V. Amino Acids and Proteins

17/10/2022
V. AMINO ACIDS
and PROTEINS
J e ssebel V . G a d o t, R C h .
Outline
I. Chemistry of Amino Acids
II. Classification of Amino Acids
III. Properties of Amino Acids
IV.Polypeptides
V. Protein Structure & Function
VI.Enzymes and Kinetics
JPVGADOT OCTOBER 2022
JPVGadot 1
17/10/2022

Amino Acids – are the building blocks for proteins
- Nearly all proteins studied are made from the twenty “standard” amino
acids.
- All of the standard amino acids are amino acids (except for proline, an imino
acid).
- At neutral pH (pH =7) both the acid and amine groups will be ionized to give
the so-called zwitterion form.
- There is no pH at which the amino acid structure will have no ionized groups.

Amino Acids – are the building blocks of proteins
- They have the structure of:
- Amino acids (in general) are chiral except glycine

- Only the L form is found in proteins, although the D form of alanine is an
important component of bacterial cell walls.
JPVGadot 2
17/10/2022
Amino Acids
20 Amino Acids
& Its Chemical Properties
1. The hydrophobic amino acids are:
◦ A. Aliphatic
◦ i. glycine (Gly, G) iv. Isoleucine (lIe, I),
◦ ii. alanine (Ala, A), v. Valine (Val, V)
◦ iii. leucine (Leu, L),
JPVGadot 3
17/10/2022
20 Amino Acids
◦ B. Sulfur-containing:
◦ i. Methione (Met, M)
◦ C. Aromatic
◦ i. phenylalanine (Phe, F),
◦ ii. tryptophan (Trp, W).
20 Amino Acids
◦ D. Cyclic imine:
◦ i. Proline (Pro, P)
Proline has an unusual imine ring structure (a secondary

amine), where the terminal amine group is actually
incorporated into the side chain.
This causes changes to the secondary structure of a protein.
Hydrophobic residues are often found in membrane bound

proteins, and the aromatic ones contribute to protein
absorbance at 280 nm, which is an important method of
protein quantification.
JPVGadot 4
17/10/2022
20 Amino Acids
1. The polar amino acids are:
◦ A. Alcohols
◦ i. threonine (Thr, T),

◦ ii. serine (Ser, S).
20 Amino Acids
1. The polar amino acids are:
◦ B. Amides
◦ i. asparagine (Asn, N),

◦ ii. glutamine (GIn, Q).
JPVGadot 5
17/10/2022
20 Amino Acids
3. Basic Amino acids are those that can accept protons.
◦ A. Imidazole: Histidine (His, H)

◦ B. Amine: Lysine (Lys, K)
◦ C. Guanidinium: Arginine (Arg, R)
20 Amino Acids
3. Acidic Amino acids are carboxylic acids, plus an thiol (cysteine)
and a phenol (tyrosine) with dissociable S-H or O-H groups:
◦ A. Aspartic Acid (Asp, D)

◦ B. Glutamic Acid (Glu, E)
◦ C. Cysteine (Cys, C)
◦ D. Phenol: Tyrosine (Tyr, Y)
JPVGadot 6
17/10/2022
20 Amino Acids
3. Acidic Amino acids
◦ B. Glutamic Acid (Glu, E)
◦ -The sodium salt of glutamic acid is the flavour enhancer
MSG.
◦ C. Cysteine (Cys, C)
◦ -is capable of forming a dimer:
◦ Cys-SH + Cys-SH = Cys-S-S-Cys.
◦ -These disulphide bridges (confusingly known as cystine), are
responsible for a lot of protein tertiary structures.
Other Amino Acids

In addition to the amino acids found in proteins, the cell also
contains a number of other amino acids that are not normally found in
peptides.
1. Ornithine – an important intermediate in the urea cycle,
2. Selenocysteine - a very rare component of some proteins and
3. Homocysteine - an important intermediate in sulphur metabolism.
JPVGadot 7
17/10/2022
Other Amino Acids

Phosphorylated Amino Acids
- amino acids in proteins are .modified after translation to
incorporate phosphate groups by kinase enzymes;
- A common strategy for protein regulation
Other Amino Acids

Methylated Amino Acids
- The histone proteins, which regulate DNA packaging in the
nucleus are themselves regulated by methylation of their arginine
and lysine residues, and the characteristic triple helical structure of
collagen is caused by its possession of many glycine and
hydroxyproline (a post-translational modification of proline) residues.
JPVGadot 8
17/10/2022
JPVGadot 9
17/10/2022

