Biochemistry: Metabolism, Enzymes, and DNA Replication
The Glycolysis Pathway
Glycolysis is a biochemical pathway in which one molecule of glucose (a 6-carbon compound) is converted into two molecules of pyruvic acid (a 3-carbon compound) through a series of enzyme-controlled reactions. It occurs in the cytoplasm of all living cells and does not require oxygen directly, making it an anaerobic process.
During glycolysis, energy is produced in the form of ATP and NADH. It consists of two phases:
- The energy investment phase
- The energy payoff phase
Glycolysis is the first step of cellular respiration and provides energy for various cellular activities.
Electron Transport Chain (ETC)
The Electron Transport Chain (ETC) is a series of electron carriers present in the inner mitochondrial membrane. It transfers electrons from NADH and FADH₂ to oxygen through a series of oxidation-reduction reactions. During this process, energy is released and used to produce ATP by oxidative phosphorylation.
The ETC is the final stage of cellular respiration and plays an important role in energy production in cells.
Citric Acid Cycle (TCA or Krebs Cycle)
The Citric Acid Cycle, also known as the TCA cycle or Krebs cycle, is a series of enzyme-controlled reactions that occur in the mitochondria of cells. In this cycle, acetyl CoA is oxidized and broken down to produce carbon dioxide (CO₂), while energy is released in the form of ATP, NADH, and FADH₂.
It is an important stage of cellular respiration and helps in the production of energy. The cycle also provides intermediate compounds needed for the synthesis of carbohydrates, fats, and proteins.
General Reactions of Amino Acids
1. Transamination
Transamination is the transfer of an amino group (-NH₂) from an amino acid to a keto acid to form a new amino acid and a new keto acid. This reaction is catalyzed by transaminase enzymes.
2. Deamination
Deamination is the removal of an amino group (-NH₂) from an amino acid, resulting in the formation of ammonia (NH₃) and a keto acid. It mainly occurs in the liver.
3. Decarboxylation
Decarboxylation is the removal of a carboxyl group (-COOH) from an amino acid, resulting in the formation of carbon dioxide (CO₂) and an amine. This reaction is catalyzed by decarboxylase enzymes.
β-Oxidation of Fatty Acids
β-Oxidation is a metabolic process in which fatty acids are broken down into acetyl CoA units in the mitochondria. It is an important pathway for the production of energy from fats.
During β-oxidation, fatty acids undergo repeated cycles of oxidation, hydration, oxidation, and cleavage. Each cycle removes a two-carbon unit in the form of acetyl CoA and produces reduced coenzymes NADH and FADH₂. These molecules enter the Electron Transport Chain to produce ATP.
β-Oxidation is important because it provides energy during fasting, exercise, and periods when carbohydrate supply is low.
Formation and Utilization of Ketone Bodies
Ketone bodies are water-soluble compounds produced from fatty acids in the liver. They are formed when there is increased breakdown of fats, such as during fasting, starvation, or low carbohydrate availability.
Formation of Ketone Bodies
Ketone bodies are formed in the mitochondria of liver cells from acetyl CoA produced during β-oxidation of fatty acids. The main ketone bodies are:
- Acetoacetate
- β-Hydroxybutyrate
- Acetone
Utilization of Ketone Bodies
Ketone bodies are transported through the blood to tissues like the heart, muscles, and brain, where they are converted back into acetyl CoA and used to produce energy through the TCA cycle. They serve as an alternative energy source when glucose is limited.
The Urea Cycle
The Urea Cycle, also known as the Ornithine Cycle, is a series of biochemical reactions that occur mainly in the liver. It converts toxic ammonia (NH₃), produced during amino acid metabolism, into urea, which is less toxic and is excreted from the body through urine.
The urea cycle helps in the removal of excess nitrogen from the body and maintains nitrogen balance.
Replication of DNA
DNA replication is the process by which a DNA molecule makes an identical copy of itself before cell division. It occurs in the nucleus of eukaryotic cells and is a semi-conservative process, in which each new DNA molecule contains one original strand and one newly synthesized strand.
DNA replication involves enzymes like DNA helicase, DNA polymerase, and DNA ligase. It is essential for the transmission of genetic information from one generation of cells to the next.
Nomenclature and IUB Classification of Enzymes
Nomenclature of Enzymes
Enzymes are named according to their substrate or the reaction they catalyze. Most enzyme names end with the suffix “-ase”. Example: Urease, Lactase.
IUB Classification of Enzymes
Enzymes are classified into six primary classes:
- Oxidoreductases – Oxidation-reduction reactions.
- Transferases – Transfer of functional groups.
- Hydrolases – Hydrolysis reactions.
- Lyases – Removal or addition of groups.
- Isomerases – Formation of isomers.
- Ligases – Joining of molecules using ATP.
Enzyme Regulation and Enzyme Inhibition
Enzyme Regulation
Enzyme regulation is the process by which the activity of enzymes is controlled in the cell to maintain proper metabolic functions.
Enzyme Inhibition
Enzyme inhibition is the process in which the activity of an enzyme is decreased or stopped by an inhibitor. It may be reversible or irreversible depending on the type of inhibitor.
Enzyme Regulation and Enzyme Inhibition
Enzyme Regulation
Enzyme regulation is the process by which the activity of enzymes is controlled in the cell to maintain proper metabolic functions.
Enzyme Inhibition
Enzyme inhibition is the process in which the activity of an enzyme is decreased or stopped by an inhibitor. It may be reversible or irreversible depending on the type of inhibitor.
Michaelis-Menten Equation and Enzyme Kinetics
Michaelis-Menten Equation
The Michaelis-Menten equation describes the relationship between the rate of an enzyme reaction and substrate concentration. It explains how enzyme activity changes with increasing substrate concentration.
Equation: V = (Vmax * [S]) / (Km + [S])
Where:
- V = Reaction velocity
- Vmax = Maximum reaction velocity
- [S] = Substrate concentration
- Km = Michaelis constant
Enzyme Kinetics
Enzyme kinetics is the study of the rate of enzyme-catalyzed reactions and the factors affecting enzyme activity, such as substrate concentration, enzyme concentration, temperature, and pH.