CHAPTER II PROTEINS Proteins -also known as Polypeptides -are organic compounds - made of amino acids arranged in a linear chain

and joined together by peptide bonds. - higher molecular weight. - most important of all biological molecules of the cells.

Structural representation of alpha-amino acids: H

C NH2

COOH

Where:

R- hydrogen, aliphatic, aromatic, heterocyclic NH2- amino group COOH- carboxyl group C- alpha carbon

Biomedical importance of proteins in e body: 1. Enzymatic catalysis - almost all biological reactions are enzyme catalyzed. Enzymes are known to increase the rate of a biological reaction by a factor of 10 to the 6th power! There are several thousand enzymes which have been identified to date. 2. Binding, transport and storage - small molecules are often carried by proteins in the physiological setting (for example, the protein hemoglobin is responsible for the transport of oxygen to tissues). Many drug molecules are partially bound to serum albumins in the plasma.

3. Molecular switching - conformational changes in response to pH or ligand binding can be used to control cellular processes 4. Coordinated motion - muscle is mostly protein, and muscle contraction is mediated by the sliding motion of two protein filaments, actin and myosin. 5. Structural support - skin and bone are strengthened by the protein collagen

Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white).

6. Immune protection - antibodies are protein structures that are responsible for reacting with specific foreign substances in the body. 7.Generation and transmission of nerve impulses - some amino acids act as neurotransmitters, which transmit electrical signals from one nerve cell to another. In addition, receptors for neurotransmitters, drugs, etc. are protein in nature. An example of this is the acetylcholine receptor, which is a protein structure that is embedded in postsynaptic neurons.

Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen

8.Control of growth and differentiation -proteins can be critical to the control of growth,cell differentiation and expression of DNA. -For example, repressor proteins may bind to specific segments of DNA, preventing expression and thus the formation of the product of that DNA segment. -many hormones and growth factors that regulate cell function, such as insulin or thyroid stimulating hormone are proteins.

Classification of Proteins: 1. Simple proteins- true proteins found abundantly in both plants and animals. a. Albumins- are soluble in water and dilute neutral solutions. - Members include serum albumin, lactal albumin, and ovalbumin. b.Globulins- are soluble in neutral dilute salt solutions but not in water. - include legumin from peas, myosinogen from muscles.

c. Glutelins- soluble in dilute acids and alkalines but insoluble in neutral solvents. - examples are glutenin from wheat and oryzenin from rice. d. Prolamines- are insoluble in ordinary solvent but soluble in 70% alcohol at about neutral point. - Present in plants such as gliadin from wheat, zein from corn, and hordein from barley.

e. Histones- soluble in water, dilute acids and alkalines but not in dilute ammonia. - not readily coagulated by heat - strongly basic and occur in the tissues in the form of salt combinations. - examples are globin from hemoglobin, thymus histone and scobrone of mackerel.

f. Protamines- contain smaller number of amino acids. - strongly basic and form soluble salts with strong mineral acids. - e.g salmin from salmon sperm g. Scleroproteins- insluble in water and neutral solvents. - e.g keratin of the epidermal tissues, elastin from ligaments and collagen from hides, bones and cartilages

2. Conjugated Proteins a. Nucleoproteins- are combination of histones and protamines with nucleic acid. - soluble in dilute solutions of NaCl and can be extracted from the tissues by the use of this solvent. - typical examples are chromatin, and the products obtain from glandular tissues and germ of grains.

b. Glycoproteins- are compounds of proteins with a carbohydrate component. - they are utilized for lubricating purposes in view of their slimy nature. - mucin from saliva, tendomucoid from tendsons and osseomucoid from bones belong to this group. - are not digested in the GI tract and used as protection.

c. Phosphoproteins- have the posthetic group (H3PO4) joined in the protein molecule. - casein from milk and vitelline of the egg yolk are rich in this type of protein. d. Chromoproteins- are protein compounds with hematin or similar pigments in their molecule. - examples are hemoglobin, cytochromes and rhodopsin.

e. Lipoproteins- have fatty substances combined with their molecules like lecithin, cephalin, etc. - they are present in the blood serum, brain tissues, cell nuclei, egg yolk and milk.

