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Exams 1,2,3,5 study guides BCH 361
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This 78 page Study Guide was uploaded by Olivia Notetaker on Tuesday August 9, 2016. The Study Guide belongs to BCH 361 at Arizona State University taught by Alexander Green in Spring 2015. Since its upload, it has received 13 views.
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Date Created: 08/09/16
Chapter 1: Biochemistry and the unity of life Biochemistry: the study of living organisms at the molecular level o molecular basis for different diseases which can then help with detection and treatment o Manipulate biochemical processes to our own advantages (genetic engineering) o Organism are about the same on a molecular level Ex: bacteria and elephants-DNA genetic info carrier, same amino acids, use aerobic respiration Elements of life Element % in Humans Hydrogen 63 Oxygen 25.5 Carbon 9.5 Nitrogen 1.4 Calicum 0.31 Phosphate 0.22 Etc 0.07 o Hydrogen, Oxygen, and Carbon make up 98% of the human body. o Water is the matrix of life-it is needed for the presence of life on earth Humans- 65% water Cells-70% water Water dissolves many biomolecules Medium used in Brownian Motion o Molecules composed of hydrogen, oxygen and carbon can be used as biologival fuels that undergo combustion into CO2 and water o Most large molecules In life are made of carbon because of it’s unique bonding properties Ex: silicon but bonds are weaker which release less energy during combustion. Product of silicon combustion: SiO2-solid and major component in sand Classes of Biomolecules Feature Protein- Nucleic Acids Lipids Carbohydr unbranched ates polymers Structur Linear polymer Linear polymer Dual chemical Diverse e that folds into 3D that form character that structures structure predictable base create that can pairs membranes form with branched hydrophobic polymers (hides from (polymeric water) & structure hydrophilic w/occasional (dissolves in branching) water) regions Membranes separate cell contents from the external environment & different cellular components from 1 another Molecula 10 > 10 6 10 > 10 6 -1300 -180 to > r weight 10 6 Monome Amino acids Nucleotides N/A Monosaccha rs added 1 by 1 rides # of 20 4 N/A Potentially monome many rs Name of Peptide bond Phosphodiester N/A Glycosidic Polymer joins A.A bond bond bond together Major Signals- informatio fuel Fuel- function insulin n storage storage- Gluco Receptors- and produce se insulin transfer energy most receptor upon comm Structure- combusti on keratin on found Mobility- Signaling in flagella molecule starch Defense- s (plant against Barriers- s) & environme cellular glyco ntal and gen dangers intracellul (anim Catalysis- ar als) enzymes Cell identi ficatio n Cell- to-cell intera ction sites Feature DNA RNA Bases Adenine (A) Adenine (A) cytosine (C) cytosine (C) guanine (G) guanine (G) thymine (T) uracil (U) Base pairing G-C G-C A-T A-U Typical form in cell Double stranded helix Single Stranded Sugar component Deoxyribose Ribose (additional OH on 2’) Stability in cell Very stable Messenger RNA (mRNA) is frequently broken down Major functions Long term information Short term information storage; contains “parts carrier; mRNA provides list” of organism template for making proteins Central Dogma A model that describes the basic principles of biological information transfer; how we go from genetic information of DNA to the proteins that perform multiple cellular functions Francis Crick-1958 Feature Replication Transcription Translation Input DNA DNA RNA Biomolecule Output DNA RNA Protein biomolecule Enzyme DNA polymerase RNA polymerase Ribosome Step 1: Replication and DNA: Genome: contains all heritable information of an organism in the form of DNA Genes: Sequences of DNA that hold each unit of information DNA polymerase (enzyme): catalyzes DNA replication process (enhances the process without harming itself) Step 2: Transcription DNA is transcribed into RNA via enzyme RNA polymerase Genes from RNA are transcribed into mRNA Step 3: Translation mRNA is translated into protein (completely different structure) Ribosomes (proteins + RNA) finish translation process Structure Definition Function other Plasma membrane Lipid bilayers Distinguish -Impermeable to that create between the two most substances barriers to define different kinds of -Proteins enable the inside and cells selectively outside of a cell Eukaryotes: permeable to: Membrane enclose glucose, amino intracellular acids, signaling compartments molecules Prokaryotes: Lack intracellular compartments Cytoplasm Inner substance Hosts cellular of the cell processes: enclosed by the -Glucose plasma metabolism membrane that -Fatty acid and is organized by protein synthesis cytoskeletons Cytoskeleton network of -Structural support Components: structural -Localize Microtubule filaments biochemical