review_mid1

review_mid1 - Review for Midterm Chem 153A TA: Suzie I....

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Unformatted text preview: Review for Midterm Chem 153A TA: Suzie I. Buffers a. Henderson Hasselbalch Eglgtign - be able to find pH, pOH, pK., or concentrations of protonated and deprotonated forms of a compound - problem #5 on page 4 is good practice b. Titration Curves - draw a titration curve (pH vs. OH' equiv.) - change the axes to pH vs. H+, OH‘ vs. pH, and H+ vs. pH and draw the titration curves - - calculate pI; remember that this depends on the charge of the side chains and the N- and C-terminus - good practice problems: pg. 10 #1 and pg. 13 #7 *** combining these two concepts: pg. 11 #2. II. Amino Acids a. Know: - side chains - 3 letter abbreviations - pKa of side chains, - pKa of N and C termini of free and bound amino acids. b. Non-Mdgd Amino Acids ( result from post-transational modifications) - disulfide bonds form between cysteine’s - hydroxylation — adding an OH group . - phosphorylation at O or N — adding a phosphate group; this is reversible and plays a role in inactivating/activating enzymes ' - acetylation - adding acetyl group to aa - formylation — adding formyl group at OL-amino group 111. Effects of Microenvironment on animo acid’s (pK.’s) inductive effect electrostatic effect 9"!” IV. Peptides a. structur s - primary — specific amino acid sequence - secondary — specific folding patterns (oz-helix or fi-pleated sheets) - supersecondary — groups of secondary structures into a pattern (ex. series of helices followed by a sheet) - tertiary — interactions of side chains with each other - quaternary — interactions between two or more polypeptides 134.. .mm-whfimm- .. r. . V t. . b. interactions involved in folding pattng of proteins - hydrogen bonds - electrostatic interactions — hydrophobic interactions - Van der Waals forces - Covalent bonds (disulfidc bonds between 2 cys residues) . interactions involved in tertim and guatgmm structures J - electrostatic interactions ( ion-polar, ion-pairs, dipole-dipole, Van der Waals, H- bonds) - hydrophobic interactions - covalent interactions (disulfide bonds) Sequencing . Acid Hydrolysis - breaks all peptide bonds so you get the amino acid composition, not the sequence - problems with acid hydrolysis - see pg. 34 of compendium . N-terminal Identification Methods - Sanger’s Reagent - covalent bond between DNP and N-terminus of the amino acid results in a DNP-aa complex of the N-terminal aa - Dansyl Chloride — dansyl group forms a covalent bond with the N-terminus of an a forming a Dansyl-aa complex . C-terminal Identification Methods - Reduction — COOH group of the C-terminal a is reduced to CH20H - Hydrazinolysis -— C-terminal amino acid is the only one where hydrazine does not form a covalent bond - Carboxypeptidase — cleave at specific sites of a polypeptide chain; starting with the C-terminus; see the original C-terminal amino acid first, then the second, then the third, and so on. . Specific Peptide Cleavage - proteolytic enzymes — chymotrypsin (cleaves after aromatic amino acids - trp, phe, tyr - as long as they are not followed by a proline) and trypsin (cleaves after lys and arg as long as they are not followed by proline) - chemical cleavage - cyanogen bromindc (cleaves afier Met only if it is not followed by pro) Carbohydrates . 2 main classifications — monosaccharides - polysaccharides . L- vs. D- isomers - only in Fischer Projections - mirror images of eachother; orientation of OH on each carbon are opposite . gum — differ in orientation around ONE carbon d. e. f. g. VII. Enantiomers — change in configuration around ALL carbons; results in L- and D- enantiomers Cyclization - results in the formation of an anomeric carbon - this is the carbon where the ring closed; orientation of OH facing up or down fiom this carbon will result in on or B configurations in the Haworth Projection - 06- form: OH group on anomeric carbon is TRANS carbon #6 - [3- form: OH group on anomeric carbon is CIS to carbon #6 Derivatives of Monosacchariges - phosphate esters — have a phosphate group attached to the sugar, replacing an OH with a phosphate group - de-oxy sugars - missing an OH group - amino sugars — amino group replaces an OH group at some position Glycosidic Bonds . - link sugar to anything else via the anomeric carbon of nonreducing sugar; O-group is donated by reducing sugar - pyran -— 6 membered ring — furan — 5 membered ring - pyranoside or furanoside means the modification is on the anomeric carbon - can be (1 (bond from anomeric C of left sugar is facing trans to C6 of left sugar) or [3 (bond of anomeric C of left sugar is facing cis to C6 of left sugar) Disaccharide - homodimers — 2 of the same sugar molecules bound together by a glycosidic bond - heterodimers — 2 different sugar molecules bound by a glycosidic bond Lipids a. General Classification of lipids: Storage ; . lipids é - (neutral) Membrane lipids (polarij i Phonpholipidl : ‘Triacylglyeerols ‘ .3 LHM~-.....