible storage of hydrolases two step biosynthetic reactions using nucleophiles other thanwater shielding water sensitive intermediates in enzyme active site TERM 35 Water dissociation DEFINITION 35 Water dissociates into hydronium (H3O+) and hydroxyl (OH-) ions H2O + H2O H3O+ + OH- (write H+ rather than H3O+ for simplicity) H2O -> H+ + OH- TERM 46 Mulder DEFINITION 46 1800s showed albumins (milk and egg) contained C, H, O, N TERM 47 Berzelius DEFINITION 47 1838 named such substances proteins from Greek proteios "of first rank" TERM 48 proteins DEFINITION 48 large biomolecules consisting of amino acids recognize and bind different types of molecules catalyze most of the chemical reactions necessary for life TERM 49 protein functions DEFINITION 49 enzymes transport coordinated motion mechanical support immune protection generation and transmission of nerve impulses control of growth and differentiation TERM 50 alpha-amino acids DEFINITION 50 consist of an amino group, a carboxyl goup, a hydrogen atom and a distinctive R-group bonded to a carbon atom This carbon is called the alpha-carbon because it is adjacent to the carboxyl group. TERM 51 zwitterion DEFINITION 51 dipolar ions Under normal cellular conditions amino acids are zwitterions: Amino group = NH3+Carboxyl group = COO- TERM 52 Amino acids in solution DEFINITION 52 will be in a charged state the amino group and/or the carboxyl group will be charged depending upon the pH The R group may also be charged. solution pH below pKa = protonated form predominates solution pH above the pKa = deprotonated (conjugate base) form predominates TERM 53 alpha-carboxyl pKa DEFINITION 53 pKa 1.8 - 2.5 TERM 54 alpha-amine pKa DEFINITION 54 pKa8.7 - 10.7 TERM 55 protein enatiomers DEFINITION 55 amino acids are chiral (asymmetric) all amino acids except glycine can exist as enantiomers Enantiomers of amino acids are called D (right-handed) or L (left-handed) L and D refer to absolute configuration L-amino acids are the only constituents of proteins TERM 56 Classes of amino acids DEFINITION 56 aliphatic aromatic sulfur-containing alcohols bases acids amides TERM 57 Aliphatic amino acids DEFINITION 57 - alpha-carbon not chiral (4): glycine (G, Gly) alamine (A, Ala) valine (V, Val) leucine (L, Leu) - Isoleucine (Ile, I)- Proline (Pro, P) TERM 58 Aromatic amino acids DEFINITION 58 Phenylalanine (Phe, F) Tyrosine (Tyr, Y) Tryptophan (Trp, W) TERM 59 Sulfur containing amino acids DEFINITION 59 Methionine (Met, M) Cysteine (Cys, C) TERM 60 Cystine DEFINITION 60 Two cysteine side chains can be cross-linked by forming a disulfide bridge (-CH2-S-S-CH2-) Disulfide bridges may stabilize the 3D structures of proteins Intracellular proteins often lack disulfides while extracellular proteins often have them. TERM 71 How proteins can be separated DEFINITION 71 size/mass (SDS gel electrophoresis, gel filtration, chromatography, dialysis, centrifugation) solubility (salting out) charge (ion-exchange chromatography) hydrophobicity (interaction chromatography, reverse phase chromatography) binding affinity (affinity chromatography) TERM 72 separated proteins can be analyzed by DEFINITION 72 sequencing (Edman degradation [proteolysis]) 3D structure(x-ray crystallography, NMR) Synthesis(automated solid phase) TERM 73 Required to purify large amounts of proteins DEFINITION 73 An assay for the protein (enzyme, antibody, etc) A purification scheme to separate desired protein from "all" other proteins and which retains protein "activity" TERM 74 gel filtration chromotography DEFINITION 74 proteins separated by size proteins passed over a column filled with a hydrated porous beads made of a carbohydrate or polyacrylamide polymer large molecules exit (elute) first TERM 75 ion-exchange chromatography DEFINITION 75 separation of proteins over a column filled with charged polymer beads + charged beads = anion-exchange chromatography,- charged beads = cation exchange chromatography (named for what you collect!!) Positively charged proteins bind to beads of negative charge & vice versa Bound proteins are eluted with salt. Non-charged proteins and proteins of similar charge to resin will elute first. TERM 76 affinity chromatography DEFINITION 76 proteins are passed through a column of beads containing a covalently bound high affinity group for the protein of interest Bound protein is eluted by free high affinity group. TERM 77 Chromatography