AMINO ACIDS AND PROTEINS, DENATURATION OF PROTEINS

Presentation on: Amino acids and proteins
Presented by: M Archana
1st year M.Tech
MDK1702
Dairy chemistry

1
A M I N O A C I D S A N D
P R O T E I N S
Proteins and Amino Acids
(Amino Acids as Acids and Bases)
Copyright © 2007 by Pearson Education, Inc.
Publishing as Benjamin Cummings

ProteinDiversity
Proteins are molecular tools
They are a diverse and complex group of
macromolecules
From McKeeandMcKee, Biochemistry, 5th Edition, ©2011by Oxford UniversityPress
Proteins

4
Functions of Proteins
 Proteins perform many different functions in the body.
TABLE 19.1

6
Amino Acids
Amino acids





Are the building blocks of proteins.
There are 20 standard amino acids
Contain a carboxylic acid group and an amino group
on the alpha () carbon.
Are ionized in solution.
Each contain a different side group (R).
R
+ │
R
│
H2N—C —COOH
│
H
H3N—C —COO−
│
H
ionized form

7
Examples of AminoAcids
H
+ │
H3N—C—COO−
│
H glycine
CH3
+ │
H3N—C—COO−
│
H alanine

8
Types of AminoAcids
Amino acids are classified as




Nonpolar (hydrophobic)
with hydrocarbon side
chains.
Polar (hydrophilic) with
polar or ionic side chains.
Acidic (hydrophilic) with
acidic side chains.
Basic (hydrophilic) with
–NH2 side chains.
Nonpolar Polar
Acidic Basic

9
Amino Acids Classification Table

10
Nonpolar AminoAcids
A nonpolar amino acid has
 An R group that is H, an alkyl group, or aromatic.

Polar AminoAcids
A polar amino acid has
 An R group that is an alcohol, thiol, or amide.
12

Acidic and Basic AminoAcids
An amino acid is


Acidic with a carboxyl R group (COO−).
Basic with an amino R group (NH3
+).
Basic Amino Acids
13
D E

15
Optical Activity
Amino acids
 Are chiral except for glycine.
 Have Fischer projections that are stereoisomers.
 That are L are used in proteins.
L-alanine D-cysteine
CH2SH
H2N H
COOH
CH2SH
H NH2
COOH
CH3
H NH2
COOH
CH3
H2N H
COOH
D-alanine L-cysteine
Fischer Projections of Amino Acids

16
•
•
• Amino acids are amphoteric molecules have both basic
and acidic group
• Zwitterions (dipolar molecules), have charged —NH3
+
and COO- groups.
Forms when both the —NH2 and the —COOH groups
in an amino acid ionize in water.
Has equal + and − charges at the isoelectric point (pI).
+
O
║
O
║
NH2—CH2—C—OH
Glycine
H3N—CH2—C—O–
Zwitterion of glycine
Amphoteric Properties
Zwitterions and Isoelectric Points

 At physiological pH (7.4), a zwitterion forms



Both + and – charges
Overall neutral
Amphoteric


Amino group is protonated
Carboxyl group is deprotonated


Soluble in polar solvents due to ionic character
Structure of R also influence solubility
Zwitterions

In solutions more basic than the pI,
 The —NH3
+in the amino acid donates a proton.
OH–
+
H3N—CH2—COO–
Zwitterion
at pI
Charge: 0
H2N—CH2—COO–
Negative ion
pH > pI
Charge: 1−
Amino Acids asAcids
17

In solutions more acidic than the pI,
 The COO−in the amino acid accepts a proton.
+
H+
+
H3N—CH2—COO– H3N—CH2—COOH
Zwitterion
at pI
Charge: 0
Positive ion
pH< pI
Charge: 1+
Amino Acids as Bases
18

pH and Ionization
H+
OH−
+
H3N–CH2–COOH
+
H3N–CH2–COO–
H2N–CH2–COO–
positive ion zwitterion negative ion
(at low pH) (at pI) (at high pH)
19

AA have multiple pKa’s due to multiple ionizable groups
Acid-base Properties
pK1 ~ 2.2
(protonated below 2.2)
pK2 ~ 9.4
(NH3
+ below 9.4)
pKR
(when applicable)

Table 3-1
Note 3-letter and
1-letter
abbreviations
Amino acid organization chart

Electrophoresis: Separation of
22
AminoAcids
In electrophoresis, an electric current is used to separate
a mixture of amino acids, and




The positively charged amino acids move toward the
negative electrode.
The negatively charged amino acids move toward the
positive electrode.
An amino acid at its pI does not migrate.
The amino acids are identified as separate bands on
the filter paper or thinlayer plate.

