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Carbohydrates 🍚
Carbohydrates are organic compounds made up of carbon, hydrogen, and oxygen atoms, typically with a hydrogen-oxygen atom ratio of 2:1, as in water. They are a primary source of energy and also play crucial structural roles in organisms.
Structure and Classification
Carbohydrates can be classified based on the number of sugar units: ● Monosaccharides: Simple sugars like glucose (the main energy currency), fructose (found in fruits), and galactose. They are the building blocks for more complex carbohydrates. (Illustration: Chair and Haworth projections of glucose and fructose.) ● Disaccharides: Formed by the glycosidic linkage of two monosaccharides. Examples include sucrose (table sugar: glucose + fructose), lactose (milk sugar: glucose + galactose), and maltose (malt sugar: glucose + glucose). (Illustration: Formation of a glycosidic bond between two glucose molecules to form maltose.) ● Oligosaccharides: Composed of 3 to 10 monosaccharide units. Often found attached to proteins (glycoproteins) or lipids (glycolipids) on cell surfaces, playing roles in cell recognition. ● Polysaccharides: Long chains of monosaccharides. ○ Starch: Energy storage in plants (composed of amylose and amylopectin). (Illustration: Branched structure of amylopectin and helical structure of amylose.) ○ Glycogen: Energy storage in animals, primarily in the liver and muscles. Highly branched structure allowing for rapid glucose release. (Illustration: Highly branched structure of glycogen.) ○ Cellulose: Structural component of plant cell walls. A linear polymer of glucose linked by β-1,4 glycosidic bonds, making it indigestible by most animals. (Illustration: Linear structure of cellulose and hydrogen bonding between chains.) ○ Chitin: Structural polysaccharide in fungi cell walls and arthropod exoskeletons. A polymer of N-acetylglucosamine.
Metabolic Pathways
1. Glycolysis
● Description: The metabolic pathway that converts glucose (C_6H_{12}O_6) into pyruvate (CH_3COCOO^-) and a hydrogen ion, H^+. The free energy released in this process is used to form the high-energy molecules ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide). ● Location: Cytoplasm of all cells. ● Key Steps & Regulation: ○ Investment Phase: Glucose is phosphorylated twice by ATP (catalyzed by hexokinase/glucokinase and phosphofructokinase-1 (PFK-1) ). PFK-1 is a major regulatory point, allosterically inhibited by ATP and citrate, and activated by AMP and fructose-2,6-bisphosphate. ○ Payoff Phase: Two molecules of glyceraldehyde-3-phosphate are converted to pyruvate, generating 4 ATP (net gain of 2 ATP) and 2 NADH. (Diagram:
Step-by-step pathway of glycolysis showing all intermediates and enzymes.)
2. Krebs Cycle (Citric Acid Cycle or TCA Cycle)
● Description: A series of chemical reactions used by all aerobic organisms to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins into ATP and carbon dioxide. ● Location: Mitochondrial matrix in eukaryotes. ● Key Steps & Regulation: ○ Pyruvate (from glycolysis) is first converted to acetyl-CoA by the pyruvate dehydrogenase complex (PDC) , producing NADH and CO_2. PDC is a key regulatory point. ○ Acetyl-CoA (2 carbons) combines with oxaloacetate (4 carbons) to form citrate ( carbons). ○ A series of oxidative decarboxylations and rearrangements regenerate oxaloacetate, producing 3 NADH, 1 FADH_2 (flavin adenine dinucleotide), and 1 GTP (or ATP) per acetyl-CoA. ○ Regulation occurs at citrate synthase , isocitrate dehydrogenase , and α-ketoglutarate dehydrogenase. (Diagram: Circular pathway of the Krebs cycle showing all intermediates, enzymes, and points of energy/reducing equivalent production.)