Actin filament activities Intermediate -Shuttle molecules filament around the cell Organelle # of Function Other membra nes Nucleus 2 Information center that holds the DNA Nuclear pores regulat e transpo rt in and out of cell Mitochondria 2-inner -Energy production center (90%) membra -produces ATP through respiration –fuel ne is molecules undergo combustion in CO2 invaginat & H2O creating the cellular energy ed carrier(ATP) Chloroplasts 2 Photosynthesis center Plants Converts light to chemical energy and algae only Smooth E.R- 1 Processes exogenous chemicals (ex: Smooth membranous drugs) bc no sack ribosom es Rough E.R 1 Synthetization of proteins destined for Rough cellular membranes/for secretion bc of making transport vesicles ribosom es (site of protein synthes is) Golgi Complex- 1 -transport vesicles move here & stacked attach to stacked membranes membranes -involved in protein sorting before final destination -Carbohydrate modification of proteins Secretory 1 -Carry proteins destined for secretion granules -Granules fuse w/ plasma membrane (zymogen &releases proteins into extracellular granules) environments -involved in Exocytosis: process of molecules are actively transported out of the cell Endosomes 1 -Carry external chemicals into the cell (iron ions, cholesterol, vitamin B12) -Formed: plasma membrane invaginates, buds off, produced small vesicle -phagocytosis:eating of a cell when large amounts are transported into the cell. Lysosomes 1 -Contain digestive enzymes for processing external chemicals and damaged organelles -Fuse with endosomes to promote digestion which is then used as cellular building blocks Vacuoles 1 Store water, ions, and nutrients Plants 80% of cell volume only Plant Cell Wall 1 Sturdy protective wall composed of Plants cellulose only Chapter 2: Water, water bonds, and the generation of order out of chaos Transient chemical interaction form the basis of biochemistry and life itself o Use bonds that are much weaker than covalent ones and that are strongly influenced by surrounding water and its pH o Extremely weak bonds can add up to very strong forces Brownian Motion o 1827 Robert brown looked at pollen granules in water under microscope o Observed multiple and different species darting randomly when suspended in H2O o Energy fluctuations (thermal noise) cause molecules surrounding in water/gas to be more active. Extent of noise depends on: Temperature-higher temperatures lead to stronger motion Water within the cell is the medium used and facilitates multiple processes: Enzymes find substrates Release of energy from fuels Diffusion of molecules to intended destinations Water o Polar solvent: Electrons spend more time near –O compared to +H o Structure constantly being broken and reformed o Polarity + ability to form H bonds = H2O solvent for any charged/polar molecule o Nonpolar (hydrophobic) molecules are insoluble in H2O o D=80 and force is greatly reduced Bond type Mechanism Charge Bond Bond Law magnitude Distance energy (S/M/L) (A) (kJ mol -1 Covalent Shared Large -1 418 (polar/nonp electrons olar Ionic Attraction of Large 3 5.8 Coulomb’s: (electrostat oppositely F =kq1q2/Dr2 e ic) charged ions D=dielectric -water constant weakens this K=proportion ality constant Hydrogen Attraction by Medium, -2 8-20 electronegati partial e- ve atoms (N,O)and hydrogen Van der Attraction Small, 3-4 2-4 (per Waals caused by fletting atom transient asymmetrie pair) charged s asymmetries Hydrophobicity & the 2 ndLaw of thermodynamics 2ndLaw of thermodynamics: Total entropy of a system & it’s surroundings always increases in spontaneous process o H2O molecules form ordered cage around nonpolar molecules o Nonpolar molecules submerged in aqueous solution releases H2O molecules and increases net disorder/entropy o It is spontaneous and no energy input is required Action How Membrane formation -Amphipathic lipids that have hydrophilic and hydrophobic groups organize into membranes by excluding water Protein Folding Driven by release of water: counter increase in order once protein reaches 3D structure Prior: H2O molecules cage hydrophobic amino acids in proteins Interactions w/other functional groups increases stability Chapter 3: Amino Acids A set of 20 amino acids form proteins Can be subdivided into 4 chemical characterits: o Hydrophobic o Polar o Positively charged o Negatively charged Fischer projections: horizontal bonds point towards you, vertical bonds point away from you Amino Acids: Building blocks for proteins; 20 amino acid=1 protein Consists of 1 alpha carbon, 1 carboxyl group, 1 Hydrogen, 1 side chain, 1 amino attachment group Chiral: L isomer (only used in proteins), D isomer Zwitterions: negatively and positively charged Essential amino acids must be obtained from diet Nonessential are made from the body-11/20 Amino Letter Abbreviatio Essential/Nonessential/i Characteris Acid n onizable tic group