based on hydrophobicity of protein DEFINITION 77 Hydrophobic interaction chromatography (HIC) Reverse phase chromatography (RPC) both based on interactions between hydrophobic patches on the surface of a protein and on the hydrophobicity of ligands (e.g. alkyl groups) covalently attached to a gel matrix TERM 78 Reverse phase chromatography (RPC) DEFINITION 78 based on interactions between hydrophobic patches on the surface of a protein and on the hydrophobicity of ligands (e.g. alkyl groups) covalently attached to a gel matrix proteins can bind very strongly to the gel and require non-polar solvents for their elution TERM 79 Hydrophobic interaction chromatography (HIC) DEFINITION 79 based on interactions between hydrophobic patches on the surface of a protein and on the hydrophobicity of ligands (e.g. alkyl groups) covalently attached to a gel matrix protein binding is promoted by inclusion of salt in the solvent and elution of proteins is caused by decreasing or removing salt from the solvent TERM 80 Column Chromatography DEFINITION 80 Separation of a protein mixture as it moves through column with steady flow of solvent Detection of eluting protein peaks as they are collected sequentially TERM 81 gel electrophoresis DEFINITION 81 movement of charged solutes through a gel in response to an electric field TERM 82 Polyacrylamide gel electrophoresis (PAGE) DEFINITION 82 chemically inertpolymerized acrylamide matrix of controlled pore size allows separation of proteins based on mass and charge TERM 83 SDS-PAGE DEFINITION 83 PAGE with sodium dodecyl sulfate, anionic detergent It complexes with proteins (1 SDS/2 amino acids) -> denatured protein of negative charge proportional to protein mass Note: reducing agents (mercaptoethanol, dithiothreitol) are also added to reduce disulfide bonds. Smaller proteins migrate faster TERM 84 isoelectric focusing DEFINITION 84 Proteins can also be separated by electrophoresis based on their native charge electrophoresis of proteins (w/o SDS) in a pH gradient to a position in the gel at which pH = pI pH gradient formed by polyampholytes (small multi- charged polymers of many pIs). TERM 85 Western blotting / Immunoblotting DEFINITION 85 proteins are separated in an SDSPAGE gel, transferred to a polymer, and then stained with a fluorescent antibody. protein reacts with antibody, illuminate and detect antibody by fluorescent transmission protein band detected on immunoblot TERM 96 proteomics DEFINITION 96 study of large sets of proteins, such as the entire complement of proteins produced by a cell TERM 97 classes of proteins DEFINITION 97 fibrous proteins globular proteins TERM 98 fibrous proteins DEFINITION 98 water insoluble static "tough" extended provide mechanical support (alpha-keratin, collagen) not mobile TERM 99 globular proteins DEFINITION 99 compact "spherical" usually: hydrophobic interior & hydrophilic exterior enzymes hormone receptors, enzymes, antibodies TERM 100 conformation of proteins DEFINITION 100 a spatial arrangement of atoms that can not be changed without breaking covalent bonds spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation # of potential conformations of a protein is astronomical. Under physiological conditions the protein assumes a single stable shape: native conformation TERM 101 primary structure DEFINITION 101 the covalent backbone of a structure what the series of amino acids is TERM 102 secondary structure DEFINITION 102 the residue-by-residue conformation of the backbone layer of a polymer alpha-helix, beta-sheet TERM 103 tertiary structure DEFINITION 103 the 3D conformation of a polymer in its native folded state TERM 104 quaternary structure DEFINITION 104 the 3D structure of a multisubunit, particularly the manner in which the subunits fit together organization of subunits in a protein with multiple subunits - an oligomer Subunits (may be identical [aa] or different [aB]) have a defined stoichiometry and arrangement Subunits are held together by many weak, noncovalent interactions (hydrophobic, electrostatic) TERM 105 Supersecondary structure DEFINITION 105 clusters of secondary structure (e.g. beta, alpha, beta) TERM 106 resonance of a peptide bond DEFINITION 106 can be shown in three ways: as a single C-N bond (double bond with O) a C=N double bond with positive and negative charges hybrid with electrons delocalized over O, C, and N atoms bond makes peptide groups planar