Bio Molecules [Autosaved]- essential.pptx

essential topic on bio molecule:
They are naturally occurring polypeptides that contain more than 50 amino acid units. therefore a protein is a hetero polymer.
Most abundant organic molecules of the living system.
They form about 50% of the dry weight of the cell.
They are most important for the architecture and functioning
of the cell.
Proteins on complete hydrolysis yields Amino Acids
There are 20 standard amino acids which are repeatedly found in the structure of proteins – animal, plant or microbial.
Collagen is the most abundant animal protein and Rubisco is the most abundant plant protein
Protein Synthesis is controlled by DNA.
They are substituted methane (CH4)
Amino acids are group of organic compounds having 2 functional groups (-NH2) and (-COOH)
(-NH2) group is basic whereas (-COOH) is acidic
R- can be H in glycine, CH3 in alanine, Hydroxymethyl in serine
in others it can be hydrocarbon chain or a cyclic group
All amino acids contain C, H, O and N but some of them additionally contain S

Physical and chemical properties of amino acids are due to amino, carboxyl and R functional groups

1. Bio Molecules Module 1

2. P R O T E INS They are naturally occurring polypeptides that contain more than 50 amino acid units. therefore a protein is a hetero polymer. Most abundant organic molecules of the living system. They form about 50% of the dry weight of the cell. They are most important for the architecture and functioning of the cell. Proteins are polymers of amino acids Proteins on complete hydrolysis yields Amino Acids There are 20 standard amino acids which are repeatedly found in the structure of proteins – animal, plant or microbial. Collagen is the most abundant animal protein and Rubisco is the most abundant plant protein Protein Synthesis is controlled by DNA.

3. AMINO ACIDS They are substituted methane (CH 4 ) Amino acids are group of organic compounds having 2 functional groups (-NH 2 ) and (-COOH) (-NH 2 ) group is basic whereas (-COOH) is acidic R- can be H in glycine , CH 3 in alanin e, Hydroxymethyl in serine in others it can be hydrocarbon chain or a cyclic group All amino acids contain C, H, O and N but some of them additionally contain S Physical and chemical properties of amino acids are due to amino, carboxyl and R functional groups

4. Zwitter ion formation (hybrid) Zwitterion is a dipolar ion which is  formed on the combination of a carboxyl group and an amino group . As a result, it is mostly formed by an amino acid.  Simultaneously carry both positive ion and negative ion – zwitter ion They are amphoteric in nature

5. No. Nature Amino acids 1. NEUTRAL : Amino acids with 1 amino and 1 carboxyl group Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile) 2. ACIDIC : 1 extra carboxyl group Aspartic acid (Asp), Asparagine (Asn), Glutamic acid (Glu), Glutamine (Gln) 3. BASIC : 1 extra amino group Arginine (Arg), Lysine (Lys) 4. S – CONTAINING : Amino acids have sulphur Cysteine (Cys), Methionine (Met) 5. ALCOHOLIC : Amino acids having –OH group Serine (Ser), Threonine (Thr), Tyrosine (Tyr) 6. AROMATIC : Amino acids having cyclic structure Phenylalanine (Phe), Tryptophan (try) 7. HETEROCYCLIC : amino acids having N in ring structure Histidine (His), Tryptophan (try) 8 . IMINO : amino acids having - N H in stead of amino group Proline (Pro) Amino acids are differentiated into 8 groups based on their structure and reaction.

6. Aspartic acid (acidic) Alanine (neutral) Lysine (basic) Serine (alcoholic) Cysteine (suphur) Phenylalanine (aromatic)

7. PEPTIDE FO R M A TI O N Amino acids are linked serially by peptide bonds (-CONH-) formed between the (-NH2) of one amino acid and the (-COOH) of adjacent amino acid Chain having 2 amino acids linked by a peptide bond is called as a DIPEPTIDE The sequence of amino acids present in a polypeptide is specific for a particular protein. Number of peptide bonds , n=(a-1) a= total number of amino acids.

