Biological Molecules

Biochemistry

Biochemistry is a branch of biology which deals with the study of chemical components and the chemical processes occurring in living organisms.

A basic knowledge of Biochemistry is essential for understanding anatomy, physiology, because all of the structures of an organism have biochemical organization.

Chemical Composition of Protoplasm

• Approximately 25 elements out of 92 naturally occurring elements of earth are found in living beings (bioelements).
• Human body is composed of only 16 of these bioelements.
• Six common bioelements constitute 99% of protoplasm (major bioelements).
• Minor bioelements: less than 1% of protoplasm.
• Trace elements: less than 0.01% of protoplasm.

Four Fundamental Biological Molecules

1. Carbohydrates
2. Proteins
3. Lipids
4. Nucleic Acids

General Importance

• Water is the medium of life and is most abundant compound in all organisms.
• Varies from 65 to 89% in different organisms.
• Human tissues: about 20% water in bone cells and 85% in brain cells.
• Jellyfish: 99% water (body shows transparency).
• Acts as a lubricant against friction (e.g., tears protect eye surface).
• Acts as fluid cushion around organs that protect them from trauma.
• Biochemical reactions take place in the presence of water.
• Takes part in many biochemical reactions such as hydrolysis of macromolecules.
• Used as a raw material in reactions like photosynthesis.

Properties of Water

High Polarity

• Water molecules have polar covalent bonds (oxygen is more electronegative).
• Oxygen has slight negative charge; each hydrogen has slight positive charge.
• Makes water an excellent universal solvent for polar substances.

High Specific Heat Capacity

• Amount of heat required for minimum increase (1°C) in temperature of 1g of a substance.
• Water has relatively very high heat capacity due to hydrogen bonding.
• Works as temperature stabilizer or regulator for organisms.

Heat of Vaporization

• Amount of heat required to change 1g of water from liquid to gaseous state.
• Specific heat of vaporization of water is 574 Kcal/kg.
• Provides cooling effect to plants and animals.

Cohesion and Adhesion

• Cohesion: attraction among water molecules enabling them to stick together.
• Adhesion: attraction of water molecules to polar surfaces.
• Both due to hydrogen bonds among water molecules.
• Enables water to act as transport medium in living bodies.

Hydrophobic Exclusion

• Reduction of contact area between water and hydrophobic substances.
• Plays key role in maintaining integrity of lipid bilayer membrane.

Ionization of Water

• H₂O ⇌ H⁺ + OH⁻ (reversible reaction).
• At 25°C, concentration of each H⁺ and OH⁻ ions in pure water is about 10⁻⁷ moles/lit.
• Water behaves as acid or base (amphoteric) and as buffer.

Density of Water

• Ice floats on water because ice is less dense than water.
• Ice has maximum hydrogen bonding; molecules arranged in lattice structure.
• Provides environment for organisms to live under ice in freezing weather.

Introduction

• Literal meaning: ‘hydrated carbons’ – carbon associated with water.
• Composed of carbon, hydrogen, and oxygen (mostly H:O ratio 2:1 as in water).
• Chemically: ‘polyhydroxy aldehydes or ketones or complex substances which on hydrolysis yield polyhydroxy aldehyde or ketone subunits’.
• General formula: Cₓ(H₂O)ᵧ where ‘x’ is whole number from three to many thousands.
• Simple carbohydrates are main source of energy in cell.
• Some carbohydrates are main constituents of cell wall in plants, fungi and microorganisms.
• Main source: green plants via photosynthesis.
• Combine with proteins and lipids to form glycoproteins & glycolipids (glyco-conjugates).

Major Groups of Carbohydrates

Monosaccharides

• Simplest carbohydrates: polyhydroxy aldehydes or polyhydroxy ketones.
• Classified based on carbon atoms present (trioses, tetroses, pentoses, hexoses, heptoses).
• In nature, monosaccharides with 3-7 carbon atoms are found.
• Glucose: naturally produced in green plants via photosynthesis.
• Synthesis of 10g of glucose requires 717.6 Kcal of solar energy.
• Blood contains 0.08% glucose.
• Starch, cellulose, and glycogen yield glucose on complete hydrolysis.

