Enzymes: Types and Functions

Role of Enzymes in Cellular Processes

• Enzymes act as catalysts in biochemical reactions.
• They speed up chemical reactions by lowering the activation energy.
• Enzymes are mainly proteins, except for ribozymes which are RNA.
• Enzymes bind to the substrate at the active site, forming an enzyme-substrate complex.
• Enzymes are reusable as they are not consumed in the reactions they catalyze.
• Enzymes can be classified based on their functions and the reactions they catalyze.

Types of Enzymes

• Hydrolases catalyze hydrolysis reactions, breaking compounds by adding water.
  • Example: Amylase breaks down starch, Lipase breaks down fats.
• Oxidoreductases are involved in oxidation-reduction reactions, transferring electrons between molecules.
  • Example: Lactate dehydrogenase converts lactate to pyruvate.
• Transferases transfer functional groups between molecules.
  • Example: Amino transferases are for amino acid synthesis.
• Ligases catalyze the joining of molecules with covalent bonds.
  • Example: DNA ligase joins DNA fragments.
• Isomerases catalyze rearrangements within a molecule.
  • Example: Phosphoglucose isomerase converts glucose-6-phosphate to fructose-6-phosphate.
• Lyases catalyze non-hydrolytic addition or removal of groups from substrates, where C-C, C-N, C-O, or C-S bonds are cleaved.
  • Example: Decarboxylase.
• Synthetases such as Ligases, joins two molecules together by the synthesis of new C-O, C-S, C-N or C-C bonds with a simultaneous breakdown of ATP

Metabolism

• Metabolism is the sum of biochemical reactions that maintain a cell's living condition in an organism.
• Catabolism breaks down complex molecules into simpler ones, releasing energy.
  • Examples: Glycolysis, cellular respiration
• Anabolism synthesizes complex molecules from simpler ones, which requires energy.
  • Examples: Protein synthesis and DNA replication

Role of Enzymes in Metabolism

• Enzymes regulate both catabolic and anabolic pathways.
• Amylase helps break down starch into sugars.
• Ribulose-5-phosphate carboxylase (Rubisco) helps build larger molecules like glucose during photosynthesis.

Cellular Respiration

• Cellular respiration involves the conversion of glucose and oxygen into energy (ATP), carbon dioxide, and water.
• Key pathways of cellular respiration: Glycolysis, Citric Acid Cycle (Krebs Cycle), and the Electron Transport Chain.

Role of Enzymes in Cellular Respiration

• Hexokinase catalyzes the phosphorylation of glucose in glycolysis.
• Pyruvate dehydrogenase bridges glycolysis and the citric acid cycle by converting pyruvate to acetyl-CoA.
• The electron transport chain involves enzymes like cytochrome oxidase, which facilitate the transfer of electrons and generate ATP via oxidative phosphorylation.

Protein Synthesis

• Protein synthesis is the process by which the body makes proteins for structural components of cell membranes.
• It helps in cell repair, producing hormones and enzymes.
• Protein is synthesized in a process called Central Dogma: DNA → RNA → Protein.
  • DNA → RNA (Transcription).
  • RNA → Protein (Translation).

Role of Enzymes in Protein Synthesis

• Enzymes like aminoacyl-tRNA synthetase are essential for linking amino acids to tRNA molecules during translation.

DNA Replication and Repair

• DNA replication ensures the accurate copying of genetic material before cell division.
• DNA repair mechanisms correct errors or damage to maintain genomic integrity.

Role of Enzymes

• Helicase unwinds the DNA helix.
• Ligase seals gaps in the DNA backbone.
• Enzymes recognize and repair mutations, ensuring genetic stability.

Signal Transduction

• Cells communicate and respond to external signals through signaling pathways (e.g., hormone signaling).
• Receptors on the cell surface or inside the cell detect signals and activate specific cellular responses.

Role of Enzymes

• Kinases (e.g., protein kinase A) phosphorylate proteins, activating or deactivating signaling pathways.
• Phosphatases remove phosphate groups, reversing the action of kinases.
• Enzymes amplify signals through cascades, ensuring rapid and efficient cellular responses.

Homeostasis

• Homeostasis is a mechanism that maintains a stable internal environment despite external changes.
• It resists change to maintain stable internal conditions (e.g., pH balance, temperature regulation, ion concentrations).

Role of Enzymes

• Enzymes maintain pH balance by converting acidic or basic compounds into neutral forms.
  • Example: Carbonic anhydrase regulates blood pH by interconverting carbon dioxide and bicarbonate.

Photosynthesis (in Plants, Algae, and Some Bacteria)

• Photosynthesis is the process by which green plants, algae, and some bacteria turn light energy into chemical energy stored in glucose.
• It occurs in light-dependent reactions and the Calvin cycle.

Role of Enzymes

• Rubisco catalyzes the fixation of carbon dioxide in the Calvin cycle.
• Enzymes in the light-dependent reactions (e.g., ATP synthase) generate ATP and NADPH.

Apoptosis (Programmed Cell Death)

• Apoptosis is a regulated process that eliminates damaged or unnecessary cells in an orderly manner.

Role of Enzymes

• Enzymes like caspases drive programmed cell death by cleaving specific cellular proteins, ensuring orderly disassembly of cellular components.

Metabolic Pathways and Energy Production

• A metabolic pathway is a series of chemical reactions where a starting molecule is modified step-by-step, through a series of metabolic intermediates, eventually yielding a final product
• Metabolic pathways can be anabolic (energy-consuming) or catabolic (energy-producing).