3. Gluconeogenesis
● Description: The metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates. It is essentially the reverse of glycolysis, but with bypasses for the irreversible steps. ● Location: Primarily in the liver, and to a lesser extent, the kidneys. ● Key Substrates: Lactate, pyruvate, glycerol (from fat breakdown), and certain amino acids. ● Key Bypass Enzymes: ○ Pyruvate carboxylase and PEP carboxykinase (PEPCK) bypass pyruvate kinase. ○ Fructose-1,6-bisphosphatase bypasses PFK-1. ○ Glucose-6-phosphatase bypasses hexokinase/glucokinase. ● Regulation: Reciprocally regulated with glycolysis. Hormones like glucagon stimulate gluconeogenesis, while insulin inhibits it. (Diagram: Gluconeogenesis pathway highlighting the bypass reactions compared to glycolysis.)
4. Glycogen Metabolism
● Glycogenesis (Glycogen Synthesis): Glucose-6-phosphate is converted to glucose-1-phosphate, then to UDP-glucose, which is added to a growing glycogen chain by glycogen synthase. Insulin promotes glycogenesis. ● Glycogenolysis (Glycogen Breakdown): Glycogen phosphorylase breaks down glycogen into glucose-1-phosphate, which is then converted to glucose-6-phosphate. Glucagon and epinephrine stimulate glycogenolysis. (Diagram: Pathways of glycogen synthesis and breakdown, showing regulatory enzymes.)
soluble in organic solvents. They serve various crucial functions, including energy storage, structural components of cell membranes, and signaling molecules.
Structure and Classification
Lipids are broadly classified based on their structure and function: ● Fatty Acids: Long hydrocarbon chains with a carboxyl group (-COOH) at one end. ○ Saturated: No double bonds in the hydrocarbon chain (e.g., palmitic acid, stearic acid). ○ Unsaturated: One or more double bonds (e.g., oleic acid - monounsaturated; linoleic acid, alpha-linolenic acid - polyunsaturated). The presence of cis double bonds introduces kinks in the chain. (Illustration: Structures of a saturated fatty acid (palmitic acid) and an unsaturated fatty acid (oleic acid), highlighting the kink due to the cis double bond.) ● Triacylglycerols (Triglycerides): The major form of stored energy in animals and plants. Composed of a glycerol molecule esterified to three fatty acid chains. (Illustration: Formation of a triacylglycerol from glycerol and three fatty acids.) ● Phospholipids (Phosphoacylglycerols): Major components of cell membranes. Composed of a glycerol backbone, two fatty acid chains, a phosphate group, and an alcohol (e.g., choline, ethanolamine, serine). They are amphipathic, having a hydrophilic head (phosphate and alcohol) and a hydrophobic tail (fatty acids). (Illustration: Structure of a phosphatidylcholine molecule, highlighting its amphipathic nature.) ● Sphingolipids: Also important components of cell membranes, particularly in nervous tissue (e.g., sphingomyelin, cerebrosides, gangliosides). They have a sphingosine backbone instead of glycerol. (Illustration: Basic structure of a sphingolipid.) ● Steroids: Characterized by a four-ring carbon skeleton called the steroid nucleus. ○ Cholesterol: A vital structural component of animal cell membranes, precursor for steroid hormones (e.g., estrogen, testosterone, cortisol), vitamin D, and bile acids. (Illustration: Structure of cholesterol.) ● Waxes: Esters of long-chain fatty acids with long-chain alcohols. They are very hydrophobic and serve as protective coatings (e.g., on leaves, skin, fur). ● Eicosanoids: Signaling molecules derived from arachidonic acid (a 20-carbon polyunsaturated fatty acid). Include prostaglandins, thromboxanes, and leukotrienes, which are involved in inflammation, blood clotting, and smooth muscle contraction.
Metabolic Pathways
1. Lipolysis (Fatty Acid Mobilization)
● Description: The breakdown of triacylglycerols stored in adipose tissue into glycerol and free fatty acids, which are then released into the bloodstream. ● Key Enzymes: Hormone-sensitive lipase (HSL) is the key regulatory enzyme, activated by hormones like epinephrine and glucagon (via cAMP pathway) and inhibited by insulin. (Diagram: Hormonal regulation of HSL and the release of fatty acids and glycerol from adipocytes.)
