chapter 3: amino acids, peptides, proteins

Chapter 3: Amino Acids, Peptides, ProteinsHLY-JU-JS-CD

Amino Acids (AA) are the building blocks of peptides and proteinsPeptides generally contain 2-10

AAPolypeptides contain 10-100 AAProteins contain >100 AAGeneral structure of AA:

at pH ~7.4:

L-Amino Acids are the biologically relevant enantiomer

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

Of the 20 common AA, 10 of them are considered essentialsee page 67 of your bookMnemonics: MILK FTW RHV“ESSENTIAL” = cannot be

produced de novo by the bodySome AA are conditionally

essentialNote 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 classesAliphatic (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 (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0

pK1: -COOH -COO- + H+ pK2: -NH3

+ -NH2 + H+

pKR: -RH -R- + H+

Isoelectric point (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0

AA net charge is (-) if pH > pI, and (+) if pH < pIpI is estimated to be the

AVERAGE of the two pK values representing neutral species.

AA net charge is (-) if pH > pI, and (+) if pH < pICASE I: ONLY TWO IONIZABLE

GROUPS:Ex. Alanine:

AA net charge is (-) if pH > pI, and (+) if pH < pICase II: MORE THAN TWO

IONIZABLE GROUPS.Ex. Aspartic Acid

Activity, open book/notes BUT no talking (20 points)1. Determine the pI of Lysine.

Show ALL conformations and the net charges at different pH’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 pK1, at pK1, after pK1 but before pK2, etc.)

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 H2O)

AA can link together via AMIDE BOND to form peptidesVIDEO!

Peptides are cleaved via hydrolysisAcids, bases or enzymes can be

used to facilitate the hydrolysisIn 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 proteins1. Catalysts (Enzymes)

2. Transport & Storage

• The largest class of proteins, accelerate rates of reactions

DNA Polymerase

Hemoglobin

Catalase CK2 Kinase

OvalbuminSerum albumin Ion channels

There are six major classes of functions of proteins3. Structural

4. Generate MovementCollagen Keratin Silk Fibroin

Actin Myosin

There are six major classes of functions of proteins5. Regulation of Metabolism and Gene

Expression

6. Protection

Insulin Lac repressor

Immunoglobulin Thrombin and Fibrinogen

Venom Proteins

Proteins have four levels of structure