Biomolecules Biology Notes - Chemical Composition, Amino Acids, Lipids, Proteins, Nucleic Acids, Enzymes and Cofactors

Biomolecules are chemical compounds found in living organisms. They include organic and inorganic compounds.

Analysis of Chemical Composition in a Tissue

• Grind a living tissue (vegetable or piece of liver etc.) in trichloroacetic acid (Cl₃CCOOH) to get thick slurry.
• Strain this through a cheesecloth or cotton to get 2 fractions such as filtrate (acid-soluble pool) and the retentate (acid-insoluble fraction).
• The filtrate contains biomicromolecules (biomolecules having molecular weight less than 1000 Dalton).
• The retentate contains biomacromolecules (biomolecules having molecular weight higher than 1000 Dalton).

Analysis of Inorganic Compounds

• Weigh a living tissue (wet weight) and it is dried (dry weight) to evaporate water.
• It is fully burnt to oxidize all carbon compounds to gaseous form (CO₂ & water vapour). It forms ash.
• The ash contains inorganic elements (Ca, Mg, Na, K etc.) & inorganic compounds (SO₄²⁻, PO₄³⁻, NaCl, CaCO₃ etc.).

Comparison of Elements in Non-living & Living Matter

Micromolecules (Biomolecules)

Molecular weight of micromolecules found in the acid soluble pool ranges from 18 to 800 Dalton (Da). The acid soluble pool represents the cytoplasmic composition.

They include amino acids, sugars, nitrogen bases, lipids etc.

1. Amino Acids

• They are the compounds formed of an amino group (-NH2), an acid group (-COOH), H & a variable group (R).
• –NH2 & –COOH are attached to the same carbon atom (α-carbon). So, they are called α-amino acids.
• They are substituted methanes.

20 types of amino acids are used for protein synthesis. They include:

• Acidic amino acids: e.g. Glutamic acid, Aspartic acid.
• Basic amino acids: e.g. Lysine, Arginine.
• Neutral amino acids: e.g. Valine.

Some amino acids are aromatic. E.g. tyrosine, phenyl alanine, and tryptophan.

Amino acids are 2 types:

• Essential amino acids: They cannot be synthesized by the body and should be supplied through diet. E.g. Lysine, leucine, isoleucine, tryptophan etc.
• Non-essential amino acids: They can be synthesized by the body. E.g. Glycine, alanine, serine, arginine etc.

In amino acids, –NH2 & –COOH have ionizable nature. So, structure of amino acids changes in solutions of different pH.

If both –NH2 & –COOH are ionized, it is called Zwitterion.

2. Lipids

Water insoluble. Contain C, H & O but number of oxygen atoms is less.

Types of lipids:

a. Simple lipids:

• These are formed of Fatty acids and alcohol such as glycerol.
• Fatty acids are lipids with a hydrocarbon chain (R- group) ending in –COOH group. i.e. R-COOH.
• E.g. Palmitic acid has 16 carbons (CH₃ - (CH₂)₁₄ - COOH or C₁₅H₃₁ - COOH) and Arachidonic acid has 20 Carbons.

Fatty acids are 2 types:

• Saturated fatty acids: They have no double or triple bonds between carbon atoms. E.g. Palmitic acid, Stearic acid (C₁₇H₃₅COOH) etc.
• Unsaturated Fatty acids: They have one or more C=C bonds. E.g. Oleic acid (C₁₇H₃₃COOH), Arachidonic acid (C₁₉H₃₁COOH) etc.

Structure of glycerol (trihydroxy propane):

CH2-OH
|
CH-OH
|
CH2-OH

Fatty acids are esterified with glycerol through ester bond forming monoglycerides, diglycerides & triglycerides.

• 1 glycerol + 1 fatty acid → Monoglyceride
• 1 glycerol + 2 fatty acid → Diglyceride
• 1 glycerol + 3 fatty acid → Triglyceride

Based on melting point, lipids (triglycerides) are 2 types:

• Fats: Higher melting point.
• Oils: Lower melting point.

b. Compound lipids:

• These are the esters of fatty acids and alcohol with additional groups.
• E.g. They are found in cell membranes. E.g. Lecithin.

c. Derived lipids:

• These are the products of hydrolysis of simple lipids and compound lipids.
• E.g. Cholesterol.

3. Sugars (Carbohydrates)

Sugars are sweet and water-soluble carbohydrates.