2. Fatty Acid β-Oxidation
● Description: A cyclical metabolic process by which fatty acids are broken down in the mitochondria (and peroxisomes for very long-chain fatty acids) to generate acetyl-CoA, NADH, and FADH_2. ● Activation: Fatty acids are first activated to acyl-CoA in the cytoplasm by fatty acyl-CoA synthetase (requires ATP). ● Transport: Long-chain acyl-CoAs are transported into the mitochondrial matrix via the carnitine shuttle. ● β-Oxidation Spiral: A four-step cycle is repeated:
- Oxidation by acyl-CoA dehydrogenase (produces FADH_2).
- Hydration by enoyl-CoA hydratase.
- Oxidation by 3-hydroxyacyl-CoA dehydrogenase (produces NADH).
- Thiolysis by β-ketothiolase, releasing acetyl-CoA and an acyl-CoA molecule shortened by two carbons. ○ The acetyl-CoA enters the Krebs cycle, and NADH and FADH_2 enter the electron transport chain. (Diagram: The four steps of the β-oxidation spiral, showing enzyme names and cofactor involvement.)
3. Fatty Acid Synthesis (Lipogenesis)
● Description: The creation of fatty acids from acetyl-CoA and NADPH, primarily in the cytoplasm of liver, adipose tissue, and lactating mammary glands. ● Precursor Transport: Acetyl-CoA from mitochondria is transported to the cytoplasm as citrate (citrate shuttle). ● Key Enzyme: Acetyl-CoA carboxylase (ACC) carboxylates acetyl-CoA to malonyl-CoA. This is the committed and highly regulated step, activated by citrate and insulin, and inhibited by long-chain fatty acyl-CoAs and glucagon/epinephrine. ● Fatty Acid Synthase (FAS) Complex: A large, multi-enzyme complex that catalyzes a repeating four-step sequence to elongate the fatty acid chain, typically producing palmitate (16:0).
- Condensation
- Reduction (requires NADPH)
- Dehydration
- Reduction (requires NADPH) (Diagram: Overview of fatty acid synthesis, highlighting the role of ACC and the FAS complex.)
4. Cholesterol Metabolism
● Synthesis: A complex, multi-step process occurring primarily in the liver, starting from acetyl-CoA. The enzyme HMG-CoA reductase catalyzes the rate-limiting step (conversion of HMG-CoA to mevalonate) and is a major target for cholesterol-lowering drugs (statins). (Diagram: Simplified overview of cholesterol biosynthesis, emphasizing the HMG-CoA reductase step.) ● Transport: Cholesterol and other lipids are transported in the bloodstream as part of lipoprotein particles (e.g., chylomicrons, VLDL, LDL, HDL) due to their insolubility. ● Excretion: Cholesterol can be converted to bile acids in the liver, which aid in fat digestion and are an important route for cholesterol excretion.
upregulate LDL receptor expression in the liver, leading to increased clearance of LDL cholesterol from the bloodstream. (Note: This isn't a disease, but a therapeutic correlation to lipid metabolism.)
Proteins 💪
Proteins are highly complex macromolecules composed of one or more long chains of amino acid residues. They perform a vast array of functions within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules.
Structure and Classification
● Amino Acids: The building blocks of proteins. There are 20 common amino acids, each with a central carbon atom (α-carbon) bonded to an amino group (-NH_2), a carboxyl group (-COOH), a hydrogen atom, and a variable group called a side chain (R-group). The R-group determines the unique properties of each amino acid. (Illustration: General structure of an amino acid, and examples of different R-groups (e.g., nonpolar, polar uncharged, acidic, basic).) ● Peptide Bonds: Amino acids are linked together by peptide bonds, formed between the carboxyl group of one amino acid and the amino group of the next, releasing a molecule of water (dehydration synthesis). (Illustration: Formation of a peptide bond between two amino acids.) ● Levels of Protein Structure:
- Primary Structure: The linear sequence of amino acids in a polypeptide chain. Determined by the genetic code. (Illustration: A short polypeptide sequence showing amino acids linked by peptide bonds.)
