Lecture 1. Advanced Biochemistry. Introduction.

5/28/2018 Lecture 1. Advanced Biochemistry. Introduction.

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Advanced BiochemistrySY31003

Mohammad Iqbal, Ph.D., Biotechnology Research Institute

Universiti Malaysia Sabah

Email: [email protected]

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Chapter 1

Introduction and overview of basic biochemistry

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Biochemistry

A knowledge of the basics of biochemistry is importantfor the understanding of physiology. Physiology is thescience of the functioning of living systems. In

physiology, the scientific method is applied to determinehow organisms, organ systems, organ cells andbiomolecules carry out the chemical or physical functionthat they have in a living system.

Biochemistry is the study of the chemical processes inliving organisms. It deals with the structureand functionof cellular components such as proteins, carbohydrates,lipids, nucleic acidsand other biomolecules. 3
http://en.wikipedia.org/wiki/Chemistryhttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Structurehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Carbohydratehttp://en.wikipedia.org/wiki/Lipidhttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Biomoleculehttp://en.wikipedia.org/wiki/Biomoleculehttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Lipidhttp://en.wikipedia.org/wiki/Carbohydratehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Structurehttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Chemistry


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Monomers and Polymers

Carbohydrates

Lipids

Proteins

Nucleic Acids

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Carbohydrates

Monosacchrides

Disaccharides

Oligosaccharides and polysaccharides

Use of carbohydrates as an energy source

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Monomers and Polymers

Monomers and polymers are a structural basis inwhich the four main macromolecules (carbohydrates,lipids, proteins, and nucleic acids), or biopolymers, of

biochemistry are based on.

Monomers are smaller micromolecules that are puttogether to make macromolecules. Polymersare those

macromolecules that are created when monomers aresynthesized together. When they are synthesized, thetwo molecules undergo a process called dehydrationsynthesis.

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http://en.wikipedia.org/wiki/Monomershttp://en.wikipedia.org/wiki/Polymershttp://en.wikipedia.org/wiki/Macromoleculeshttp://en.wikipedia.org/wiki/Carbohydrateshttp://en.wikipedia.org/wiki/Lipidshttp://en.wikipedia.org/wiki/Proteinshttp://en.wikipedia.org/wiki/Nucleic_acidshttp://en.wikipedia.org/wiki/Biopolymershttp://en.wikipedia.org/wiki/Dehydration_synthesishttp://en.wikipedia.org/wiki/Dehydration_synthesishttp://en.wikipedia.org/wiki/Dehydration_synthesishttp://en.wikipedia.org/wiki/Dehydration_synthesishttp://en.wikipedia.org/wiki/Dehydration_synthesishttp://en.wikipedia.org/wiki/Biopolymershttp://en.wikipedia.org/wiki/Nucleic_acidshttp://en.wikipedia.org/wiki/Nucleic_acidshttp://en.wikipedia.org/wiki/Nucleic_acidshttp://en.wikipedia.org/wiki/Proteinshttp://en.wikipedia.org/wiki/Lipidshttp://en.wikipedia.org/wiki/Carbohydrateshttp://en.wikipedia.org/wiki/Macromoleculeshttp://en.wikipedia.org/wiki/Polymershttp://en.wikipedia.org/wiki/Monomers


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Carbohydrates

Carbohydrates in general are polyhydroxy aldehydes orketones or compounds which yields these on hydrolysis.

Carbohydrates are widely distributed both in animal andplant tissues.

Animal-glucose and glycogen

Plants-cellulose and starch

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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, wheren

is at least 3).

Glucose, one of the most important carbohydrates, is anexample of a monosaccharide. So is fructose, the sugar

that gives fruitstheir sweet taste.

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http://en.wikipedia.org/wiki/Monosaccharidehttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Glucosehttp://en.wikipedia.org/wiki/Fructosehttp://en.wikipedia.org/wiki/Fruithttp://en.wikipedia.org/wiki/Fruithttp://en.wikipedia.org/wiki/Fructosehttp://en.wikipedia.org/wiki/Glucosehttp://en.wikipedia.org/wiki/Glucosehttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Monosaccharide


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ContMonosacchrides

Monosaccharides can be grouped into aldoses (havingan aldehydegroup 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 tocreate larger structures.