They are formed of C, H, and O in the ratio of 1:2:1.

4. Nitrogen Bases

These are the nitrogen-containing cyclic compounds found in nucleic acids.

They are 2 types:

• a. Purines: Includes Adenine (A) & Guanine (G).
• b. Pyrimidines: Includes Cytosine (C), Thymine (T) & Uracil (U).

Nitrogen base + Sugar → Nucleoside

Adenine + Sugar → Adenosine

Guanine + Sugar → Guanosine

Cytosine + Sugar → Cytidine

Thymine + Sugar → Thymidine

Uracil + Sugar → Uridine

Nitrogen base + Sugar + Phosphate → Nucleotide

Adenine + Sugar + Phosphate → Adenylic acid

Guanine + Sugar + Phosphate → Guanylic acid

Cytosine + Sugar + Phosphate → Cytidylic acid

Thymine + Sugar + Phosphate → Thymidylic acid

Uracil + Sugar + Phosphate → Uridylic acid

Nucleotides are heterocyclic compounds.

Nucleic acids (DNA & RNA) are made up of nucleotides.

Biomacromolecules (Macromolecules)

These are biomolecules having molecular weight greater than 1000 Da. They include:

• Proteins
• Polysaccharides
• Nucleic acids

Their molecular weight is 10,000 Da and above.

Acid insoluble fraction (macromolecular fraction) includes macromolecules from cytoplasm and organelles.

Lipid is not strictly a macromolecule as its molecular weight does not exceed 800 Da. But it comes under acid insoluble fraction because many lipids are arranged into structures like cell membranes. When a tissue is grinded, cell membranes are broken and form water insoluble vesicles. They cannot be filtered along acid soluble fraction.

1. Proteins

• Proteins are heteropolymer of amino acids.
• They are polypeptides, i.e., linear chains of amino acids linked by peptide bonds.
• Peptide bond is formed when –COOH group of one amino acid reacts with NH₂ group of next amino acid by releasing a molecule of water (dehydration).

Functions of Proteins

• For growth and tissue repair.
• Transport nutrients across cell membranes. E.g., GLUT-4 enables glucose transport into cell.
• Acts as intercellular ground substance. E.g., collagen.
• Acts as antibodies to fight infectious organisms.
• Acts as receptors. E.g., receptors of smell, taste, hormones.
• Some are hormones (e.g., Insulin), enzymes (e.g., trypsin), pigments (e.g., hemoglobin) etc.

Most abundant protein in animal world: Collagen.

Most abundant protein in the biosphere: Ribulose bisphosphate carboxylase - oxygenase (RuBisCO).

Structural Levels of Protein

• Primary structure: It describes the sequence of amino acids, i.e., the positional information in a protein.
• Secondary structure: Here, one or more polypeptide chains are folded in the form of a helix. It has only right-handed helices. E.g., Keratin, Fibroin (silk fibre).
• Tertiary structure: Here, helical polypeptide chain is further folded like a hollow woolen ball. It gives 3-D view. Tertiary structure is necessary for many biological activities of proteins. E.g., Myoglobin, enzymes.
• Quaternary structure: Here, more than one polypeptide chains form tertiary structure and each chain functions as subunits of protein. E.g., Haemoglobin. It has 4 subunits (2 α subunits and 2 β subunits).

2. Polysaccharides (Complex Carbohydrates)

These are polymers of sugars (monosaccharides). E.g.:

• Starch (homopolymer of glucose)
• Cellulose (homopolymer of glucose)
• Glycogen (homopolymer of glucose)
• Inulin (homopolymer of fructose)

There are complex polysaccharides formed of amino-sugars (e.g., glucosamine, N-acetyl galactosamine etc.).

Chitin is the homopolymer of N-acetyl glucosamine. It is seen in exoskeleton of arthropods and fungal cell wall.

Glycosidic bond in polysaccharides: It is the bond formed when individual monosaccharides are linked between 2 carbon atoms by dehydration.

Starch forms helical secondary structure. It can hold iodine molecules in the helical portion giving blue colour.

Cellulose has no complex helices and so cannot hold iodine.

Diagrammatic Representation of a Portion of Glycogen

3. Nucleic Acids (DNA & RNA)

Nucleic acids are heteropolymer of nucleotides. i.e., many nucleotides are linked to form polynucleotide.

Nucleic acids are 2 types: DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid).