- Secondary Structure: Local, regular folding patterns of the polypeptide backbone, stabilized by hydrogen bonds between peptide bond C=O and N-H groups. Common structures include: ■ α-helix: A right-handed coil. ■ β-pleated sheet: Formed by hydrogen bonds between adjacent polypeptide strands (parallel or antiparallel). (Illustration: α-helix and β-pleated sheet structures, highlighting hydrogen bonding.)
- Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between the R-groups of the amino acids. These interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces, and disulfide bridges (covalent bonds between cysteine residues). (Illustration: A globular protein showing various R-group interactions contributing to its tertiary structure.)
- Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) to form a functional protein complex. Not all proteins have quaternary structure. (e.g., hemoglobin, which has four subunits). (Illustration: Hemoglobin molecule showing its four subunits.) ● Classification by Function: ○ Enzymes: Catalyze biochemical reactions (e.g., amylase, pepsin). ○ Structural Proteins: Provide support and shape (e.g., collagen, keratin).
○ Transport Proteins: Carry substances (e.g., hemoglobin, albumin). ○ Hormonal Proteins: Regulate physiological processes (e.g., insulin, growth hormone). ○ Receptor Proteins: Mediate cellular responses to stimuli (e.g., G-protein coupled receptors). ○ Contractile Proteins: Involved in movement (e.g., actin, myosin). ○ Defensive Proteins: Protect against disease (e.g., antibodies). ○ Storage Proteins: Store amino acids or ions (e.g., ferritin stores iron).
Metabolic Pathways
1. Protein Digestion and Amino Acid Absorption
● Digestion: Begins in the stomach with the action of pepsin (secreted as inactive pepsinogen and activated by low pH), which breaks proteins into smaller peptides. Continues in the small intestine where pancreatic proteases (e.g., trypsin, chymotrypsin, elastase, carboxypeptidases , secreted as zymogens) and intestinal peptidases further hydrolyze peptides into amino acids, dipeptides, and tripeptides. (Diagram: Overview of protein digestion in the GI tract, indicating key enzymes and their sites of action.) ● Absorption: Amino acids and small peptides are absorbed by intestinal epithelial cells via various specific transporters.
2. Amino Acid Catabolism (Degradation)
● Overview: Surplus amino acids are not stored; they are catabolized. The α-amino group is removed, and the remaining carbon skeleton is converted into major metabolic intermediates that can be used for energy production (via Krebs cycle), gluconeogenesis, or fatty acid synthesis. ● Transamination: The first step in the catabolism of most amino acids is the transfer of their α-amino group to α-ketoglutarate to form glutamate and an α-keto acid. This is catalyzed by aminotransferases (transaminases) , which require pyridoxal phosphate (PLP, a derivative of vitamin B6) as a cofactor. (Diagram: General transamination reaction.) ● Oxidative Deamination: Glutamate is then oxidatively deaminated by glutamate dehydrogenase in the mitochondria, releasing ammonia (NH_4^+) and regenerating α-ketoglutarate. This reaction uses NAD^+ or NADP^+ as a cofactor. (Diagram: Oxidative deamination of glutamate.) ● Urea Cycle: ○ Purpose: Ammonia is toxic, especially to the brain. The urea cycle converts ammonia into urea (a less toxic compound) in the liver for excretion in urine. ○ Location: Mitochondrial matrix and cytoplasm of liver cells. ○ Key Steps:
- Formation of carbamoyl phosphate from NH_4^+, HCO_3^-, and 2 ATP (catalyzed by carbamoyl phosphate synthetase I - the rate-limiting step).