Oligosaccharides

• Disaccharides: yield two monosaccharides on hydrolysis.
• Trisaccharides: yield three monosaccharides on hydrolysis.
• Covalent bond between monosaccharides: glycosidic bond.
• Important disaccharides: maltose, sucrose, lactose (C₁₂H₂₂O₁₁).

Polysaccharides

• Formed by several monosaccharide units linked by glycosidic bonds.
• Act as structural components, food and energy stores.
• Homo-polysaccharides: formed by condensation of only one kind of monosaccharide (e.g., starch, glycogen, cellulose, chitin).
• Hetero-polysaccharides: formed by condensation of different kinds of monosaccharides (e.g., agar, pectin, peptidoglycan).

Introduction

• Most abundant organic compounds found in cells (>50% of total dry weight).
• Human body has more than 10,000 proteins.
• Polymers of amino acids (contain C, N, O, H, and some contain S).
• Chemically: ‘polymers of amino acids or polypeptides chains’.

Functions of Proteins

Amino Acids

• Building blocks of proteins.
• About 170 types found in cells and tissues.
• Only 25 are constituents of proteins; most proteins made of 20 types.
• Basic structure: central alpha carbon attached to H atom, amino group (-NH₂), carboxylic group (-COOH), and R-group.
• R-group determines individual chemical properties.

Protein Structure

Primary Structure

• Sequence of amino acids determined by F. Sanger.
• Determined by order of nucleotides in DNA.
• Sickle cell anemia: caused by point mutation in β-globin gene.
• Glutamic acid replaced by valine at position number six in hemoglobin.

Secondary Structure

• α-helix: uniform geometric structure with 3.6 amino acids per turn.
• β-pleated sheet: formed by folding back of polypeptide.

Tertiary Structure

In aqueous environment, hydrophobic amino acids buried inside while hydrophilic amino acids on surface.

Quaternary Structure

Polypeptide tertiary chains aggregated and held together by various bonds and interactions.

Classification of Proteins

Introduction

• Collective term for variety of organic compounds: fats, oils, waxes, steroids.
• Heterogeneous group of organic compounds mostly related to fatty acids.
• Insoluble in water but soluble in organic solvents.
• Hydrophobic nature makes them best suited as structural component of cell membranes.
• Store double the amount of energy as compared to same amount of carbohydrates.
• May act as insulating layer (e.g., waxes in exoskeleton of insects).

Classification of Lipids

1. Simple lipids: esters of fatty acids with various alcohols (e.g., acylglycerols, waxes).
2. Complex lipids: contain other groups in addition to alcohol and fatty acids (e.g., phospholipids, glycolipids, lipoproteins).
3. Derived lipids: derivatives of simple and complex lipids (e.g., terpenes, steroids, prostaglandins, cholesterol).

Acylglycerols

• Most abundant lipids in living things.
• Chemically: ‘esters of glycerol and fatty acids’.
• Glycerol: tri-hydroxy alcohol with three carbons, each bearing OH group.
• Monoacylglycerol: glycerol + one fatty acid.
• Diacylglycerol: glycerol + two fatty acids.
• Triacylglycerol: glycerol + three fatty acids (also called ‘neutral lipids’).

Fatty Acids

• Organic compound containing one carboxylic acid group attached to hydrocarbon chain.
• Contain even number of carbon atoms (2-30).
• Represented as R-COOH, where R is hydrocarbon tail.
• Fats and oils are lighter than water (Specific gravity ~0.8).

Other Lipid Types

Waxes

• Highly hydrophobic compounds.
• Natural waxes: esters of long chain fatty acids and long chain alcohols (e.g., bee’s wax, cutin).
• Synthetic waxes: derived from petroleum or polyethylene (e.g., paraffin wax).
• Functions: protective functions in plants and animals, machine lubricants.

