Chapter Notes: Biomolecules

Table of Contents
1. What is a Biomolecule?
2. How to Analyse Chemical Composition of Living Tissue
3. Key Classes of Biomolecules
4. Primary and Secondary Metabolites
5. Biomacromolecules and Molecular Weight
6. Proteins
7. Polysaccharides
8. Nucleic Acids - Structure and Components
9. Metabolic Basis for Living Organisms
10. Enzymes
11. Classification and Nomenclature of Enzymes
12. Co-Factors (Non-Protein Components Required for Activity)
13. Summary
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In our world there are many different kinds of living things. Do they all have the same building blocks? When we compare plants, animals or microbes with non-living matter such as soil or rocks, we find the same chemical elements - notably carbon, hydrogen and oxygen - but living systems contain proportionally more carbon and hydrogen. This higher concentration of certain elements, and the specific ways they are assembled, give living matter its characteristic chemistry and functions.

What is a Biomolecule?

Biomolecules are chemical compounds present in living organisms that are essential for their structure, function and regulation. They range from small molecules involved in metabolism to large macromolecules that form cellular structures and perform complex functions. Major classes include proteins, carbohydrates, lipids, nucleic acids and certain regulatory molecules such as hormones and vitamins.

Types of Biomolecules

Biomolecules can be classified by size and function. Small molecules that play roles in basic metabolic reactions are often called micromolecules (or primary metabolites). Large polymers and complexes such as proteins, nucleic acids and many polysaccharides are termed macromolecules. Both types are essential for the living state.

Biomolecules

How to Analyse Chemical Composition of Living Tissue

To determine which chemical species occur in living tissue, investigators separate and identify the different compounds present in a sample. A classical approach begins by disrupting tissue and partitioning components according to solubility.

• Initial extraction: Tissue is often homogenised and treated with an acid such as trichloroacetic acid to precipitate large macromolecules and leave small soluble compounds in the filtrate.
• Filtration: The homogenate is filtered to obtain an acid-soluble pool (filtrate) containing small molecules and an acid-insoluble fraction (pellet/retentate) containing macromolecules.
• Compound isolation: Techniques such as chromatography and electrophoresis are used to separate and purify individual compounds from the acid-soluble pool.
• Identification: Analytical methods (elemental analysis, mass spectrometry, NMR, IR, etc.) determine molecular formula and probable structure. Biologically relevant classification then groups compounds into categories such as amino acids, nucleotide bases and fatty acids.

Key Classes of Biomolecules

Amino Acids

Amino acids are organic molecules in which an amino group (-NH2) and a carboxyl group (-COOH) are attached to the same carbon atom called the α-carbon. This is why they are called α-amino acids. Each α-amino acid has four substituents on the α-carbon: a hydrogen atom, a carboxyl group, an amino group and a variable side chain denoted R. There are 20 standard amino acids commonly found in proteins; their side chains determine whether an amino acid is acidic, basic, polar, nonpolar or aromatic (for example, tyrosine and phenylalanine are aromatic).

B is called zwitterionic form

Amino acids are amphoteric: they can ionise differently depending on pH (zwitterions), and this property affects protein structure and behaviour.

Lipids

Lipids are a diverse group of molecules that are generally insoluble in water but soluble in nonpolar solvents. Simple lipids include fatty acids, which have a terminal carboxyl group attached to an alkyl chain (the R group). Fatty acids vary by chain length and degree of unsaturation. For example, palmitic acid contains 16 carbons while arachidonic acid has 20 carbons. Fatty acids may be saturated (no C=C double bonds) or unsaturated (one or more C=C).

Glycerol (a trihydroxypropane) combines with fatty acids to form mono-, di- and triacylglycerols (fats and oils). Phospholipids (e.g., lecithin) contain glycerol, fatty acids and a phosphate-containing head and are major components of cell membranes. Nervous tissues and some membranes contain more complex lipids.

Carbohydrates, Amino acids, Fats and oils (lipids)

Nucleic Acids

Nucleic acids (DNA and RNA) are polymers of nucleotides. Each nucleotide consists of a nitrogenous base (a heterocyclic compound), a five-carbon sugar (ribose or deoxyribose), and one or more phosphate groups. When a base is linked to a sugar without phosphate it is a nucleoside; when phosphate is present it is a nucleotide. Common nitrogenous bases are adenine, guanine, cytosine, thymine (DNA only) and uracil (RNA only).