- Carbamoyl phosphate reacts with ornithine to form citrulline (in mitochondria).
- Citrulline is transported to the cytoplasm and reacts with aspartate (donor of the second nitrogen atom of urea) to form argininosuccinate (requires ATP).
the essential amino acid phenylalanine to tyrosine. ○ Pathophysiology: Without functional PAH, phenylalanine accumulates in the blood and tissues. High levels of phenylalanine and its metabolites (like phenylpyruvate, phenylacetate, and phenyllactate) are neurotoxic and can cause severe intellectual disability, seizures, microcephaly, and behavioral problems if untreated. Tyrosine becomes an essential amino acid. ○ Diagnosis and Management: Most newborns are screened for PKU. Treatment involves a lifelong diet severely restricted in phenylalanine (low-protein foods) and supplementation with tyrosine and special medical formulas. Early and consistent dietary management can lead to normal development. (Clinical Scenario: A newborn screening test comes back positive for PKU. The infant is immediately placed on a special low-phenylalanine formula, and the parents receive extensive dietary counseling.) ● Urea Cycle Disorders: ○ Description: A group of genetic disorders caused by defects in any of the enzymes or transporter proteins involved in the urea cycle. This leads to the accumulation of ammonia (hyperammonemia) and other toxic precursors in the blood. ○ Symptoms: Can present in newborns with lethargy, vomiting, poor feeding, seizures, and coma. If untreated, can lead to brain damage and death. Milder, late-onset forms also exist. ○ Example: Ornithine Transcarbamylase (OTC) Deficiency: The most common urea cycle disorder, X-linked. ○ Management: Acute management involves reducing ammonia levels (e.g., dialysis, nitrogen-scavenging drugs). Long-term management includes a low-protein diet, essential amino acid supplementation, and medications to help remove nitrogenous waste. (Clinical Scenario: A neonate develops rapidly worsening neurological symptoms and is found to have extremely high blood ammonia levels, suggestive of a urea cycle disorder.) ● Sickle Cell Anemia: ○ Description: A genetic disorder caused by a point mutation in the gene for β-globin, one of the subunits of hemoglobin. This results in the substitution of valine for glutamic acid at the sixth position of the β-globin chain (HbS). ○ Pathophysiology: Under low oxygen conditions, HbS molecules polymerize, causing red blood cells to become rigid and sickle-shaped. These abnormal cells can block small blood vessels (vaso-occlusion), leading to pain crises, organ damage, and increased destruction of red blood cells (hemolytic anemia). ○ Correlation: While primarily a genetic disease affecting protein structure, it illustrates the profound impact a single amino acid change can have on protein function and human health. The altered primary structure leads to abnormal quaternary structure interactions under deoxygenated conditions. (Clinical Scenario: A child of African descent presents with recurrent episodes of severe pain in the limbs and abdomen, along with anemia.)
Nucleic Acids 🧬
Nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are biopolymers essential for all known forms of life. They carry genetic information that is read in cells to make
the RNA and proteins by which living things function.
Structure and Classification
● Nucleotides: The monomeric units of nucleic acids. Each nucleotide consists of three components:
- A Pentose Sugar: ■ Deoxyribose in DNA (lacks an oxygen atom at the 2' carbon). ■ Ribose in RNA (has a hydroxyl group at the 2' carbon).
- A Nitrogenous Base: ■ Purines: Adenine (A) and Guanine (G) – have a double-ring structure. ■ Pyrimidines: Cytosine (C), Thymine (T) (only in DNA), and Uracil (U) (only in RNA) – have a single-ring structure.