Alanine A Ala NE Hydrophobic Arginine R Arg NE-IONIZABLE Positive Asparagine N Asn NE Polar Aspartate D Asp NE- IONIZABLE Negative Cysteine C Cys NE- IONIZABLE Polar Glutamate E Glu NE- IONIZABLE Negative Glutamine Q Gln NE Polar Glycine G Gly NE Hydrophobic Histidine H His E- IONIZABLE positive Isoleucine I Ile E Hydrophobic Leucine L Leu E Hydrophobic Lysine K Lys E- IONIZABLE Positive Methionine M Met E HP Phenylalan F Phe E HP ine Proline P Pro NE HP Serine S Ser NE POL Threonine T Thr E POL Tryptophan W Trp E HP Tyrosine Y Tyr NE- IONIZABLE POL Valine V Val E HP Chapter 4: Protein structure Type Definition Formation Properties Structure Primary The Alpha- Polypeptide: -repeated feature of sequence carboxyl Multiple AA’s structure of amino group of 1 AA joined by -side chains: vary & acids to + alpha-amino peptide point out at backbonds form a group of other bonds; each Carbonyl groups: protein -Condensation has serve as H bond held reaction directionality acceptors together (release of (polarity); Amino groups: serve by peptide H2O) written from as H bond donors bonds =peptide N-terminal-C- bond that terminal requires input residue of energy Residue: amino acid unit inside the polypeptide Second Regular Hydrogen Alpha helix: Coiled coil: 2 right- ary structures bonds on the coiled handed alpha-helices in proteins backbone (CO structure coil into left handed caused by and NH 4 stabilized by superstructure via van backbone residues intrachain der waals H-bonding away-all hydrogen interactions/disulfide participate in Beta sheets: bonds H bonding)) + Formed from a-keratin: hair, horns, protein = hydrogen nails secondary bonding Collagen helix: 3- structure between strand super helical (alpha helix) polypeptide cable formed by strands hydrogen bonds between strands ex: collagen: tendons, ligaments,skin Tertiary Longer Disulfide Myoglobin: transports range bonds: oxygen from interaction occurs when bloodmitochondria. 8 between 2 cysteine a-helices & heme: side chains residues in a enables oxygen and protein transport. Has residues interact. Form hydrophobic residues crosslinks b/t interior of protein as a distant binding pocket for cysteines heme. Pair of histidine’s either same enable binding of iron + strand or oxygen atoms of heme different Motifs: globular units that ranging from 30- 400 residues. Connected by flexible residues to assist in folding Helix-Turn-Helix Motif: commonly used to stabilize interaction b/t protein & DNA Domains: compact globular units that are part of polypeptide chain Quatern Interaction Subunit: ary s between polypeptide different chain that is polypeptid part of the e chains protein quaternary structure ex: Cro repressor, Hemoglobin, DNA pol. III Primary: Peptide bonds are planar because of their double-bond character which provides the 3D structure of protein Mostly all of them are in trans position to give it the most stable structure because of steric clashes. Bonds of the alpha carbon can rotate providing some degree of freedom during folding process (Secondary mostly) Ramachandran diagram defines possible combinations- top left: beta-sheets, top right, left-handed alpha helix, bottom left, right handed alpha helices Difference Alpha beta Rise per residue 1.5 A Sdfsdsdfbksjdbf.kjsdbf.ksjbdf.kjsbdf.jsb Rotation per turn 100 degrees df.ksjdfh Residues per turn 3.6 Helical pitch 5.4 A (1.5 x 5.4) 3.5 A features -Mostly all are right -Parallel, anti-parallel, combination handed -Side chain above and below -Amino acids that -Loops and turns enable chains to turn disrupt this: back on themselves often have branched side hydrophilic R groups groups hydrogen bond donors, proline (missing H donor, can’t form) Thermodynamics and protein structure The native structure is always the most stable Proteins fold by progressive stabilization of intermediates –usually starts as the N-terminal residues are leaving the ribosomes Nucleation-Condensation model: local and long-range interactions that occur simultaneously to fold the protein Not all proteins have a stable/structured final configuration Intrinsically unstructured proteins (IUPS)-not well defined 3D stuctures; can switch states upon interaction w/another protein; important for signaling and regulation Metamorphic proteins: Proteins that exist in an ensemble of stuctures of approximately equal energies Prions and misfolded proteins: 1 misfold and triggers infections-catalyzes itself and makes normal proteins like the infectious 1 Prion: a proteinaceous infectious particle (protein + infection)-exception to central dogma PrP : Less stable than Prp Creutzfeldt-Jakob disease (CJD) Prion associated incurable neurological condition Accumulation of misfolded proteins leads to exponential growth of insoluble material and eventual cell death Transmission of infection: o Can occur spontaneously o Contaminated impants o Consuming animals with disease o Cannibalism