Proteins and amino acids

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 Proteins
Proteins are essential biomolecules that perform a wide variety of functions within living
organisms.
The functions of proteins.
1. Structural Support: Proteins like collagen, keratin, and elastin provide structural
support to cells and tissues. Collagen, for example, is a major component of connective
tissues like skin, tendons, and bones.
2. Enzymatic Activity: All enzymes are proteins.
3. Transport: Proteins are involved in the transport of molecules across cell membranes
(e.g., ion channels and transporters) or within the body. Hemoglobin is an example,
transporting oxygen in the blood.
4. Immune Response: Antibodies are specialized proteins that recognize and neutralize
foreign invaders like bacteria, viruses, and toxins. They are a key component of the
immune system.
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 The functions of proteins.
5- Cell Signaling: Many proteins function in signal transduction pathways, helping cells
communicate with each other. Receptor proteins on cell surfaces bind to signaling
molecules (e.g., hormones) and initiate cellular responses.

6- Movement: Proteins such as actin and myosin are essential for muscle contraction
and movement. These proteins interact within muscle cells to produce contraction and
allow movement of the body.

7- Storage: Some proteins serve as storage molecules for important substances. For
example, ferritin stores iron, and casein in milk stores amino acids for the developing
infant.

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 The functions of proteins.
8- Gene Expression and Regulation: Certain proteins (e.g., transcription factors)
are involved in regulating the expression of genes, controlling which proteins are
made in the cell.
9- pH and Fluid Balance: Some proteins, like albumin in blood plasma, help
maintain the osmotic balance and regulate fluid distribution within tissues and the
blood.
10- Energy Source: Although not their primary role, proteins can be broken down
to provide energy when carbohydrates and fats are unavailable, though this is a last-
resort mechanism.

Overall , proteins are macromolecules, composed of amino acids as the basic units.

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 Structure of the Amino Acids

• Each amino acid (except proline) has a carboxyl group,

an amino group, a hydrogen atom and a distinctive
side chain (“R-group”) bonded to the α-carbon atom.

• At physiologic pH, all amino acids have a negatively

charged group (COO-) and a positively charged group
(NH3+), both attached to the α-carbon.
• Substances, such as amino acids, that can act either as
an acid or a base are defined as amphoteric.
• the nature of the side chains that ultimately dictates the
role an amino acid plays in a protein.

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Zwitterions
A zwitterion is a molecule that has both a positive and a negative charge, but the
overall charge of the molecule is neutral. This typically happens in molecules that
contain both acidic and basic functional groups, such as amino acids. The charges are
localized on different parts of the molecule, so the net charge is zero.

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 Classification of amino acids.
The 20 amino acids can be classified according to the
polarity of their side chains into:

1. Amino acids with nonpolar side chains

Alanine, Valine, Leucine, Isoleucine, Glycine, Proline,

Methionine, phenylalanine and Tryptophan.

Each of these amino acids has a nonpolar side chain that

does not bind or give of protons or participate in hydrogen
or ionic bonds. Proline differs from other amino acids in that
it contains an imino group, rather than an amino group.
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1. Amino acids with nonpolar side chains

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2. Amino acids with uncharged polar side chains
Serine, Threonine, Tyrosine, asparagine , glutamine and Cysteine
These amino acids have zero net charge at neutral pH. The side chain of cysteine contains a
sulfhydryl group (-SH), which is an important component of the active site of many
enzymes.

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3. Amino acids with acidic side chains

The amino acids aspartic acid ( Asp) and glutamic acid ( Glu) are proton donors.

At physiologic pH, the side chains of these amino acids are fully ionized, containing a
negatively charged carboxylate group (–COO-).

They are, therefore, called aspartate or glutamate.

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4- Amino acids with basic side chains

Arginine, Lysine, and Histidine. The side chains of the basic amino acids accept
protons. At physiologic pH the side chains of Lysine and Arginine are fully ionized and
positively charged. In contrast, histidine is weakly basic, and the free amino acid is
largely uncharged at physiologic pH.

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Abbreviations and symbols for
commonly occurring amino acids

Each amino acid name has an

associated three-letter abbreviation
and a one-letter symbol as shown in
the table .

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Nutritionally, amino acids are classified as
1- Essential amino acids
2- Non-essential amino acids
3- semi-essential amino acids.
1- Essential amino acids: These are not synthesized by the body and must be taken in
diet.They include valine, leucine, isoleucine, phenylalanine, threonine, tryptophan,
methionine and lysine.
2- Non-essential amino acids: They can be synthesized by the body and may not be the
requisite components of the diet such as Alanine, Glycine, Proiine
3- Semi-essential amino acids: These are growth promoting factors since they are not
synthesized in sufficient quantity during growth. They include arginine and histidine.
They become essential in growing children, pregnancy and lactating women.

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Optical properties of amino acids
Optical activity: the ability of substance to rotate the plan of the
polarized light to the left or to the right.
Any substance containing asymmetric carbon atom has optical
activity.
Asymmetric(chiral) carbon atom is the carbon atom which
bonded to 4 different chemical atoms or molecules.