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http://en.wikipedia.org/wiki/Aldoseshttp://en.wikipedia.org/wiki/Aldehydehttp://en.wikipedia.org/wiki/Ketoseshttp://en.wikipedia.org/wiki/Ketonehttp://en.wikipedia.org/wiki/Ketonehttp://en.wikipedia.org/wiki/Ketoseshttp://en.wikipedia.org/wiki/Aldehydehttp://en.wikipedia.org/wiki/Aldoses


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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 aglycosidic 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 linkage14


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Cont Disacchrides

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Oligosacchrides

Oligosaccharides yield 2-10 monosaccharide units onhydrolysis example maltotriose.

Synthesized through the action of specific enzyme,glycosyltransferases, which catalyze the formation ofglycosidic bonds.

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Polysacchrides

Polysacchrides contain more than ten monosaccharidesunits, and can be hundreds of sugar units in length.

Homopolysaccharides-polysaccharides having only onetype of monosaccharides.

Heteropolysaccharides-polysaccharides having morethan one type of monosaccharides.

Starch (reserve carbohydrate in plants)

Glycogen (reserve carbohydrate in animals)

Cellulose (chief carbohydrate in plants) 17


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ContPolysacchrides

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Mucopolysacchrides

Mucopolysacchrides or glycosaminoglycans arecarbohydrates 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 ofmany 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


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Proteins

Proteins are polymers of amino acids. They containcarbon, hydrogen, oxygen and nitrogens. Some proteinsmay contain sulphur, phosphorus, trace elements suchas copper or iron. Amino acids are referred to asbuilding blocks of proteins.

Proteins occupy a central position in the architecture

and functioning of living matter. The chemical andphysical activity that constitutes the life of the cell, iscatalyzed by enzymes, all of which are proteins.

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Cont Proteins

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Some proteins serve as structural, extracellular elements,for example, as hair, wool and the collagen ofconnective tissue.

Other proteins may be hormones or oxygen-carriers,participate in muscular contraction, are associated withthe genes and are concerned with immunological

defense mechanisms as antibodies etc.


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Cont Proteins

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Essential Amino Acids

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Essential amino acids (total 10) are those which can notbe synthesized in sufficient quantities by the body andare needed for the normal functioning of animals. Adeficiency in any one prevents growth in younganimals, 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 insufficient quantities by the body are designed nutritionallynon-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 linkedby 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. Theseinclude several types such as:

(i) Fibrous proteins-insoluble animals proteins,

elongated molecules. This group includes the protein ofsilk, skin, hair, nails, connective tissue and bone. Thisgroup may be subdivided into several distinct types:

Collagens

Elastins

Keratins

Myosin

Ossein 29


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Cont...Simple proteins

(ii) Globular proteins-spherical or ovoid in shape,soluble in water, includes enzymes, oxygen carryingproteins 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


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Conjugated Proteins

Conjugated proteins are complex proteins in which theprotein molecule is combined with characteristic non-amino acid substances. These include several typessuch 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 ofnatural 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 33


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Lipids

Lipids may be defined as compounds which arerelatively insoluble in water, but freely soluble innonpolar 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 otherhigher 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 inaddition they contain other groups. They aresubclassified as:

a. Phospholipids, containing phosphoric acid b. Non-phosphorylated lipids

c. Sulpholipids or sulfatides

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C C d Li id


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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 39


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Derived Lipids

They are compounds which are derived from lipids orprecursors 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 acidthat usually has between 12 and 24 carbon atoms thathas 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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http://en.wikipedia.org/wiki/Lauric_acidhttp://en.wikipedia.org/wiki/Myristic_acidhttp://en.wikipedia.org/wiki/Palmitic_acidhttp://en.wikipedia.org/wiki/Stearic_acidhttp://en.wikipedia.org/wiki/Arachidic_acidhttp://en.wikipedia.org/wiki/Arachidic_acidhttp://en.wikipedia.org/wiki/Arachidic_acidhttp://en.wikipedia.org/wiki/Arachidic_acidhttp://en.wikipedia.org/wiki/Stearic_acidhttp://en.wikipedia.org/wiki/Stearic_acidhttp://en.wikipedia.org/wiki/Stearic_acidhttp://en.wikipedia.org/wiki/Palmitic_acidhttp://en.wikipedia.org/wiki/Palmitic_acidhttp://en.wikipedia.org/wiki/Palmitic_acidhttp://en.wikipedia.org/wiki/Myristic_acidhttp://en.wikipedia.org/wiki/Myristic_acidhttp://en.wikipedia.org/wiki/Myristic_acidhttp://en.wikipedia.org/wiki/Lauric_acidhttp://en.wikipedia.org/wiki/Lauric_acidhttp://en.wikipedia.org/wiki/Lauric_acid


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Unsaturated Fatty Acids

They are similar to saturated fatty acids in the reactionof the carboxylic group but also show properties due tothe 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 besynthesized 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 andtransfer 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 49


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Bases Present in the Nucleic Acids

2 types of nitrogenous bases; the purines andpyrimidines are present in nucleic acids.