Chapter 33: DNA and RNA structure Word Definition Bases (building block) Hold genetic info Sugars (building block) DNA or RNA –given #’s depending on location Phosphate (building block) Phosphate group connects sugars on backbones Phosphodieter linkages Negative charge; link 5’ & 3’ carbons Nucleoside triphosphate 3 phosphates that are monomers to form DNA&RNA Nucleoside Sugar +base Nucleotide Sugar + base + phosphate Purines -osine suffix Pyrimidine -idine suffix Base stacking Stacking of bases 1 atop the other leading to Van der waals interaction-cumulative effect on interaction is strong Helicases Enzymes that separate DNA Double helices Denaturation Process of the addition of heat to melt the H- bonds and van der waals interactions Melting temperature (T ) m Temperature at which helices separate Annealing/renaturation Spontaneous rehybridization of separated complementary strands when temperature falls below Tm Supercoiling over or underwinding of a DNA strand negative (subtracting coils) or positive (extra twists) Histones Proteins essential for condensing DNA -5 major ones: H1, H2A, H2B, H3, H4. Have tails that stick out of the DNA that are important for regulation Histone octamers Forms when all pairs except for H1 interact Nucleosomes Histone octamers wrapped with DNA in a left- handed arrangement Repeating unit of core particle + linker DNA Nucleosome core particles: 145-bp of DNA (associated with histone octamers) – separated by linker DNA Chromatin Entire complex of DNA and histones within the cell Each bead is 10 nm in diameter Arranged as 30 nm-thick fibers Ribozymes RNA molecules that perform catalyzes on reactions with a complex RNA structure RNA World Hypothesis All current life on Each descended from systems that employed RNA exclusively for information storage, replication and catalysis Cas9/Crispr Enzyme discovered in bacteria that is used to guide RNA to precisely cut a target DNA sequence in the genome First enzyme found to make precise cuts in DNA Adenine Guanine Cytosine Thymine/Ura (purine) (purine) (Pyrimidine) cil (Pyrimidine) DNA Deoxyadenosi Deoxycytidine Deoxyguanosi thymidine ne ne RNA Adenosine Cytidine Guanosine uridine A form B form-common Z Form form Shape Stocky (short and Intermediate Lanky (tall and wide) thin) Rise per bp 2.3 A 3.4 A 3.8 A Helix diameter -26 A -20 A -18 A Screw sense Right handed Right handed Left-handed Bp per turn 11 10.4 12 Pitch per turn 25.3A 35.4 A 45.6A (=rise per bp X bp per turn) Tilt of bases 19 degrees (high) 1 degree (low) 9 degrees perpendicular to (medium) helical axis Biological RNA, RNA-DNA DNA-3 million base Under occurrence hybrids, pairs investigation-more dehydrated DNA prevalen ton sites of active transcription Major and Minor grooves Base pairing occurs off central axis of B form double helix creating major and minor grooves Major groove is wider and deeper than minor groove to provide more sequence-dependent features for DNA recognition Both grooves provide H-bond donors and acceptors to interact with DNA- binding process Chapter 6: Basic conceptions of enzymes Enzyme: Macromolecule that acts as a catalyst for a biochemical reactions o Most are proteins but some aren’t o 3D structure enables them to act as powerful and highly specific catalysts o Often able to increase reaction rates by over a million s folds Catalysts: Chemical that enhances the rate of chemical reactions w/o being permanently altered itself Carbonic Anhydrase: fastest known enzyme that facilitates transport for CO2 into the lungs and maintains pH level of the blood while also catalyzing the addition of CO2 in water o Converts 10 molecules of CO2 per second o Reaction is reversible and the enzyme can catalyze both reactions OMP Decarboxylase: Performs essential step on synthesis of pyrimidine nucleotides that increases rate to 1017 o Catalytic reaction rate:-20 miliseconds o Uncatalytic reaction rate: 78million years Substrate: Reactant of an enzymatic reaction o Enzymes can usually only catalyze one reaction/similar reactions in sets o Vary in degrees of specificity on the substrate Proteolytic enzymes: Catalyze proteolysis of peptide bonds Thrombin that is used in blood clotting targets arg-Gly bonds in particular Papin from papaya is largely indiscriminating Enzyme class Function Ex Oxidoreductases Transfer elections Lactate between molecules dehydrogenase: used in glycolysis Transferases Transfer functional groups Aminotransferases: AA between molecules synthesis and degradation Isomerases Move functional groups Triose phosphate: Used between molecules in glucose Lyases Add atoms or functional Lyase fumerase: citric group to a double bond or acid cycle remove them to form a double bond Ligases Join 2 molecules in a DNA ligase: joins DNA reaction powered by ATP strands together hydrolysis Hydrolyses Cleaves molecules Thrombin: Arg-Gly bond through the addition of breakage