Charge: -1
Charge: +1
Pka=2
H
2
OH-
Pka=10
OH-
Charge: 0 (When aa have a net charged of zero
its called a Zwitterion)
PH=1
Low PH
PH=7
Adding a base
PH=12
High PH
9.60
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
2.34
X
9.60
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
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?
Pka: 2.19
Pka: 6.97
1. PH
2. 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).
1. PH< PK1 (All Protonated)
2. PH> PK1 COOH COO3. PH> PKR COOHR COO4. PH>PK2 H3N+ H2N
X
Pka: 4.25
X
Write equations for the dissociation of aspartate and calculate its pI.
Pka: 9.8
Pka: 2.1
Pka: 3.9
pH = 3.0
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=6
H+
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!
Protein Structure
 Peptide: A short chain of amino acids.
 Polypeptides: A long chain of amino acids.
 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 bond
Primary
Assembly
Secondary
Folding
Tertiary
Packing
Quaternary
Interaction
PROCESS
STRUCTURE
Protein Structure: The different levels…………….
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
-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.
R groups are not involved in forming peptide bonds!
Primary
Assembly
Secondary
Folding
Tertiary
Packing
Quaternary
Interaction
PROCESS
STRUCTURE
Protein Structure: The different levels…………….
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-sheet
• β-strands connected by hydrogen bond to form a βsheet.
• Less common than α-helix
Types of β-sheet