- A Phosphate Group: One, two, or three phosphate groups attached to the 5' carbon of the sugar. (Illustration: Structures of deoxyribose and ribose. Structures of the five nitrogenous bases. General structure of a nucleotide, showing the sugar, base, and phosphate.) ● Polynucleotide Chains: Nucleotides are linked together by phosphodiester bonds formed between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of the next nucleotide. This creates a sugar-phosphate backbone with the nitrogenous bases projecting outwards. (Illustration: Formation of a phosphodiester bond between two nucleotides.) ● Deoxyribonucleic Acid (DNA): ○ Structure: Typically a double-stranded helix (B-DNA is the most common form). The two strands run antiparallel (one 5' to 3', the other 3' to 5'). ○ Base Pairing: Adenine (A) pairs with Thymine (T) via two hydrogen bonds. Guanine (G) pairs with Cytosine (C) via three hydrogen bonds (Chargaff's rules). This specific pairing is crucial for DNA replication and transcription. ○ Function: Stores the genetic blueprint of the organism. Contains the instructions for building and maintaining an organism. (Illustration: Double helix structure of DNA, showing antiparallel strands, sugar-phosphate backbone, and A-T, G-C base pairing with hydrogen bonds.) ● Ribonucleic Acid (RNA): ○ Structure: Usually single-stranded, but can form secondary structures (e.g., hairpin loops) through intramolecular base pairing (A with U, G with C). ○ Types and Functions: ■ Messenger RNA (mRNA): Carries genetic information transcribed from DNA to the ribosomes for protein synthesis. ■ Transfer RNA (tRNA): Acts as an adaptor molecule in protein synthesis. Each tRNA carries a specific amino acid and has an anticodon that base-pairs with the corresponding codon on mRNA. (Illustration: Cloverleaf structure of a tRNA molecule.) ■ Ribosomal RNA (rRNA): A major structural and catalytic component of ribosomes, the machinery for protein synthesis. ■ Other RNAs: Small nuclear RNAs (snRNAs), microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs) – involved in gene regulation and other cellular processes.
● Description: The process by which a DNA molecule is duplicated to produce two identical DNA molecules. It is semi-conservative (each new DNA molecule contains one old strand and one new strand). ● Key Enzymes and Proteins: ○ Helicase: Unwinds the DNA double helix. ○ Single-Strand Binding Proteins (SSBs): Stabilize the separated strands. ○ Primase: Synthesizes short RNA primers to provide a 3'-OH group for DNA polymerase. ○ DNA Polymerase: Catalyzes the synthesis of new DNA strands by adding nucleotides complementary to the template strand in the 5' to 3' direction. Requires a template and a primer. Has proofreading activity (3' to 5' exonuclease) to correct errors. ○ Leading Strand: Synthesized continuously in the 5' to 3' direction towards the replication fork. ○ Lagging Strand: Synthesized discontinuously in short fragments (Okazaki fragments) away from the replication fork, also in the 5' to 3' direction. ○ DNA Ligase: Joins Okazaki fragments together. ○ Topoisomerases: Relieve supercoiling stress ahead of the replication fork. (Diagram: Replication fork showing leading and lagging strand synthesis, and the key enzymes involved.)
4. Transcription (RNA Synthesis)
● Description: The process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA) or other RNA types. ● Key Enzyme: RNA Polymerase. Binds to specific DNA sequences called promoters to initiate transcription. Does not require a primer. ● Steps:
- Initiation: RNA polymerase binds to the promoter, unwinds the DNA, and initiates RNA synthesis.
- Elongation: RNA polymerase moves along the DNA template strand, synthesizing a complementary RNA molecule in the 5' to 3' direction using ribonucleoside triphosphates (ATP, UTP, CTP, GTP).
- Termination: RNA polymerase reaches a terminator sequence on the DNA, and the RNA transcript is released. ● RNA Processing (in Eukaryotes): ○ 5' Capping: Addition of a modified guanine nucleotide to the 5' end of pre-mRNA. ○ 3' Polyadenylation: Addition of a poly-A tail (multiple adenine nucleotides) to the 3' end. ○ Splicing: Removal of non-coding regions (introns) and joining of coding regions (exons). (Diagram: Overview of transcription, showing RNA polymerase, DNA template, and the growing RNA transcript. Separate diagram for eukaryotic RNA processing.)