The protein amino acids are classified according to the chemical
nature of their R groups as aliphatic, aromatic, heterocyclic and sulfur
containing amino acids.
More meaningful classification of amino acids is based on the polarity

of the R groups. The polarity of the R groups varies widely from totally
non-polar to highly polar. The 20 amino acids are classified into four
main classes.
1. Non-polar or hydrophobic, aliphatic R Groups

2. Non-polar aromatic R Groups
3. Polar Uncharged R Groups
4. Charged R Groups
JPVGadot 10
17/10/2022

Nonpolar Nonpolar Polar Charged
Aliphatic Aromatic Uncharged
Glycine Phenylalanine Serine Acidic Basic
Alanine Tyrosine Threonine Aspartic Acid Lysine
Valine Tryptophan Cysteine Glutamic Acid Arginine
Leucine Methionine Histidine
Isoleucine Asparagine
Proline Glutamine

Essential Amino Acids
- The other amino acids, which are needed for normal functioning of
the body but cannot be synthesized from metabolic intermediates.
-These must be obtained from the diet and a deficiency in anyone of
the amino acids prevents growth and may even cause death.
1. Methionine, 6. Leucine,
2. Threonine, 7. Phenylalanine
3. Tryptophan, 8. Lysine are the
4. Valine, 9. Histidine and
5. Isoleucine, 10. Arginine
JPVGadot 11
17/10/2022
II. Properties of Amino Acids

A. Physical Properties
1. Amino acids are white crystalline substances.
2. Most of them are soluble in water and insoluble in non-polar organic
solvents.
3. Aliphatic and aromatic amino acids particularly those having several carbon
atoms have limited solubility in water but readily soluble in polar organic
solvents.
4. They have high melting points varying from 200-300 degC or even more.
5. They are tasteless, sweet or bitter. Some are having good flavor.
6. Amphoteric nature of amino acids as they contain both acidic (COOH) and
basic (NH2) groups. The amino acids possessing both positive and negative
charges are called zwitterions.
7. Isomerism - All amino acids except proline, found in protein are a-amino
acids because NH2 group is attached to the a-carbon atom, which is next to
the COOH group.
II. Properties of Amino Acids

B. Chemical Properties
1. Reaction with formaldehyde (Formal titration) to find out the
amount of total free amino acids in plant samples.
2. Reaction with nitrous acid to liberate nitrogen gas
3. Reaction with oxidant, ninhydrin produce a purple colored
compound known as Ruhemann's purple which is used in the
quantitative determination of amino acids.
4. Decarboxylation such as production of the vasoconstrictor agent,
histamine is produced from histidine.
JPVGadot 12
17/10/2022
IV. Polypeptides
Amino acids are linked together by formation of covalent bonds.
The covalent bond is formed between the a-carboxyl group of one
amino acid and the a-amino group of the next amino acid.
The bond is called as a peptide bond and the compound formed is a
peptide.
V. Protein Structure & Function

A. Classification of Protein
1. Solubility and composition.
2. Function.
3. Size & Shape.
JPVGadot 13
17/10/2022
A. Based on Solubility and

Composition
Proteins are again divided into three main groups as:
1. Simple Proteins
- Simple proteins yield on hydrolysis, only amino acids. These
proteins are further classified based on their solubility in different solvents
as well as their heat coagulability.
2. Conjugated or Compound Proteins
- These are simple proteins combined with some non-protein
substances known as prosthetic groups. The nature of the non-protein or
prosthetic groups is the basis for the sub classification of conjugated
proteins.
3. Derived proteins
- These are proteins derived by partial to complete hydrolysis from
the simple or conjugated proteins by the action of acids, alkalies or enzymes.
They include two types of derivatives, primary-derived proteins and
secondary-derived proteins.
1. Simple Proteins
Compound Description and Functions
1. Albumin Albumins are readily soluble in water, dilute acids and alkalies
and coagulated by heat. Seed proteins contain albumin in lesser
quantities. Example - Serum albumin and ovalbumin (egg white).
2. Globulin Globulins are insoluble or sparingly soluble in water, but their
solubility is greatly increased by the addition of neutral salts such
as sodium chloride. Example -Serum globulin, Fibrinogen,
Myosin of muscle and Globulins of pulses.
3. Prolamin Prolamins are insoluble in water but soluble in 70-80% aqueous
alcohol. They are deficient in lysine. Example - Gliadin of wheat
and Zein of corn.
4. Glutelin Glutelins are insoluble in water and absolute alcohol but soluble
in dilute alkalies and acids. They are plant proteins. Example -
Glutenin of wheat.
JPVGadot 14
17/10/2022
1. Simple Proteins
5. Histone Histones are small and stable basic proteins and contain fairly large
amounts of basic amino acid, histidine. They are soluble in water, but
insoluble in ammonium hydroxide. They occur in globin of
haemoglobin and nucleoproteins.
6. Protamine Protamines are the simplest of the proteins. They are soluble in water
and are not coagulated by heat. Protamines are found in association
with nucleic acid in the sperm cells of certain fish.
7. Albuminoids They are highly resistant to proteolytic enzymes. They