Phospholipids

• Derivatives of phosphatidic acid by addition of nitrogenous base.
• Head (phosphate group + nitrogenous compound): polar and hydrophilic.
• Tail (fatty acid side chains): non-polar and hydrophobic.
• Example: Phosphatidylcholine (lecithin).
• Function: form biological membranes, regulate cell permeability.

Terpenes

• Synthesized from isoprene unit (C₅H₈).
• Two isoprene units: monoterpene (e.g., menthol).
• Four isoprene units: diterpene (e.g., vitamin A).
• Six isoprene units: triterpene (e.g., ambrein) and polyterpene (e.g., carotenoids).
• Important carotenoids: plant pigments (chlorophyll, cytochromes).

Steroids

• Type of terpenoids with high molecular weight that can be crystallized.
• Steroid nucleus: 17 carbon atoms arranged in four attached rings.
• Cholesterol is precursor of many steroids (bile salts, testosterone, progesterone, estrogen).

Prostaglandins

• Derived from arachidonic acid.
• Exist in virtually every mammalian cell; act as local hormone.
• Functions: regulate B.P and blood flow, induce fever and inflammation, intensify pain sensation, regulate platelet aggregation, induce labour.
• Aspirin reduces fever and pain by inhibiting prostaglandin synthesis.

Introduction

• First isolated from nucleus of pus cells, originally named “Nuclein”.
• Renamed nucleic acid due to acidic properties.
• Two types: DNA and RNA (linear unbranched polymers of nucleotides).

Chemical Composition of Nucleotides

• Each nucleotide consists of:
  1. Pentose sugar (ribose in RNA, deoxyribose in DNA)
  2. Phosphate group
  3. Nitrogen containing base
• Ribose: C₅H₁₀O₅
• Deoxyribose: C₅H₁₀O₄
• Phosphate group provides acidic properties to DNA and RNA.
• Nitrogenous bases:
  • Pyrimidines (single ring): cytosine (C), thymine (T), uracil (U)
  • Purines (double ring): adenine (A), guanine (G)
• Thymine only in DNA; uracil only in RNA.
• Nucleoside: nitrogenous base + pentose sugar.
• Nucleotide: nucleoside + phosphate group.
• Nucleotides connected via phosphodiester linkage.
• Polynucleotides have free 5′ phosphate group at one end and free 3′ hydroxyl group at other end.

Important Nucleotides

• ATP: energy currency of the cell.
• ATP → ADP releases 7.3 Kcal/mole or 31.81 KJ/mole energy.
• NAD⁺ (Nicotinamide adenine dinucleotide), NADP, FAD: important dinucleotides used in oxidation-reduction reactions.

Ribonucleic Acid (RNA)

• Polymer of ribonucleotides.
• Single strand, may fold back to give double helical characteristics.
• Synthesized from DNA via transcription.

Types of RNA

Messenger RNA (mRNA)

• Takes genetic message from nucleus to ribosome.
• Single strand of variable length.
• Length depends on size of gene/protein.
• Every three nucleotides encode specific amino acid (codons).

Transfer RNA (tRNA)

• Smallest in size (75-90 nucleotides).
• Single stranded but shows duplex appearance in some regions.
• Flat cloverleaf shape in 2D views.
• 5′-end terminates in guanine; 3′-end terminates with CCA.
• Has three loops: middle loop contains anti-codon.
• At least 20 kinds (one for each amino acid).
• Human cells contain about 45 different kinds.

Ribosomal RNA (rRNA)

• Major portion of RNA in cell (up to 80%).
• Largest size among RNA types.
• Acts as machinery for protein synthesis.
• Strongly associated with ribosomal proteins (40-50%).

Difference Between DNA and RNA

Two different molecules, belonging to different categories, combine together to form conjugated molecules.