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LLecture 2 Objectives.pdf

by: Anita Cheung

LLecture 2 Objectives.pdf BMB507

Marketplace > University of Miami > Bioxhemistry > BMB507 > LLecture 2 Objectives pdf
Anita Cheung
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Lecture 2 Objectives for the course
Class Notes




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This 5 page Class Notes was uploaded by Anita Cheung on Sunday September 25, 2016. The Class Notes belongs to BMB507 at University of Miami taught by in Fall 2016. Since its upload, it has received 2 views. For similar materials see Proteins in Bioxhemistry at University of Miami.


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Date Created: 09/25/16
Lecture Objectives – Lecture 2 1. Learn about the pH scale and the Henderson-Hasselbalch equation to solve problems pH + - Keq [H ][OH ] / [H 2] Ion product for water K w [H ][OH ] = 10 -14at 25 degrees pH = -log 10 [H ] pH of pure water is 7 High [H ] is acidic  low pH + Low [H ] is basic  high pH Acids and Bases Acids are proton donors Bases are proton accepts The strength of an acid reflects its tendency to release a proton pKa is the pH at which the acid and base exist 50/50 HA  H + A - + - Keq [H ][A ] / [HA] pKa = -log[K] Henderson Hasselbalch Equation - pH = pKa + log [A ]/[HA] Work out example problems from lecture 2. Understand that amino acids are zwitterionic, and learn their chemical structures, ionization properties, and stereochemistry  Amino acids are chiral o Natural AAs are in L-form o  Hydrophobic Amino Acids: o Alanine (Ala or A) o Valine (Val or V) o Isoleucine (Ile or I) o Leucine (Leu or L) o Methionine (Met or M) o Phenylalanine (Phe or F) (aromatic) o Tyrosine (Tyr or Y) (aromatic) o Tryptophan (trp or W) (aromatic)  Hydrophilic Amino Acids o Basic  Lysine (Lys or K)  Arginine (Arg or R)  Histidine (His or H) o Acidic  Aspartate (Asp or D)  Glutamate (Glu or E) o Uncharged  Serine (Ser or S)  Asparagine (Asn or N)  Threonine (Thr or T)  Glutamine (Gln or Q)  Special o Cysteine (Cys or C)  Form disulfide bonds that can be reduced via DTT or B-ME o Glycine (Gly or G) o Proline (Pro or P)  Can be cis in extended chains  Isomerization is rate-limiting in protein folding  Catalyzed by Peptidyl Prolyl cis-trans Isomerases (PPIs) 3. Know the approximate pKa’s of side chains and how they are affected by their environment 4. Learn about the mechanism of Aspartyl proteases, and how pKa modulation is important for their mechanism • Dielectric constant o Decrease in dielectric constant increases the electrostatic attraction between acetate ion and proton o This increases the pKa • Hydrogen bonding o Formation of hydrogen bonds increases the pKas of acidic groups • Temperature Proteins can alter the pKa of side chains in two main ways • If a side chain is in a hydrophobic environment, it will prefer to be uncharged o  increases pKa of acidic side chains (a lower proton concentration is required to protonate them) o  decreases pKa of basic side chains • Acidic side chain next to charged groups o Putting an acidic side chain close to a positively charged group will make it prefer to be deprotonated  lower pKa o Putting an acidic side chain close to a negatively charged group will make it prefer to be protonated  higher pKa • Aspartyl Proteases o Family of proteases with broad specificity – two types  Pepsin type protease with acidic optimum pH  Retroviral proteases o Active site has two conserved aspartate residues that use an acid base mechanism  One Asp activates a coordinated water molecule that then attacks the carbonyl bond to break the peptide bond o o Pepsin type  The low pH of these enzymes is because 50% of the catalytic Asps need to be protonated  The two catalytic Asps are not equivalent, and their pKas are modulated by neighboring side chains  o HIV-1 Protease  Dimeric with one catalytic Asp on each monomer  Optimal pH around 7  Movement of the flaps are correlated with structural reorganization of the catalytic Asps


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