H

OH-

OH-

2

Charge: +1

Charge: 0 (When aa have a net charged of zero its called a Zwitterion)

Charge: -1

Low PH High PHAdding a base

PH=1 PH=7PH=12

Pka=10

Pka=2

PH/ increasing OH

Pka (Low will lose first)

Pka1 (for carboxyl H 2.34),

Pka2 (for amino group H 9.60) PI is PH when aa is neutral

PI (isoelectric point)= (Pka1+PKa2)/2

X X9.60

2.34

1. pH < pKaC Almost all monopositive form Avg. net charge +1

2. pH = pKaC Half monopositive, half isoelectric Avg. net charge = +0.5

3. pH = 1/2(pKaC + pKaN) All isoelectric form Avg. net charge = 0

4. pH = pKaN Half isoelectric, half mononegative Avg. net charge = -0.5

5. pH > pKaN Almost all mononegative Avg. net charge -1

9.60

2.34

Calculate the pI of methionine.

Methionine has Ka values pKaC = 2.1 and pKaN = 9.3.

pI = 1/2(pKaC + pKaN)

pI = 1/2(2.1 + 9.3)

pI = 5.7

WHAT ABOUT THE R Groups?

1. PH2. Pka (Low will lose first)3. Pk1 (for carboxyl H 2.19), Pk2 (for amino group H 9.67),

PKR (for R group H 4.25).

4. PH< PK1 (All Protonated)

5. PH> PK1 COOH COO-

6. PH> PKR COOHR COO-

4. PH>PK2 H3N+ H2N

X X

Pka: 2.19

Pka: 6.97

Pka: 4.25

Write equations for the dissociation of aspartate and calculate its pI.

A zwitterion is a molecule with both positive and negative charges, but with a net charge of zero.

The isoelectric form is found after the first dissociation, between pKaC and pKaR

pI = 1/2(pKaC + pKaR)

pI = 1/2(2.1 + 3.9)

pI = 3.0

•If the pH is less than the pI, the amino acid will have a net positive charge.

•If the pH is greater than the pI, the amino acid will have a net negative charge.

•If the pH equals the pI, the amino acid will have no net charge (this is the definition of pI.)

Pka: 2.1

Pka: 3.9

Pka: 9.8

pH = 3.0

H+

Histidine: side chain can be a proton donor and a proton acceptor

Histidine: weakly basic, but uncharged at physiological PH (7.4)

PH> Pka , Lose the proton!

H+

Pka=6

Protein Structure

Protein: A protein is a biological polymer of amino acids bonded together by peptide bonds between the carboxyl (-COOH) and amino (-NH2) groups of adjacent amino acid residues and folds into a defined three dimensional structure.

Peptide: A short chain of amino acids.

Polypeptides: A long chain of amino acids.

peptide bond

Protein Structure: The different levels…………….

Primary

Secondary

Tertiary

Quaternary

Assembly

Folding

Packing

Interaction

S T

R U

C T

U R

E P R O C E S S

The Primary Structure: Amino acids joined by peptide bonds!

Defining the primary structure of a protein

The primary structure of a designated protein is the

amino acid sequence of the protein!

Chemistry of peptide bond formation

R groups are not involved in forming peptide bonds!

-α-carboxyl of one amino acid is joined to α -amino of a second amino acid (with removal of water).

-Peptide bond has a partial double bond character.

- It is a rigid bond that is shorter than a single bond.

Protein Structure: The different levels…………….

Primary

Secondary

Tertiary

Quaternary

Assembly

Folding

Packing

Interaction

S T

R U

C T

U R

E P R O C E S S

Defining the secondary structure of a protein

local sub-structures in a polypeptide chain

predominantly formed by the participation of hydrogen-bond

Understanding the H-bond

A hydrogen bond is the interaction of a hydrogen atom with an electronegative atom. Ex: nitrogen, oxygen etc.

α-Helix α-helix is a right-handed spiral conformation

Every N-H group of the amino group forms a hydrogen bond with the C=O group of the carboxylic acid group of an amino acid four residues earlier

• Short peptides do not form α-helix

• The side chains of the amino acids face outward!

• Formed by the same groups that are involved in the formation of peptide bond (Amino group and carboxylic acid group)!.

peptide bond

• Some amino acids can disrupt the α-helix structure:

-Proline: Insert a Kink in the chain.

- Large numbers of charge amino acids (Glutamate, aspartate, histadine, Lysine and arginine) can also disrupt the helix by forming ionic bonds!

Keratin………………..• Keratin structure is nearly entirely α-Helical

• Major component of tissue Such as hair and skin.

• β-strands connected by hydrogen bond to form a β-sheet.

• Less common than α-helix

β-sheet

Types of β-sheet