by restricting movement TERM 107 conformations of a peptide group DEFINITION 107 cis conformation is less favorable than trans due to steric interference of alpha-carbon side chains trans conformation is established in protein during synthesis nearly all peptide groups in proteins are in trans conformation TERM 108 Ramachandran plot DEFINITION 108 steric contour diagram of allowed values of rotation permitted about the N-C alpha (phi) and C-alpha -C (psi) bonds. How much freedom of rotation do we have? TERM 109 Phi bonds in peptides DEFINITION 109 N - C(alpha) bond rotation is possible TERM 110 Psi bonds in peptides DEFINITION 110 C(alpha) - C bond rotation is possible TERM 121 Loops DEFINITION 121 often contain hydrophilic residues and are found on protein surfaces TERM 122 turns DEFINITION 122 loops containing 5 residues or less type I and type II TERM 123 B-turns (reverse turns) DEFINITION 123 connect different antiparallel B-strands also called hairpin loop TERM 124 Type I turn DEFINITION 124 4 AAs stabilized by H-bonds between a-carbonyl O of residue n and a-NH of residue (n+3) Pro is often 2nd residue TERM 125 Type II turn DEFINITION 125 also called glycine turn, B-bend like Type I Turn, but 3rd residue is Gly TERM 126 motifs DEFINITION 126 recurring protein structures TERM 127 domains DEFINITION 127 independently folded, compact, distinct structural unit in proteins ~25 to ~300 amino acid residues connected to each other by loops, bound by weakinteractions between side chains domains have separate functions and may fold as independent, compact units illustrate evolutionary conservation of protein structure TERM 128 Four categories of protein domains DEFINITION 128 All a: almost entirely a-helices and loops All B: only B-sheets and non-repetitivestructures that link the B-strands Mixed a/B: alternate regions of a-helix and B-strand (e.g. aBa motif) a + B: local clusters of a-helices and B-sheet in separate, contiguous regions of the polypeptide chain TERM 129 folds DEFINITION 129 combination of secondary structures that form the core of a domain Some domains have simple folds, others have more complex folds TERM 130 domain structure and function DEFINITION 130 A single domain may have a particular function interfaces between 2 domains provide crevices, grooves, and pockets on the surface of a protein for binding or catalytic sites In multifunctional enzymes, each catalytic activity can be on one of several domains TERM 131 oligomer DEFINITION 131 A polymer that consists of two, three, or four monomers TERM 132 denaturation DEFINITION 132 partial or complete unfolding of native conformation causes loss of biological activity caused by heat, extreme pH, detergents, chaotropic agents due to disruption of non-covalent interactions some proteins can be refolded or renatured most denatured proteins adopt a random-coil conformation TERM 133 chaotropic agents DEFINITION 133 "chaos-promoting" chemicals that denature proteins (e.g. urea, guanidinium chloride) do NOT cleave covalent bonds, disrupt 2, 3and 4structure, but interrupt noncovalent interactions interrupt hydrophobic interactions by disordering water molecules adjacent to protein increase entropy of system TERM 134 What are two chaotropic agents? DEFINITION 134 urea guanidinium chloride TERM 135 Tm DEFINITION 135 melting temperature temperature when 50% of protein is denatured TERM 146 prosthetic groups DEFINITION 146 a metal ion or other non-amino acid molecule tightly bound to a protein and essential for its activity heme TERM 147 holoprotein DEFINITION 147 active protein with all its cofactors TERM 148 apoprotein DEFINITION 148 protein without its cofactors TERM 149 myoglobin DEFINITION 149 Binds O2 Stores & transports O2 in muscle Prosthetic group: heme = Fe-protoporphyrin IX Single polypeptide (153 aa) + heme Globular protein with 8 a- helices Oxygenated myoglobin = oxymyoglobin All polar residues (except 2 His's) are locatedon protein surface has 8 a-helices TERM 150 oxymoglobin DEFINITION 150 oxygenated myoglobin TERM 151 myoglobin and hemoglobin prosthetic group DEFINITION 151 Fe-protoporphyrin IX TERM 152 Hemoglobin DEFINITION 152 Binds O2 Transports O2 in vertebrate blood Prosthetic group: heme = Fe-protoporphyrin IX Tetramer: a2B2; a has 141 aa; B has 146 aa; acts as dimer of aB 3structure of each subunit similar to myoglobin allosteric protein - O2 binding shifts position