Nucleic acids store genetic information (DNA) and transmit it via RNA to direct synthesis of proteins and regulate cellular activities.

Nucleic Acids

Primary and Secondary Metabolites

• Metabolites are the chemical compounds produced or used in an organism's metabolic reactions.
• Primary metabolites are produced by all cells and have direct roles in growth, development and reproduction (for example, amino acids, sugars, nucleotides).
• Secondary metabolites are compounds found especially in plants, fungi and microbes (examples: alkaloids, flavonoids, essential oils). Their biological roles can include defence, signalling and ecological interactions; many have useful applications for humans (rubber, medicinal alkaloids, spices).
• Animal tissues typically contain a wide range of primary metabolites; secondary metabolites are especially diverse in plants and microorganisms.

Some Secondary Metabolites

Biomacromolecules and Molecular Weight

• The acid-soluble pool (small molecules) typically contains compounds with molecular weights from about 18 to ~800 daltons (Da).
• The acid-insoluble fraction contains macromolecules such as proteins, nucleic acids, polysaccharides and many structural or membrane lipids with molecular weights usually well above ten thousand daltons.
• Biomolecules are therefore described as micromolecules (MW < 1000 Da) and macromolecules (polymers and large complexes).
• Some lipids though small in monomeric mass are classified with macromolecular structures because they occur in membrane assemblies and complexes disrupted during tissue grinding.
• The acid-soluble fraction largely reflects cytoplasmic composition, while macromolecules include cytoplasmic and organelle components.
• Water is the most abundant chemical in living organisms by quantity and is essential to biomolecular structure and reactions.

Average Composition of Cells

Proteins

Proteins are polypeptide chains formed by the linkage of amino acids via peptide bonds between the amino group of one residue and the carboxyl group of the next. There are 20 common amino acids that make up proteins.

1. Essential amino acids: cannot be synthesised in sufficient quantities and must be obtained in the diet.
2. Non-essential amino acids: can be synthesised by the body from metabolic intermediates.

The major roles of proteins in cells include:

1. Transport of nutrients and molecules across membranes (transport proteins).
2. Immune defence (antibodies and other defence proteins).
3. Catalysis of biochemical reactions (enzymes).

Some Proteins and their Functions

Collagen is the most abundant protein in the animal kingdom; it provides structural strength to skin, bone and connective tissue.

Structure of Proteins

(a) Primary Structure

The primary structure is the linear sequence of amino acids in a polypeptide chain. The end with the free amino group is called the N-terminal, and the end with the free carboxyl group is the C-terminal.

(b) Secondary Structure

Secondary structure arises from hydrogen bonding between backbone atoms. Common motifs are:

• α-helix: the polypeptide chain coils in a right-handed helix stabilised by hydrogen bonds.
• β-pleated sheet: two or more segments of the polypeptide lie side by side and are linked by hydrogen bonds.
• Collagen triple helix: three polypeptide strands coil together, characteristic of collagen.

(c) Tertiary Structure

Tertiary structure is the three-dimensional folding of a single polypeptide chain due to interactions between side chains (hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide bridges), giving the protein its specific shape and active sites.

(d) Quaternary Structure

Quaternary structure exists when two or more polypeptide chains (subunits) assemble into a functional protein complex. For example, adult haemoglobin is composed of four subunits: two α and two β subunits.

Polysaccharides

• Polysaccharides are long chains of monosaccharide units linked by glycosidic bonds.
• They may be homopolymers (one type of monosaccharide) or heteropolymers (different monosaccharides).
• Cellulose is a homopolymer of glucose and a primary structural component of plant cell walls.
• Starch (plant storage) and glycogen (animal storage) are glucose polymers that differ in branching; glycogen is highly branched.
• Inulin is a fructose polymer found in some plants.
• Polysaccharide chains have a reducing end and one or more non-reducing ends; branching affects their physical properties and enzymatic breakdown.
• Starch forms a helical structure that binds iodine (I2) producing a blue colour; cellulose does not form the same helices and does not give the same iodine reaction.