Secondary Structure of DNA (Watson - Crick Double Helix Model)

• There are more than a dozen forms of DNA such as A, B, C, D, E, Z etc.
• DNA consists of 2 polynucleotide strands arranged antiparallelly as a double helix.
• In DNA, a nucleotide consists of nitrogen base, deoxyribose sugar and phosphate group.
• Backbone (strands) of DNA is formed by the sugar-phosphate-sugar chain.
• Steps are formed of Nitrogen base pairs.
• Nitrogen bases include Adenine (A), Guanine (G), Thymine (T) and Cytosine (C). Uracil absent.
• A pairs with T (A=T) by 2 hydrogen bonds.
• G pairs with C (G≡C) by 3 hydrogen bonds.
• A phosphate molecule links the 3’-carbon of the sugar of one nucleotide to the 5’-carbon of the sugar of the next nucleotide. The bond between the phosphate and –OH group of sugar is an ester bond. As there is one such ester bond on either side, it is called phosphodiester bond.
• The bond between sugar and nitrogen base is called N-glycosidic bond.

In B-DNA

• One full turn of helical strand has 10 steps (10 base pairs).
• Length of one full turn = 34 Å (i.e. 3.4 Å for each step).
• At each step, the strand turns 36⁰ (360⁰ for a full turn).

Metabolism

All the biochemical reactions taking place inside a living system together constitute metabolism. E.g.:

• Removal of CO2 from amino acids to form amine.
• Removal of amino group in a nucleotide base.
• Hydrolysis of a glycosidic bond etc.

The intermediate products of metabolic reactions are called Metabolites.

Flow of metabolites in metabolic pathway has a definite rate & direction like automobile traffic. This metabolite flow is called dynamic state of body constituents.

Metabolites are 2 types:

• Primary metabolites: They have identifiable functions in physiological processes and necessary for life. E.g., amino acids, sugars, nucleic acids, lipids, vitamins etc.
• Secondary metabolites: They are not directly involved in normal growth, development or reproduction. They are found in plant, fungal and microbial cells. E.g.:
• Pigments: Carotenoids, Anthocyanins etc.
• Alkaloids: Morphine, Codeine etc.
• Terpenoids: Monoterpenes, Diterpenes etc.
• Essential oils: Lemongrass oil etc.
• Toxins: Abrin, Ricin etc.
• Lectins: Concanavalin A.
• Drugs: Vinblastine, curcumin etc.
• Polymeric substances: Rubber, gums, cellulose etc.

In metabolism, there is a series of linked multistep chemical reaction called metabolic pathways. It is 2 types:

The energy released through catabolism is stored in the form of chemical bonds. When needed, this bond energy is utilized for biosynthetic, osmotic and mechanical works.

The most important energy currency in living system is the bond energy in adenosine triphosphate (ATP).

The Living State

In organisms, the metabolites are present in different concentrations. E.g., Blood concentration of glucose in a normal person is 4.2 - 6.1 mmol/L. Concentration of hormones is nanograms/mL.

Systems at equilibrium cannot perform work. As living organisms work continuously, they cannot reach equilibrium. i.e., “The living state is a non-equilibrium steady-state to be able to perform work”.

Living process is a constant effort to prevent falling into equilibrium. This is achieved by energy input obtained from metabolism. So, no living state without metabolism.

Enzymes

• Enzymes are biological catalysts which influence the speed of biochemical reactions.
• All enzymes are proteins but all proteins are not enzymes.
• Enzymes are specific. i.e., each enzyme has its own substrate.
• Ribozymes: Nucleic acids (RNA) that behave like enzymes.
• Enzymes form tertiary structure (3D) with some crevices (pockets) called ‘active site’ into which the substrate fits.

Chemical Reactions

Chemical compounds undergo two types of changes:

• Physical change: A change in shape or state of matter without breaking bonds. E.g., ice melts into water, water becomes vapour.
• Chemical change (chemical reaction): In this, bonds are broken and new bonds are formed. It may be organic or inorganic reaction. E.g.

Rate of a physical or chemical process = Amount of product formed per unit time. i.e., δp/δt.

Rate is called velocity if the direction is specified.

Rates of physical and chemical processes are influenced by factors such as temperature. Generally, rate doubles or decreases by half for every 10°C change in either direction.

Rate of enzyme catalysed reactions is very high. E.g., Carbonic anhydrase is the fastest enzyme. It accelerates the following reaction 10 million times.

