Bio 230 Exam 2 Study Guide
Bio 230 Exam 2 Study Guide Bio 230
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This 16 page Study Guide was uploaded by Kiara Lynch on Tuesday February 2, 2016. The Study Guide belongs to Bio 230 at La Salle University taught by TBA in Summer 2015. Since its upload, it has received 29 views. For similar materials see EVOLUTION & ECOLOGY in Biology at La Salle University.
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Date Created: 02/02/16
Biochem exam 2 notes Chapter 7- Hemoglobin: Portrait of a Protein in Action Hemoglobin vs. Myoglobin o Hemoglobin 4 polypeptide chains Cooperative- if one chain binds the others are more likely to Efficient- 90% use of potential O2 carrying capacity o Myoglobin Single polypeptide 7% use of potential O2 carrying capacity Organic portion named based on side chain; inorganic portion- heme, interacts with O2 6 coordination positions in hemoglobin o 4 heme groups o 1 protein o 1 oxygen Whale myoglobin o Alpha helices and turns o 1 3D protein structure known o ¼ of cells in body are RBC’s; b/w 20 and 30 trillion; life span of 120 days Myoglobin o Stays in muscles for oxygen storage o Only 1 oxygen binding site o Proximal histidine When oxygen binds, iron is pulled into the plane and the heme flattens Still connected to histidine but there is a change in location o Distal histidine Doesn’t form bond with anything in heme Takes up space Oxygen is forced to bond at an angle Oxygen competes with CO for binding to iron CO binds to Fe in heme 25k times better than oxygen but there is more oxygen in the air H bond to bound oxygen molecule helps stabilize oxymyoglobin o 3D shape of myoglobin vs hemoglobin Virtually the same shape even though there are different amino acids and different amounts Hemoglobin- 2 alpha and 2 beta chains held together by noncovalent bonds Allosteric- protein that changes shape in reaction to binding or interaction with another molecule o Holds oxygen better when changing shape o Relaxed conformation (changed shape) holds onto O2 better o Tense conformation- releases O2 easier Hemoglobin o 4 myoglobin like subunits o 2 alpha and 2 beta chains Related by divergent evolution Conservation of key residues (proximal and distal histidines) o Alpha helices o Globin fold Oxygen binding parabolic saturation curve for myoglobin o Y axis- fractional saturation Fraction of possible binding sites that contain oxygen At 100% every molecule is bound to an oxygen Does not need a lot of oxygen to be saturated Low oxygen levels in muscle Binds tightly o X axis- pO2 (torr) Amount of oxygen available in environment How much pressure oxygen is putting on the molecule to accept it Sigmoidal oxygen saturation curve of hemoglobin o Hemoglobin is cooperative- interacting binding sites o Need more oxygen to saturate hemoglobin ½ saturation at 26 torr Tense at bottom of curve, relaxed at top o Allosteric- happens 4 times (4 chains) Significance of cooperativity of hemoglobin o Hemoglobin releases 66% of oxygen under stressed conditions while myoglobin only releases 7% o Without cooperativity, hemoglobin would only release 38% of oxygen o Oxygen must be transported into blood from the lungs, where the partial pressure is relatively high (100 torr) into metabolizing tissue, where the partial pressure is lower (20 torr) o Hemoglobin becomes 98% saturated in the lungs After it moves into tissue, it is only 38% saturated 66% of potential oxygen binding sites contribute to oxygen transport Cooperative release of O2 favors more complete unloading of O2 in tissues o If myoglobin was used for oxygen transport: 98% saturated in lungs, and 91% saturated after transport to tissue Binds too tightly to oxygen to be useful for transport Exercise effects o Some hemoglobin recycles and doesn’t release oxygen o Hemoglobin is effective in providing O2 to exercising tissue 21% at rest Additional 45% during exercise Rotation o As hemoglobin binds to oxygen, there are quaternary structural changes Rotates 15 degrees on oxygenation R state- “relaxed” Increased binding affinity Need indirect mechanisms because of large separation of Fe sites Internal changes o Location of Fe in heme Iron associated histidine brought toward porphyrin ring Alpha helix also moves Amino acids also move with the entire backbone Models of allosteric changes o The bigger the arrow, the more likely that the reaction is going to take place as you add more oxygen, the more likely it is to relax o Sequential Change one at a