Biomolecules

Learning outcomes

1. Understand the basic chemical composition of living organisms.
2. Differentiate between organic and inorganic constituents in biological systems.
3. Grasp the role and structure of biomolecules such as amino acids, lipids, and nucleic acids.
4. Comprehend the functional classification of primary and secondary metabolites.
5. Explore macromolecular structures such as proteins, polysaccharides, and nucleic acids.
6. Learn about the dynamic state of biomolecules in metabolism and the catalytic action of enzymes.

Living organisms, regardless of their size or complexity, exhibit a remarkable similarity in their chemical composition. Both organic compounds and inorganic elements are found within these organisms. The elemental composition of a living organism and non-living matter may appear similar when qualitatively analyzed, but a closer look reveals that living systems have a higher relative abundance of carbon, hydrogen, and oxygen.

Chemical Composition of Living Organisms

In living tissues, biomolecules are found that fall under two categories: organic and inorganic compounds. The chemical composition of living organisms can be studied by breaking down a tissue sample into acid-soluble and acid-insoluble fractions. This method allows scientists to determine the molecular composition and classify the biomolecules.

1. Organic Compounds in Living Organisms: Organic compounds such as amino acids, lipids, and nucleic acids are prevalent in the acid-soluble fraction of living tissues. These molecules have molecular weights of up to 800 daltons (Da) and form the basic building blocks of life.
2. Inorganic Constituents: Inorganic elements like calcium, magnesium, and phosphate can be found in the ash obtained after complete oxidation of biological matter. Inorganic molecules play critical roles in structural support and metabolic pathways.

Important Note: Biomolecules include not only carbon-based compounds but also inorganic elements. This highlights the interdependence of organic and inorganic chemistry in biological systems.

Amino Acids and Their Significance

Amino acids are crucial organic compounds, characterized by an amino group (–NH2) and a carboxyl group (–COOH) attached to the same carbon atom, known as the α-carbon. These amino acids are substituted methanes where the other positions are filled by hydrogen and a variable R group.

1. Classification Based on R Group:
   R groups vary among amino acids, leading to a wide variety of structures. Examples include glycine (with a hydrogen as R group), alanine (methyl group as R), and serine (hydroxymethyl group).
2. Physical and Chemical Properties: Amino acids can be classified as acidic (e.g., glutamic acid), basic (e.g., lysine), or neutral (e.g., valine), depending on their functional groups.
3. Ionizable Nature: Amino acids can exist in different forms based on pH, with the ionizable nature of the amino and carboxyl groups leading to changes in their structure. At neutral pH, most amino acids exist in the zwitterionic form.

Lipids: Structure and Function

Lipids are a diverse group of water-insoluble molecules that play critical roles in cell membrane structure and energy storage. They are composed of fatty acids and glycerol, forming various esterified compounds.

1. Fatty Acids: These have a carboxyl group attached to a long R group. The R group can vary from saturated (without double bonds) to unsaturated (with one or more double bonds). Palmitic acid and arachidonic acid are examples of fatty acids with different carbon chain lengths.
2. Glycerol: This is a trihydroxy propane molecule that forms the backbone of many lipid structures such as triglycerides. Phospholipids are lipids containing phosphorus, which are important for the structure of the cell membrane.
3. Complex Lipids: Lipids found in neural tissues often exhibit more complex structures. Cholesterol and lecithin are examples of lipids that play significant roles in membrane fluidity and cell signaling.

Primary and Secondary Metabolites

Living organisms produce a wide array of organic compounds, which are classified into primary and secondary metabolites based on their roles and functions in physiology.

1. Primary Metabolites: These are compounds like amino acids, sugars, and nucleotides that are involved in basic physiological functions and are found across all living organisms.
2. Secondary Metabolites: Found mainly in plants, fungi, and microorganisms, secondary metabolites such as alkaloids, flavonoids, essential oils, and antibiotics do not participate in normal metabolic processes but have significant ecological and pharmacological roles.

Important Note: While primary metabolites are essential for life, secondary metabolites often provide adaptive advantages to organisms, such as defense against herbivores or pathogens.

Macromolecules and Their Functions

Macromolecules such as proteins, nucleic acids, and polysaccharides play vital roles in cellular processes. These compounds, with molecular weights above 10,000 Da, are typically polymeric, meaning they are composed of repeating units called monomers.

1. Proteins: Proteins are heteropolymers composed of amino acids. The sequence of amino acids defines a protein’s primary structure, while further folding leads to secondary, tertiary, and quaternary structures. Collagen and RuBisCO are examples of proteins with structural and enzymatic roles, respectively.
2. Polysaccharides: These are long chains of monosaccharides that serve structural or storage functions. For example, cellulose is a homopolymer of glucose and forms the cell wall in plants, while starch and glycogen serve as energy reserves in plants and animals.
3. Nucleic Acids: DNA and RNA are polynucleotides made of nucleotides linked by phosphodiester bonds. They carry genetic information and direct the synthesis of proteins in cells.