Diagrammatic representation of a portion of glycogen

Nucleic Acids - Structure and Components

Nucleic acids are polynucleotides built from repeating nucleotide units. Each nucleotide has three chemically distinct parts: a nitrogenous base, a five-carbon sugar (ribose in RNA, deoxyribose in DNA) and phosphate groups.

• Nucleic acids that contain deoxyribose are called DNA (deoxyribonucleic acid) and those that contain ribose are called RNA (ribonucleic acid).
• Biomolecules are continually synthesised and degraded; the ensemble of chemical reactions that build and break biomolecules is called metabolism.
• In living organisms, almost all metabolic reactions are enzyme-catalysed. Proteins that accelerate biochemical reactions are called enzymes.

Metabolic Basis for Living Organisms

• Pathways that build complex molecules from simpler ones are called anabolic (biosynthetic) pathways.
• Pathways that break down complex molecules into simpler ones are called catabolic pathways.
• Examples: photosynthesis and protein synthesis are anabolic; respiration and digestion are catabolic.
• ATP (adenosine triphosphate) is the main energy currency used to drive many biochemical reactions.
• Living systems operate in a non-equilibrium steady state, maintaining concentrations of metabolites that allow continuous performance of work and regulation.

Enzymes

Enzymes are biological catalysts that accelerate chemical reactions without being consumed. Most enzymes are proteins; some RNA molecules (called ribozymes) also have catalytic activity.

• As proteins, enzymes have primary, secondary and tertiary structures. The folded tertiary structure creates crevices or pockets; one of these is the active site where catalysis occurs.
• The active site binds specific substrates and brings them into orientations that favour the chemical transformation, greatly increasing the reaction rate.

Enzyme Catalysts versus Inorganic Catalysts

• Inorganic catalysts can operate at high temperatures and pressures; most biological enzymes are sensitive to temperature and denature at elevated temperatures (often above ~40°C for mesophilic enzymes).
• Enzymes from thermophilic organisms (from hot vents or hot springs) can be stable and active at very high temperatures (sometimes up to 80-90°C).
• Enzymes show high specificity for substrates and often large rate accelerations compared with uncatalysed reactions.

Chemical Reactions and Rate of Reaction

Chemical change involves breaking and forming of covalent bonds; physical change involves change of state or shape without bond breakage.

Example of a chemical reaction:

Ba(OH)₂ + H₂SO₄ → BaSO₄ + 2H₂O

The rate of a process is the amount of product formed per unit time and can be expressed as:

rate = δP / δt

Reaction rates depend on factors such as temperature, concentration, surface area, catalysts, and for enzymes: pH and ionic environment. A rough rule often observed is that reaction rates change noticeably with a 10°C change in temperature (rates approximately double or halve depending on direction), though this is only an approximate guide and varies by reaction and system.

Catalysis by Enzymes - An Example

• Enzyme-catalysed reactions are many orders of magnitude faster than uncatalysed equivalents. For example, the enzyme carbonic anhydrase accelerates the hydration of CO₂ to carbonic acid dramatically: without enzyme ~200 molecules formed per hour; with enzyme ~600,000 molecules per second - an increase of around 10 million-fold.

Metabolic Pathways

• Cellular metabolism comprises many enzyme-catalysed reactions arranged as metabolic pathways.
• Glucose catabolism to pyruvate is a sequence of ten enzyme-catalysed reactions; under different physiological conditions the pathway yields different end products: in anaerobic muscle → lactic acid; in aerobiosis → pyruvate (further oxidised); in yeast fermentation → ethanol.
• Overall: Glucose → 2 Pyruvic acid

How Do Enzymes Give Such High Reaction Rates?

Enzymes lower the activation energy required to reach the transition state, making substrate conversion to product much more likely at physiological conditions.

Enzyme-Substrate Interaction

• The substrate (S) binds into the enzyme's active site to form an ES complex. This binding is usually rapid and reversible.
• Binding often induces a conformational change in the enzyme (the induced fit), aligning catalytic residues and placing strain on substrate bonds to facilitate conversion into a high-energy transition state.
• After bond breaking and formation the product (P) is formed and released, regenerating the free enzyme.
• Symbolically: E + S ⇌ ES → EP → E + P

Concept of activation energy

Energy Profile and Activation Energy

• Reaction progress can be represented on an energy diagram: potential energy (y-axis) versus reaction coordinate (x-axis).
• The substrate must reach the higher energy transition state before converting to product; the energy difference between substrate and transition state is the activation energy.
• Enzymes stabilise the transition state and thus reduce the activation energy, speeding up the reaction.
• If product energy is lower than substrate energy the reaction is exothermic (energy releasing); if higher it is endothermic (requires input of energy).