time No full conversion from T into R state but still increases binding affinity Influence on other subunits Anything that binds with oxygen becomes relaxed and makes other subunits want to be relaxed o Concerted All change at same time At each level of oxygen loading, equilibrium exists between T and R states R state has a greater affinity for oxygen o Combined model describes hemoglobin Conerted- tetramer with 3 sites occupied by oxygen- primarily R state Sequential- tetramer with 1 site occupied by oxygen- primarily T state but binds to oxygen 3x as fully deoxygenated hemoglobin does Shape change o No oxygen iron out of heme o Add oxygen iron into heme heme flattens histidine gets tugged and pulled down Disappearance of cavity after 15 degree rotations o Cavity is just big enough to fit 2,3-BPG 2,3-BPG o Pure hemoglobin binds to oxygen more tightly than does hemoglobin in blood Due to presences of 2,3-BPG in RBCs o Binds in center of molecule in pocket present in T form Interacts with 3 positive charged groups on beta chains Locks hemoglobin in T conformation o T to R when oxygen is present pocket collapses and 2,3-BPG is released o Hemoglobin remains in T state until higher oxygen concentration is reached o Equimolar concentration in RBCs o Same amount as hemoglobin 1:1 o Not big; 2 charges; allosteric o Sigmoidal oxygen saturation curve Fetal RBCs have a higher affinity for oxygen because they do not bind to 2,3-BPG as well as maternal RBCs Fetal- 2 alpha chains and 2 Y chains 2 less + charges (SerHis) 1 amino acid side chain gets switched from charged to uncharged 2,3-BPG does not bind as well; fetal- relaxed easier; gets oxygen from mother’s blood easier o Bohr Effect As pH decreases, oxygen affinity also decreases Lowering of pH from 7.4 to 7.2 results in release of oxygen from oxyhemoglobin Salt bridges o Salt bridges form to stabilize the quaternary structure Stabilizes T state tendency to release oxygen o Formation depends on presence of added proton on histidine Negative aspartate favors protonation of histidine o As pH drops, histidine is protonated, a salt bridge forms, and T state is stabilized o As [CO2] increases, pH decreases Carbon dioxide stimulates oxygen release by two mechanisms o High carbon dioxide concentration causes a drop in pH in the RBCs CO 2 H O2+ enzyme (carbonic anhydrase- abundant in RBCs) H2CO 3 - + Carbonic acid dissociates HCO +3H which leads to a pH drop which stabilizes the T state o Direct interaction between carbon dioxide and hemoglobin Attached carbamate Carbon dioxide effects o Stabilizes deoxyhemoglobin by reacting with the terminal amino group o Forms negative carbamate groups Mechanism for oxygen transport from tissues to lungs- 14% Participates in salt bridge interactions; stabilizes T state, releases oxygen Sickle-Cell Anemia o Electrical field Difference in rate molecules move because of different charges o 1 molecular disease to be figured out o Hemoglobin precipitated (no longer soluble) leads to sickle cell shape gets stuck in capillaries o 2-D chromatography Size and charge Take alpha and beta chains and cut them using a protease Separate pieces 2 dimensionally Edman degradation performed on Hemoglobin A and S molecules Chain goes from charged to hydrophobic o Caused by 1 codon change (GluVal) Hydrophobic cavity o Hydrophobic/hydrophilic interactions leads to this disease Hydrophobic patch- Phe 85, Val 88 Oxyhemoglobin S in R state Phe 85 and Val 88 are buried inside Leads to aggregation sickle cell hemoglobin fibers formed o Sickle cell traits and malaria Correlation between regions with high frequency of Hemoglobin S allele and regions with a high prevelance of malaria Chapter 8- Enzymes: Basic Concepts and Kinetics Characteristics of enzymes o Immense catalytic power o Highly specific Specificity is due to the precise interaction of the substrate with the enzyme. Precision is the result of the intricate 3D structure of enzyme protein o Highly regulated- variety of ways to turn on and off (ex: phosphorylation) Enzymes end the way they started and can be catalyzed again o The product is the substance the enzyme releases o The substrate is the substance the enzyme is working on k- rate constant; how many reactions take place per second Protease- proteins that break peptide bonds Proteolysis- hydrolysis of peptide bonds (C—N) o Trypsin cleaves on the carboxyl side of Arg and Lys residues o Thrombin cleaves Arg-Gly bonds in particular sequences only Cofactors o Ex: luminescence of