Glycolysis

• Glycolysis is a metabolic process that breaks down glucose into pyruvate and produces ATP.
• It is the initial metabolic pathway of cellular respiration and occurs in both aerobic and anaerobic organisms.
• The process takes place in the cytoplasm and consists of energy-requiring and energy-releasing steps.
• Energy yield: 2 ATP and 2 NADH per glucose molecule.
• It is also known as the glycolytic pathway or Embden-Meyerhof-Parnas pathway

TCA Cycle

• The TCA cycle, also known as the Krebs cycle or citric acid cycle, is a series of biochemical reactions that occur in the mitochondria.
• It involves the oxidation of acetyl-CoA derived from carbohydrates, fats, proteins, and alcohol, that releases stored energy and generates ATP.
• Energy yield: 3 NADH, 1 FADH2, and 1 GTP (ATP) per cycle.

Oxidative Phosphorylation

• Oxidative phosphorylation is the process by which ATP is synthesized using energy derived from the transfer of electrons through the electron transport chain (ETC)
• Electron transfer happens via transmembrane protein complexes in the inner mitochondrial membrane, which makes a proton gradient which is the used to drive ATP synthesis

Electron Transport Chain

• The ETC is a series of protein complexes and electron carriers embedded in the inner mitochondrial membrane, consisting of 4 main complex
• Complex I (NADH: Ubiquinone Oxidoreductase): NADH from glycolysis and the TCA cycle donates electrons to Complex I.
• Complex II (Succinate Dehydrogenase): Electrons from FADH2 are transferred to ubiquinone, unlike Complex I, Complex II does not pump protons.
• Ubiquinone (Coenzyme Q) acts as a lipid-soluble carrier that shuttles electrons
• Complex III (Cytochrome bc₁ Complex): Transfers electrons from ubiquinone to cytochrome c.
• Complex IV (Cytochrome c Oxidase): Accepts electrons from cytochrome c and reduces oxygen (O2) to water (H₂O).
• Protons flow back into the matrix through ATP synthase via Chemiosmosis, catalyzing the conversion of ADP and inorganic phosphate (Pi) into ATP

ATP Production

• Each NADH generates 2.5 ATP and each FADH2 generates 1.5 ATP in the ETC
  • Glycolysis Yields 2 ATP from substrate-level phosphorylation and 3 from NADH
  • Conversion of Pyruvate to acetyl CoA yields 5 ATP
  • Citric Acid cycle yield 2 ATP from substrate level phosphorylation and up to 18 from NADH and FADH
• Total ATP generated from a glucose molecule = 32 ATP

Beta Oxidation

• Beta oxidation is the catabolic process by which fatty acid molecules are broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acetyl-CoA
• Acetyl CoA enters the citric acid cycle, generating NADH and FADH2, which are electron carriers used in the electron transport chain.
• The resulting acetyl CoA enters the CA cycle

Mechanism

• It is named as such because the beta carbon of the fatty acid chain undergoes oxidation and is converted to a carbonyl group to start the cycle again
• The number of cycles that happens is predicted by: (n/2)-1, where n is number of carbon chain and 2 is number of acetyl CoA produced per cycle
  • E.g Palmitic acid has 16 carbons, the cycle will be (16/2)-1 = 7 cycles

ATP Production

• Each Beta oxidation yields 1 NADH, 1 FADH2 and 2 acetyl CoA

• The acetyl CoA enters into the TCA cycle and generates 3 NADH, 1 FADH2, 1 GTP (ATP): yielding an addition 10 ATP in the ETC

  • The number of acetyl CoA is given by n/2, where n is number of carbon chains

• The net ATP generated can be predicted by a formula:

  • ATP from acetyl CoA = (n/2) x 10
  • ATP from Beta oxidation cycle = ((n/2)-1) x 4
  • ATP used for driving beta oxidation = 2

• An example, Palmitic acid with 16 carbons will yield:

  • ATP from acetyl CoA = (16/2) x 10 = 80 ATP
  • ATP from Beta oxidation cycle = ((16/2)-1) x 4 = 28 ATP
  • ATP used for driving beta oxidation = 2 ATP
  • Total ATP left = 80 + 28 – 2 = 106 АТР

Protein Catabolism

• Protein catabolism is the breakdown of proteins into smaller peptides and ultimately into amino acids.
• It begins with pepsin where it converts proteins into polypeptides
• In the intestine, the small peptides are broken down into amino acids to be absorbed into the bloodstream

Outcomes

• During the amino acid metabolism, where they are utilized as an energy source a converted into new proteins via the Krebs cycle.
• The amount amino acid yeild is dependent of the type of amino acid
• Glucogenic amino acids enters into a gluconeogentic pathway to form pyruvate or into TCA to from oxaloacetate and a-ketoglutarate.
  • Amino acids of this type are; Alanine, Glutamate, Methionine, Histidine, Aspartate, Proline, Asparagine, Glutamine, Glycine, Serine, Arginine, Cysteine, Valine.
• Ketogenic are metabolized to acetyl CoA or channelled into the TCA cycle
  • Example: Leucine and Lysine.
  • Other amino acids that can also be ketogenic; Isoleucine, Phenylalanine, Tyrosine, Tryptophan, Threonine
• However, breaking down proteins into amino acids will not yeild any ATP, with the exceptions of the carbon-skeleton producing ammonia
  • The ammonia is converted to urea in, which consumes 4 ATP