Chapter Notes

How to Analyse Chemical Composition?

All living organisms, from plants to animals to microbes, are made of chemicals. When we compare the elements found in living tissue with those in non-living matter like the Earth's crust, we find a similar list of elements. However, the key difference lies in their abundance. Living organisms have a significantly higher relative abundance of carbon and hydrogen compared to the Earth's crust.

To understand the chemical makeup of living tissue, we can perform two main types of analysis:

1. Analysis of Organic Compounds

This method helps us identify the carbon-based compounds, or biomolecules, present in living things.

• Procedure:
  1. Take a living tissue (like a vegetable or a piece of liver).
  2. Grind it in trichloroacetic acid ($Cl_3CCOOH$) to create a thick slurry.
  3. Strain the slurry through cheesecloth or cotton.
• Results: This process separates the slurry into two parts:
  • The Acid-Soluble Pool (Filtrate): This liquid part contains thousands of organic compounds with small molecular weights, generally from 18 to 800 daltons (Da). These are often called micromolecules.
  • The Acid-Insoluble Fraction (Retentate): The solid material left behind contains larger organic compounds, called biomacromolecules.

2. Analysis of Inorganic Compounds

This is a destructive method used to identify the inorganic elements and compounds.

• Procedure:
  1. Weigh a small amount of living tissue (this is the wet weight).
  2. Dry the tissue completely to evaporate all the water. The remaining material gives the dry weight.
  3. Burn the dried tissue completely. All carbon compounds are oxidized and removed as gases ($CO_2$, water vapor).
• Result: The remaining substance is called ash. This ash contains inorganic elements like calcium and magnesium, and inorganic compounds like sulphates and phosphates.

From these analyses, we can classify the chemical constituents of living tissues into various categories like amino acids, fatty acids, and nucleotide bases.

Amino Acids

Amino acids are the building blocks of proteins.

• Structure: They are organic compounds that have both an amino group ($-NH_2$) and an acidic carboxyl group ($-COOH$) attached to the same carbon, called the α-carbon.
• They are essentially substituted methanes, with four groups attached to the central carbon:
  1. A hydrogen atom (H)
  2. A carboxyl group ($-COOH$)
  3. An amino group ($-NH_2$)
  4. A variable group called the R group.
• Types: There are 20 different types of amino acids that make up proteins, distinguished by their unique R group.
  • If the R group is a hydrogen (H), the amino acid is glycine.
  • If the R group is a methyl group ($-CH_3$), it is alanine.
  • If the R group is a hydroxy methyl ($-CH_2OH$), it is serine.
• Classification based on R group:
  • Acidic: e.g., glutamic acid
  • Basic: e.g., lysine
  • Neutral: e.g., valine
  • Aromatic: e.g., tyrosine, phenylalanine, tryptophan
• Zwitterionic Form: The amino and carboxyl groups are ionizable. In a solution, an amino acid can exist as a zwitterion, which is an ion carrying both a positive and a negative charge.

Lipids

Lipids are a broad group of naturally occurring molecules that are generally insoluble in water.

• Fatty Acids: A simple lipid consisting of a carboxyl group attached to an R group. The R group is a hydrocarbon chain that can have from 1 to 19 carbons.
  • Saturated Fatty Acids: Have no carbon-carbon double bonds ($C=C$) in their chain.
  • Unsaturated Fatty Acids: Have one or more carbon-carbon double bonds in their chain.
  • Examples include palmitic acid (16 carbons) and arachidonic acid (20 carbons).
• Glycerol: A simple lipid that is a trihydroxy propane.
• Fats and Oils: Many lipids are formed when fatty acids are esterified with glycerol. They can be monoglycerides, diglycerides, or triglycerides. The main difference between fats and oils is their melting point; oils have a lower melting point and remain liquid in winter.
• Phospholipids: These are complex lipids that contain phosphorus. They are a major component of cell membranes. Lecithin is an example of a phospholipid.

Nitrogenous Bases, Nucleosides, and Nucleotides

These are carbon compounds with heterocyclic rings.

• Nitrogenous Bases: There are five main types: adenine, guanine, cytosine, uracil, and thymine.
  • Adenine and guanine are purines.
  • Cytosine, uracil, and thymine are pyrimidines.
• Nucleosides: A nitrogenous base attached to a sugar. Examples include adenosine, guanosine, and cytidine.
• Nucleotides: A nucleoside with a phosphate group also attached to the sugar. Examples include adenylic acid and thymidylic acid.
• Nucleic Acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers made of nucleotides. They function as the genetic material of an organism.

Primary and Secondary Metabolites

The thousands of biomolecules found in living organisms can be called metabolites. They are divided into two main categories:

• Primary Metabolites: These are compounds like amino acids and sugars that are found in animal tissues and have known, identifiable roles in normal physiological processes.
• Secondary Metabolites: When we analyze plants, fungi, and microbes, we find thousands of other compounds like alkaloids, rubber, essential oils, antibiotics, and spices. These are called secondary metabolites. While their direct functions in the host organisms are not always clear, many are very useful to humans (e.g., drugs, rubber, pigments). Some also have ecological importance.