8. PROTEINS Function Chemical nature and solubility Nutritional i mp o rtance On the basis of production in body: essential: not produced by body , essential to be taken in diet Non- essential:produced by body, not essential to be taken Semi essential:produced at very low rate, partially eaten

9. Functional classification Structural proteins e.g. keratin, collagen Enzymatic proteins e.g. pepsin Transport proteins e.g. Haemoglobin Hormonal proteins e.g. Insulin, Growth hormone Contractile proteins e.g. Actin, myosin Storage proteins e.g. Ovalbumin Genetic proteins e.g. Nucleoproteins Defence proteins e.g. Imunoglobulins Receptor proteins e.g. for hormones and viruses

10. Classification based on chemical nature and solubility 1. Simple proteins : They are composed only of amino acid residues Conjugated proteins : Along with amino acids , there is a non-protein prosthetic group. Derived proteins : They are denatured or degraded products of the above two

11. Proteins S i mple Conjugated De r i v e d Nucleoproteins Glycoproteins Mucoprote i ns Lipoproteins Phosphoproteins Chro moprote i ns Metalloproteins Globular Fibrous Albumin Globulin H i stones Collagen Elastin K e r a t i n Primary Secondary Coagu l a t ed proteins Proteans Metaproteins Proteoses protones Peptides Only amino acids are present Along with amino acids + Prosthetic group

12. STRUCTURE OF PROTEIN 4 basic structural levels are assigned to proteins – primary , secondary, tertiary and quaternary PRIMARY The primary structure refers to the number and linear sequence of amino acids in the polypeptide chain and the location of the disulphide bridges The primary structure is responsible for the function of the protein. (Immature Protein- formed in ribosome ) The 1 st aminoacid is N-terminal , written on the left side whereas the last amino acid C- terminal , is written on the right side

13. SECONDARY The folding of the linear chain into a specific coiled structure is called as secondary structure. It is developed from primary structure by their peptide bonds formation of intra or inter poly-peptide bonds , which make proteins functional 3 types : α- helix, β- pleated sheet and collagen helix α- helix β- pleated sheet Collagen helix Primary structure does not give any information about the functional properties of the protein

14. α – Helix: A poly peptide chain which forms a regular spiral or coil around an imaginary axis is called α – helix. Some of the structures which show α – helix are keratin of hair, fur, claws, feathers etc … The coils of α – helix are held together by intramolecular hydrogen bonds between NH and O groups of amino acids of successive turns of the coil parallel to the main axis of the fibre . R- groups occur towards the outer side of the α – helix.

15. β - Pleated sheet: When two or more peptide chains are inter connected by hydrogen bonds to produce a pleated sheet like structure known as β - pleated sheet. Chains may be parallel or anti parallel. Straight hydrogen bonds occur between amide group (-NH) and carboxyl group (-CO-) group of adjacent polypeptide. Cross linkages help in stabilization of β – pleated sheet . In parallel chain, N- atoms of adjacent strands of poly-peptides point in the same directions ( keratin and feathers) In anti – parallel pleated sheet, N atoms are in opposite directions ( silk, fibroin)

16. Collagen helix: collagen has large number of glycine and proline hence it cannot form alpha – helix. Three poly peptide chains come together and run parallel to form a right handed super helix that is stabilized by hydrogen bonds among the three. The triple helix of collagen is called Tropo collagen . It is present in the connective tissue tendons and bones.

17. TERTIARY It is a 3D arrangement of all atoms in the protein, important for biological activity. Ex: Enzymes (tertiary str.) The helical polypeptide may fold upon itself and assume a complex but specific form – spherical, rod like or something in between. These geometrical shapes are known as tertiary (3 ) structure QUATERNARY Proteins are said to be quaternary in structure If they have 2 or more polypeptide chains Haemoglobin is an excellent example - ( 2 α ,2 β ) polypeptide chains

18. With the water, I say, Touch me not, To the tongue, I am tasteful, Within limits, I am dutiful, In excess, I am dangerous LIPIDS

19. Lipids are the chief concentrated storage form of energy forming about 3.5% of the cell content. Lipids are small molecular weight compounds. Lipids are organic substances relatively insoluble in water but soluble in organic solvents (alcohol, ether) Functions : They are the concentrated fuel reserve of the body. Lipids are constituents of membrane structure and regulate the membrane permeability . They serve as source of fat soluble vitamins [ Vit ADEK] Lipids are important cellular metabolic regulators Lipds protect the internal organs and serve as insulating materials Like in neurons ,it has myelin sheath which is made up of lipids 6. Shape and contour to body 7. Makes food taste & palatability

20. LIPIDS S i mple Complex De r i v e d Phospholipids Glycolipids L i poprot e i ns Fats & Oils W a x es Steroids T erpenes General formula of Fatty acid is C n H 2n O 2

