Chapter 3 Amino Acids Peptides Proteins HLYJUJSCD Amino

Chapter 3: Amino Acids, Peptides, Proteins HLY-JU-JS-CD

Amino Acids (AA) are the building blocks of peptides and proteins Peptides generally contain 2 -10 AA Polypeptides contain 10 -100 AA Proteins contain >100 AA General structure of AA: at p. H ~7. 4:

L-Amino Acids are the biologically relevant enantiomer

Of the 20 common AA, 10 of them are considered essential see page 67 of your book

Of the 20 common AA, 10 of them are considered essential see page 67 of your book Mnemonics: MILK FTW RHV “ESSENTIAL” = cannot be produced de novo by the body Some AA are conditionally essential Note though that there are now more than 20 AA! (but we will only focus on the 20)

Selenocysteine is a derivative of Cys used to derive protein structures

The 20 AA can be grouped according to functional classes Aliphatic (GAVLIMP) Aromatic (WYF) Polar, uncharged (CHNQST) Polar, charged – acidic (DE) Polar, charged – basic (RK) *Histidine is basic but uncharged See structures on page 70 of your book.

There are 7 AA With Aliphatic Side Chains

Pro is an aliphatic AA with the amino and the acid group in one 5 -membered ring

There are 3 AA with Aromatic Side Chains

Of the 6 polar uncharged AA, 2 have Hydroxyl Side Chains (except Tyr)

One AA has a Sulfhydryl (-SH) Side Chain

There are 3 AA With Basic Side Chains, 2 of them ccharged (RK)

Two AA have acidic side chains (DE). Their amide counterparts (NQ) are polar, uncharged

Chemical reactivity of AA are dependent on their “R group” AA structures and reactivity will be important in understanding protein structures and functions AA electric charges also affects protein structure and function

Isoelectric point (p. I) of an AA (or peptide/protein) is equal to the p. H when net charge = 0

Isoelectric point (p. I) of an AA (or peptide/protein) is equal to the p. H when net charge = 0 p. K 1: -COOH -COO- + H+ p. K 2: -NH 3+ -NH 2 + H+ p. KR: -RH -R- + H+

AA net charge is (-) if p. H > p. I, and (+) if p. H < p. I is estimated to be the AVERAGE of the two p. K values representing neutral species.

AA net charge is (-) if p. H > p. I, and (+) if p. H < p. I CASE I: ONLY TWO IONIZABLE GROUPS: Ex. Alanine:

AA net charge is (-) if p. H > p. I, and (+) if p. H < p. I Case II: MORE THAN TWO IONIZABLE GROUPS. Ex. Aspartic Acid

Activity, open book/notes BUT no talking (20 points) Determine the p. I of Lysine. Show ALL conformations and the net charges at different p. H’s. 2. Draw the titration curve for Lysine. 3. Determine the inflection points, and draw the structure/s of Lysine at each interval (i. e. , before p. K 1, at p. K 1, after p. K 1 but before p. K 2, etc. ) 1.

AA can link together via AMIDE BOND to form peptides • Two ends are form: amino or N terminus and carboxyl or C terminus • Peptide formation is a condensation reaction (loss of H 2 O)

AA can link together via AMIDE BOND to form peptides VIDEO!

Peptides are cleaved via hydrolysis Acids, bases or enzymes can be used to facilitate the hydrolysis In our stomach or intestine, peptidases or proteases are present Enzymes specific to some AA are used for protein analysis (more of this later )

Proteins in our body play different important roles Biological functions of proteins depend on the AA sequence (central dogma!) Six major classes of protein functions: ◦ Enzyme ◦ Transport and Storage Proteins ◦ Structural Proteins ◦ Muscle Contraction and Mobility Proteins ◦ Regulatory and Receptor Proteins ◦ Immune or Defense Proteins

There are six major classes of functions of proteins 1. Catalysts (Enzymes) • The largest class of proteins, accelerates of reactions DNA Polymerase 2. CK 2 Kinase Catalase Transport & Storage Hemoglobin Serum albumin Ion channels Ovalbumin

There are six major classes of functions of proteins 3. Structural Collagen 4. Keratin Silk Fibroin Generate Movement Actin Myosin

There are six major classes of functions of proteins 5. Regulation of Metabolism and Gene Expression Lac repressor Insulin 6. Protection Immunoglobulin Thrombin and Fibrinogen Venom Proteins

Proteins have four levels of structure