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BCHM 307 Exam 1 Study Guide

by: Sean Anderson

BCHM 307 Exam 1 Study Guide BCHM 307

Marketplace > Purdue University > BCHM 307 > BCHM 307 Exam 1 Study Guide
Sean Anderson
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These notes cover all of the topics we have covered thus far. All the main concepts are in bold and graphs and tables are supplied within the guide for easier understanding.
Dr. Stefan Paula
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This 24 page Study Guide was uploaded by Sean Anderson on Monday September 26, 2016. The Study Guide belongs to BCHM 307 at Purdue University taught by Dr. Stefan Paula in Fall 2016. Since its upload, it has received 3 views.


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Date Created: 09/26/16
Sean Anderson Dr. Stefan Paula BCHM 307 9/22/16 BCHM 307 Exam 1 Study Guide Water   Water has a tetrahedral geometry because of its electronic structure  Water is polar and has a dipole movement (up)  Water can form H-bonds….requirements: o H-bond donor (H-A) o H-bond acceptor (B)  H-bonds are partially covalent (1.8A) o Covalent bond (1.0A) o No bond (2.7A)  Water can have H-bonds with other molecules o Water-Alcohol o Water-Amine *The hydroxyl and amine groups are key players in hydrogen bonding in biomolecules  H-bonds in DNA (very weak) o C-G (3 H-bonds) o A-T (2 H-bonds)  Strength of intermolecular forces o Covalent bond > Ionic interactions > H-bond > van der Waals interactions  Water molecules orient so that oxygen atoms are always pointing towards hydrogen atoms o Four neighbors o Tetrahedral structure  Water is highly cohesive  Water as a solvent o Ions and polar compounds  “like dissolves like” o Nonpolar compounds  Non-polar molecules such as oil are not miscible with polar solvents such as water  Nonpolar molecules tend to aggregate in polar solvents o The hydrophobic effect is the phenomenon by which nonpolar molecules aggregate to avoid contact with hydrophilic molecules, particularly water  Amphiphilic Molecules o Fatty acids (lipid) o Hydrophilic (polar) – head group o Hydrophobic (nonpolar) – hydrocarbon tail  Most lipids are amphiphilic  Some amphiphilic molecules form micelles in aqueous solutions  Some amphiphilic molecules form bilayers in aqueous solutions Auto-dissociation of water + - o H 2  H + OH o K=[H ]x[OH ]/[H O] 2 o K = [H ]x[OH ]=10 -14 w o K w Ionization constant & Ionic product  pH definition + - -14 o K w [H ]x[OH ]=10 o Pure water, [H ]=[OH ]=10 M -7 o Pure water is neutral (pH=7) + -7 o Solutions in which [H ] > 10 M = Acidic o Solutions in which [H ] <10 M = Basic o pH=-log[H ]+  pH=7—neutral  pH<7—acidic  pH>7—basic o Example: 0.5L water, 0.025L of 0.025M HCl 1. M 1 1M V 2 2 2. 0.025Mx0.025L=0.525LxM 2 3. M 20.0012 4. pH=-log[0.0012] 5. pH=2.9 (acidic)  Acids and Bases o Acid: proton donor o Base: proton acceptor + - o HA + H 0 2 H 0 +3A o Acid + BaseConjugate Base + Conjugate Acid  Strong and weak acids/bases o Strong acids/bases completely dissociate in water  HCl, HNO ,3KOH, NaOH… o Weak acids/bases partially dissociate in water  Acetic acid o Stronger acid = higher Ka = lower pKa o Weaker acid = lower Ka = higher pKa o pH=pK + log[A ]/[HA] o Example: 0.025L of 0.01M HAC, 0.025L of 0.03M AC , pKa=4.76  HAC=(0.01Mx0.025L)/1.05L=0.00024M  AC =(0.03Mx0.025L)/1.05L=0.0007M  pH=4.76+log{[0.0007M]/[0.00024M]}=5.23 (acidic)  pK and pH convey protonation states o pH<3.5: Amino acid has both protons and a net positive charge  COOH and NH 3+ o 3.5<pH<9.0: Amino acid loses the proton on the carboxyl carbon and becomes a zwitterion that has a neutral charge  COO and NH + 3 o pH>9.0: Amino acid loses both protons and has a net negative charge -  COO and NH 2  