21. SIMPLE LIPIDS They are esters of fatty acids with alcohol. They are of 2 types : Neutral or true fats : Esters of fatty acids with glycerol Waxes : Esters of fatty acids with alcohol other than glycerol. Neutral / True fats True fats are made up of C, H, & O but O is less A fat molecule is made up of 2 components : GLYCEROL (1 mol) FATTY ACIDS (1-3 mol, of same or diff long chained)

22. G l y c e r o l A glycerol mol has 3 carbons each bearing a –OH group Fatty acid A fatty acid mol is an unbranched chain of C- atoms. It has a –COOH group at one end and a H bonded to almost all the C-atoms Fatty acids may be saturated or unsaturated

23. Unsaturated fatty acids (oils) may further divided as 1. mono unsaturated fatty acid – containing one double bond Ex: oleic acid 2. poly unsaturated fatty acid – containing 2 or more double bonds Ex: linoleic acid, arachidonic acid

24. COMPL E X LIPIDS They are derivatives of simple lipids having additional group like phosphate, N 2 -base, Protein etc. They are further divided into Phospholipids, Glycolipids, Lipoproteins . Phospholipid They are made up of a molecule of glycerol Or other alcohol having A phos group at 1 of its –OH groups 2 fatty acid molecules at other 2 –OH groups A nitrogen containing base attatched to phos group A phospholipid molecule has a hydrophobic tail (fatty acids) and a hydrophilic head(phos group)

25. Glycolipid They are components of cell membranes, particularly myelin sheath and chloroplast membranes CEREBROSIDE are the most simplest form of glycolipids

26. Lipoprotein They contain lipids and proteins in theirmolecules . They are main constituent of membranes. They are found in milk and Egg yolk. Lipids are transported in blood and lymph as lipoproteins. 5 types of lipoproteins : chylomicrons VLDL LDL HDL Free fatty acid albumin complex

27. D E RIV E D LIPIDS They are derivatives obtained on the hydrolysis of the simple and complex lipids. e.g. steroids, terpenes and prostaglandins Ster o id The steroids do not contain fatty acids but are included in lipids as they have fat-like properties. They are made up of 4 fused carbon rings Cholesterol, Vit D, testosterone, adrenocortical hormones. The most common steroids are STEROLS. Common sterols are Cholesterol and ergosterol

28. Terpenes Terpenes are a major component of essential oils produced by plants. They give fragrance to the plant parts. Vitamins A, E and K contain a terpenoid called phytol Carotenoid pigment is precursor for Vitamin A Lycopene , a pigment present in tomatoes is a terpenoid Gibberellin s, the plant hormone is also a terpene

29. On the basis of production in body 1. essential fatty acids- not produced by body 2. non essential fatty acids – can be synthesized in body LDL and HDL: Low density lipo proteins transport cholesterol from liver through blood to the tissues (Bad cholesterol) High density Lipo proteins transports cholesterol from blood to the liver where it is metabolized ( Good Cholestrol ) LDL – high risk of heart attack HDL – Low risk of heart attack

30. ENZYMES

31. Enzymes are a group of catalysts functioning in a biological system They are usually proteinaceous substances (2° and 3° structure) produced by the living cell Without themselves getting affected. Enzymes enhance the rate of reaction and are formed in the cell under the instructions of genes ENZYMOLOGY is the branch of science that deals with the study of Enzymes in all the aspects like nomenclature, reactions and functions Enzymes occur in colloidal state and are often produced in inactive form called proenzymes (zymogen), which are converted to their active forms by specific factors like pH, substrate etc. The enzymes that are produced within a cell for metabolic activities are known as endoenzymes and those which act away from the site of synthesis are called exo - enzymes

32. GENERAL PROPERTIES OF ENZYME AND FACTORS AFFECTING THEIR ACTIVITY Enzymes accelerate the reaction but do not initiate it. Enzymes themselves do not participate in the reaction and remain unchanged at the end of the reaction. Enzymes, are therefore, needed in small amounts . The molecule of an enzyme is larger than that of substrate molecule and hence during reaction a specific part of enzyme molecule comes in contact with the substrate molecule. That part is called active site of enzyme. Amphoteric nature: Chemically most of the enzymes are proteins and, therefore, show amphoteric nature. The enzymes can react with acidic substances as well as alkaline substances.

33. Specificity: Most of the enzymes are specific in their action. A single enzyme acts upon a single substrate or a group of closely related substrates. For example, the enzyme urease can act only upon urea , invertase can act upon sucrose only A slight change in the configuration of the substrate molecule requires action by a different enzyme. Colloidal nature: All enzymes are colloidal in nature and thus provide large surface area for reaction to take place. Colloids (colloids- gel like) are mixtures of two components i.e. dispersed particles and dispersion medium. The size of the dispersed particles is larger than dispersion medium.