water Cofactors: Small molecules that are required for certain enzymes to function divided into 2 groups o Metals: Metal ions w/ binding pocket in the apoenzyme 3+ Carbonic anhydrase 2+quies Zn EcoRV requires Mg o Coenzymes: Organic molecules derived from vitamins Prosthetic group is tightly bound coenzyme Pyruvate dehydrogenase requires TPP (thiamine pyrophosphate) Pyruvate carboxylase requires biotin o Other: Myoglobin and hemoglobin require heme Apoezymes: inactive enzymes lacking cofactor Holoenzyme: Catalytically active enzyme in complete form with it’s cofactor Enzyme thermodynamics: The ability of a reaction to occur spontaneously is related to the thermodynamic free energy G o Reactions are asses by net charge in free energy ΔG <0 : spontaneous reactions ΔG > 0: addition of energy for reaction to occur ΔG=0: system is in equilibrium Enzymes can only be applied to reactions that are spontaneous where the change is G is less than zero, it’s it’s greaten than zero, the enzyme is inactive and needs more energy Free energy is correlated with energy that is needed to start conversion of reactants into products o Transition is what enzymes modify in order to speed up chemical reaction o Enzymes only modify reaction rates Change in free energy: Exergonic o Reactions that release energy during a reaction o Spontaneous reactions only occur if ΔG < 0. Endergonic o Reactions that require addition of energy o Reactions that aren’t spontaneous bc ΔG > 0 Equilibrium o ΔG = 0 o No net charge in concentrations of products and reactants Reaction path o ΔG is independent of the reaction path and only depends on the end point of the reaction o Enzymes alter their reaction path Rate of reaction o ΔG doesn’t work to find the rate of reaction ‡ o Free energy of activation ΔG determines reaction rate Transition state: Transition state of higher free energy o Chemical reaction going from reactant R to product P that passes through a fleeting molecular structure that is in between ‡ S X P Activation energy: Energy needed to reach the transition state o ΔG = ΔG Gs Enzymes enable the formation of transition state by lowering the energy of activation (ΔG ) to make it more accessible to more molecules Active sites: Bind substrates and promote formation of transition state 3D cleft formatted by residues of different regions in the protein primary structure Only takes up small portion of protein Have unique microenvironments because substrates are bound to enzymes by multiple weak attractions Binding is specific and depends on the arrangement of atoms in the active site o Lock and key: Enzyme fits perfectly for binding substrate Perfect fit Substrate + active site in enzyme= enzyme-substrate complex o Induced fit model: Flexible enzymes that have interactions between substrate and active sites which lead to dynamic conformational changes Conformation selection: substrates bind only in particular conformations of enzymes ΔG reduction mechanism Substrates bind to active site through noncovalent interactions that all realease energy (binding energy) Combined effect of all interactions facilitates formation of transition state Inhibiting substrate: Using a transition state analog that outcompetes substrate for active site Chapter 7: Kinetics and Regulation Kinetics define the rate of reaction o Thermodynamics define if the reaction can occur spontaneously or not Micahelis-Menten model of enzyme kinetics can be used to understand the properties of enzymes Allosteric enzymes combine catalysis and information processing and are essential for cellular metabolism Kinetics and rate of reaction: See slide 3 Michaelis-Menten Model Describes initial reaction velocity vs. concentration of the substrate to form an equation where substrate binds reversibly to enzyme to make complex which then reacts irreversible to make the product in order to regenerate free enzymes. V max (s) (velocity maximum of substrate), K (cMnstant-50% vMax s) and S (substrate) are needed Reciprocal of Michaelis-Menton equation gives you the Lineweaver-Burk equation: Slope= Km/Vmax Intercept = 1/vmax Intercept= -1/kM Y (V0)=m (Vmax) X( S) + b (vmax) KM significance o Equal to concentration of substrate when the enzyme is half oxxupid o Varies depending on the pH, temp and ions present o For most enzymes, this lies bwtween 10 -1and 10 -7M which corresponds to physiological levels of substrates enabling it for better tuning of enzyme activity Vmax significance o Related to turnover number of enzyme (k cat o Turnover number ((k ): catf substrate molecules that an enzyme can convert into product per unit time when the enzyme if fully saturated with substrate (kcat= Vmax/ ( E ) r o Carbonic anhydrase has 1 of highest known turnover numbers: 6 x10 5 -1 s or 1.7 us per reaction The specificity constant: kcat/m o Provides info on the specificity of interaction of enzyme w/ particular substrate Higher