Titration of acetic acid with NaOH o Rule of thumb for “buffer zone”: pH=pK ±1 Amino Acids (AA)   Most AA are chiral  In proteins, the L-form is exclusively present  Thalidomide (morning sickness drug for pregnant women) o S form: sedative o R form: teratogenic (birth defects, miniature arms)  There are 20 unique AA that make up proteins in general  Each 20 different AA have different R-groups  The 20 AA differ in the polarity of their R-groups o Three categories of R-groups:  Hydrophobic AA: nonpolar R-groups (remains inside the core of the protein)  Hydrophilic AA: polar R-groups (remains on outside surface of the protein)  Polar R-groups can be charged or uncharged  Naming of AA o Full name (glycine) o 3 letter code (Gly) o 1 letter code (G)  Hydrophobic AA—all these reside in the core of the protein structure o Proline o Valine o Tryptophan o Methionine *PVT MAIL P o Alanine o Isoleucine o Leucine o Phenylalanine  Polar uncharged AA—all these reside on the surface of the protein structure o Cysteine o Asparagine o Serine o Threonine *CAST THGG o Tyrosine o Histidine o Glutamine o Glycine  Charged AA o Glutamate (-) o Aspartate (-) *GALA o Lysine (+) o Arginine (+)  Cysteine residues: disulfide bridge o Disulfide bridges can form intra-strand crosslinks o When a protein contains more than one polypeptide chain, disulfide bonds can also form inter-chain crosslinks  Histidine o Can be charged at certain pH values (pH 3 = +1)  Peptides o AA are linked by peptide bonds to form polypeptides o AA within the peptide are called ‘AA residues’ because only the residual atoms remain  2 AA’s: 20AA x 20 combinations = 400 AA possibilities  3 AA’s: 20AA x 400 combinations = 8000 AA possibilities  Prediction of total charge of a peptide *(make flashcards) Group pK C-terminus 3.5 Aspartate 3.9 Glutamate 4.1 Histidine 6.0 Cysteine 8.4 N-terminus 9.0 Tyrosine 10.5 Lysine 10.5 Arginine 12.5  When 3.5<pH<9.0 the structure of a generic AA is Zwitterion forms (+ and – charge present) o Carboxyl group is acidic at neutral pH (pK=3.5) o Amino group is basic at neutral pH (pK=9.0) Protein Structures   Different levels of protein structures o Primary structure  Sequence of AA residues o Secondary structure  Localized conformation of the polypeptide backbone o Tertiary structure  Three-dimensional structure of an entire polypeptide, including all its side chains o Quaternary structure  Spatial arrangement of polypeptide chains in a protein with multiple subunits  The peptide bond o Peptide group is planar  The planarity of the peptide group  The two torsion angles of a peptide bond  Steric constraints limit relative position of peptide planes  The alpha helix o 3.6 residues per turn  Pitch = 5.4Å o 2 nm in diameter o 3.4 nm per 360˚ turn of DNA  0.34 nm between base pairs  10 base pairs per 360˚ turn o Core densely packed  van der Waals interactions occur o H-bonds: C=O bonds with NH that is 4 positions away o Glycine and proline are rare o R-groups point toward N-terminus  1Å=10 m-10  β-pleated sheets o Top: parallel CN, CN o Bottom: anti-parallel CN, NC  Arrow always points to C-terminus  Look for α-carbon when determining direction of arrow  α-carbon is to the left of N group: CN  α-carbon is to the right of N group: NC  Proteins can be grouped into four classes (CATH) a) α-protein (alpha helix only) b) β-protein (beta sheets only) c) α/β-protein (alpha helix and beta sheets) d) Protein with very little secondary structure Proteins   Location of AA in a globular protein o A folded polypeptide assumes a shape with a hydrophilic surface and a hydrophobic core  Location of α-helices and β-sheets o Secondary structure elements are often found in the core  Ion pairs (salt bridges) o 2 ion pair+ found-in the core of myoglobin  Lys —Glu  