01 · Explore
Analysing Chemical Composition
Living organisms possess a diverse range of chemicals. While the elements found in living tissue are similar to those in the earth's crust, their relative abundance differs significantly.
To identify the organic compounds in a living tissue, such as a vegetable or liver, the tissue is ground in trichloroacetic acid (Cl₃CCOOH) using a mortar and pestle. This process creates a thick slurry. When strained through cheesecloth, two fractions are obtained: the filtrate (acid-soluble pool) and the retentate (acid-insoluble fraction). The acid-soluble pool contains thousands of small organic compounds.
Inorganic constituents are analysed through a 'destructive' experiment. A tissue sample is weighed (wet weight), dried to remove water (dry weight), and then fully burnt. Burning oxidises carbon compounds into gaseous forms (CO₂ and water vapour), leaving behind 'ash'. This ash contains inorganic elements like calcium and magnesium, as well as compounds like sulphate and phosphate.
Elemental analysis reveals that living organisms have a higher relative abundance of carbon and hydrogen compared to the earth's crust. For instance, carbon makes up 18.5% of human body weight but only 0.03% of the earth's crust.
| Element | % Weight in Earth's Crust | % Weight in Human Body |
|---|---|---|
| Hydrogen (H) | 0.14 | 9.5 |
| Carbon (C) | 0.03 | 18.5 |
| Oxygen (O) | 46.6 | 65.0 |
| Nitrogen (N) | very little | 3.3 |
| Sulphur (S) | 0.03 | 0.3 |
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What are the two fractions obtained during the chemical analysis of living tissue using trichloroacetic acid?
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02 · Explore
Amino Acids and Lipids
Small molecular weight organic compounds include amino acids and lipids, which serve as building blocks or structural components.
Amino acids are organic compounds containing an amino group (-NH₂) and an acidic carboxyl group (-COOH) on the same carbon, the α-carbon. They are essentially substituted methanes where four groups—hydrogen, carboxyl, amino, and a variable 'R' group—occupy the valency positions. There are 20 types of amino acids found in proteins, differing by their R group (e.g., H in glycine, CH₃ in alanine).
Lipids are generally water-insoluble molecules. Fatty acids consist of a carboxyl group attached to an R group. The R group can be a methyl, ethyl, or a higher number of CH₂ groups (1 to 19 carbons). For example, palmitic acid has 16 carbons including the carboxyl carbon, while arachidonic acid has 20 carbon atoms including the carboxyl carbon. They can be saturated (no double bonds) or unsaturated (one or more C=C bonds).
Glycerol is a simple lipid known as trihydroxy propane. Many lipids have both glycerol and fatty acids, where fatty acids are esterified with glycerol to form monoglycerides, diglycerides, or triglycerides. Phospholipids are complex lipids containing a phosphate group and are vital components of cell membranes; lecithin is a prominent example. In solutions of varying pH, amino acids can exist in a zwitterionic form where both the amino and carboxyl groups are ionised.
Formation of Glycerides
- 1
Glycerol
A three-carbon alcohol (trihydroxy propane) serves as the backbone.
- 2
Esterification
Fatty acids react with the hydroxyl groups of glycerol.
- 3
Triglyceride
Three fatty acid chains are attached to one glycerol molecule, forming a fat or oil.
The sequential process of esterifying fatty acids to a glycerol backbone to form complex lipids.
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What defines an α-amino acid?
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03 · Explore
Metabolites and Biomacromolecules
Biomolecules are categorised based on their molecular weight and their role in the organism's metabolism.
Primary metabolites, such as amino acids and sugars, have identifiable functions in normal physiological processes. Secondary metabolites, found in plants, fungi, and microbes, include alkaloids, flavonoids, rubber, and essential oils. While their specific roles in the host are not always clear, many are useful for human welfare (e.g., drugs like vinblastin or spices).
Biomolecules are divided into two types based on molecular weight. Micromolecules (or simply biomolecules) are found in the acid-soluble pool and have molecular weights ranging from 18 to around 800 daltons (Da) approximately. Biomacromolecules are found in the acid-insoluble fraction and have weights exceeding 10,000 Da. These include proteins, nucleic acids, and polysaccharides.
Lipids are an exception. Although their molecular weight does not exceed 800 Da, they appear in the acid-insoluble fraction. This is because lipids are part of cell membranes; when tissue is ground, membranes break into water-insoluble vesicles that separate with the macromolecular fraction.
| Category | Examples |
|---|---|
| Pigments | Carotenoids, Anthocyanins |
| Alkaloids | Morphine, Codeine |
| Toxins | Abrin, Ricin |
| Drugs | Vinblastin, Curcumin |
| Polymeric substances | Rubber, Gums, Cellulose |
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Why are lipids found in the acid-insoluble fraction despite their low molecular weight?
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04 · Explore
Proteins and Polysaccharides
Proteins and polysaccharides are essential polymers that provide structure and perform vital biological functions.
Proteins are heteropolymers of amino acids linked by peptide bonds. Because there are 20 different amino acids, proteins are never homopolymers. Essential amino acids must be obtained through diet, while non-essential ones are made by the body. Collagen is the most abundant protein in animals, while RuBisCO is the most abundant in the entire biosphere.
Polysaccharides are long chains of sugars (monosaccharides). Cellulose is a homopolymer of glucose and a primary component of plant cell walls. Starch (in plants) and glycogen (in animals) serve as energy stores. Inulin is a polymer of fructose. Complex polysaccharides like chitin form the exoskeletons of arthropods.
