The Chemistry of life

All living things are composed of and use chemicals More than 100,000 chemicals are used by living organism for defence communication aggression reproduction and various other activities

 These chemicals may be organic/inorganic The branch of biology that deals with the study of chemistry of living things is called BIOCHEMISTRY

Four major organic molecules living things are associated with Carbohydrates: Polymers of sugars Lipids: Macromolecules constructed from fatty acids & glycerol Proteins: Polymers of amino acids Nucleic Acids: Polymers of nucleotides

 Biological polymers are formed by a common reaction known as CONDENSATION or DEHYDRATION SYNTHESIS REACTION Water is removed (dehydration) to form a bond between the growing polymer and the next monomer subunit.

 Large biological polymers are broken down through the reverse reaction HYDROLYSIS Water (H-OH) is added to break a covalent bond between subunits in a polymer.

Dehydration

Hydrolysis

CARBOHYDRATES
A class of organic molecules Hydrates of carbon Cn(H20)n Eg:C6H12O6 , (CH20)6, C6(H2O)6 Monomers called monosaccharides or simple sugars No.of carbon atoms with a ose indicates a carbohydrate

Glucose is an example of a hexose or simple sugar.

C6 (H2O)6

E vs. F sugars

 Simple sugars combine with each other by dehydration synthesis reaction to form complex carbohydrates. In this reaction, a macromolecule is formed when water is removed from smaller component parts. When one monomer with OH group attaches with H of other dehydration synthesis reaction results.

Disaccharides
Two monomeric units bonded together Bonds are specifically called GLYCOSIDIC BONDS Sucrose = glucose + fructose

Held together by a Glycosidic bonds

Glycosidic Bonds Link Monosaccharides Sucrose= a disaccharide made from glucose and fructose.

Glycosidic Bond E1, 2 linkage

Lactose: A Dissacharide The glycosidic bond is a F 1,4 linkage

The glycosidic bond

Polysaccharides(complex carbohydrates)
More than 2 monomeric units joined by glycosidic linkage by dehydration synthesis reaction Eg: Starch(Plants), glycogen(storage form in animals) Breaking of these polymers to individual subunits is done by hydrolysis.

Cellulose

Cellulose

Cellulose: Another polysaccharide

Constructing the cell walls of plant cell Humans cannot hydrolyse cellulose as they lack cellulase Hence, cellulose not used as energy source However, this adds bulk/fibre to our diet Helps in proper digestion, reduce risk of colon cancer etc.

Function of Carbohydrates
Storage substances of potential energy Sugar can be used by the cell as a component of other complex molecules such as DNA , RNA, ATP. Important for cell-cell recognition & communication

LIPIDS
Large non polar organic molecules Insoluble in water Soluble in organic solvents like ethers or acetone Amount of oxygen is less as compared to hydrogen and carbon

Classification of Lipids
Simple lipids  Steroids  Prostaglandin  Cannot be hydrolyzed to get the monomeric unit

Complex Lipids
True fats Phospholipids Waxes Can be hydrolyzed to get soaps

True Fats
Glycerol Fatty Acid

Depending on the R group, these compounds have very different properties. Saturated Fatty acid (Animal fat)

Unsaturated Fatty acid (plant fat)

Saturated fatty acid: A saturated fatty acid is fully loaded with hydrogen atoms and contain only single bonds between carbon. Generally found in animal tissues Solid at room temperature Ex. Stearic acid (found in solid meat)

Unsaturated fatty acids:

Carbon double bonded to each other in the chain at one or more positions Generally Present in plants ( peanut oil, olive oil) Liquid at room temperature Example: Linoleic acid (Also an essential fatty acid for humans)*

 The occurence of double bonds in fatty acids is indicated by Greek letter followed by a number indicating the location of first double bond in the molecule. E.g: Oleic acid C18:1 9 Linoleic acid - C18: 2 6 (Omega 6 Fatty acid) Linolenic acid - C18: 3 3 (Omega 3 fatty acid)

Synthesis of triglycerides
Glycerol + 3 fatty acids= Triglycerides

Phospholipids
Fatty acids containing phosphates Major components of membranes Separates cell contents for external environment

Phospholipids

Some phospholipids are also known as Lecithins

Phospholipids

Lecithins
Another class of phospholipids Important constituent of cell membranes Emulsification of fats (present in choclates) Fatty acids
acids

Smaller fatty

Easy for the body to absorb

Steroids
Lipid molecules with a typical interlocking ring structure Many of them acts as hormones Steroid hormones are lipid soluble Example: Cholesterol, testosterone, estradiol etc.

Cholesterol
Found in blood associated with lipoproteins Excessive deposits can cause Atherosclerosis Used to synthesize bile salts and cell membranes
Used as compenents of cell membrane Necessary for the synthesis of Vit.D

Importance of fats
Molecules for storing energy Energy of 1g fat = 2g sugar Acts as a insulating layer under skin Prevents heat loss from body (whales, seals and walruses Prevents damage to many organs by acting as a cushion (Eyes and kidneys)

END OF LECTURE

Chapter 3 The Chemistry of life

Proteins
Polymers of amino acids Amino acids - short carbon skeleton having amino (NH2)group on one end and carboxyl group on the other end.