34. Enzyme optima : Enzymes generally work best under certain narrowly defined conditions referred to as optima. These include appropriate temperature and PH. Temperature sensitivity : Since the enzymes are proteins, they are affected by change in temperature. With increase in temperature, increase in enzyme activity takes place (up to 40 C). However, when temperature increases above 60 C the proteins undergo denaturation or even complete breakdown . When the temperature is reduced to freezing point or below freezing point the enzymes become inactivated but they are not destroyed. The rate of reaction is more at optimum temperature. pH sensitivity : Most of the enzymes are specific to pH and remain active within particular range of pH. The strong acid or strong base denatures enzymes. Most of the intracellular enzymes function best around neutral pH

35. Concentration of enzyme and substrate : The rate of reaction is proportionate to the concentration of the reacting molecules. If the substrate concentration is increased the rate of enzyme action also increases up to certain limit. Beyond a certain concentration, the enzyme molecules remain saturated with substrate molecules and the activity becomes steady. Enzyme inhibitors : Enzyme inhibitors are certain products which inhibit enzyme activity. During the reaction, if the active site of enzyme is occupied by these inhibitors instead of substrate molecules and the activity of enzyme is lost . These substances are like substrate molecules in their structure and are called competitive inhibitors .

36. ENZYME INHIBITION: The activity of an enzyme is sensitive to the presence of specific chemicals that bind to the enzyme. when the bonding of a chemical shuts off enzyme activity, the process is called Inhibition and the chemical is called inhibitor. Foreign substances can block the catalytic effects of enzymes. These substances Are called enzyme inhibitors There are 2 types Competitive inhibition Non competitive inhibition

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38. Competitive inhibition: These inhibitors resembles the structure of substrates, also Called as “ substrate analogues ”. Ex: malonic acid is a competitive inhibitor for succinic dehydrogenase enzyme Non-Competitive inhibition: Inhibitors which do not resemble the substrate in structure But decrease the activity of the enzyme. They bind at any other place other than active site and renders It inactive. Ex: salts of heavy metals like copper, mercury, Ag etc

39. The protein chain folds up on itself, the chain criss-crosses itself and hence, many crevices or pockets are formed. one such pocket is called ACTIVE SITE. The chemical which is converted into a product is called a ‘substrate’. The enzymes(proteins with 3D structures) including active site, convert a substrate (S) in to a product (P). During the state where substrate is bound to the enzyme active state, a new Structure of the substrate called transition state structure is formed. Bond breaking Or making is completed. The product is released from the active site.

40. The energy level difference between S and P. If P is at a lower level than S, the reaction is an exothermic reaction . (need not to supply Energy (heating) to form product) and vice versa. Whether it is an exothermic or endothermic reaction, the “S” has to go through a much high energy state or transition state. The difference of average energy content of S from That of this transition state is called “ Activation energy ”

41. Classification and nomenclature of enzymes Enzymes are divided in to 6 classes each with 4-13 subclasses and named accordingly by a four- digit number. They are named by adding the suffix ‘ ase ’ to the root word of the substrate. i.e enzymes that act on sucrose – sucrase, lipid –lipase , protein – protease, nucleic acid – nuclease respectively. Some enzymes are named according to their reaction they catalyze. Ex: dehydrogenase - dehydrogenation, polymerase – polymerization Also, some enzymes are named after their sources. Ex: papain from papaya.

42. Some enzymes like pepsin, trypsin, renin and casein do not end up with suffix ‘ ase ’, The detailed method of naming enzymes has been developed by International union of biochemistry and molecular biology ( IUBMB)

43. Group of Enzymes Reactions catalysed Examples 1. Oxidoreductases Transfer of O 2 or H 2 atoms or electrons from one substrate to another D e h y dr o gena s e Oxidases 2.Transferases Transfer of a specific group (other than H) from one substrate to another Transaminase 3.Hydrolases Hydrolysis of a ester, peptide, glycosidic bonds Digestive enzymes 4. Isomerases Change of the molecular form of the substrate ( interconversion of geometric or positional isomers) Phospho Hexo isomerase 5.Lyases removal of groups from substrates other than hydrolysis leaving double bonds D e c arb o x y l ase Aldolase 6. Ligases Joining of 2 molecules by formation of new bonds Citric acid syn t h et ase