Arg —Asp -  Stabilization of protein structure o Delicate balances between forces o Interactions to consider:  Hydrophobic interactions  H-bonds  Electrostatic:  Charge/charge  van der Waals interactions  Disulfide bonds  Hydrophobic interactions o Folded—Favorable (hydrophobic core) o Unfolded—Unfavorable (hydrophobic core exposed)  Protein flexibility o Proteins are flexible, not static  Domains and quaternary structure o A single chain can form local 3D structures called domains o Two or more separate chains (subunits) can orient in 3D space to give quaternary structure  Protein purification o Separate proteins present in a large mixture, using differences in physical properties  Charge  Size  Solubility  Polarity  Binding affinity  Chromatography o A technique for separating molecules on the basis of a physical property; use of a mobile and immobile phase o Commonly used chromatography methods in biochemistry:  Gel filtration (size exclusion) chromatography  Ion exchange chromatography  Affinity chromatography  Gel filtration (size exclusions) chromatography o Separation is based on size  Larger proteins elute faster  Smaller proteins elute slower since they have to diffuse between all the gel beads  Ion exchange chromatography o Separation based on charge  Resins have either diethylaminoethane (DEAE) or carboxymethyl (CM) functional groups  Affinity chromatography o Separates biochemical mixtures based on a highly specific interaction  Such as that between antigen and antibody, enzyme and substrate, or receptor and ligand  SDS-PAGE o Before SDS  Protein is folded with a hydrophobic core and polar charged R- groups on the surface o After SDS  Protein is unfolded (linear) with a negatively charged surface  Due to sample traveling to anode (+)  Protein sequencing o Determining the primary structure of a protein o Two methods:  Edman Degradation  Chemical method that removes and identifies AA from their N-terminus  Mass Spectrometry  Faster method  Measures mass/charge (m/z) ratios  Sequencing by mass spectrometry o ESI: Electrospray Ionization  Create “flying” protein fragments  ProteinIonizationMS (isolation)—selected peptideCollision chamber (fragmentation) MS2 (mass analysis)  MS-1 isolates a single fragment  MS-2 determines its sequence o Each AA has a unique m/z ratio  Determination of protein tertiary structure o Three methods:  X-ray diffraction  NMR spectroscopy  Cryo-electron microscopy  X-ray diffraction o Requires protein crystals which are hard to obtain (trial and error) o Uses electron density maps o X < 4Å is good atomic resolution  NMR spectroscopy o NMR requires a strong magnetic field and operates with radio waves (low energy, large wavelengths) o The exact (relative) wavelength of resonance depends on the environment of the nuclei (bonds, neighbors in space) o NMR spectroscopy of proteins:  NMR provides distance constraints  Frequently, a family (ensemble) of similar structures is obtained  Cryo-electron microscopy (Cryo-EM) o Application of transmission electron microscopy to a thin film of frozen biological molecules o Captures images of molecules from different angles and orientations, the 3D-structure is reconstructed computationally Myoglobin and Hemoglobin   Myoglobin and hemoglobin o O transport: critical for sustaining life 2 o Myoglobin (Mb): Oxygen storage in tissue (muscle) o Hemoglobin (Hb): Oxygen transport in blood  Hemoglobin and myoglobin structure o Myoglobin—1 heme group (1 Fe ) 2+ 2+ o Hemoglobin—4 heme groups (4 Fe )  The heme group o Prosthetic group: Non-amino acid in nature, essential for a protein’s function o Heme: Porphyrin ring with central Iron atom (Fe ) 2+  Oxygen binding by Mb o MbO 2 Mb + O 2 o K= [Mb][O ]/2MbO ] 2 o K: dissociation constant  Measures for O 2ffinity of Mb (the smaller the number, the tighter the binding) o Fractional saturation (Y): the proportion of myoglobin molecules that have bound O 2 o Y=(pO 2/(K+pO )2 *Hyperbolic graph o Mb binds O i2 a hyperbolic fashion  The meaning of K o P50 oxygen partial pressure at which 50% of all Mb molecules bind oxygen o K = P 50 o Example:  K= 3 torr. pO =20 torr. Y=??  