are fibrous in nature and form most of the supporting structures of
animals. They occur as chief constituent of exoskeleton structure such
as hair, horn and nails.
2. Compound Proteins
1. Nucleoproteins Nucleoproteins are simple basic proteins (protamines or

his tones) in salt combination with nucleic acids as the
prosthetic group. They are the important constituents of
nuclei and chromatin.
2. Mucoproteins These proteins are composed of simple proteins in

combination with carbohydrates like
mucopolysaccharides, which include hyaluronic acid and
chondroitin sulphates.
3. Chromoproteins These are proteins containing coloured prosthetic groups
e.g., haemoglobin, flavoprotein and cytochrome.
JPVGadot 15
17/10/2022
2. Compound Proteins
4. Lipoproteins These are proteins conjugated with lipids such as neutral fat,
phospholipids and cholesterol.
5. These are metal-binding proteins. A B-globulin, termed

Metalloproteins transferrin is capable of combining with iron, copper and
zinc. This protein constitutes approximately 3 % of the total
plasma protein. Another example is ceruloplasmin, which
contains copper.
6. These are proteins containing phosphoric acid. Phosphoric
Phosphoproteins acid is linked to the hydroxyl group of certain amino acids like
serine in the protein, Example- casein of milk.
3. Derived Proteins
1. Primary a. Proteans Proteans are insoluble products formed by the

Derived action of water, dilute acids and enzymes.
Example - myosan from myosin, fibrin from
fibrinogen.
b. These are formed by the action of acids and

Metaproteins alkalies upon protein. They are
insoluble in neutral solvents.
c. Coagulated Coagulated proteins are insoluble products

Proteins formed by the action of heat or alcohol on
natural proteins. Example - cooked meat and
cooked albumin.
JPVGadot 16
17/10/2022
3. Derived Proteins
Compound Description Grouped According to average MW
and
Functions
2. These a. Proteoses - are hydrolytic
Secondary proteins are products of proteins, which are soluble in water and
Derived formed in are not coagulated by heat.
the
progressive b. Peptones - are hydrolytic products, which have
hydrolytic simpler structure than proteoses. They are soluble in
cleavage of water and are not coagulated by heat.
the peptide
bonds of
protein c. Peptides –are composed of relatively few amino
molecule. acids. They are water-soluble and not
coagulated by heat.
B. Based on Function
Proteins are again divided into 10 main groups as:
1. Catalytic Proteins - Enzymes

- The most striking characteristic feature of these proteins is their
ability to function within the living cells as biocatalysts. These biocatalysts are
called as enzymes. Enzymes represent the largest class. Nearly 2000 different
kinds of enzymes are known, each catalyzing a different kind of reaction. They
enhance the reaction rates a million fold.
2. Regulatory Proteins – Hormones
- These are polypeptides and small proteins found in relatively lower
concentrations in animal kingdom but play highly important regulatory role in
maintaining order in complex metabolic reactions. Example- growth hormone,
insulin etc.
3. Protective Proteins – Antibodies
- These proteins combine with foreign protein and other substances
and fight against certain diseases. Example immunoglobulin. These proteins are
produced in the spleen and lymphatic cells in response to foreign substances
called antigen.
JPVGadot 17
17/10/2022
4. Storage Proteins
- A major class of proteins which has the function of storing amino
acids as nutrients and as building blocks for the growing tissues. Storage
proteins are source of essential amino acids such as is globulins and
prolamins in cereals. But in rice the major storage protein is glutelins.
Albumin of egg and casein of milk are also storage proteins.
5. Transport Proteins
- Some proteins are capable of binding and transporting specific
types of molecules through blood. Haemoglobin is a conjugated protein
composed of colourless basic protein that transports oxygen through blood
to various tissues
6. Toxic Proteins
- Ricin present in castor bean is extremely toxic to higher animals in
very small amounts. Lectin, a toxic protein present commonly in legumes,
agglutinates red blood cells. A bacterial toxin causes cholera, which is a
protein. Snake venom is protein in nature.
7. Structural Proteins
- Examples of structural proteins are myosin of muscles, keratin of
skin and hair and collagen of connective tissue. Carbohydrates, fats, minerals
and other cellular components are organized around such structural proteins
8. Contractile Proteins
- Proteins like actin and myosin function as essential elements In
contractile system of skeletal muscle.
9. Secretary Proteins
- Fibroin is a protein secreted by spiders and silkworms to form
webs and cocoons.
10. Exotic Proteins
- Antarctic fishes live in -1.90C waters, well below the temperature
at which their blood is expected to freeze. These fishes are prevented from
freezing by antifreeze glycoproteins present in their body.
JPVGadot 18
17/10/2022
B. Based on Size and Shape