jellyfish Specific sequences of amino acids need cofactors Cofactors take in oxygen and calcium which converts the cofactor to a different form This causes the release of CO2 and light Reaction would happen on its own without cofactors but would take a long time o 99.9% of enzymes are proteins (exception: RNA) o Catalysis- accelerates the rate of a reaction by a substance that is not permanently affected by this process Apoenzyme + cofactor holoenzyme o Many enzymes require cofactors o 2 groups of cofactors Metals Coenzymes- small organic molecules Often derived from vitamins Loosely bound- cosubstrates (bind and release from enzyme; reused) Tightly bound- prosthetic groups Enzymes convert energy o Photosynthesis: light sugar o Cellular respiration: sugar ATP o Myosin in muscles: ATP mechanical work o Membrane transport: ATP electrical gradients Thermodynamics- science concerned with the relationship between heat and work o 1 law The total energy of a system and its surroundings is constant Must set boundaries for system and surroundings ∆E = Eb – Ea = Q – W Eb- end energy; Ea- beginning energy Q= heat absorbed by system W= work done by system o 2nd law A process can occur spontaneously only if the sum of the entropies of the system and its surroundings increases. If (∆S system + ∆S surroundings) > 0, then spontaneous o Free energy, ∆G A reaction is spontaneous only if ∆G is negative (exergonic) A system at equilibrium and no net charge can take place if ∆G=0 A reaction is not spontaneous if ∆G is positive ∆G= free energy of the products - free energy of the reactants ∆G is independent of path transformation ∆G gives no info on the rate of the reaction Rate of the reation depends on free energy of activation Only focus on system; energy available to the system to do work Enthalpy ∆G = ∆H system - T∆S system < 0 Heat content of system Disorder in water occurs spontaneously o ∆G= ∆G + RT ln ([products]/[reactants]) o ∆G= ∆G -2.303 RT log K’10 eq o K= equilibrium constant= [products]/[reactants] ° As K increases, standard ∆G decreases o Standard conditions, ∆G ° 1 M 1 atm ° 25 C pH 7 o Enzyme alters reaction rate not equilibrium; K is not effected by enzyme o Transition state Enzyme lowers point of transition state Activation energy is lowered when catalyzed ES Complex o Enzyme + substrate enzyme substrate complex enzyme + product o Evidence of ES complex Constant  rate of reaction increases with increase of [substrate] until maximal velocity Kinetic data o Reaction velocity (how quickly product is forming) vs. substrate concentration (varies) Physical reaction between substrate and enzyme X-ray crystallography Active site surrounded by residues from enzyme Presence of heme cofactor Enzymes fold into specific shapes and have an active or binding site where the reaction takes place o Substrate interacts with specific site Spectroscopy Colored prosthetic group Substrate has effect on shape of enzyme Common features of enzyme active sites o Entire sequence positions important amino acids properly o 3-D cleft/crevice o Takes up small part of total volume of an enzyme o Unique microenvironments Ex: nonpolar microenvironment enhances binding of substrates and catalysis o Substrates are bound to enzymes by multiple weak attractions Ex: noncovalent bonds- electrostatic, hydrogen, van der waals Enzyme and substrate have complementary shapes high degree of specificity o Specificity of binding depends on the precisely defined arrangement of atoms in active sites o Lock and key model Short range forces require close contact complementary shapes o Induced fit model Enzyme changes shape on substrate binding Used when you don’t want side products Enzyme kinetics o Amount of product formed as a function of time Initial velocity is the slop at the beginning of the reaction where the reverse reaction is insignificant Certain amount of buffer and enzyme Vary amount of substrate to see how fast product forms Pre steady state Couple of milliseconds Everything is still mixing, enzyme is trying to find substrate Steady state ES complex concentration becomes constant o Initial velocity (reaction velocity) vs. [substrate] Enzyme is one monomer and one substrate, nonallosteric Steady state portion of curve is where product formation is constant Km is the substrate concentration at half the Vmax Ratio of rate constants (K2+ K )-1 1 o Michaelis-Menten Kinetics K 1 K E + S ES 2→ E + P ←K −1 ❑ V= (k2/Km)*[E][S] When [S] is low, [E] is near [ET] V= (k2/Km)* [E ][S] T