III. Derived Proteins- substances formed from simple and conjugated proteins. a. Primary protein derivatives- are proteins which have undergone intramolecular rearrangement through the hydrolytic action of certain physical and chemical agents. - They are synonymous with denatured proteins.

1. Proteans- are insoluble substances resulting from the premilinary action of water, dilute acids, or enzymes. - myosan from myosin and edestan from edestin are good examples. 2. Metaproteans- are product of further hydrolysis. - soluble in weak acids and alkalies, but insoluble in neutral salt solutions. -acid metaproteans(acid albuminate); alkali metaproteans (alkali albuminate

3. Coagulated proteins- are insoluble products resulting from either the action of heat, alcohol, ultraviolet are or even simple mechanical shaking. -cooked egg albumin, cooked meat,etc.

b. Secondary protein derivatives- are products of more extensive hydrolysis. 1. Primary proteoses- are soluble in water, precipitated by concentrated nitric acid. - not coagulated by heat. 2. Secondary proteoses- precipitated only by complete saturation with ammonium sulfate but not with nitric or picric acid.

3. Peptones- are insoluble in water, not coagulated by hear and not precipitated by ammonium sulfate but by certain alkaloidal reagents such as phosphotungstic and tannic acids. 4. Peptides- are combinations of two or more amino acids , the carboxyl group of one being united with the amino group of the other. -same properties with peptones. -ex: di,tri,tetra, penta,poly

Classification of protein according to pattern of structure: 1. Primary protein structure- the main mode of linkage is the peptide bond. - the amino acid sequences is often referred to as covalent structure. -individual proteins may consist of one or more peptide chains.

2. Secondary protein structure- where the peptide chains are folded regularly , the folding resulting from the linkage of the carbonyl group of one peptide chain with the amine group of another chain, by means of hydrogen bonds. - the hydrogen bonding produces a regular coiled arrangement called helix. -refers to the arrangement of amino acids that are close together in a chain .

. An alpha helix is a tightly coiled, rodlike structure which has an average of 3.6 amino acids per turn. The helix is stabilized by hydrogen bonding between the backbone carbonyl of one amino acid and the backbone NH of the amino acid four residues away.

Cartoon representation of a helix secondary protein structure

The beta pleated sheet- is composed of two or more straight chains that are hydrogen bonded side by side. If the amino termini are on the same end of each chain, the sheet is termed parallel, and if the chains run in the opposite direction (amino termini on opposite ends), the sheet is termed.All of the amides are hydrogen bonded except those on the outer strands. Pleated sheets may be formed from a single chain if it contains a beta turn, which forms a hairpin loop structure.

3. Tertiary protein structure- where the helical arrangement is periodically interrupted, permitting numerous bonds with additional foldings. - the spatial configuration is threedimensional and is maintained by covalent bonds. -tertiary structure refers to the arrangement of amino acids that are far apart in the chain.

4. Quarternary protein structure- the protein organization is produced by fitting together separate coiled and folded structures to form an aggregate functional structure. -complex of several protein molecules or polypeptide chains, usually called protein subunits in this context, which function as part of the larger assembly or protein complex

Quarternary structure: Hemoglobin

Models of different Protein Structures

Protein Structure: From primary to quarternary

Physical and Chemical Properties of Proteins: 1. When pure, proteins are generally tasteless except with hydrolates. 2. Mostly colorless. 3. Insoluble in fat solvents and present varied degrees of solubility in water, salt solution, dilute acids and alkalies. 4. Proteins are amphoteric. 5. Proteins are very reactive and highly specific.

Solubility of Proteins: (Major influences) 1. The effect of neutral salt. 2. The effect of pH. 3. The effect of organic solvents. Actions of Heat- when burned, proteins decompose and liberate a characteristic odor of burned hair or feather. - solutions of proteins when heated between 38-60 degrees centigrade, undergo slight intramolecular rearrangements. - ( DENATURATION)

Precipitations: 1. By acids 2. By salts of Heavy metals 3. By alcohol Hydrolysis: 1. Dilute acids; alkalies or enzymes - due to addition of elements in the peptide bond/ linkage.