Y=(20)/(20+3) = 0.869  Oxygen binding by Hb o Binding curve is Sigmoidal, not hyperbolic like Mb  Cooperativity  Oxygen affinities of Mb and Hb are different o P50= 26 torr (Hb)—(greater number=greater affinity)—due to more heme groups o P = 2.8 torr (Mb)—(lesser number=greater affinity)—due to less 50 heme groups  The Perutz mechanism of Hb o Blue: deoxy form, bent porphyrin ring (no oxygen)  T (“tense”) form o Purple: oxy form, planar porphyrin ring (oxygenated)  R (”relaxed”) form  The TR transition in Hb o Tense (deoxy) form is a larger appearing quaternary structure o Relaxed (oxy) form is a smaller appearing quaternary structure  The Bohr effect o pH high (basic) oxygen affinity of Hb is larger (greater affinity) o pH low (acidic) oxygen affinity of Hb is lower (lesser affinity) o Amino termini of α-chains o His residues near C-termini of β-chains o If protonated (lower pH), the T-form is stabilized  Oxygen release due to lower affinity (tissue) o If deprotonated (higher pH), the R-form is stabilized  Oxygen uptake due to higher affinity (lungs) o pH in tissue is lower than in lungs o Oxygen needs to be released in the tissues and taken up by in the lungs Lungs Tissue Slightly Basic Slightly Acidic R-form T-form Oxy- Deoxy- High affinity Low affinity Left curve shift Right curve shift Oxygen uptake Oxygen release Deprotonated Protonated  The effect of BPG o BPG lowers O a2finity o BPG binds only to the T-form conformation of Hb and stabilizes it o Curve shifts to the right with BPG  Carbon monoxide poisoning o CO binds better to Hb than O2and displaces it  Comparison of Hb sequences o Invariant Essential for function o Conservatively substitutedSomewhat important for function o Variable Not important for function  Sickle cell anemia o Fiber formation (Hb) inside red blood cells  Bursting of red blood cells (anemia)  Clogging of blood vessels (tissue death) o Glu Val mutation o Conveys some protection against malaria  Possibly from fiber formation?? Enzymes and Chemical Reactions  How can we increase the rate of a chemical reaction? o Increase temperature o Increase the [substrate] o Add a catalyst  Biocatalystsenzymes  Mostly proteins (exception: ribozymes are RNA-based)  Rate enhancements typical for enzymes o Enzymes speed up biochemical reactions significantly  10 -10 12times faster  Enzyme structure o Substrates bind to enzymes at the active site o High specificity for the substrate (reactant)  Summary of enzyme properties o Great rate enhancement o Catalysis under mild conditions (T, P, pH) o Great specificity o Regulation by effectors (inhibitors, activators)  Naming of enzymes o The name of the substrate (1) and the catalyzed reaction (2) are the enzymes name  Pyruvate decarboxylase removes a carboxylate group from the substrate pyruvate o There are six major classes of enzymes: Class of Enzyme Type of Reaction Catalyzed Oxidoreductases Oxidation-reduction reactions Transferases Transfer of function groups Hydrolases Hydrolysis reactions Lyases Group elimination to form double bonds Isomerases Isomerization reactions Ligases Bond formation coupled with ATP hydrolysis o Example: This is a Lyases reaction, due to a C2 group being eliminated and a double bond is formed to produce the CO 2  2-oxo-acid-carboxy-lyase  Thermodynamics of reactions o The sign of ∆G indicated the spontaneity of a reaction (not a measure for its