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Advanced Biochemistry SY31003

Mohammad Iqbal, Ph.D., Biotechnology Research Institute Universiti Malaysia Sabah Email: miqbal@ums.edu.my

Chapter 1

Introduction and overview of basic biochemistry

Biochemistry

A knowledge of the basics of biochemistry is important for the understanding of physiology. Physiology is the science of the functioning of living systems. In physiology, the scientific method is applied to determine how organisms, organ systems, organ cells and biomolecules carry out the chemical or physical function that they have in a living system. Biochemistry is the study of the chemical processes in living organisms. It deals with the structure and function of cellular components such as proteins, carbohydrates, 3 lipids, nucleic acids and other biomolecules.

Monomers and Polymers

Carbohydrates Lipids

Proteins
Nucleic Acids

Carbohydrates

Monosacchrides Disaccharides

Oligosaccharides and polysaccharides


Use of carbohydrates as an energy source

Monomers and Polymers

Monomers and polymers are a structural basis in which the four main macromolecules (carbohydrates, lipids, proteins, and nucleic acids), or biopolymers, of biochemistry are based on. Monomers are smaller micromolecules that are put together to make macromolecules. Polymers are those macromolecules that are created when monomers are synthesized together. When they are synthesized, the two molecules undergo a process called dehydration synthesis.
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Carbohydrates

Carbohydrates in general are polyhydroxy aldehydes or ketones or compounds which yields these on hydrolysis. Carbohydrates are widely distributed both in animal and plant tissues. Animal-glucose and glycogen Plants-cellulose and starch

Classification of Carbohydrates

Monosaccharides Disaccharides Oligosaccharides

Polysaccharides
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Monosacchrides

The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar that gives fruits their sweet taste.

ContMonosacchrides

Monosaccharides can be grouped into aldoses (having an aldehyde group at the end of the chain, e. g. glucose) and ketoses (having a keto group in their chain; e. g. fructose). Monosacchrides can be linked by glycosidic bonds to create larger structures.

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ContMonosacchrides

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ContMonosacchrides

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ContMonosacchrides

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Disacchrides

It consist of 2 monosaccharides and is joined by a glycosidic or ether bond. Most well known examples are sucrose, lactose, maltose and isomaltose. Sucrose (non reducing) = glucose + fructose Lactose (reducing)= glucose + galactose Maltose (reducing) = 2 glucose with -1,4 linkage Isomaltose (reducing) = 2 glucose with -1,6 linkage
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Cont Disacchrides

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Oligosacchrides

Oligosaccharides yield 2-10 monosaccharide units on hydrolysis example maltotriose. Synthesized through the action of specific enzyme, glycosyltransferases, which catalyze the formation of glycosidic bonds.

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Polysacchrides

Polysacchrides contain more than ten monosaccharides units, and can be hundreds of sugar units in length. Homopolysaccharides-polysaccharides having only one type of monosaccharides. Heteropolysaccharides-polysaccharides having more than one type of monosaccharides. Starch (reserve carbohydrate in plants) Glycogen (reserve carbohydrate in animals) Cellulose (chief carbohydrate in plants)

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ContPolysacchrides

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Mucopolysacchrides

Mucopolysacchrides or glycosaminoglycans are carbohydrates containing uronic acid and amino sugars. Examples: Hyaluronic acid (connective tissues, tendons) Heparin (anticoagulant) Chondrointin sulfate (connective tissues, tendons) Keratan sulfate (cornea and tendons) Dermatan sulfate (skin, blood vessel, heart valves)
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Cont Mucopolysacchrides

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Biological Significance of Carbohydrates

Carbohydrates are the main source of energy in the body. Brain cells and RBCs are almost wholly dependent on carbohydrates as the energy source.
Carbohydrates also serve as a structural component of many organisms, including the cell wall of bacteria, exoskeleton of many insects and the fibrous cellulose. Carbohydrates play a key role in the metabolism of amino acids and fatty acids. 21

Proteins

Proteins are polymers of amino acids. They contain carbon, hydrogen, oxygen and nitrogens. Some proteins may contain sulphur, phosphorus, trace elements such as copper or iron. Amino acids are referred to as building blocks of proteins. Proteins occupy a central position in the architecture and functioning of living matter. The chemical and physical activity that constitutes the life of the cell, is catalyzed by enzymes, all of which are proteins.
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Cont Proteins

Some proteins serve as structural, extracellular elements, for example, as hair, wool and the collagen of connective tissue. Other proteins may be hormones or oxygen-carriers, participate in muscular contraction, are associated with the genes and are concerned with immunological defense mechanisms as antibodies etc.

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Cont Proteins

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Essential Amino Acids

Essential amino acids (total 10) are those which can not be synthesized in sufficient quantities by the body and are needed for the normal functioning of animals. A deficiency in any one prevents growth in young animals, and may even cause death. Examples are : Arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.

