Proteins-Biomolecules

Building Blocks- amino acid

I. Introduction

To a large extent, cells are made of protein, which constitutes more than half of their dry weight
Proteins are the most versatile class of molecules in living organisms. Amongst their functions are:
catalysis (enzymes), transport, storage (casein), contraction (muscles), protection (antibodies), attack
(toxins), hormones (insulin, growth hormone) and structure (collagen). All proteins contain C, H, N, O
some S, P, Fe, Zn, Cu.

Most of the chemical reactions of the cell are carried out by proteins. Proteins also are the
major structural components of most cells and tissues. Proteins are often called polypeptides in
reference to the fact that they are composed of amino acids held together by peptide bonds. Peptide
bonds actually are amide bonds which are formed by the condensation of the carboxyl groups and
amino groups of consecutive amino acids in the polymer chain. The so-called peptide backbone of a
protein is a monotonous, regularly repeating structure. Projecting out from the backbone are the R-
groups which are the side-chains of the amino acids.

The biomolecules such as proteins that are present in living organisms are carbon-based
compounds. Carbon is the third most abundant element in living organisms (relative abundance H > O >
C > N > P > S). The most common ions are Ca+2, K+ , Na+ , Mg+2, and Cl- . The properties of
biomolecules, such as shape and chemical reactivity, are best described by the discipline of organic
chemistry
 The major function of amino acids is to act as the building blocks of proteins.
Amino acids themselves can be used by the cell to produce energy and are the starting
point for making many nitrogen-containing compounds.

amino acids-Peptides-Polypeptides-Proteins

-Proteins are composed of series of polypeptides with forces

1. Covalent interactions- peptide bonds, amide bonds, ester bonds, disulfide bonds
2. Non-covalent – H-bonding
3. Hydrophobic interactions
4. Van der Waal’s force
 II. General Structure of amino acid

A. Formula

As the name implies, amino acids contain two functional groups, a carboxylic
acid group and an amino group. The common amino acids are α-amino acids where
both functional groups are attached to the same carbon atom.

Also attached to the central carbon are a hydrogen atom and an R group, which
is different in each amino acid.

The form above is called the non-ionic form. Both the amino group and carboxyl
group are capable of ionizing. At neutral pH, which is normal for biological systems,
both groups are ionized.

This doubly ionized form is called the zwitterion (hybrid ion with one positive charge and one
negative charge) and overall has a zero charge. Crystalline amino acids have this structure, and the
electrostatic forces between molecules explain the higher-than-expected melting points of amino acids.
 There are 20 common or major amino acids that are found in proteins. They are divided into
groups based on the nature of the R group. However, not every amino acid falls neatly into a category,
so there can be variations in how amino acids are classified. For instance, the glycine R-group is
sometimes classified as hydrophilic and sometimes as hydrophobic. Each amino acid can be designated
by a three-letter abbreviation, or by a one-letter abbreviation.

Nonpolar aliphatic R groups The R group of these amino acids is hydrophobic, but not the entire
amino acid. The R groups are mainly hydrocarbon in nature.

1. Nonpolar aliphatic R groups- Hydrophobic

AA/aa 3 1 Other Specification/Uses

letters letter
Alanine Ala A Mother of all amino acid
Valine Val V Essential amino acid in the human system
Important to functioning of the nervous system
Leucine Leu L Essential amino acid in the human system
Associated with digestive enzymes
Isoleucine Ile I Associated with digestive enzymes
Methionine Met M Initiates protein synthesis
R group containing “S” in the structure
Proline Pro P Does not contain a primary amino group
Disrupt the a-helical configuration of -COOH “Helix Breaker”
Less Flexible
2. Aromatic R-Groups
The R groups of these amino acids are aromatic and will absorb UV light at 280 nm.

AA/aa 3 1 Other Specification/Uses

letters letter
Phenylalanine Phe F (non-polar)
-an essential amino acid in the human system
-important in utilization of Vitamin C and production of thyroxine
-should be converted to tyr from the diet. If not will become
phenylpyruvic acid can lead to:
1. Mental retardation (infants)
2. Pku disease phenylketonuvia.

Tyrosine Tyr Y (Slightly polar)

-needed in synthesis of some thyroid hormone

Tryptophan Trp W (polar)

-important in utilization of B-vitamins and synthesis of
neurotransmitters.
- found in charred portion of broiled fish
3. Polar, uncharged R groups (at pH = 7.0)
The R groups of these amino acids are hydrophilic

AA/aa 3 1 Other Specification/Uses

letters letter
Serine Ser S -OH group
-a component of phosphoprotein (phosphate group attached to
serine.
Threonine Thr T -OH group
-important in building tissues and utilization of nutrients
Asparagine Asn N -amide group
Glutamine Gln Q -amide group
Cystein Cys C -S group
-(The R group is a thiol or sulfydryl group.)
-found in curly hair
Glycine Gly G - H group
-The hydrogen R group is not really hydrophilic, but this amino acid
has similar properties to the others (hydrophobic-non polar)
-simplest amino acid
-a major excitatory neurotransmitter
-detoxification of benzoic acid
 4. Negatively-charged R groups (at pH 7.0)

These amino acids are acidic and contain an extra carboxyl group

AA/aa 3 1 Other Specification/Uses

letters letter
Aspartic Acid Asp D - Aspartate (salt of aspartic acid)
-major excitatory neurotransmitter

Glutamic Acid Glu E - Glutamate (salt of glutamic acid)

-major excitatory neurotransmitter
-MSG (monosodiumglutamate)-Additive Ajinomoto

5. Positively-charged R groups (at pH 7.0) These amino acids are basic and contain an extra basic
group.

AA/aa 3 1 Other Specification/Uses

letters letter
Lysine Lys K -found in collagen
-helps in assimilation of amino acids.
Arginine Arg R -guanido or guanidium group
Histidine His H - The R group is an imidazole group. This is the only amino acid with
an R group that ionizes around neutral pH (buffer) , creating two
forms of the amino acid.
-Histidine-Histamine