making it have a higher affinity at other binding sites TERM 153 Conservative substitutions DEFINITION 153 AA changes that do NOT significantly effect conformation (i.e. Val to Ile) TERM 154 nonconservative substitutions DEFINITION 154 AA changes thatDO effect conformation (i.e. Glu to Val) TERM 155 p50 DEFINITION 155 partial pressure at half saturation TERM 156 Sigmoidal curve DEFINITION 156 s-like shape shows positive cooperativity of binding onoxygen binding curve TERM 157 Hyperbolic curve DEFINITION 157 r type shape showssingle equilibrium constant on oxygen binding curve TERM 158 oxygen binding curve DEFINITION 158 comparison of O2 binding to Mb and Hb Fractional Saturation = Y, pO2 = X Y =[MbO2] / ([MbO2] + [Mb]) TERM 159 allosteric protein DEFINITION 159 regulatory protein whose activity is modulated by noncovalent binding of a specific metabolite at a site other than the active site allosteric regulation is caused by small changes in native conformation of a protein TERM 160 allosteric effectors DEFINITION 160 small molecules that bind to allosteric proteins and regulate their activity TERM 171 isomerases DEFINITION 171 enzymes thatcatalyze isomerization reactions (rearranging of molecules) TERM 172 Ligases DEFINITION 172 AKA Synthases enzymes thatcatalyze the joining (ligation) of two substrates requires chemical energy (ATP) 2 -> 1 TERM 173 first order rate equation DEFINITION 173 [P] / t = v = k[s] v = velocity p = product s = substrate k = rate constant (1/s) TERM 174 second order rate equation DEFINITION 174 bimolecular v = k * [S1]^1 * [S2]^1 k = rate constant (1/Ms) TERM 175 pseudo first order reaction DEFINITION 175 If concentration of a reactant is so high that it remains constant during reaction = zero-order v =k * [S1]^1 * [S2]^0 =k[s1]^1 TERM 176 Enzyme-substrate complex DEFINITION 176 complex formed when specific substrates fit into the enzyme active site E+S -->ES -->E+P When [S] >> [E], every enzyme binds a molecule of substrate (enzyme is saturated with substrate) Under these conditions the rate depends only upon [E], and the reaction is pseudo-first order TERM 177 enzyme kinetics DEFINITION 177 study of the rates of enzyme-catalyzed reactions enzyme kinetics gives information about:enzyme catalysis, enzyme mechanisms, regulation of enzyme activity (i.e. inhibitors & activators), basis of enzyme assays Effect of enzyme concentration [E] on velocity (v) TERM 178 The kinetics of an enzyme are affected by: DEFINITION 178 [enzyme] [substrate] pH & temperature coenzymes, activators, inhibitors TERM 179 Km DEFINITION 179 Michaelis constant usually 10-1 to 10-7M concentration of substrate needed for 1/2 maximum velocity [S] at which reaction is half its maximal value the lower the Km value, the greater the affinity of E for S Km values for enzymes are typically just above [S], so that the enzyme rate is sensitive to small changes in [S]. Km depends on enzyme, pH, temperature and ionic strength of environment Km = (k-1 + k2) / k1 TERM 180 Michaelis-Menten assumptions DEFINITION 180 no product reverts to S, true in initial stage of reaction, k-2 = ) (initial velocity = Vo) Steady state conditions (i.e. concentration of ES stays the same while concentration of E and S changes). Occurs when formation of ES = breakdown of ES TERM 181 Kcat DEFINITION 181 catalytic constant turnover number number of catalytic events per second per enzyme For most cases, Kcat is a measure of the catalytic activity of the enzyme. Thus, the greater Kcat, the faster the reaction. TERM 182 Michaelis-Menten equation DEFINITION 182 vo = (Vmax[S]) / (Km + [S]) Equation describes vo versus [S] plots TERM 183 turnover number DEFINITION 183 number of S molecules converted into P by E per second when E is fully saturated with S. k2 = kcat = s^-1 can be calculated from Vmax =k2[ET] Turnover number of most enzymes is from 1 to 10,000 per sec TERM 184 Values of kcat/Km DEFINITION 184 kcat/Km can approach rate of encounter of two uncharged molecules in solution (108 to 109M^-1s^-1) kcat/Km is also a measure of enzyme specificity for different substrates (specificity constant) rate acceleration = kcat/kn (kn = rate constant in the absence of enzyme) allows for comparison of effectiveness of enzyme TERM 185 Lineweaver-Burk plot DEFINITION 185 a straight line plot of 1/v vs. 1/[S] 1/vo = (Km/vmax)(1/[S]) + (1/Vmax) slope = Km / Vmax Y-intercept = 1/Vmax X-intercept = -1/Km