V=(Vmax/Km)* [S] k2= k cat= [ET]= Vmax Free enzyme  = E ET= total enzyme ES= enzyme substrate Need high Vmax to Km ratio High velocity, low Km binds to substrate well and little substrate needed Diffusion is the rate limiting factor reacts as fast as substrate can get there Sequential reactions o Sequential reactions- all substrates must bind to enzyme before any product is released Ordered- substrates bind enzyme in a defined sequence Random o At least 2 substrates o Ordered sequential Ex: Lacatate dehydrogenase Pyruvate reduction to lactate Coenzyme binds first, and lactate is released first Requires that NADH binds first Pyruvate can’t bind to enzyme without NADH Only want it acting on enzyme when oxygen levels are low Many enzymes that have NAD+ or NADH o Random sequential Ex: Creatine kinase Stored to later be converted into ATP o Energy source in muscle Either one can leave first or bind first Double Displacement/ “ping-pong” o 1 or more products are released before all substrates bind the enzyme o Substitute enzyme intermediate- enzyme is temporarily modified o Enzyme binds first to substrate and accepts amino group Substrate enzyme intermediate- takes part and holds on (covalent bond) o Enzyme releases product o Binds to second substrate o Releases second product o Reactions that shuttle amino groups between amino acids and ketoacids are usually double displacement reactions o Ping pong effect- binds, releases, binds, releases Allosteric enzymes o Do not follow Michaelis- Menten kinetics Sigmoidal curve not hyperbolic o Key regulators of metabolic pathways o Change shape when bound to enzyme o Binding of substrate to one active site can alter the properties of other active sites in the same enzyme molecule o Examples: Cooperativity Activity may also be altered by regulatory molecules that are reversible bound to specific sites other than catalytic sites Inhibitors o Irreversible inhibitors dissociates slowly from enzyme because they are tightly bound (covalently or noncovalently) Ex: penicillin o Reversible inhibitors Rapid dissociation of ES Complex Reversible, weak noncovalent bonds (H bond, hydrostatic) Can bind at other places besides active site o Competitive inhibitor Competes with substrate for active site Resembles substrate similar shape Fits into and binds to active site Can be relieved by increasing [substrate] successfully competes Enzyme binds to substrate or inhibitor but not both Diminishes rate of catalysis by reducing proportion of enzyme molecules bound to substrate o Uncompetitive inhibitor Binds to ES complex Only binds to enzyme if substrate is already bound Cannot be relieved by increase of [substrate] Binding site created on interaction of enzyme and substrate o Noncompetitive inhibitor Inhibitor and substrate can bind simultaneously to enzyme at different binding sites Can bind to free enzyme or ES complex Binds somewhere else besides active site at any time Alters the active site Decreases  of functional enzyme rather than diminishing proportion of enzyme molecules bound to substrate Net effect decrease turnover # Cannot be overcome by increasing substrate o Graphs Competitive Relative rate vs. [substrate] o As  of competitive inhibitor increases, higher concentration of substrate is required to attain a particular reaction velocity o Shows how high [substrate] can relieve competitive inhibition o Possible to reach Vmax o Km increases with inhibitor 1/V vs. 1/[S] o Vmax unaltered o Km increased Uncompetitive Relative rate vs. [substrate] o Inhibitor binds only to ES complex o Vmax cannot be attained even at high [substrate] o Km value is lowered and becomes smaller as more inhibitor is added o If inhibitor binds, enzyme becomes inactive 1/V vs. 1/[S] o Inhibitor does not effect the slope o Vmax and Km are reduced by equal amounts Noncompetitive Relative rate vs. [substrate] o Inhibitor binds both to free enzyme and ES complex o Vmax cannot be attained o Km remains unchanged so reaction rate increases more slowly at low substrate concentrations 1/V vs. 1/[S] o Km unaltered o Vmax decreased o Irreversible inhibitors Group specific reagents chemicals that react with certain amino acid side chains doesn’t look like substrate just has to be small enough to fit into active site ex: DIPF o reacts with highly reactive serine side chains o inhibits enzymes by covalently bonding and modifying crucial serine residue o enzyme is no longer functional o proteins digested Affinity labeling Looks like substrate React with