values usually means greater affinity ( relationship) for the substrate o Upper limit is set by the rate constant of k 1 describes rate of formation of the ES complex Max value is limited by diffusion to 10 10 9 s-M -1 o A lot of enzymes actually reach specificity constants that are equal to the upper bound and actually reach kinetic perfection Sequential reactions Multiple substrate reaction in which both substrates have to bind to enzymes before reaction can continue o EnzymeNADHPyruvatelactateNAD+ enzyme Double displacement reactions o 1 or more products are released before all substrates bind with the enzyme o Have a substituted enzyme intermediate o Allosteric enzymes and Metabolism Allosteric enzymes are essential for regulating/routing a cell’s metabolism o Inhibit and promote catalysis o Carry our feedback inhibition o Regulated by molecules that bind to sites other than active sites o Always catalyze the committed step of metabolic pathways o Show a sharper increase of V0 in the middle of the curve compared to Michaelis-Menten General S shape called sigmoidal curve Metabolism: Set of chemical pathway of cells that are used to extract energy from the environment and apply it to biosynthesis Ex of metabolic pathway: Pathway for UTP synthesis w/ OMP decarboxylase A 5 enzyme pathway o Initial substrate is transformed by 5 different enzymes into a final product F E1, e2, e3, e4,e5 o Each substrate and product in pathway is a potential useful compound for use inside the cell o Cell ensures the optimum use of compounds by the Feedback inhibition Intermediates B, C, D, and E aren’t very important to the cell A is important and shouldn’t be wasted Process of A B is called the committed step in the overall pathway E1 carries out the feedback inhibition because it is an allosteric enzyme which always catalyzes the committed step of metabolic pathways. The concerted Model o Explains general properties of allosteric enzymes o 3 principle assumptions Have multiple active sites on different polypeptide chains Can exist in 2 distinct conformations or states Related: active, catalytic state Tense: significantly less active L0=T/R: allosteric constant typically in the 100s T & R are in equilibrium and can switch states easily Symmetry rule: All subunits in the enzyme must be in the same state. If one subunit switches to R the others have to as well. o Behaviors of model: @ low (S), T state & hard for S to bind When finally binds, induces change of state for all subunits Disrupts equilibrium in favor of R leading to sharp increase in V0 Threshold behavior: enables tight control reaction rate compared to MM kinetics Regulator molecules o Shift equilbirum between T and R Enzyme in T form enzyme in R form = activator = heterotrophic effects Enzyme in R form enzyme in T form=inhibitor =heterotrophic effects Enzyme in T form enzyme with 1 S bound = substrate= homotropic effects Sequential Model o Assumes that subunits undergo sequential changes in structure o Binding of substrate to 1 subunit influences the conformation of neighboring subunits o Can have negative cooperativity T state enzyme w/ 1 S boundEnzyme w/ 2 S boundenzyme w/ 3 S bound enzyme w/ 4 S bound Chapter 8: Mechanisms and Inhibitors Enzymatic reactions are affected by factors that influence chemical reactions in general: o Temperature Reaction rates increase as temp increases (Brownian motion) unless they are weak bonds that are disrupted in high temps Holds until enzyme becomes denatured o pH Enzyme pH dependence can arise from ionizable groups in the protein Chymotrypsin and pepsin are both proteolytic enzymes Chymotrypsin: small intestine at pH 8 Pepsin: stomach @ pH 1-2 Inhibitors o Molecules that bind to enzymes to decrease enzymatic activity o Regulate allosteric enzymes & are important source of drugs o Can either be reversible or Irreversible Reversible inhibitors Feature Competitive Uncompetitive Noncompetitive Define Compete for Inhibitor binds to Inhibitor binds to binding to enzyme ES complex site on enzyme active site that isn’t active site Forms E1 Yes No Yes complex Forms ES1 No Yes Yes complex app Effect on Vmax No change- Decrease Decrease constant 1/Vmax app 1/Vmax app app increases increases Effect on Km Increase Decrease No change (1/Km ap) (1/Km ap) increases decreases Example drugs Sulfanilarride Roundup Doxycycline (antibiotic), (Herbicide) (antibiotic) Ibuprofen Double Reciprocal plots: W/ Lineweaver-Burk equation enable rapid identification of inhibitor mechanism o Slide 22**** Irreversible inhibitors: Unbind very slowly/are bound to the enzyme covalently Type Definition Group Specific Modify specific R groups of amino acids Affinity labels Covalently modify active-site residues & are structurally similar to an enzymes substrate Suicide inhibitors Chemically modified substrates that become reactive after the enzyme acts on them Transition-state