Biomacromolecules

Based on the chemical analysis of living tissue, biomolecules can be divided into two types based on their molecular weight:

1. Micromolecules: Found in the acid-soluble pool, with molecular weights from 18 to 800 daltons (Da).
2. Biomacromolecules: Found in the acid-insoluble fraction, with molecular weights of ten thousand daltons and above.

The acid-insoluble fraction contains four main types of organic compounds: proteins, nucleic acids, polysaccharides, and lipids.

The acid-soluble pool roughly represents the composition of the cytoplasm, while the acid-insoluble fraction consists of macromolecules from the cytoplasm and organelles. Together, they represent the entire chemical composition of a living organism.

Average Composition of a Cell

As you can see, water is the most abundant chemical in living organisms.

Proteins

Proteins are large biomolecules, or macromolecules, that are essential for life.

• Structure: They are polypeptides, which means they are linear chains of amino acids linked together by peptide bonds.
• Heteropolymers: A protein is a heteropolymer because it is made from 20 different types of amino acid monomers. A homopolymer, in contrast, has only one type of repeating monomer.
• Essential Amino Acids: Some amino acids cannot be made by our bodies and must be obtained through our diet. These are called essential amino acids, and dietary proteins are their source.
• Functions: Proteins perform a vast array of functions in living organisms:
  • Enzymes: Catalyze biochemical reactions (e.g., Trypsin).
  • Structural: Provide support (e.g., Collagen, the intercellular ground substance).
  • Transport: Move substances across cell membranes (e.g., GLUT-4 for glucose transport).
  • Hormones: Act as chemical messengers (e.g., Insulin).
  • Defense: Fight infectious agents (e.g., Antibodies).
  • Receptors: For sensory reception (smell, taste, etc.).

• Collagen is the most abundant protein in the animal world.
• Ribulose bisphosphate Carboxylase-Oxygenase (RuBisCO) is the most abundant protein in the whole biosphere.

Polysaccharides

Polysaccharides are long chains of sugars (monosaccharides) and are another class of macromolecules.

• Cellulose: A homopolymer consisting only of glucose units. It is the main structural component of plant cell walls. Paper and cotton fiber are cellulosic.
• Starch: A polymer of glucose used as an energy storehouse in plants. It forms helical structures that can hold iodine ($I_2$) molecules, giving a characteristic blue color in tests.
• Glycogen: The energy storage polysaccharide in animals. It is also a polymer of glucose but is more branched than starch.
• Inulin: A polymer of fructose.
• Chitin: A complex polysaccharide found in the exoskeletons of arthropods (like insects and crustaceans). It is a homopolymer of modified sugar units.

Nucleic Acids

Nucleic acids are macromolecules found in the acid-insoluble fraction of any living tissue.

• Structure: They are polynucleotides, meaning they are polymers of building blocks called nucleotides.
• Components of a Nucleotide: Each nucleotide has three distinct parts:
  1. A heterocyclic compound (a nitrogenous base).
  2. A monosaccharide (a sugar).
  3. A phosphoric acid or phosphate group.
• Sugars in Nucleic Acids:
  • Ribonucleic acid (RNA) contains the sugar ribose.
  • Deoxyribonucleic acid (DNA) contains the sugar 2' deoxyribose.
• Nitrogenous Bases:
  • Purines: Adenine (A) and Guanine (G).
  • Pyrimidines: Cytosine (C), Thymine (T), and Uracil (U). (Uracil is found in RNA instead of Thymine).

Structure of Proteins

Biologists describe protein structure at four different levels, each building upon the last.

Primary Structure

This is the simplest level. The primary structure is the unique sequence of amino acids in a polypeptide chain. It describes which amino acid is first, second, third, and so on. The first amino acid is called the N-terminal amino acid, and the last is the C-terminal amino acid.

Secondary Structure

The polypeptide chain doesn't remain a straight, rigid rod. It folds into regular, repeating patterns. This local folding is the secondary structure. A common secondary structure is the α-helix, which resembles a right-handed revolving staircase.

Tertiary Structure

This refers to the overall three-dimensional shape of a single polypeptide chain. The long chain is folded upon itself like a hollow woolen ball. This tertiary structure is absolutely necessary for the biological activity of most proteins.

Quaternary Structure

Some proteins are made of more than one polypeptide chain, or subunit. The quaternary structure describes how these individual subunits are arranged with respect to each other. [!example] Adult human haemoglobin (Hb) is a great example of a protein with a quaternary structure. It consists of four subunits: two identical α-type subunits and two identical β-type subunits, which all fit together to form the functional protein.

Enzymes

Enzymes are biological catalysts that speed up chemical reactions in living cells.