enzyme- covalent bond Not enzyme specific Ex: TPCK o Reactive analog of normal substrate for chymotrypsin o Binds at active site of chymotrypsin and modifies essential histidine residue o Cuts peptide bond after phenylalanine Suicide inhibition Looks like substrate Reaction mechanism takes place in active site Intermediate in reaction binds to active site and inhibits reaction Ex: FAD o Cofactor for monoamine oxidase o N, N-Dimethylpropargylamine inhibits monoamine oxidase by covalently modifying prosthetic group after inhibitor is oxidized o N-flavin stabilized by addition of proton o Dopamine and serotonin Something binds to active site; inhibitor reacts with prosthetic group Control levels to stop parkinsons Ex: Penicillin o Covalently modifies the enzyme transpeptidase and prevents synthesis of bacterial walls which kills the bacteria o Irreversibly inactivates key enzyme in bacterial cell wall synthesis o Cell wall is a single large bag shaped macromolecule because of cross linking Formation of cross links in stapholococcus aureus peptidoglycan Terminal amino group of penta-glycine bridge in cell wall attacks peptide bond between 2 D-alanine residues to form a cross link Acyl enzyme intermediate formed in transpeptidation reaction leading to cross link formation Acyl enzyme intermediate- covalent bond between part of substrate and enzyme o Made up of sugars, amino acids, and covalent bonds 4 alanine 5 glycine penta-glycine bridge o There is a high possibility of bacteria undergoing extreme osmotic stress, so cell walls coat the bacteria. Without the cell wall, the bacterial cells burst and die. o R-D-Ala-D-Ala peptide blocks entrance of penicillin into active site inhibits reaction; cell can burst and die o Formation of penicilloyl enzyme complex Penicillin reacts with transpeptidase to form an inactive complex which is indefinitely stable Highly strained 4 membered beta lactam ring of penicillin makes it especially reactive On binding to transpeptidase the serine residue at active site attacks the carbonyl carbon atom of the lactam ring to form the penicilloyl-serine derivative Ex: Aspirin o Covalently modifies cyclooxygenase which reduces synthesis of signaling molecules in inflammation Chapter 9- Catalytic Strategies Catalytic Principles o Binding Energy Lowering of activation energy that enzyme provides All bonds contribute to lowering the activation energy o Covalent Catalysis active site contains reactive group (usually a powerful nucleophile) that becomes temporarily covalently attached to part of the substrate during catalysis Ex: chymotrypsin- cuts peptide bond after large hydrophobic side chains o General Acid-Base Catalysis Molecule other than water, usually an amino acid side chain, plays role of proton donor/acceptor Ex: Chymotrypsoin uses the Histidine residue as a base catalyst to enhance nucleophilic power of serine Ex: Carbonic anhydrase uses Histidine residue to remove H+ ion from Zinc-bound water molecule to form OH- Ex: Phosphate groups of ATP substrates in mysosin serve as base to promote its own hydrolysis o Catalysis by Approximation Usually 2 substrates Reaction rate may be enhanced by bringing substrates together along a single binding surface on an enzyme “blind-date” strategy- two substrates need to react, enzyme brings them together Ex: carbonic anhydrase binds carbon dioxide and water in adjacent sites to facilitate reaction o Metal Ion Catalysis Metal ion may facilitate formation of nucleophiles such as hydroxide by direct coordination Ex: Zinc in catalysis by carbonic anhydrase A metal may serve as an electrophile stabilizing a negative charge on a reaction intermediate Ex: Mg in EcoRV A metal may also serve as a bridge between enzyme and substrate increasing binding energy and holding substrate in place Ex: myosins and all enzymes that use ATP as substrate Triggers covalent catalysis Proteases o Form peptide bonds, can be broken Rigid and planar (partial double bond character) Prevents from breaking easily need enzyme to break it Resistant to hydrolysis o Rarely goes backward o Chymotrypsin Specificity Cleaves proteins on carboxyl side of aromatic or large hydrophobic amino acid side chains Inactivated by treatment with DIPF which only reacts with Ser 195 Chymotrypsin has an active serine side chain that reacts with DIPF becomes inactive irreversible Substrate analog- looks like substrate but isn’t substrate Chymotrypsin’s substrate analog has a phenylalanine Catalysis Cleavage by chymotrypsin Deprotonation