analogs Mimic transition state of the reaction Catalysis Type Definition Covalent Catalysis Active site contains a reaction group that becomes temporarily modified during reaction General acid-base Catalysis A molecule other than water is used as the proton donor/acceptor Metal Ion Catalysis Used as an electrophilic catalyst to influence acidity or by binding to the substrate Approximation and Orientation Catalysis More than 1 substrate reaction where enzyme can bring reactants together in the correct position & orientation for the reaction to occur Chymotrypsin o Proteolytic enzyme/protease that breaks peptide bonds by a hydrolysis reaction o Breaks bonds on the carboyl-terminal side of the large hydrophobic AAs o Has both covalent and general acid-base catalysis strategies o Chromogenic substrate produces a color product when it is acted on by an enzyme P-Nitrophenolate has yellow color when produced by chymotrypsin o Obeys Michaelis-Menten kinetics but differs @ start of reaction Start: rapid increase in product but soon slows down to reach steady-state rate Suggests the reaction is occurring in 2 stages Covalent intermediate state formed during catalysis o Is an acyl-enzyme complex o Hydrolysis eventually leads to release of acyl from enzyme creating steady state phase Molecular mechanism o Oxygen atom of Ser 195 makes a nucleophilic attack on carbonyl carbon atom o Carbon has 4 atoms bonded to it thus becoming negatively charged, unstable, tetrahedral intermediate Oxyanion hole: Pocket in active site of enzyme that stabilizes an oxygen w/ negative charge o Intermediate collapses to form the acyl enzyme Oxyanion hole: packet in active site of enzyme o His 57 donates proton to enable the amine component to free the enzyme (acid-base catalyst in reaction) o H20 molecule enters active site & donates proton to His 57 o OH- results & attacks carbonyl atom to create another tetrahedral intermediate Oxyanion hole: stabilizes oxygen w/ negative charge o Intermediate collapses & forms carboxylic acid product o Enzyme & catalytic triad return to their initial state Oxyanion hole o Formed in Chymotrypsin by Hydrogen bonds provided by amino groups of ser 195 & Gly 193 o Hydrogen bonds stabilize the O- of the tetrahedral intermediate Chapter 9: Hemoglobin-An allosteric Protein Hemoglobin: o Oxygen-carrying metal ion proteins that transports oxygen from the lungs into the tissues and o Made of 4 iron ions + subunits held together by hydrophobic interactions & salt bridges o Prophryn ring attached contains both pyrrole rings and iron o Increases oxygen carrying capacity of blood by 70-fold o First allosteric protein studied in detail o Present in red blood cells of nearly all vertebrate ex: crocodile icefish family o 96% of dried blood cell mass is made of hemoglobin (35% if h20 included) o Has sigmoidal curve characteristic of cooperative allosteric behavior o Releases 60-66% O2 into tissues from the lungs bc allosteric regulators; o Releases 8% of O2 to tissues o T (deoxyhemoglobin) and R (oxyhemoglobin) states that differ by 15 degree rotation. 2,3 BPG: allosteric regulator that binds to hemoglobin in central pocket of T state & has very anionic charge (-5) but interacts w/ 3 positive AAs in each Beta subunit (regulation of Affinity) T state has lower affinity for oxygen than R state Myoglobin: o Facilitates the diffusion of O2 to tissues o Provides a reserve supply of O2 o Closely related protein to hemoglobin o Shows Hyperbolic behavior meaning that there is an absence oh allosteric interactions o Going from the lungs to tissues O2 release 7% bc no quaternary structure Heme o Prosthetic group for hemoglobin & myoglobin o Has Protoporphyrin2+)ganic component & central iron atom o Iron in ferrous (Fe state & is bonded to 4 nitrogen atoms Can form 2 additional bonds above & below heme plane 5th Fe coordination site bonds to proximal histidine Deoxyhemoglobin (No O2) –inactive T state 2+ Prevents oxidation of Fe & reduces carbon monoxide bonding O2 forms a hydrogen bond w/ distal histidine th 6 fe coordination site can bind to oxygen Oxyhemoglobin (bound O2)-active R state Fe shifts 0.4A into protoporphyrin plane Causes structural changes in the heme and surrounding proteins Hemoglobin subunits o 2 alpha o 2 beta o Form subunits of dimer pairs Alpha1beta1 and alpha2 beta2 o Substantial surface in contact b/t dimers Structural change o Binding to O2 causes a shift in Fe which shifts the proximal histidine causing the alpha helix to shift changing alpha1beta1- alpha2beta2 interface which results in changes from T to R transition o pH active muscle is lower than that found in the lungs. pH change shifts hemoglobin to T state Fetal hemoglobin adaptation: o Obtains O2 from moms hemoglobin o Have altered form with subunits 72% identical to Beta subunits Modifications to these subunits reduce the charge of the 2,3-BPG binding pocket reducing