Table 1: Comparison of Macromolecules in Living Systems

Macromolecule	Monomer	Function
Proteins	Amino acids	Enzymes, structural roles
Polysaccharides	Monosaccharides	Energy storage, structure
Nucleic Acids	Nucleotides	Genetic information
Lipids	Fatty acids, glycerol	Energy storage, membranes

Dynamic State of Biomolecules

In living organisms, biomolecules are constantly in a state of flux. This dynamic nature is a key characteristic of life, where biomolecules undergo continuous transformations through metabolic pathways.

1. Metabolism: Refers to the sum of all chemical reactions that occur within living organisms. These reactions are categorized as either anabolic (building complex molecules from simpler ones) or catabolic (breaking down complex molecules into simpler ones).
2. Enzymes: These are biocatalysts that accelerate chemical reactions without being consumed in the process. Enzymes lower the activation energy required for a reaction to proceed, enabling cellular processes to occur at biologically feasible rates.

Important Note: Enzymes are specific to their substrates and operate under specific conditions of temperature and pH. Any deviation from these conditions can lead to enzyme inactivation or denaturation.

Structure of Proteins

Proteins are vital macromolecules with multiple levels of structural complexity.

1. Primary Structure: This refers to the linear sequence of amino acids in a protein, with each amino acid linked by a peptide bond.
2. Secondary Structure: Involves the folding of the protein chain into structures like alpha-helices or beta-pleated sheets, stabilized by hydrogen bonds.
3. Tertiary Structure: The 3D conformation of a protein that arises from further folding of the secondary structure. The active sites of enzymes are formed at this level.
4. Quaternary Structure: Some proteins are composed of multiple polypeptide subunits. For instance, hemoglobin has a quaternary structure consisting of four subunits.

Nucleic Acids: DNA and RNA

Nucleic acids are polymers made up of nucleotides, each containing a nitrogenous base, a pentose sugar, and a phosphate group.

1. DNA Structure: DNA is composed of two **

antiparallel strands** of nucleotides that form a double helix. The Watson-Crick model describes the structure, where adenine pairs with thymine and guanine pairs with cytosine through hydrogen bonds.

2. RNA Structure: RNA is usually single-stranded and differs from DNA by containing uracil instead of thymine and ribose instead of deoxyribose.

Table 2: Comparison between DNA and RNA

Component	DNA	RNA
Sugar	Deoxyribose	Ribose
Nitrogenous Bases	Adenine, Thymine, Guanine, Cytosine	Adenine, Uracil, Guanine, Cytosine
Strands	Double-stranded	Single-stranded
Function	Genetic information storage	Protein synthesis

Metabolism and Energy

The metabolic pathways in living organisms allow for the conversion of biomolecules into energy or other compounds required for growth and maintenance. Catabolic reactions release energy, while anabolic reactions consume energy. The energy from these reactions is often stored in the form of ATP (adenosine triphosphate), the energy currency of the cell.

1. Glycolysis: A key metabolic pathway that converts glucose into pyruvate through a series of enzyme-catalyzed reactions, producing ATP in the process.
2. Bioenergetics: This sub-discipline studies how organisms capture, store, and utilize energy through metabolic pathways.

MCQ
Which macromolecule serves as the primary storage form of energy in animal cells?
Answer: Glycogen.

Enzymes: Catalysts of Life

Enzymes are proteins that act as catalysts for biochemical reactions. They are highly specific to their substrates and can increase the rate of reactions by millions of times.

1. Catalytic Mechanism: Enzymes work by lowering the activation energy required for a reaction to proceed. They do this by forming an enzyme-substrate complex and stabilizing the transition state.
2. Factors Affecting Enzyme Activity: Enzyme function is influenced by temperature, pH, and substrate concentration. Each enzyme operates at an optimum temperature and pH, beyond which its activity declines.

Table 3: Factors Affecting Enzyme Activity

Factor	Effect on Enzyme Activity
Temperature	Activity peaks at optimum temperature; high heat denatures enzymes
pH	Each enzyme has an optimum pH; extreme pH levels denature enzymes
Substrate Concentration	Increases activity up to saturation point (Vmax)

3. Enzyme Inhibition: Inhibitors are molecules that bind to enzymes and reduce their activity. Competitive inhibitors resemble the substrate and compete for the active site, while non-competitive inhibitors bind elsewhere and alter the enzyme’s conformation.

Co-factors and Co-enzymes

Co-factors are non-protein molecules required by some enzymes to function. They can be:

1. Prosthetic Groups: Tightly bound organic molecules, like haem in peroxidase.
2. Co-enzymes: Organic compounds that bind transiently to enzymes, like NAD and NADP.
3. Metal Ions: Inorganic ions such as zinc that form coordination bonds with the enzyme to assist in catalytic activity.

Important Note: Enzyme activity is lost when the co-factor is removed, demonstrating their essential role in catalysis.

In conclusion, biomolecules form the basis of life, driving all metabolic functions and energy transformations through the coordinated action of enzymes, supported by the precise interplay of macromolecular structures.