Electrophoresis
With an electric current, a mixture of lysine, aspartate,
and valine are separated.
23

Essential amino acids




Must be obtained
from the diet.
Are the ten amino
acids not
synthesized by the
body.
Are in meat and
diary products.
Are missing (one or
more) in grains and
vegetables.
Essential AminoAcids
TABLE 19.3
24
Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Amino Acids and Proteins
Formation of Peptides
Copyright © 2007 by Pearson Education, Inc
25

30
The Peptide Bond
A peptide bond


Is an amide bond.
Forms between the carboxyl group of one amino acid
and the amino group of the next amino acid.
+
O
||
CH3 O
+ | ||
H3N—CH2—C—O– + H3N—CH—C—O–
O H CH3 O
|| | | ||+
H3N—CH2—C—N—CH—C—O– + H2O
peptide bond

Formation of ADipeptide
27

Naming Dipeptides
A dipeptide is named with


A yl ending for the Nterminal amino acid.
The full amino acid name of the free carboxyl group
(COO) at the Cterminal end.
28

Protein Structure: Primary and
Secondary Levels
29

ProteinDiversity
From McKeeandMcKee, Biochemistry, 5th Edition, ©2011by Oxford UniversityPress
Proteins

Primary Structure of Proteins
The primary structure of a protein is


The particular sequence of amino acids.
The backbone of a peptide chain or protein.
Ala─Leu─Cys─Met
O-
31
CH3
CH3 S
CH CH3 SH CH2
CH3 O CH O CH2 O CH2 O
H3N CH C N CH C N CH C N CH C
H H H

Primary Structures
The nanopeptides oxytocin and vasopressin


Have similar primary structures.
Differ only in the amino acids at positions 3 and 8.
32

45
Primary Structure
of Insulin
Insulin



Was the first protein to
have its primary structure
determined.
Has a primary structure of
two polypeptide chains
linked by disulfide bonds.
Has a chain A with 21
amino acids and a chain B
with 30 amino acids.

46
Secondary Structure – Alpha Helix
The secondary structures of proteins indicate the
three-dimensional spatial arrangements of the
polypeptide chains.
An alpha helix has


A coiled shape held in place by hydrogen bonds
between the amide groups and the carbonyl
groups of the amino acids along the chain.
Hydrogen bonds between the H of a –N-H group
and the O of C=O of the fourth amino acid down
the chain.

47
Secondary Structure – Alpha Helix

Secondary Structure – Beta
36
Pleated Sheet
A beta-pleated sheet is a secondary structure that




Consists of polypeptide chains arranged side by
side.
Has hydrogen bonds between chains.
Has R groups above and below the sheet.
Is typical of fibrous proteins such as silk.

Secondary Structure: β-Pleated
Sheet
37

Secondary Structure: Triple Helix
A triple helix



Consists of three alpha
helix chains woven
together.
Contains large amounts
glycine, proline, hydroxy
proline, and
hydroxylysine that contain
–OH groups for
hydrogen bonding.
Is found in collagen,
connective tissue, skin,
tendons, and cartilage.
50

Protein Structure: Tertiary and
Quaternary Levels
39

The tertiary structure of a protein
 Gives a specific three dimensional shape to the
polypeptide chain.
 Involves interactions and cross links between
different parts of the peptide chain.
 Is stabilized by
Hydrophobic and hydrophilic interactions.
Salt bridges.
Hydrogen bonds.
Disulfide bonds.
40
Tertiary Structure

Tertiary Structure
 The interactions
of the R groups
give a protein its
specific three-
dimensional
tertiary
structure.
41

Tertiary Structure
TABLE 19.5
42

57
Globular Proteins
Globular proteins



Have compact,
spherical shapes.
Carry out synthesis,
transport, and
metabolism in the
cells.
Such as myoglobin
store and transport
oxygen in muscle.
Myoglobin

58
Fibrous Proteins
Fibrous proteins



Consist of long, fiber-like shapes.
Such as alpha keratins make up hair, wool, skin,
and nails.
Such as feathers contain beta keratins with large
amounts of beta-pleated sheet structures.

Quaternary Structure
The quaternary structure



Is the combination of two or
more tertiary units.
Is stabilized by the same
interactions found in tertiary
structures.
Of hemoglobin consists of two
alpha chains and two beta
chains. The heme group in
each subunit picks up oxygen
for transport in the blood to the
tissues.
45
hemoglobin

Summary of Protein Structure
46

63
Summary of Protein Structures

Protein Hydrolysis and Denaturation
48

Protein hydrolysis
 Splits the peptide bonds to give smaller peptides
and amino acids.
 Occurs in the digestion of proteins.
 Occurs in cells when amino acids are needed to
synthesize new proteins and repair tissues.
49
Protein Hydrolysis

Hydrolysis of a Dipeptide


+
H2O, H
+
CH3 O
H3N CH COH
heat,
+
In the lab, the hydrolysis of a peptide requires acid or
base, water and heat.
In the body, enzymes catalyze the hydrolysis of
proteins.
OH
+ CH3 O CH2 O
H3N CH C N CH C OH
H OH
+
CH2 O
H3N CH C OH
50

Denaturation involves
 The disruption of bonds in the secondary, tertiary
and quaternary protein structures.
 Heat and organic compounds that break apart H
bonds and disrupt hydrophobic interactions.
 Acids and bases that break H bonds between polar
R groups and disrupt ionic bonds.
 Heavy metal ions that react with S-S bonds to form
solids.
 Agitation such as whipping that stretches peptide
chains until bonds break.
51
Denaturation

Denaturation of protein occurs
when




An egg is cooked.
The skin is wiped with
alcohol.
Heat is used to cauterize
blood vessels.
Instruments are sterilized in
autoclaves.
Applications of Denaturation
52

•
•
•
Ribonuclease is a small protein that
contains 8 cysteins linked via four
disulfide bonds
Urea in the presence of 2-
mercaptoethanol fully denatures
ribonuclease
When urea and 2-mercaptoethanol
are removed, the protein
spontaneously refolds, and the
correct disulfide bonds are reformed
•
•
The sequence alone determines the
native conformation
Quite “simple” experiment, but so
important it earned Chris Anfinsen
Ribonuclease
Refolding
Experiment

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