Nature of Enzyme Action

• Binding of substrate to enzyme active site forms an enzyme-substrate (ES) complex.
• Induced fit: enzyme changes conformation to fit the substrate more closely, facilitating catalysis.
• Transition to an enzyme-product (EP) complex follows bond reorganisation, after which the product dissociates and the enzyme is free to catalyse another turnover.

Factors Affecting Enzyme Activity

• Enzyme activity depends on the integrity of the protein's tertiary structure. Factors that alter this structure will affect activity.
• Temperature: each enzyme has an optimum temperature; activity falls at lower temperatures (reduced kinetic energy) and at higher temperatures (denaturation).
• pH: each enzyme has an optimum pH; deviations alter ionisation of amino acid side chains and substrate binding.
• Substrate concentration: increasing [substrate] increases reaction rate until a maximum velocity (Vmax) is reached when all enzyme active sites are occupied (saturation).

Effect of change in : (a) pH (b) Temperature and (c) Concentration of substrate on enzyme activity

Enzyme Inhibition

• Certain chemicals bind to enzymes and reduce activity; these are called inhibitors.
• Competitive inhibitors resemble the substrate and compete for the active site, reducing substrate binding (example: malonate inhibits succinic dehydrogenase by resembling succinate).
• Inhibitors can be used therapeutically or to control microbial pathogens.

Classification and Nomenclature of Enzymes

Enzymes are classified by the type of chemical reaction they catalyse. There are six major classes, each with several subclasses. The commonly used classification follows the International Union of Biochemistry (EC numbers), but the classes can be described conceptually as:

Classification of Enzymes​

1. Oxidoreductases (Dehydrogenases)

These catalyse oxidation-reduction reactions between two substrates (one is oxidised while the other is reduced).

• General form: S (reduced) + S' (oxidised) → S (oxidised) + S' (reduced)

2. Transferases

Transferases transfer specific functional groups (other than hydrogen) from one molecule to another.

• General form: S-G + S' → S + S'-G

3. Hydrolases

Hydrolases catalyse hydrolytic cleavage of bonds by addition of water, including:

• ester bonds, ether bonds, peptide bonds, glycosidic bonds, C-C bonds, C-halide bonds, P-N bonds

4. Lyases

Lyases remove groups from substrates (or add groups to double bonds) without hydrolysis, often forming double bonds or rings.

5. Isomerases

Isomerases catalyse rearrangements within a molecule converting optical, geometric or positional isomers.

6. Ligases

Ligases join two molecules together, usually with the expenditure of chemical energy (often from ATP) to form bonds such as C-O, C-S, C-N or P-O.

Co-Factors (Non-Protein Components Required for Activity)

Some enzymes require non-protein components to be catalytically active. The protein part alone is called the apoenzyme. With its non-protein component it forms the active enzyme or holoenzyme. Cofactors are of three main types:

Types of Cofactors

• Prosthetic groups: tightly or permanently bound organic groups that form an integral part of the enzyme (example: haem in catalase or peroxidase).
• Coenzymes: organic molecules that bind temporarily and participate in the catalytic process. Many coenzymes are derived from vitamins (for example, NAD and NADP contain niacin).
• Metal ions: metal cofactors (e.g., Zn2+, Mg2+, Fe2+/Fe3+) that form coordination bonds with side chains at the active site and sometimes with the substrate (example: zinc in carboxypeptidase).

Removing an essential cofactor disables the enzyme's catalytic activity, showing the importance of these components for many enzyme systems.

Summary

Biomolecules - including proteins, carbohydrates, lipids and nucleic acids - form the chemical basis of life. They range from small metabolites to large macromolecules and perform structural, catalytic, information-carrying and regulatory roles. Metabolism is the set of enzyme-catalysed reactions that build and break these molecules; enzymes lower activation energy, display specificity and are regulated by temperature, pH, substrate concentration and cofactors. Understanding composition, structure and function of biomolecules is fundamental to biology and to applications in medicine, agriculture and biotechnology.