velocity)  ∆G<0 = spontaneous reaction—exergonic  ∆G>0= non-spontaneous reaction—endergonic o The height of the activation energy barrier determines the rate of the reaction  High activation barrier = slow reaction  Low activation barrier = fast reaction o Enzymes work by providing a pathway with a lower activation energy barrier for a reaction  Fundamental mechanisms for enzyme catalysis o Acid-base catalysis  An enzyme can use acid catalysis, base catalysis, or both o Covalent catalysis  Also called nucleophilic catalysis o Metal Ion Catalysis  Acid-base catalysis: Keto-enol tautomerization o Acid catalysis—(proton donors) o H transfer from an acid lowers the free energy (∆G) of the transition state o B+se Catalysis—(proton acceptors) o H is abstracted by a base to lower the free energy (∆G) of the transition state  AA that can play a role in acid-base catalysis + o Essentially any AA that has a NH , -SH, or –OH end  Covalent catalysis: decarboxylation of acetoacetate  Some AA that can play a role in covalent catalysis  Metal ion catalysis: alcohol dehydrogenase  Proteases o Protease: enzyme catalyzing the hydrolysis of a peptide bond  Example: Serine proteases o A triad conserved AA (including serine) in the active site  Features of the serine protease mechanism (part 1) *Carbonyl C: location of nucleophilic attack  Features of the serine protease mechanism (part 2) o A portion of the substrate protein (C-terminal) is gone, the remaining part is still covalently attached to Ser-195 *Acyl-enzyme intermediate o Enzyme is regenerated catalyst o Rest of protein (N-terminal) is released  Enzymes stabilize the transition state o Enzymes bind tightly to the transition state (more so than to substrates, intermediates, or products), thereby stabilizing it and lowering its activation energy barrier o Lower activation energy  Serine proteases: stabilization of intermediates via the oxyanion hole  Different serine proteases have different specificities Specificities of Some Proteases Protease Residue Preceding Cleaved Peptide Bond Chymotrypsin Phe, Trp, Tyr Elastase Ala, Gly, Ser, Val Thermolysin Ile, Met, Phe, Trp, Tyr, Val Trypsin Arg, Lys o Cleavage does not occur if the following residue is Proline o Ser + Gly = Oxyanion hole  The substrate binding sites of serine proteases  Enzymes: biomolecular reactions o When enzymes bind substrates, the substrates are brought into proximity and in the correct orientation to make a chemical reaction favorable  Enzyme kinetics o Enzyme kinetics is the study of rates of reactions catalyzed by enzymes o The reaction rate (velocity, v) can be described in two ways:  Disappearance of substrate, S  Appearance of product, P  Definition of reaction velocity o As [GAP] decreases, [DHAP] increases (inverse relationship)  V=-∆[S]/∆t=∆[P]/∆t  Velocity as a function of enzyme concentration o Linear relationship o As the [enzyme] increases, so does the reaction velocity  Velocity as function of substrate concentration o Shape is hyperbolic (like Mb) o Enzyme gets saturated at high [substrate] o E + S  ES o As the [substrate] increases, so does the reaction velocity until the [substrate] plateaus  Enzymes: reaction rate vs substrate concentration o Goal: equation that expresses velocity as a function of [S]  Rate laws o A unimolecular reaction has a velocity (rate) that is dependent on the concentration of only one substrate  A  P  V = k[A] = k[A] 1 -1  k; rate constant, has units of s  First order  Order: sum of exponents in rate law = 1 o A bimolecular reaction has a velocity (rate) that is dependent on two substrate concentrations  A + B  P 1 1  V = k[A][B] = k[A] [B]  k: rate constant, has units of M s1 -1  Second order  Order: sum of exponents in rate law = 2  Rate laws: enzymes