Starch forms helical secondary structures that can trap iodine (I₂) molecules, resulting in a characteristic blue colour. Cellulose lacks these complex helices and therefore does not react with iodine.
| Protein | Function |
|---|---|
| Collagen | Intercellular ground substance |
| Trypsin | Enzyme |
| Insulin | Hormone |
| Antibody | Fights infectious agents |
| GLUT-4 | Enables glucose transport into cells |
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What is the difference between a homopolymer and a heteropolymer in the context of biomolecules?
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05 · Explore
Nucleic Acids
Nucleic acids are the genetic material of living organisms, existing as long polymers of nucleotides.
Nucleic acids are polynucleotides found in the acid-insoluble fraction. Each nucleotide consists of three parts: a heterocyclic nitrogenous base, a monosaccharide pentose sugar, and a phosphate group. The nitrogenous bases are adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U).
Adenine and guanine are substituted purines (double-ring structures), while cytosine, thymine, and uracil are substituted pyrimidines (single-ring structures). The sugar is either ribose (in RNA) or 2'-deoxyribose (in DNA).
A nucleoside is formed when a base is attached to a sugar; examples include adenosine, guanosine, thymidine, uridine, and cytidine. When a phosphate group is esterified to the sugar of a nucleoside, it becomes a nucleotide, such as adenylic acid, thymidylic acid, guanylic acid, uridylic acid, or cytidylic acid. DNA and RNA consist of nucleotides only and function as genetic material.
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What are the three components of a nucleotide?
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06 · Explore
Levels of Protein Structure
Biologists describe protein structure at four distinct levels of complexity, which are essential for their biological activity.
The primary structure is the linear sequence of amino acids. It provides positional information, identifying the first (N-terminal) and last (C-terminal) amino acids. The secondary structure occurs when the polypeptide chain folds into specific shapes, most commonly the right-handed alpha-helix or beta-pleated sheets.
The tertiary structure is the folding of the protein chain upon itself like a hollow woolen ball, creating a 3-dimensional shape. This level is absolutely necessary for the biological activities of proteins, as it creates active sites for enzymes. The quaternary structure refers to the arrangement of multiple polypeptide subunits in a complex protein.
Human haemoglobin is an example of quaternary structure, consisting of four subunits: two α-type and two β-type chains working together to transport oxygen.
Hierarchy of Protein Folding
- 1
Primary
Linear sequence of amino acids held by peptide bonds.
- 2
Secondary
Local folding into alpha-helices or beta-sheets via hydrogen bonds.
- 3
Tertiary
Overall 3D shape of a single polypeptide chain.
- 4
Quaternary
Assembly of multiple folded subunits into a functional unit.
The four levels of protein structure, from a simple sequence to a complex multi-subunit assembly.
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Which level of protein structure is essential for the catalytic activity of enzymes?
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07 · Explore
Enzymes and Chemical Reactions
Enzymes are biological catalysts, mostly proteins, that dramatically increase the rate of chemical reactions.
Enzymes possess an 'active site', a pocket into which a specific substrate fits. Unlike inorganic catalysts, enzymes are sensitive to high temperatures and usually denature above 40°C, though thermophilic organisms have enzymes stable up to 90°C. They accelerate reactions by lowering the activation energy required to reach the transition state.
The rate of a reaction is the amount of product formed per unit time (δP/δt). Enzymes can increase this rate by millions of times. For example, carbonic anhydrase facilitates the formation of 600,000 molecules of carbonic acid per second, compared to only 200 molecules per hour without the enzyme.
A multistep chemical reaction, where each step is catalysed by enzymes, is called a metabolic pathway. For example, glucose becomes pyruvic acid (C₆H₁₂O₆ + O₂ → 2C₃H₄O₃ + 2H₂O) through ten different enzyme-catalysed reactions. The catalytic cycle involves the substrate binding to the active site, inducing a shape change in the enzyme for a tighter fit, forming a transient enzyme-substrate (ES) complex, and finally releasing the product.
Enzymatic Acceleration
CO₂ + H₂O → H₂CO₃
In the presence of carbonic anhydrase, the reaction rate increases from 200 molecules/hour to 600,000 molecules/second, an acceleration of about 10 million times.
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How do enzymes increase the rate of a chemical reaction?
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08 · Explore
Factors Affecting Enzyme Activity
Enzyme activity is highly regulated and depends on specific environmental conditions and the presence of other molecules.
Enzymes function within a narrow range of temperature and pH. Each has an 'optimum' value where activity is highest. Low temperatures temporarily inactivate enzymes, while high temperatures cause permanent denaturation. Substrate concentration also affects velocity; the rate increases until all enzyme active sites are saturated (Vmax).
Inhibition occurs when specific chemicals shut off enzyme activity. In competitive inhibition, the inhibitor closely resembles the substrate and competes for the active site (e.g., inhibition of succinic dehydrogenase by malonate). Enzymes are classified into 6 classes, each with 4-13 subclasses, and named by a four-digit number.
Many enzymes require non-protein 'co-factors' to be active. The protein part is called the apoenzyme. Co-factors include prosthetic groups (tightly bound, e.g., haem), co-enzymes (transiently bound vitamins like niacin), and metal ions (e.g., zinc for carboxypeptidase).
| Class | Type of Reaction Catalysed |
|---|---|
| Oxidoreductases | Oxidation and reduction between substrates |
| Transferases | Transfer of a group (other than hydrogen) |
| Hydrolases | Hydrolysis of bonds (ester, peptide, etc.) |
| Lyases | Removal of groups leaving double bonds |
| Isomerases | Inter-conversion of isomers |
| Ligases | Linking of two compounds (e.g., C-O, C-N) |
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What is a competitive inhibitor?
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What happens to an enzyme when the co-factor is removed?
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