Proteins

Criteria

1. Level of organization
2. According to function
3. According to composition
4. Whether they contain essential amino acids
5. According to structure

1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure

Primary structure

This is a linear sequence of amino acids joined together by peptide bonds. Disulphide bonds may also be found.

Secondary structure

This is due to coiling or twisting of the polypeptide.

Diagram

α helix

This is due to attraction of various amino acids. This is a component of hair, claws, nails, as well as skin.

β pleated sheets (zigzag structures)

Collagen is a compound of tissues like bones and cartilage. Collagen is an example of β pleated sheets.

Tertiary structure

Tertiary structure is due to coiling and twisting of the polypeptide helix forming a globular or spherical shape.

Bonds present in the coiled structure are ionic bonds, hydrogen bonds, hydrophobic interactions, and disulphide bridges.

Examples of tertiary structures (they are very soluble).

1. Immunoglobins (antibodies)
2. Hormones
3. Enzymes

Quaternary structure

Quaternary structure is due to coiling and twisting of various polypeptide chains. Usually the structure is associated with non-protein parts called prosthetic groups, e.g., hemoglobin.

Hemoglobin has four polypeptide chains, two α-chains and two β-chains, each surrounding an iron atom.

The hemoglobin consists of protein parts. The protein part consists of 4 polypeptide chains; of the four polypeptide chains, 2 are α chains and 2 are β chains, and is called globin.

The non-protein part is called haem and consists of porphyrin surrounding an iron atom.

Essential amino acids vs. non-essential amino acids

Essential amino acids are those which cannot be synthesized by human cells but are obtained from food.

All of the 20 α-amino acids are needed to make different proteins in the body of a human.

Twelve of these amino acids can be synthesized by the cells from other substances that are present in the body; these are called non-essential amino acids.

The other eight cannot be synthesized by the body and must be included in the person's diet; these are called essential amino acids.

1. Simple proteins: Simple proteins are made up of amino acids only. E.g., histones (nucleoprotein), globulin (immunoglobulin), scleroproteins (e.g., keratin), albumins, and protamines.
2. Conjugated proteins: Made up of amino acids; these are globular proteins associated with non-protein materials. E.g., haemoglobin, glycoproteins (components of cell membrane), mucin (component of saliva), and lipoproteins (components of cell membrane).

NOTE: These are also functions of proteins.

This is because their side chains have no charge at the pH of body cells.

Thus they are divided into: natural hydrophobic amino acids and natural hydrophilic amino acids.

Natural hydrophobic amino acids

Seven natural amino acids have side chains (R) that are non-polar or hydrophobic. These hydrophobic groups are either alkyl or aromatic in nature.

1. Alanine (Ala)
2. Valine (Val)
3. Leucine (Leu)
4. Isoleucine (Ile)
5. Proline (Pro)
6. Phenylalanine (Phe)
7. Tryptophan (Trp)

Neutral hydrophilic amino acids

Eight amino acids are classified as hydrophilic.

1. In general, these amino acids are more soluble than hydrophobic amino acids.
2. The side chain of glycine (Gly) is just hydrogen. The other seven neutral hydrophilic amino acids have side chains that can form either strong or weak hydrogen bonds with water.
3. These have a hydroxyl group in either side chain: serine (Ser), threonine (Thr), or tyrosine (Tyr). Two contain an amino functional group: asparagine (Asn) and glutamine (Gln). The remaining two contain a sulphur atom: cysteine (Cys) and methionine (Met).

Others include: tyrosine, asparagine, cysteine, glutamine, and methionine.

Acidic amino acids have side chains that contain a second carbonyl group.

At the pH of cells in the body, these carboxylic groups exist primarily as negatively charged carboxylate ions, and they interact strongly with water molecules.

1. Aspartic acid (Asp)
2. Glutamic acid (Glu)

Three of the amino acids contain a side chain that acts as a proton acceptor or base. They are thus classified as basic amino acids: lysine (Lys), arginine (Arg), and histidine (His).

a. Fibrous proteins

1. Have a secondary structure and little or no tertiary structure.
2. Insoluble in water.
3. Physically tough.
4. Form long polypeptide chains cross-linked at intervals, forming long fibres or sheets.

Functions of fibrous proteins

Perform structural functions in cells and organisms, e.g., collagen (tendons, bones, connective tissues), myosin in muscles, silk (spider webs), keratin (nails, hair, feathers).

b. Globular proteins

1. Found mostly in tertiary structure.
2. Polypeptide chain highly folded to form spherical shape.
3. Easily soluble in water.

Functions of globular proteins

Form enzymes, antibodies, and some hormones, e.g., insulin.

Intermediate proteins

Fibrous in nature but soluble in water, e.g., fibrinogen.

Function of intermediate proteins

Fibrinogen forms insoluble fibrin when blood clots.

Like proteins, nucleic acids are largely polymers made up of a small number of different building blocks called nucleotides.

Each nucleotide is in turn composed of three smaller parts:

1. A phosphate group
2. A monosaccharide
3. A nitrogen-containing base

The term nucleotide is used to refer to a nitrogenous base bound to a monosaccharide.

And the nucleotide is a nucleotide phosphate.

There are two major types of nucleic acids:

1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)

Diagrams

There are two main differences between the deoxyribonucleotide components of DNA and the ribonucleotide components of RNA.

The bonds that hold these polymers together are ester linkages formed between the phosphate on the number 5 carbon of ribose in one nucleotide and the hydroxyl on the number 3 carbon of ribose in the next nucleotide (deoxyribose in the case of DNA).

Two nucleic acids are said to have a 3′5′ phosphate ester bridge/bond between their nucleotide components.

Diagram of a long nucleic acid

1. The DNA consists of two long polynucleotide strands, and the base components of each nucleotide on one strand can form hydrogen bonds with only one specific nucleotide base on the other strand.
2. Guanine (G) can hydrogen bond only to cytosine in another DNA strand to form a base pair.
3. Adenine (A) can hydrogen bond with thymine (T).