o Michaelis-Menten approach: o E + S (k 1r k -1 ES (k )2 E + P o ES (k 2 E + P Rate limiting step—very slow o V = ∆[P]/∆t = k 2ES] o Example:  t=0s has a 10mM [S]  t=10s has a 2mM [S] -1  V = -∆[S]/∆t = (10-2)/10-0) = 0.8mMs o Example:  t=0s has a 0mM [P]  t=5s has a 20mM [P]  V = ∆[P]/∆t = (20-0)/(5-0) = 4mMs -1  Michaelis-Menten kinetics o E + S (k 1r k )-1ES (k )2 E + P  Express [ES] in other terms o ∆[ES]/∆t = k [1][S] –k [-1]—k [ES2  k [E][S]  formation of ES 1  –k -1S]—k [E2]  depletion of ES o For most of the duration of the reaction, [ES] remains steady as substrate is converted to product o As [S] decreases, [P] increases Assume steady state equilibrium o ∆[ES]/∆t = 0 = k [1][S] –k [-1]—k [ES2 o [E] total [ES] + [E] o [E] = [E] total [ES] o K M (k +-1)/2 “M1chaelis constant” o V Max = k 2E] total k catE] o The Michaelis-Menton equation:  V = V Max[S]/K M [S] o V Max is where the reaction velocity reaches its plateau o K Ms the substrate concentration at ½ V Max o Example:  What is the velocity of the reaction?  K M 1mM  V Max= 5nMs -1  [S] = 0.25 mM -1  V = (5nM*0.25nM)/(1mM+0.25mMs) = 1nMs o Example:  KM= K M  [S] = 0.75 kM  VMax= V Max  V = V Max(0.75k Mk M0.75k )M  V = V Max(0.75k M1+0.75k )M= V Max0.428  The meaning of K M o K is a measure of the affinity of E for S M o Low K M high affinity o High K M low affinity  The meaning of K cat o K cat catalytic rate constant, turnover number  A measure of how fast the enzyme converts bound substrates to product o High K cat fast turnover o K cat= k2 o K cat= V Max[E]total  Catalytic efficiency o K catMatio indicates catalytic efficiency o 10 M S = enzyme reaches catalytic perfection o Enzymes reach catalytic perfection when their rate is diffusion- controlled  Each collision of S with E leads to formation of P  Enzyme + Substrate  Product  Each E and S collision leads to a P due to it having enough energy to reach the transition state  Linearizing the Michaelis-Menton equation o V = V Max[S]/KM+ [S]  Take reciprocal of both sides: (makes graph linear)  1/v = (KM/V Max(1/[S]) + 1/VMax  Lineweaver-Burk plot  Enzyme inhibition o Enzyme inhibitors interfere with the function of an enzyme o Uses/occurrences of enzyme inhibitors:  Pesticides  Drugs  Natural poisons  Reversible enzyme inhibition o Competitive inhibitors resemble the substrate and therefore bind to the same site (=active site) as the substrate  K Mhanged  increased  V Maxunchanged  α: degree of inhibition, inhibition factor  α = 1 + [I]/K1  Slope = αK /M Max  K 1 [E][I]/[EI] (dissociation constant)  K 1easures for affinity of inhibitor for enzyme  Transition state analogs o Enzymes bind most tightly to the transition state  Compound resembling the transition state will have high affinity  Transition stage analogs  Other types of enzyme inhibition o Irreversible inhibitors bind covalently to enzyme (won’t come off) o Noncompetitive inhibitors   o Both V Max(smaller) and K Mlarger) are affected  Enzyme regulation in Nature o Negative effectors: inhibitors o Positive effectors: activators o Other regulatory mechanisms: 1. Rate of enzyme synthesis/degradation 2. Enzyme location (inside cell or on surface) 3. Effectors (inhibitors or activators) 4. Covalent modification (phosphorylation—can turn enzyme on or off)  Drug development o Goal: obtain an effector of therapeutic value o Rational drug design:  Active site structure is known  find inhibitor that “fits” o Requirements for a “good” drug candidate (in vitro and in vivo)  Tight binding  High specificity  leave other enzymes alone/side effects  Pharmacokinetics:  Solubility in water and lipids  Stability against other enzymes (P450 liver enzymes), etc..  Performance in clinical trials -


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