In the absence of enzyme, only 200 molecules of H₂CO₃ are formed in an hour. In the presence of carbonic anhydrase, about 600,000 molecules are formed per second.

In a metabolic pathway, each step is catalysed by different enzymes.

E.g., In glycolysis [Glucose (C₆H₁₂O₆) → 2 Pyruvic acid (C₃H₄O₃)], ten different enzymes take part.

Nature of Enzyme Action (Catalytic Cycle)

Enzyme acts with substrate like a lock & key model action.

It includes the following steps:

• The substrate binds to the active site of enzyme (E+S).
• This induces some changes in enzyme so that the substrate is tightly bound with active site of enzyme to form enzyme-substrate complex (ES).
• The active site breaks chemical bonds of substrate to form enzyme-product complex (EP).
• The enzyme releases the products and the free enzyme is ready to bind to other molecules of the substrate (E+P).

This pathway goes through some unstable transition state structures.

How do Enzymes Speed up a Chemical Reaction? (Concept of Activation Energy)

• Activation energy is the additional energy required to start a chemical reaction.
• In an exothermic or endothermic reaction, the substrate must go through a much higher energy state. It is called transition state energy. Therefore, activation energy is the difference between average energy of substrate and transition state energy.
• If the product (P) is at a lower energy level than the substrate (S), the reaction is an exothermic reaction (spontaneous reaction). It requires no energy (by heating) to form the product.
• In a biochemical reaction, enzymes lower the activation energy. As a result, speed of the reaction increases.

Factors Affecting Enzyme Activity

a) Temperature and pH

Enzymes show highest activity at optimum temperature & pH. Activity declines below and above optimum value.

At low temperature, enzyme temporarily inactive.

At high temperature, enzymes destroy because proteins are denatured by heat.

Inorganic catalysts work at high temperature & pressure. But enzymes get damaged at high temperature (> 40°C).

Thermophilic organisms have enzymes which are stable at high temperature (up to 80-90°C).

b) Concentration of Substrate

With the increase in substrate concentration, the velocity of enzyme action rises at first and reaches a maximum velocity (Vmax). This is not exceeded by further rise in concentration because enzyme molecules are fewer than the substrate molecules i.e., No free enzyme molecules to bind with additional substrate molecules.

c) Presence of Inhibitor

The binding of specific chemicals (inhibitor) shuts off the enzyme activity. This is called inhibition.

The inhibitor closely similar to the substrate is called competitive inhibitor. It competes with the substrate for the binding site of the enzyme. As a result, the substrate cannot bind and the enzyme action declines. E.g., Malonate is similar to the substrate succinate. So, it inhibits succinic dehydrogenase in the following reaction.

Competitive inhibitors are used to control bacterial pathogens.

Classification and Nomenclature of Enzymes

• Oxido-reductases / Dehydrogenases: Catalyze oxido-reduction b/w two substrates.

S reduced + S’ oxidized → S oxidized + S’ reduced

• Transferases: Catalyze transfer of a group (other than hydrogen).

S-G + S’ → S’-G + S

• Hydrolases: Catalyze hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide or P-N bonds.
• Lyases: Catalyze removal of groups by mechanisms other than hydrolysis leaving double bonds.

X-C-C-Y → X-Y + C=C

• Isomerases: Catalyze inter-conversion of optical geometric or positional isomers.
• Ligases: Catalyze the linking of 2 compounds together. E.g., enzymes catalyzing joining of bonds like C-O, C-S, C-N, P-O etc.

Co-factors

These are non-protein constituents bound to the enzyme to make the enzyme catalytically active.

Apo-enzyme: Protein portion of the enzyme.

Co-factor + Apoenzyme = Holoenzyme.

When the co-factor is removed from the enzyme, its catalytic activity is lost.

Co-factors are 3 types:

• Prosthetic group: Organic. Tightly bound to apoenzyme. E.g., Haem. It is a part of the active site of peroxidase and catalase. These enzymes catalyze breakdown of H₂O₂ to water & O₂.
• Co-enzymes: Organic. Transient binding to apoenzyme. Many co-enzymes contain vitamins. E.g., nicotinamide adenine dinucleotide (NAD) and NADP contain niacin.
• Metal ions: They form co-ordination bonds with side chains at active site and one or more co-ordination bonds with the substrate. E.g., Zn is a cofactor for Carboxypeptidase.