Purine bases present in DNA and RNA are same;adenine and guanine.

Pyrimidine bases present in the nucleic acids arecytosine, thymine and uracil. Cytosine is present in bothDNA and RNA. Thymine is present in DNA and uracilin RNA.

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Nucleosides

Nucleosides are formed when bases are attached to thepentose 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 thatcontains the genetic instructions used in thedevelopment and functioning of all known livingorganismsand someviruses.

The main role of DNA molecules is the long-termstorage of information. The DNA segments that carry

this genetic information are called genes.

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http://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Geneticshttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Moleculehttp://en.wikipedia.org/wiki/Informationhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Informationhttp://en.wikipedia.org/wiki/Moleculehttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Geneticshttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleic_acid


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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 importanttype of molecule that consists of a long chain ofnucleotide units. Each nucleotide consists of anitrogenous base, a ribosesugar, and a phosphate.

RNA is transcribedfrom DNA by enzymescalled RNApolymerasesand is generally further processed by other

enzymes. RNA is central to protein synthesis.

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http://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Ribosehttp://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/Protein_synthesishttp://en.wikipedia.org/wiki/Protein_synthesishttp://en.wikipedia.org/wiki/Protein_synthesishttp://en.wikipedia.org/wiki/Protein_synthesishttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Ribosehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Nucleotide


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ContRribonucleic acid (DNA

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Enzymes

Enzymes are protein catalysts for biochemical reactionsin living cells.

The substance upon which enzyme acts, is calledsubstrate. The enzyme will convert the substrate intoproduct.

All enzymes are proteins.

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Classification of Enzymes

Classification of enzymes is based on their reactionspecificity. 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 bymechanism other than hydrolysis, leaving double bonds)

5. Isomerases (catalyze isomeration reactions)

6. Ligases or Synthetases (catalyze synthesis by thecondensation of two groups requiring ATP or similar

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Chemical Nature of Enzymes

Enzymes are the largest and most specialized class ofprotein molecules. They are of two types: simple andconjugated (holoenzymes) enzymes.

Simple enzymes: are simple proteins such as trypsin,pepsin.

Conjugated enzymes : Many enzymes posses chemicalgroup that are non amino acid in nature.

Conjugated protein enzyme (holoenzyme)= Apoenzyme(protein part) + Non protein cofactor (prostheticgroup/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 mustundergo limited proteolysis, to become catalyticallyactive. (conversion of pepsinogen to pepsin catalyzedby H+ or pepsin).

Isoenzymes, has multiple molecular forms in the sameorganism catalyzing the same reaction example lactate

dehydrogenase which can occur in 5 possible forms inblood 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., cytochromeoxidase.

On the contrary, certain enzymes are liberated by livingcells 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 insmall amounts compared with other components suchas protein, carbohydrate or fat and the absence of

which leads to a deficiency disease.

Nine vitamins are water soluble, whereas four vitaminsare fat soluble.

Vitamins are required to perform specific cellularfunctions, for example precursor of coenzyme in

metabolic pathways. 64


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Cont...Vitamins

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Dietary Minerals

Dietary mineralsare the chemical elementsrequired byliving organismsfor optimal health, other than the fourelements carbon, hydrogen, nitrogen, and oxygenpresentin 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
http://en.wikipedia.org/wiki/Chemical_elementhttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Carbonhttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Nitrogenhttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Organic_chemistryhttp://en.wikipedia.org/wiki/Organic_chemistryhttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Nitrogenhttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Carbonhttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Chemical_element


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Essential Macrominerals

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Essential Microminerals


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Essential Microminerals

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References

Lippincotts Biochemistry, 2ndEdition J.M.Berg, J.L.Tymoczko & L.Stryer: Biochemistry, 5thEdn

T.M.Devlin: Text book of Biochemistry

D.M.Vasudevan & S.Sreekumari: Textbook ofBiochemistry (For Medical Students) 3rdEdn. Jaypee Bros

D.B.Marks, A.D.Marks & C.M.Smith: Basic MedicalBiochemistry: A Clinical Approach

S.Benyon: Metabolism and Nutrition

E.L.Fox, R.W.Bowers & M.L.Foss: The physiological basisfor exercise and sport.

Lecture 1. Advanced Biochemistry. Introduction.

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Transcript of Lecture 1. Advanced Biochemistry. Introduction.