Proteins are again divided into 2 main groups as:
1. Globular
- are mostly water-soluble and fragile in nature. Example-
enzymes, hormones and antibodies.
2. Fibrous
- Fibrous proteins are tough and water-insoluble. They are used
to build a variety of materials that support and protect specific tissues.
Example-Skin, Hair, Fingernails and Keratin.
Conformation of Proteins
JPVGadot 19
17/10/2022
VI. Enzymes & Kinetics

Enzymes are the heart of Biochemistry.
Protein based catalysts.
Enormously effective catalysts: typically enhance rates by 10^6 to
10^12 fold.
Operate under mild conditions: 0 - 100 degC, 20 - 40 degC for most
organisms; and low pressures (atmospheric).
Very Specific: Generally catalyze reaction for a very restricted group of
molecules, sometimes for a single naturally occurring molecule of a
single chirality.
Characteristics of Enzymes
1. Enzymes being proteins exhibit all properties of proteins. They have their
specific isoelectric points at which they are least soluble.
2. They can be denatured by changes in pH and temperature.
3. Enzymes exhibit enormous catalytic power.
4. Enzymes are specific in the reaction catalyzed and in their choice of
substrates.
a. Absolute S -When enzymes catalyse only one particular reaction
they are said to exhibit absolute specificity. e.g., Urease acts only on urea.
b. Group S - Amylase hydrolyses the group of substances like starch,
dextrin and glycogen, which have the same type of glycosidic linkages (a. 1,4).
c. Optical S - Maltase catalyses the hydrolysis of alpha but not beta-
glycosides. (D or L-amino acids)
JPVGadot 20
17/10/2022
JPVGadot 21
17/10/2022
Factors Affecting Enzyme

Reaction
The factors that mainly influence any enzyme-catalysed reaction are:
1. Substrate concentration
2. Enzyme concentration
3. Temperature
4. pH
5. Inhibitors
Other factors such as state of enzyme (oxidation), time and activators

also affect enzyme-catalysed reaction to certain extent.
JPVGadot 22
17/10/2022
REFERENCES:
1. Gajera, H.P. (2008). Fundamentals of Bicohemistry A Textbook.
International Book Distributing
JPVGadot 23

V. Amino Acids and Proteins

Uploaded by

Document Information

Original Description:

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

V. Amino Acids and Proteins

Uploaded by

Copyright:

Available Formats

17/10/2022

JPVGADOT OCTOBER 2022

I. Chemistry of Amino Acids

JPVGADOT OCTOBER 2022

I. Chemistry of Amino Acids

- Amino acids (in general) are chiral except glycine

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

Proline has an unusual imine ring structure (a secondary

This causes changes to the secondary structure of a protein.

Hydrophobic residues are often found in membrane bound

JPVGADOT OCTOBER 2022

◦ i. threonine (Thr, T),

JPVGADOT OCTOBER 2022

◦ i. asparagine (Asn, N),

JPVGADOT OCTOBER 2022

◦ A. Imidazole: Histidine (His, H)

JPVGADOT OCTOBER 2022

◦ A. Aspartic Acid (Asp, D)

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

Other Amino Acids

JPVGADOT OCTOBER 2022

Other Amino Acids

JPVGADOT OCTOBER 2022

Other Amino Acids

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

II. Classification of Amino Acids

More meaningful classification of amino acids is based on the polarity

1. Non-polar or hydrophobic, aliphatic R Groups

JPVGADOT OCTOBER 2022

II. Classification of Amino Acids

JPVGADOT OCTOBER 2022

II. Classification of Amino Acids

JPVGADOT OCTOBER 2022

II. Properties of Amino Acids

JPVGADOT OCTOBER 2022

II. Properties of Amino Acids

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

V. Protein Structure & Function

JPVGADOT OCTOBER 2022

A. Based on Solubility and

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

7. Albuminoids They are highly resistant to proteolytic enzymes. They

JPVGADOT OCTOBER 2022

1. Nucleoproteins Nucleoproteins are simple basic proteins (protamines or

2. Mucoproteins These proteins are composed of simple proteins in

JPVGADOT OCTOBER 2022

5. These are metal-binding proteins. A B-globulin, termed

JPVGADOT OCTOBER 2022

1. Primary a. Proteans Proteans are insoluble products formed by the

b. These are formed by the action of acids and

c. Coagulated Coagulated proteins are insoluble products

JPVGADOT OCTOBER 2022

JPVGADOT OCTOBER 2022

1. Catalytic Proteins - Enzymes