• Composition: Almost all enzymes are proteins. Some RNA molecules can also act as enzymes; these are called ribozymes.
• Structure and Function: Like other proteins, enzymes have a tertiary structure. This 3D folding creates crevices or pockets on their surface called the active site. The substrate (the molecule the enzyme acts on) fits into this active site, allowing the enzyme to catalyze the reaction at a very high rate.
• Enzymes vs. Inorganic Catalysts:
  • Inorganic catalysts often work best at high temperatures and pressures.
  • Enzymes are damaged by high temperatures (above 40°C), a process called denaturation.
  • However, enzymes from organisms living in extreme heat (like hot springs) can be stable at temperatures up to 80-90°C.

Chemical Reactions

A chemical reaction involves the breaking of old chemical bonds and the formation of new ones. The rate of a reaction is the amount of product formed per unit of time ($rate = \delta P / \delta t$).

Enzymes dramatically increase the rate of reactions. [!example] The reaction of carbon dioxide and water to form carbonic acid: $CO_2 + H_2O \longleftrightarrow H_2CO_3$ Without an enzyme, only about 200 molecules of $H_2CO_3$ are formed per hour. With the enzyme carbonic anhydrase, the rate skyrockets to 600,000 molecules per second—an acceleration of about 10 million times!

A series of linked, enzyme-catalyzed reactions is called a metabolic pathway. For example, the conversion of glucose to pyruvic acid involves ten different enzyme-catalyzed steps.

How do Enzymes bring about such High Rates of Chemical Conversions?

To understand this, we need to look at the energy of a reaction.

• The chemical that is converted into a product is called the substrate (S).
• For a reaction to occur, the substrate must pass through a high-energy transition state before it can become the product (P).
• The energy required to get the substrate to this transition state is called the activation energy.

Enzymes work by lowering the activation energy of a reaction. They create an "easier" pathway for the conversion of substrate to product, which makes the reaction happen much faster. An enzyme does this by binding the substrate at its active site, forming a temporary enzyme-substrate (ES) complex, which helps stabilize the transition state.

Nature of Enzyme Action

The catalytic cycle of an enzyme can be described in four steps:

1. The substrate (S) binds to the active site of the enzyme (E).
2. This binding causes the enzyme to change its shape slightly, fitting more tightly around the substrate.
3. The active site then breaks or forms chemical bonds in the substrate, converting it into the product (P) while it is still bound to the enzyme (forming an EP complex).
4. The enzyme releases the product(s), and the free enzyme is ready to bind to another substrate molecule.

The overall process can be shown as: $E + S \longleftrightarrow ES \longrightarrow EP \longrightarrow E + P$

Factors Affecting Enzyme Activity

Several factors can affect how well an enzyme works by altering its tertiary structure.

• Temperature and pH:

  • Each enzyme has an optimum temperature and optimum pH at which it shows the highest activity.
  • Activity declines above and below these optimal values.
  • Low temperatures temporarily inactivate the enzyme, while high temperatures permanently destroy it (denaturation).

• Concentration of Substrate:

  • As substrate concentration increases, the reaction rate also increases.
  • However, the rate eventually reaches a plateau, a maximum velocity called Vmax.
  • This happens because the enzyme molecules become saturated—all active sites are occupied, and they cannot process the substrate any faster, no matter how much more is added.

• Inhibitors:

  • These are specific chemicals that bind to an enzyme and shut off its activity.
  • A competitive inhibitor is a molecule that closely resembles the normal substrate. It competes with the substrate for the active site. When the inhibitor binds, the substrate cannot, and the enzyme's action declines.
  • An example is the inhibition of succinic dehydrogenase by malonate, which resembles the substrate succinate.

Classification and Nomenclature of Enzymes

Enzymes are classified into 6 major classes based on the type of reaction they catalyze:

1. Oxidoreductases/dehydrogenases: Catalyze oxidation-reduction reactions.
2. Transferases: Transfer a group (other than hydrogen) between two substrates.
3. Hydrolases: Break bonds by adding water (hydrolysis).
4. Lyases: Remove groups from substrates by means other than hydrolysis, often creating a double bond.
5. Isomerases: Catalyze the inter-conversion of isomers (e.g., optical, geometric, or positional).
6. Ligases: Join two compounds together by forming new bonds (e.g., C-O, C-S, C-N).

Co-factors

Many enzymes require a non-protein chemical component called a co-factor to be catalytically active.

• The protein portion of such an enzyme is called the apoenzyme.
• The complete, active enzyme (apoenzyme + co-factor) is called a holoenzyme.

There are three kinds of co-factors:

1. Prosthetic Groups: These are organic compounds that are tightly bound to the apoenzyme. For example, haem is the prosthetic group in the enzymes peroxidase and catalase.
2. Co-enzymes: These are also organic compounds, but their association with the apoenzyme is transient (temporary), usually only during catalysis. Many vitamins are essential components of co-enzymes (e.g., the vitamin niacin is part of the co-enzymes NAD and NADP).
3. Metal Ions: A number of enzymes require metal ions for their activity. These ions form coordination bonds with side chains at the active site and with the substrate. For example, zinc is a co-factor for the enzyme carboxypeptidase.