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Non-Essential Amino Acids

Those amino acids (total 10) that can be synthesized in sufficient quantities by the body are designed nutritionally non-essential amino acids.

Examples are : Alanine, Aspargine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Proline, Serine, Tyrosine.

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Peptides

A peptide consists of two or more amino acids linked by peptide bonds. Dipetide (2 amino acids) Tripeptide (3 amino acids)

Polypeptide (many amino acids)

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Classification of Proteins

Simple proteins Conjugated proteins Derived proteins

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Simple proteins

Simple proteins consist solely of amino acids. These include several types such as: (i) Fibrous proteins-insoluble animals proteins, elongated molecules. This group includes the protein of silk, skin, hair, nails, connective tissue and bone. This group may be subdivided into several distinct types: Collagens Elastins Keratins Myosin 29 Ossein

Cont...Simple proteins

(ii) Globular proteins-spherical or ovoid in shape, soluble in water, includes enzymes, oxygen carrying proteins and protein hormones like ACTH, oxytocin, vasopressin, glucagon and insulin. This group may be subdivided into several distinct types: Albumins Globulins Histones Protamines Glutelins Prolamines 30

Conjugated Proteins

Conjugated proteins are complex proteins in which the protein molecule is combined with characteristic nonamino acid substances. These include several types such as: Nucleoproteins Mucoproteins Glycoproteins Chromoproteins Lipoproteins Metalloproteins Flavoproteins Phosphoproteins
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Derived Proteins

Derived proteins are not present in nature as such. They are obtained as a result of partial hydrolysis of natural proteins.

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Biological Significance of Proteins

Structural components of cells Food stuffs Biocatalyst (enzymes) Hormones Oxygen carriers Protection against diseases Growth and repair Formation of rhodopsin Synthesis of melanin Urea formation

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Lipids

Lipids may be defined as compounds which are relatively insoluble in water, but freely soluble in nonpolar organic solvents like benzene, chloroform, alcohol , acetone etc.

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Cont...Lipids

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Classification of Lipids

Simple lipids Compound lipids

Derived lipids
Lipids complexed to other compounds

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Simple Lipids

They are esters of fatty acids with glycerol or other higher alcohols. They are sub classified: (i) Tiacyl glycerol or triglycerides or neutral fat (ii) Waxes

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Compound Lipids

They are fatty acids esterifies with alcohol; but in addition they contain other groups. They are subclassified as: a. Phospholipids, containing phosphoric acid b. Non-phosphorylated lipids c. Sulpholipids or sulfatides

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Cont...Compound Lipids

1. Phospholipids, containing phosphoric acid


a. Nitrogen containing glycerophosphatides (lecithin, cephalin) b. Non-nitrogen containing glycerophosphatides (phosphatidyl inositol) c. Plasmalogens containing long chain alcohol (choline plamalogen) d. Phosphosphingosides, containing sphingosine

2. Non-phosphorylated lipids
a. Cerbrosides b. Globosides c. Gangliosides

3. Sulpholipids or sulfatides
a. Sulfated cerebrosides b. Sulfated globosides c. Sulfated gangliosides

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Derived Lipids

They are compounds which are derived from lipids or precursors of lipids, e.g. fatty acids, steroids, prostaglandins, leukotrienes, terpenes, dolichols, etc.

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Lipids Complexed to Other Compounds

Proteolipids
Lipoproteins

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Biological Significance of Lipids

Chief food storage compounds Structural components of cells

Rich source of respiratory energy


Carriers of essential compounds Enzyme activation
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Cont... Biological Significance of Lipids

Hormone synthesis Heat insulation

Mechanical protection
Adding taste and palatability to food Giving shape and contour to the body
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Fatty Acids

Fatty acids are obtained from the hydrolysis of fats. Fatty acids are of 2 types: a. Saturated fatty acids b. Unsaturated fatty acids

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Saturated Fatty Acids

Saturated fatty acids are a long-chain carboxylic acid that usually has between 12 and 24 carbon atoms that has no double bonds.

Example are Lauric acid (12 C), Myristic acid (14 C), Palmitic acid (16 C), Stearic acid ( 18 C), Arachidic acid (20 C).

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Unsaturated Fatty Acids

They are similar to saturated fatty acids in the reaction of the carboxylic group but also show properties due to the presence of double bond.

a. Monounsaturated acids= one double bond b. Polyunsaturated acids= more than one double bond

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Essential Fatty Acids

Linolenic and linoleic acids (polyunsaturated fatty acids) are called essential fatty acids, because they can not be synthesized by the body and have to be supplied in diet.

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Nucleic Acids

Nucleotides are precursors of the nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Nucleic acids are concerned with the storage and transfer of genetic information.