of p-nitrophenol at pH 7 Spectrophotometer- the higher the absorbance, the more product is released Absorbance vs. time Not a parabolic curve (not Michaelis-Menten) Rapid burst- pre steady state o Acyl group covalently bonds to enzyme and substrate and p-nitrophenolate is released Steady state o Intermediate is hydrolyzed and carboxylic acid is released o Free enzyme regenerated 2 steps of covalent catalysis Acylation to form acyl-enzyme intermediate o Release of part of substrate; other parts form covalent bond with serine residue enzyme stuck Deacylation to regenerate free enzyme o Water severs bond; part stays with product and part goes to enz X-ray crystallography Spherical, 3 polypeptide chains linked by disulfide bonds chymotrypsinogen Active site- serine 195 o Hydrophilic Catalytic triad- serine, histidine, aspartate Catalytic Triad Serine 195 helps create a good nucleophile Histidine- positions serine side chain and polarizes its hydroxide group so it is ready for deprotonation Aspartate- negative charge balances out positive charges of histidine Substrate binding nucleophilic attack of serine on the peptide carbonyl group collapse of tetrahedral intermediate release of amine component water binding nucleophilic attack of water on acyl enzyme intermediate collapse of tetrahedral intermediate release of carboxylic acid component Oxyanion hole o Proposed mechanism- everything that should work with this enzyme o Stabilizes tetrahedral intermediate o H bonds link peptide NH groups and negatively charged oxygen atoms of the intermediate o Deep pocket lined with hydrophobic residues Favors binding of residues with long hydrophobic side chains o Active site serine is positioned to cleave peptide backbone between residue in the pocket and next residue in chain o Substrate specificity Chymotrypsin cuts after large hydrophobic side chains Fit into active site big hydrophobic pocket with catalytic triad at top Families of proteins o Mutations over time o Genes change independently look different o Catalytic triad conserved evolutionarily o Divergent evolution Common ancestor Chymotrypsin and trypsin have similar structures o Residues and their side chains determine specificity Chymotrypsin- favors large hydrophobic side chains Trypsin- favors positive side chains because of negative charge of Asp Elastase- favors small hydrophobic side chains b/c of two Val (take up room) o Convergent evolution Completely different chains that evolve to be similar Ex: evolve to have same reaction mechanism catalytic triad Used to cut peptide bonds Carboxypeptidase II is a very different looking protease than chymotrypsin but still uses the triad o Enzyme NH groups in oxyanion hole stabilize the negative charge o Prove hypothesis Clone- enzyme + plasmid Plasmid- vehicle for moving DNA, can cause mutations Site directed mutagenesis- alter specific nucleotides to target triad All members of the triad are critical to the mechanism Mostly serine and histidine Mutate each member of the triad one at a time and then all at once and compare activity to the wild type and uncatalyzed reactions Replace amino acids with alanines Why does it occur better with no enzyme? Binding energy stress on peptide bond not usually there, more likely to break enzyme substrate complex o Cysteine proteases Help create nucleophiles Cysteine, aspartyl, and metalloproteases all have different active sites despite similar reactions Peptide carbonyl group attacked by: Histidine activated cysteine Aspartate activated water molecule o Microenvironment of active site Aspartic acid normal- proton from water to create nuc Unprotonated aspartic acid- H bond with oxygen and draw electron up to create nuc Metal activated water molecule o Zn involved o Base- often glutamate; helps deprotonate the metal bound water molecule o Metal interacts with water, base accepts proton from water, nucleophile created to attack C HIV virus o Cells infected o Releases genome- uncoded and converted into DNA o DNA integrates in host DNA o Compact genome 1 giant continuous gene o Produces viral RNAs translated 4-5 proteins connected together Need to be spliced Protease produced by virus splices proteins o HIV protease Flaps close down after substrate has been bound Dimer of aspartyl protease Active site Need to design something to inhibit virus from spreading Irreversible inhibitor- indinavir Binds to active site Prevents further clipping Viral cycle interrupted
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