5. Translation (Protein Synthesis)
● Description: The process by which the sequence of codons in an mRNA molecule directs the incorporation of amino acids into a polypeptide chain.
● Location: Ribosomes in the cytoplasm. ● Key Players: ○ mRNA: Carries the genetic code from DNA. Codons are three-nucleotide sequences that specify particular amino acids. ○ tRNA: Adaptor molecules with an anticodon that base-pairs with an mRNA codon, and a corresponding amino acid attached. Aminoacyl-tRNA synthetases attach the correct amino acids to their respective tRNAs ("charging"). ○ Ribosomes: Composed of rRNA and ribosomal proteins. Have a small and a large subunit. Contain binding sites for mRNA and tRNAs (A site: aminoacyl-tRNA; P site: peptidyl-tRNA; E site: exit). ● Steps:
- Initiation: The small ribosomal subunit binds to mRNA and the initiator tRNA (carrying methionine in eukaryotes). The large subunit then joins to form the initiation complex.
- Elongation: ■ Codon Recognition: An incoming aminoacyl-tRNA binds to the codon in the A site. ■ Peptide Bond Formation: The polypeptide chain on the P site tRNA is transferred to the amino acid on the A site tRNA, catalyzed by peptidyl transferase activity of rRNA (a ribozyme). ■ Translocation: The ribosome moves one codon down the mRNA. The tRNA from the P site moves to the E site and exits; the tRNA from the A site (now carrying the growing polypeptide) moves to the P site.
- Termination: A stop codon (UAA, UAG, UGA) in the mRNA reaches the A site. Release factors bind to the stop codon, causing the polypeptide to be released and the ribosomal complex to dissociate. (Diagram: Ribosome structure with A, P, and E sites, showing the steps of translation: initiation, elongation (codon recognition, peptide bond formation, translocation), and termination.)
Enzyme Mechanisms (Example)
● DNA Polymerase (during DNA replication): ○ Reaction: Catalyzes the template-directed synthesis of DNA by adding deoxyribonucleotides to the 3'-OH end of a growing DNA strand. (dNMP)n + dNTP \rightarrow (dNMP){n+1} + PP_i ○ Mechanism:
- Substrate Binding: The correct deoxyribonucleoside triphosphate (dNTP) whose base is complementary to the template base binds to the active site. The active site "selects" the correct dNTP based on its ability to form proper Watson-Crick base pairs with the template.
- Nucleophilic Attack: The 3'-hydroxyl group of the primer strand (or growing DNA strand) performs a nucleophilic attack on the \alpha-phosphate of the incoming dNTP.
- Phosphodiester Bond Formation: A phosphodiester bond is formed, and pyrophosphate (PP_i) is released. The hydrolysis of PP_i by pyrophosphatase drives the reaction forward.
- Translocation: The enzyme (or DNA) translocates to position the new 3'-OH end in the active site for the next addition.
● Anticancer Drugs Targeting Nucleotide Metabolism: ○ Rationale: Rapidly dividing cancer cells have a high demand for nucleotides for DNA and RNA synthesis. Therefore, enzymes involved in nucleotide metabolism are attractive targets for chemotherapy. ○ Examples: ■ Methotrexate: An antifolate drug that inhibits dihydrofolate reductase (DHFR). This enzyme is crucial for regenerating tetrahydrofolate, a cofactor required for thymidylate synthesis (conversion of dUMP to dTMP by thymidylate synthase) and de novo purine synthesis. Inhibition of DHFR depletes tetrahydrofolate, thus blocking DNA synthesis. ■ 5-Fluorouracil (5-FU): A pyrimidine analog that is converted in cells to FdUMP (fluorodeoxyuridine monophosphate). FdUMP irreversibly inhibits thymidylate synthase , thereby blocking the synthesis of dTMP and thus DNA replication. (Note: This illustrates therapeutic targeting of nucleic acid metabolism rather than a specific disease caused by its defect, but is highly relevant clinically.)