-‘... .. ,__. .,. b. MW: see pg. 55 of compendium c. Triac r e: 1. name FA, dropping —ic or —ate ending and adding -oyl 2. name the carbon # it is on 3. name parent compound (glycerol) d. W: 1. name FA, dropping —ic or -ate ending and adding -oyl 2. name the carbon # it is on (either 1 or 2) 3. name phosphate alcohol group (“X” on the below table) 4. name parent compound (“name of glycerophospholipid column on table below) "*recognize, don't memorize! *** Curdlollpin 6- 1. indicate whether substitution of FA is at O or N 2. name FA, dropping ending and adding -oyl 3. name the X group appropriately 4. name parent compound (“Name of sphingolipid” column in table below) VIII. a. b. C. Nan-d flyeofipids . Gluooayleaobtoflde hero-fiesta:le (a ghboside) ‘W (33112 Enzymes 6 main classes — see page 65 of compendium; be able to write a reaction based on the enzyme name and be able to name the enzyme based on the reaction type. Michaelis-Menten Model - 5 Assumptions Model: E+S 6—5? ESg-EE? E+P, A 1. For initial velocities, we have not made any product yet (i.e. [P] = 0). Therefore the rate ofE + P 3%EP is 0. V= k2 [E][P] = 0 2. The overall reaction rate depends on the rate limiting step, which is assumed to be ES 9 E + P. Therefore, the actual equation for initial reaction rates is V0 = k; [ES]. ' 3. [ES] always comes to steady state. Therefore it’s concentration will remain constant. In other words, it is being made at the same rate that it is being used up. 4. [S] >>>>>> [ES]. Therefore, [S] does not change significantly at early time points. 5. [Emu] = [Em] + [ES] Total enzyme concentration is equal to the concentration of free enzyme plus the concentration of bound enzyme. Remember we can only measure total enzyme concentration. Michael's-M nten uation & - plot V0 vs. [S] a 11 V0 = anxlslla‘M + . 4.. kw Mame”. d. Lineweaver-Burk Plot -. plot (1N0) vs. (l/[S]) - need to convert Michaelis-Menten equation into the equation of a line (y = mx + b) — y represents l/Vo - m represents the slope (Kmme) - x represents 1/ [S] - b represents the y-intercept (1N max) - the x-intercept value is —1/Km e. Eadig-Hofstee Plot - plot Vo vs. (V o/ [S]) - need to convert Michaelis-Menten equation into the equation of a line (y = mx + b) - y represents V0 - m represents the slope (-Km) - x represents (Vol [8]) — b represents the y-intercept (V max) - the x—intercept value is Vmax m f. Factors Afiegting Enzyme Agtivig 1. pH -— changes properties of enzymes and substrates; effects binding 2. Temperature — disrupts H-bonding and other interactions, denaturing enzymes; increases the energy of the substrate molecule 3. Inhibitors a. Competitive -— compete with substrate for the same binding site I. No change in me - at high [S], the substrate out-competes the inhibitor in binding to the enzyme 2. Apparent increase in Km - at low [S] the inhibitor is more likely to bind to enzyme and inactivate it, so it appears that we would need more substrate to reach Vm/Z MM mar J. Mat. EUR”!— Vg v0 / *1 b. Noncon'ipe‘titive V [51 V°/[sj — Do not compete with substrate for the same binding site —— These inhibitors will bind to the regulatory site of the enzyme Whether or not substrate is bound to the enzyme. — Influence on kinetics: 1. decrease in V.mm — at any given [S] (big or small), there is always a pool of enzymes that will bind inhibitor and become inactive; degree of inhibition is the same at all [S]’s. 2. no apparent change in Km — inhibitor binding does not effect b b' d' su strate in mg Lb PM. E“ PM“. V0 4 > *1 Viz/[c] vc. Uncompetitive - Inhibitor only binds to the enzyme when substrate is bound to the enzyme - Influence on kinetics: 1. decrease in Vmx — at high [S] you make more E-S complex so the inhibitor will be most likely to bind and inactivate the enzyme 2. apparent decrease in Km - at low [S], less E-S complex made so less inhibition occurs, so we are able to reach the new (lower) Vm/Z with less [S]; i vmx o: t Km 5% Vlo‘l' +1 V foil V°I r51 Mechanisms of Enzyme Catalysis a. Two Theories of Enzyme-Subsgate Binding 1. Lock and Key Model — substrate fits exactly, into the enzyme binding site . 2. Induced Fit Model — substrate causes the enzyme to undergo a conformational change so the substrate can fit better. . Acid-Bge Catalysis —- protons are transfered —- - Acid Catalysis —— active site provides the acid which will donate the proton - Base Catalysis - active site acts as the proton acceptor via the substrate and water ***these two reactions do not happen without each other*** . Covalent Catalysis — form a covalent bond between the substrate and enzyme . Electrosgic _C_atalysis — electrostatic interactions, between charged side chains on enzyme and substrate or betWeen 2 charged side chains on the enzyme, accelerate the reaction rate . Metal Ion Catalysi - some are also electrostatic 2 classes: 1. Metalloenzymes — always there; tightly bound metal ions 2. Metal-activated enzymes - not stably associated with enzyme; loosely bound Proximng and Og'entation Effects — all enzyme mechanisms involve this because the substrate must always be in the correct proximity and orientation to come in contact with the active site of the enzyme . Pref rential in ' of ran " n tate Co lex - get binding when there is electrostatic stabilization - electrostatically, the substrate and enzyme prefer to be near eachother (opposite charges attract) - when the binding of the substrate destabilizes the substrate and induces bond angle strain; when the intermediate forms, the bond angle strain is relieved. EXAM MATERIAL INCLUDES, BUT IS NOT EXCLUSIVE TO, THIS BE SURE YOU ALSO STUDY YOUR NOTES, THE COMPENDIUM, AND THE PRACTICE PROBLEMS. **GOOD LUCK!** ...
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This test prep was uploaded on 04/10/2008 for the course CHEM 153A taught by Professor Staff during the Spring '05 term at UCLA.

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review_mid1 - Review for Midterm Chem 153A TA: Suzie I....

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