Amino acids that have an asymmetric center at the α-carbon can

exist in two forms, designated D and L, that are mirror images of
each other. The two forms in each pair are termed stereoisomers

All amino acids found in proteins are of the L-configuration.

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Glycine is the exception because its α-carbon has two hydrogen substituents and,
therefore, is optically inactive.

The isoelectric point (PI) , is the pH at which an amino acid is electrically neutral- that is
where the sum of the positive charges equals the some of the negative charges.

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 Peptide bond
Amino acids are commonly joined together by an amide linkage, called a peptide bond.
The peptide bond is formed by a condensation reaction between two amino acids where
one loses a hydroxyl from its carboxyl group (-COOH), and the other loses a hydrogen
from its amino group (-NH2).

By convention, the free amino end of the peptide chain (N-terminal) is written to the left and
the free carboxyl end (C-terminal) to the right. Therefore, all amino acid sequences are read
from the N- to the C-terminal end of the peptide. Each component amino acid in a
polypeptide is called a “residue”.
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 Structure of proteins
Primary Structure of Proteins
• Primary structure is the linear sequence of amino acids by peptide bonds in a
protein molecule.
• The sequence is determined by the gene encoding the protein.
• The specific order of amino acids dictates how the protein will fold and ultimately
determine its function.
• Many genetic diseases result in proteins with abnormal amino acid sequences.

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The biologically important peptides.
1- Glutathione: protects cells from the destructive effects
of oxidation by reacting with peroxides.

2- Oxytocin : stimulates contraction of uterine muscles

during childbirth and the ejection of milk by mammary
glands during lactation.

3- Vasopressin: stimulates the kidneys to retain water.

4- Opioid peptides found in nervous tissue cells : they relieve pain and produce pleasant
sensations.

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Secondary structure, is the local folding of the polypeptide chain into regular structures,
mostly by hydrogen bonding.
Common secondary structures include Alpha-helix, and Beta-pleated sheet
1- Alpha-helix: A right-handed coil where the backbone's N-H group of one amino acid
forms a hydrogen bond with the C=O group of another amino acid four residues away.

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β-sheet
Beta-pleated sheet: A structure formed when
segments of the polypeptide chain lie side by side
and are held together by hydrogen bonds, creating a
sheet-like shape.
The chains may run in the same direction, forming a
parallel β-sheet or run in opposite directions ,
forming antiparallel β- structure.

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 Tertiary structure
• Tertiary structure is the three-dimensional shape of a
single polypeptide chain.

• It is essential for the protein's specific function.

• Tertiary structure is stabilized by various

interactions, such as: hydrogen bonds, ionic bonds,
hydrophobic interactions, and disulfide bonds.
The structure of myoglobin

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The ionic bonds , hydrophobic interactions, disulfide bonds, and hydrogen bonds contribute to tertiary structure.

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Quaternary structure
Quaternary structure is the structure of proteins
which are composed of two or more polypeptide
chains (subunits).

The responsible bonds are usually of the same types

of those involved in stabilizing tertiary structure.

Hemoglobin is a classic example, as it consists of

four polypeptide subunits that work together to bind The structure of hemoglobin

oxygen.

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 Proteins are classified according to their composition into three groups:
1. Simple proteins: on complete hydrolysis they yield only amino acids such as
albumin and globins.

2. Compound proteins: consist of protein part which called apoprotein and non
protein part which called prosthetic group such as; lipoproteins, glycoproteins,
phosphoproteins, nucleoproteins and chromoproteins.

3. Derived proteins: they are produced from simple and/ or compound proteins
either by hydrolysis, digestion or denaturation. Examples coagulate proteins,
metaproteins and peptides.

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 Classification of proteins
Proteins are also classified based-on shape:
1- Fibrous proteins such as collagen.
1. Globular proteins such as hemoglobin

Hemoglobin

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 Denaturation of proteins
• Protein denaturation refers to the process in which a protein loses its native,
functional three-dimensional structure due to various external factors.
• The denaturation process can disrupt the protein's biological function because its
specific shape is often essential for its activity.
Factors that Cause Denaturation
1-Heat: High temperatures cause break the weak bonds that maintain a protein's shape.
2- pH Changes.
3- Chemicals: chemicals, such as urea, detergents, or alcohol, can interfere with the
protein's structure by disrupting hydrophobic interactions and breaking bonds.
4- Salts: High salt concentrations can disrupt ionic bonds

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 Denaturation Effects

1. Loss of Function: Denatured proteins usually lose their ability to perform their
biological function, (e.g., enzymes losing their catalytic ability).
2. Irreversibility: Some proteins can refold back into their active shape when the
denaturing conditions are removed, but others may remain permanently denatured,
especially if their structure is irreversibly altered.

Differences between Denaturation and Degradation

Denaturation refers to the unfolding or alteration of a protein’s structure without
breaking its primary structure .
Degradation( hydrolysis) involves the breakdown of the protein’s primary structure
(peptide bonds are destroyed ), often leading to complete loss of the protein’s
function.

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