Classification of Amino acids: - According to the number of amino acids and carboxyl groups presented in their molecules. 1. Neutral amino acids- equal numbers of amino and carboxyl groups. a. Aliphatic amino acids- where R stands for either a hydrogen or an aliphatic radical. .

Examples of aliphatic amino acids:

H H C NH2 COOH CH3 H C NH2 COOH CH2 OH H C NH2 COOH

Glycine/ glycocol/amino acetic acid

Alanine( alphaamino propionic cid

Serine ( a-amino bhydroxy propionic acid

H CH2 CH3 C NH2 COOH CH2CH2 CH3

H C NH2 COOH CH3CH CH3

H C NH2 COOH

Amino butyric acid

N-amino valeric acid

Valine (a-amino isovaleric acid

b. Aromatic amino acids- are those in which R represents an aromatic group.

c. Thionine group - sulfur containing amino acids.

Cysteine

Methionine

d. Secondary amino acids - amino acids contain secondary, imino, rather than the primary amino group. - The nitrogen is present in pyrrolidine ring.

Proline (Pyrrolidine carboxylic acid)

2. Acid amino acids - are monoamino dicarboxylic acids and are acid in reaction.

Aspartic acid (amino succinic acid)

Glutamic acid
(a-amino glutaric acid)

3. Basic amine acids - are diamino monocarboxylic acids. -alkaline in reaction.

Histidine

Arginine

General Properties of Amino Acids: I. Physical Properties: 1. White crystalline 2. Soluble in cold water, except cysteine and tyrosine. 3. Most are insoluble in alcohol. 4. Most are sweet like glycine, alanine, serine and proline. 5. Others like leucine are tasteless; while some are bitter like arginine.

II. Chemical Properties: 1. Amino acids are amphoteric. 2. They form esters with alcohol. 3. Amino acids can be acetylated, benzylated or methylated. 4. All amino acids except proline and hydroxyproline react with nitrous acid with the liberation of nitrogen gas.

CLINICAL SIGNIFICANCE OF PROTEIN: 1. The substitution of a hydrophobic amino acid (V) for an acidic amino acid (E) in the -chain of hemoglobin results in sickle cell anemia (HbS). This change of a single amino acid alters the structure of hemoglobin molecules in such a way that the deoxygenated proteins polymerize and precipitate within the erythrocyte, leading to their characteristic sickle shape.

2. Collagens are the most abundant proteins in the body. Alterations in collagen structure arising from abnormal genes or abnormal processing of collagen proteins results in numerous diseases, including Larsen syndrome, scurvy, osteogenesis imperfecta and Ehlers-Danlos syndrome. a. Ehlers-Danlos syndrome is actually the name associated with at least ten distinct disorders that are biochemically and clinically distinct yet all manifest structural weakness in connective tissue as a result of defective collagen structure.

b. Osteogenesis imperfecta also encompasses more than one disorder. At least four biochemically and clinically distinguishable maladies have been identified as osteogenesis imperfecta, all of which are characterized by multiple fractures and resultant bone deformities. c. Marfan syndrome manifests itself as a disorder of the connective tissue and was originally believed to be the result of abnormal collagens. However, recent evidence has shown that Marfan syndrome results from mutations in the extracellular protein, fibrillin, which is an integral constituent of the non-collagenous microfibrils of the extracellular matrix.

3. Several forms of familialhypercholesterolemia are the result of genetic defects in the gene encoding the receptor for low-density lipoprotein (LDL). These defects result in the synthesis of abnormal LDL receptors that are incapable of binding to LDLs, or that bind LDLs but the receptor/LDL complexes are not properly internalized and degraded. The outcome is an elevation in serum cholesterol levels and increased propensity toward the development of atherosclerosis.

4. A number of proteins can contribute to cellular transformation and carcinogenesis when their basic structure is disrupted by mutations in their genes. These genes are termed proto-oncogenes. For some of these proteins, all that is required to convert them to the oncogenic form is a single amino acid substitution. The cellular gene, RAS, is observed to sustain single amino acid substitutions at positions 12 or 61 with high frequency in colon carcinomas. Mutations in RAS are most frequently observed genetic alterations in colon cancer.