Amino acids

Amino acid cont.

Total of 20 different amino acids found in nature that differ in the R group and are very important to cells. These are the building blocks of the millions of different proteins found in living systems Out of these 20, 9 are called essential amino acids as these cannot be synthesized by body and needs to be supplied in diet. (Meth, val, leu,Iso,His, Phe,threo,trypto, lysine)

Amino Acids Cont..

Amino acids are bound to one another by dehydration synthesis reaction Carboxyl acid group of one will form Covalent bond with the amino group of the another amino acid by removal of water molecule This covalent bond which joins the amino acids together is called as the peptide bond

Amino Acid Cont..

The long chain of amino acids formed is called polypeptide chain. A specific polypeptide chain is composed of a specific sequence of amino acids bonded end to end.

Four levels of protein structure

Primary structure Secondary structure Tertiary structure Quaternary structure

Primary structure
 Actual sequence of amino acids in a protein  This primary structure is encoded by various genes present in the DNA The primary structure of a protein is linear.

Secondary Structure
Twisted primary structure Hydrogen bonding stabilizes these structures Generally found of two types  Alpha helix  Beta Sheets

-helix
Similar to the shape of a coiled telephone cord The helical shape is maintained by hydrogen bonds between the amino acid side chains at different locations Ex. Hair

Beta sheets
Formed from two chain lying parallel or anti parallel to each other Flat sheet like structure Hydrogen bonds are the major forces which stabilizes this structure Ex. Silk

Beta Pleated sheet

Tertiary structure
Coiled telephone cord coils around itself many times Contains both alpha and beta sheets Both intermolecular and intramolecular hydrogen bonds are formed Ex. Myoglobin (Oxygen holding protein containing 153aa)

Structure of Myoglobin

Quaternary structures
Several tertiary polypeptides coil around each other Forms a large globular structure with different interacting polypeptide chains Disulphide bonds, covalent bonds and hydrogen bonds are present Ex: Haemoglobin, Insulin, Antibodies

Quaternary structure

Immunoglobulins

Importance of protein structure

Structure is closely related to its function Any changes in the arrangement of amino acids can have far-reaching effects on its function Ex. haemoglobin made up of 2 types of polypeptide chains - alpha and beta Change in one amino acid of one chain(glutamic acid replaced by valine in sixth position)---Chains folds in different pattern -Sickle cell anemia

Protein folding
Either Helix or Beta sheet Improper folding may result into Alzheimers disease, Bovine Spongiform encephalitis, Cruetzfeldt Jacobs disease All resulting from improper folding of helix or beta sheets

Reasons for Changes in protein structure

Because of altered amino acid sequence Changing environmental conditions Ex. Change in pH, ionic strength of the solution , Temperature

Protein denaturation
Denaturation: Irreversible loss of physical and chemical properties of proteins Caused by excessive heating which disrupts the hydrogen bonds of the protein Common example: yellow portion of egg changing to white solid mass when heated Insulin kept in dark bottles to prevent Denaturation by light

Types of protein and functions

Structural proteins  Maintains the shape of cell and organism  Makes muscle cells, cell membrane, tendons and blood cells  Provides rigidity and flexibility for body movements

Regulatory proteins
Regulates the various biochemical activities of the body Enzymes and hormones are regulatory proteins Insulin (Hormone): produced by pancreas and regulates the amount of glucose in the blood If produced in less amount ----- Diabetes Excess sugar eliminated form through urine

Oxytocin
Another regulatory hormone Secreted by pituitary gland Stimulates the contraction of uterus during child birth Pitocin artificial homologue of Oxytocin

Nucleic acids
Complex polymeric molecules which store and transfer information within a cell Constructed from basic monomeric units known as Nucleotides Nucleotide= sugar + phosphate+ organic nitrogenous bases Sugars: Ribose, Deoxyribose

Nucleic acids cont.

1) 2) 3) 4) 5) Nitrogenous bases Adenine Guanine Thymidine Cytosine Uracil (in case of RNA)

Nucleic acids two types

DNA- Deoxyribonucleic acid - deoxyribonucleotides - Has deoxyribose sugar - Has adenine, guanine, cytosine and thymine - Usually double stranded - Two strands joined by hydrogen bonds - Adenine thymine pairing - Guanine Cytosine Pairing RNA-Ribonucleic acid Ribonucleotides Has ribose sugar Has adenine, guanine, cytosine and uracil Usually single stranded Secondary structure Adenine uracil pairing guanine cytosine pairing

DNA(deoxyribonucleic acid)
Hereditary molecule (stores all the information needed for protein synthesis) Molecular model proposed by Watson and Crick in 1953 Has a double helix structure Two strands are interwined in clock wise direction in right hand helix

DNA Cont
The strand completes a turn each 34 Ao Each nucleotide occupies 3.4 Ao Thus there are 10 nucleotides per turn Width of DNA molecule is 20 Ao Each step in DNA ladder made up of purine and pyrimidine pair No. of purines = No. of pyrimidines

DNA Structure

RNA structure

Phosphodiester bonds

RNA (Ribonucleic acid)

. Contains the information needed for protein synthesis Synthesized from DNA by a process known as transcription