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Exam 2 Review -Additional Notes

by: Rachael Couch

Exam 2 Review -Additional Notes biol 3361

Marketplace > University of Texas at Dallas > biol 3361 > Exam 2 Review Additional Notes
Rachael Couch
GPA 3.9
Biochemistry 1
Dr. Lee

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About this Document

Additional notes for preparing for exam 2. Includes information from suggested problems in the textbook, cengage, and posted exam review.
Biochemistry 1
Dr. Lee
Class Notes
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This 3 page Class Notes was uploaded by Rachael Couch on Monday October 12, 2015. The Class Notes belongs to biol 3361 at University of Texas at Dallas taught by Dr. Lee in Summer 2015. Since its upload, it has received 53 views.


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Date Created: 10/12/15
Exam 2 Additional information Chapter 5 0 Carboxypeptidase A Cleaves C term AA all but ArgLysPro 0 Carboxypeptidase B Cleaves C term ArgLys 0 Carboxypeptidase CY Cleaves any C term AA 0 Clostripain Cleaves after Arg Chapter 13 0 MM equations 8 vs v 0 Km S at 12 Vmax 0 v VmaxS Km S O kcat VmaxEt 0 Catalytic efficiency kcatKm 0 LB equations 1S vs UV 0 X intercept 1Km 0 Yintercept 1V max 0 Slope KmV max 0 LB plot change 0 Competitive Same Yintercept increased slope O Noncompetitive Same Xintercept increased slope O Uncompetitive Same slope shifted left Chapter 14 0 Nucleophile base donates an electron pair usually 0 N or S 0 Base can handle losing an electron pair becoming positive 0 Electrophile acid accepts electron pair usually alkenes 0 Acid can handle losing an H can handle negative charge 0 Covalent catalysis O Nucleophilic Amines NR3 carboxylates RCOO hydroxyls OH imidazole N ring structure in histidine thiol SH I Nucleophilic residues mainly serine histidine cysteine andlysine O Electrophilic targets on substrate phosphoryl acyl CO 0 Mechanisms in actual enzymes 0 Serine proteases Ping pong mechanism covalent catalysis general acidbase catalysis 39 Chymotrypin Oxyanion hole transition state stabilization O Aspartic proteases general acidbase catalysis 0 pnitrophenylacetate hydrolysis 0 Example of specific acid or general base catalysis 0 Example of transition state analog that proves burst phase kinetics I Reaction changes to a slower rate after all enzymes are acetylated waiting for water to release them in the rate limiting step 0 Carbonic anhydrase 0 Example of metal ion catalysis 0 Has Zn2 which polarizes water 0 OH39 then attacks C02 0 Prolyl isomerase specifically human cyclophilin A 0 Example of protein motion catalysis O Catalyzes interconversion between trans and cis conformations in peptides 0 Polarcharged and polaruncharged amino acids engage directly in catalytic effects in enzyme active sites by acting as nucleophiles facilitating substrate binding and stabilizing transition states 0 pH in uence on aspartic protease 0 Have a pH optimum significantly impaired function outside of pH optimal range 39 Acidic 245ish 0 Cysteine protease O Degrade proteins hydrolysis of peptide bonds Nucleophilic cysteine Basic amino acid histidine deprotonates cysteine s thiol SH S Deprotonated cysteine attacks sulfur on substrate carbonyl carbon Release N term deprotonates histidine O Creates thioester intermediate that is hydrolyzed to generate a carboxylic acid 0 O O O 0 Lysozymes O Damage bacterial cell walls 0 Active site Gly and Asp 0 General acid catalysis Chapter 6 0 Alpha helix length 015nmresidue 0 Beta turn Hydrogen bonds between i and i3 residues 0 Proline is the least common in alpha helices because proline cannot function as a hydrogen bond donor but the most common in beta turns because it stabilizes the vis bond that beta turns require 0 More glycine in proteins than any other amino acid because it has a small side chain that can be accommodated in smalltight bends that are required in the compact proteins 0 H bond donors Have an H Lysine arginine tryptophan 0 H bond acceptors Lone pair of electrons aspartic acid glutamic acid 0 Donors and acceptors Asparagine glutamine serine threonine histidine tyrosine 0 All have a heteroatom with a hydrogen connected OH NH SH 0 Not threonine because N is in ring 0 Proteins in their native structure are dynamic 0 Have different conformations and can change 0 Changes tofrom different conformations occur by transient H bondlocalized not global changes that pass through the unfolded state


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