allosteric effect Bohr effect o Christian Bohr observed effect in 1904 o Inter and intra subunit of salt-bridge forms in hemoglobin w/ Co2 and Hydrogen ions being allosteric regulators of it o Metabolizing tissues release hydrogen ions and CO2 heterotrophic effects that enhance O2 release @ tissues o H response: @ low pH: His 146 in the Beta subunit becomes protonated Can form hydrogen bond w/ Asp 94 stabilize T states o CO2 response: Binds to hemoglobin in form of Carbamate (blood+ amino group) @ terminal amino groups Carbamate groups further stabilize the T state o Bound Co2 + H on hemoglobin are transported back into lungs- accounts only for 14% of total transport of these species to lungs o CO2 release is favored o Sickle-cell anemia o Disorder Due to a mutation of a single Beta nucleotide in hemoglobin o Resistant to malaria-evolutionary advantage o Replaces glutamate w/ valine (GAG to TGT) Encourages polymerization of hemoglobin & eventually cell deformation that stick together in capillaries & reduce normal blood flow to tissues o Disease happens if there are 2 copies of the abnormal gene o People w/ sickle trait are Heterozygous for the abnormal hemoglobin gene but white ppl are homozygous for the abnormal hemoglobin gene o Conformational change is fundamental aspect Brings hydrophobic patch to surface that can interact w/ mutated amino acid on the other subunit Functional Magnetic resonance imaging (fMRI) o Useful tool for brain imaging function o Relies on the movement of iron within hemoglobin o Can reveal differences in the amounts of oxyhemoglobin in a region of the brain Plausible pathogenic scenario: o A mutation that eliminates the activity of an enzyme involved in porphyrin synthesis leads to increased anemia o A mutation that allows normal fetal hemoglobin to continue being produced into adulthood would enhance symptoms of sickle-cell disease Carbohydrates Isomers o Constitutional: Differ in order of attachment o Stereoisomer: differ in spatial arrangement but have same order Enantiomers: non-superimposable mirror images Diastereomers: not mirror images Anomers: differ at new asymmetric carbon atoms that form a ring Epimers: differ at several asymmetric carbon atoms Glycosidic bonds o Glycosyltransferases: Catalyze glycosidic bond formation by condensation reaction o Glycoside: Sugar w/ glycosidic bond o Grouped into O-,N-,C-, S-glycosidic bonds Depends on new element bonded to anomeric carbon Glycoproteins: Proteins w/ at least 1 covalently attached carbohydrate group Class Structure Function Carb vs protein Glycoprotein Proteins that have Protein Cell membrane undergone components glycosylation at cell adhesion asparagine (N- Blood serum linkage) & components serine/threonine (O- linkage) side chains Proteoglycans Glycoproteins where Lubricants and Carb protein is attached structural to: components of glycosaminoglycan connective Polysaccharides tissue cell adhesion bind factors related to cell proliferation Mucins Glycoproteins where Lubricants Protein protein component Protective is extensively barriers glycosylated at S Hydrating and T by N- underlying acetylgalactosamine cells Roles in fertilization and immune response Lipids Lipids: Water-insoluble molecules highly soluble in organic solvents that can’t form polymers like carbohydrates, proteins and nucleic acid can o Energy storage o Membranes o Signal transduction Fatty acids (14) o Hydrocarbon chains w/ carboxylic acid terminate group (R-C(=O)-OH) o More reduced form than carbohydrates bc they have more hydrogens, Makes it easier to store more energy for combustion Saturation o Saturated fats : hydrocarbons w/ single bonds o Unsaturated fats: Hydrocarbons w/ 1 or more double bond creating a kink in the molecule Naming (16) o C-1 (carbon 1 ): carboxylic acid carbon (OH-C(=O)-R) o C2: alpha-carbon o C3: Beta carbon o w-1: 1 carbon from opposite side o w-2: 2ndcarbon from opposite side o w-3: 3 carbon from opposite side o Cis vs. Trans Trans: alpha carboxylic acid carbon attachment Cis: beta carboxylic acid carbon attachment Fatty acid Nomenclature o Base fatty acid names by # of carbons: # of Prefix Postfix 12 Dodec- 14 Tetradec- 16 Hexadec- -anoate/anoic aicd 18 Octadec- 20 Eicos- 22 Docos- 24 Tetracos- n o Double bonds: ▲ if b/t Cn and Cn+1 #: -en, -aiden, -atrien-, atetraen-, apentaen- o Cis& trans Start of name to specify double bond configuration-usually in cis o N-prefix Simple saturated fatty acids Fatty acids melting point (19): o Increased melting points are associated with higher numbers of Chain length Trans Trans-oelate: 45 degrees Celsius Cis-kinked so lower melting point: 13.4 degrees Celsius Saturation Stearate: 69.6 degrees Celsius Triacylglycerol o Storage form of fatty acids that are hydrophobic and stored in anhydrous form (w/o water) 1 glycogen holds 2 parts H20 by mass 6x more en
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