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Nucleotides

Nucleotide is made up of three components: a. Nitrogenous base (a purine or a pyrimidine) b. Pentose sugar, either ribose or deoxyribose c. Phosphate groups esterified to the sugar Adenylic acid Guanylic acid Thymidylic acid Cytidic acid Uridylic acid

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Bases Present in the Nucleic Acids

2 types of nitrogenous bases; the purines and pyrimidines are present in nucleic acids. Purine bases present in DNA and RNA are same; adenine and guanine. Pyrimidine bases present in the nucleic acids are cytosine, thymine and uracil. Cytosine is present in both DNA and RNA. Thymine is present in DNA and uracil in RNA.
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Nucleosides

Nucleosides are formed when bases are attached to the pentose sugar, D-ribose or 2-deoxy D-ribose. Adenosine Guanosine Cytidine Uridine

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Types of Nucleic Acids

Two general classes of nucleic acids a. Deoxyribonucleic acid (DNA)

b. Ribonucleic acid (RNA)

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Deoxyribonucleic acid (DNA)

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. The DNA segments that carry this genetic information are called genes.

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ContDeoxyribonucleic acid (DNA)

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Functions of DNA

Self replication or duplication Protein synthesis

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Ribonucleic Acid (RNA)

Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis.

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ContRribonucleic acid (DNA

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Enzymes

Enzymes are protein catalysts for biochemical reactions in living cells. The substance upon which enzyme acts, is called substrate. The enzyme will convert the substrate into product.

All enzymes are proteins.

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Classification of Enzymes

Classification of enzymes is based on their reaction specificity. Six classes have been recognized: 1.Oxidoreductases (catalyze oxidation-reduction reactions) 2. Hydrolases (catalyze hydrolytic reactions) 3. Transferases (catalyze group transfer reactions) 4. Lyases (catalyze removal of groups from substrates by mechanism other than hydrolysis, leaving double bonds) 5. Isomerases (catalyze isomeration reactions) 6. Ligases or Synthetases (catalyze synthesis by the condensation of two groups requiring ATP or similar triphosphate) 59

Chemical Nature of Enzymes

Enzymes are the largest and most specialized class of protein molecules. They are of two types: simple and conjugated (holoenzymes) enzymes. Simple enzymes: are simple proteins such as trypsin, pepsin. Conjugated enzymes : Many enzymes posses chemical group that are non amino acid in nature. Conjugated protein enzyme (holoenzyme)= Apoenzyme (protein part) + Non protein cofactor (prosthetic group/coenzyme/metal activator)
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General properties of Enzymes

Remains unaltered in the end Required in small quantities Protein in nature Accelerate the rate of reaction Reversibility of enzyme action Enzyme specificity

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Proenzymes and Isoenzymes

Proenzymes, are catalytically inactive which must undergo limited proteolysis, to become catalytically active. (conversion of pepsinogen to pepsin catalyzed by H+ or pepsin). Isoenzymes, has multiple molecular forms in the same organism catalyzing the same reaction example lactate dehydrogenase which can occur in 5 possible forms in blood sera and tissues of most vertebrates.

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Endo and Exoenzymes

Enzymes acts with in the cells are called endoenzymes, hence they are metabolic enzymes e.g., cytochrome oxidase.

On the contrary, certain enzymes are liberated by living cells and catalyze vital reactions in the cells environment. These are called exoenzymes e.g., the digestive enzymes: amylase, lipase, proteases etc.

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Vitamins

A complex organic substance required in the diet in small amounts compared with other components such as protein, carbohydrate or fat and the absence of which leads to a deficiency disease. Nine vitamins are water soluble, whereas four vitamins are fat soluble. Vitamins are required to perform specific cellular functions, for example precursor of coenzyme in metabolic pathways. 64

Cont...Vitamins

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Dietary Minerals

Dietary minerals are the chemical elements required by living organisms for optimal health, other than the four elements carbon, hydrogen, nitrogen, and oxygen present in common organic molecules. Dietary minerals may be divided into 2 groups: 1. Macrominerals, which are required in amounts greater than 100 mg/d. 2. Microminerals (Trace Elements), which are required in amounts less than 100 mg/d.
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Essential Macrominerals

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Essential Microminerals

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References

Lippincotts Biochemistry, 2nd Edition J.M.Berg, J.L.Tymoczko & L.Stryer: Biochemistry, 5th Edn T.M.Devlin: Text book of Biochemistry D.M.Vasudevan & S.Sreekumari: Textbook of Biochemistry (For Medical Students) 3rd Edn. Jaypee Bros D.B.Marks, A.D.Marks & C.M.Smith: Basic Medical Biochemistry: A Clinical Approach S.Benyon: Metabolism and Nutrition E.L.Fox, R.W.Bowers & M.L.Foss: The physiological basis for exercise and sport.
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