Biochemistry
Basic Biochemistry and the Cell
Basic biochemistry for MBBS: water, pH and buffers, the Henderson-Hasselbalch equation, and the metabolic role of cell organelles, mapped to NMC code BI1.1.
MedNext Academy | 3 min read
Basic Biochemistry and the Cell
Basic biochemistry for MBBS: water, pH and buffers, the Henderson-Hasselbalch equation, and the metabolic role of cell organelles, mapped to NMC code BI1.1.
Basic biochemistry sets the physical and cellular groundwork for the whole subject. It covers water, pH and buffers, the properties of biomolecules in solution, and the molecular organisation of the cell and its organelles, each of which is the site of a specific set of metabolic reactions.
High-yield: Basic Biochemistry and the Cell
- Water is the biological solvent; its polarity and hydrogen bonding drive the hydrophobic effect that folds proteins and forms membranes.
- The Henderson-Hasselbalch equation, pH equals pKa plus log of base over acid, underlies buffer action and blood pH control.
- The bicarbonate buffer is the main extracellular buffer; its pKa of 6.1 works because the lungs and kidneys keep carbon dioxide and bicarbonate open-ended.
- Normal arterial blood pH is tightly held between 7.35 and 7.45.
- Cell membranes are a fluid mosaic of phospholipid bilayer with embedded proteins; cholesterol modulates fluidity.
- The mitochondrion is the site of the citric acid cycle, beta-oxidation and oxidative phosphorylation, and it carries its own circular DNA.
- The rough endoplasmic reticulum synthesises secretory and membrane proteins; the smooth reticulum handles lipid synthesis and drug detoxification.
- The Golgi apparatus modifies, sorts and packages proteins, adding sugars during glycosylation.
- Lysosomes contain acid hydrolases active at pH 5; their deficiency causes lysosomal storage diseases such as Tay-Sachs.
- Peroxisomes carry out very-long-chain fatty acid oxidation and generate and detoxify hydrogen peroxide with catalase.
- The nucleus stores genomic DNA as chromatin and is the site of replication and transcription.
- Amphipathic molecules with polar and non-polar ends, such as phospholipids and bile salts, form micelles and bilayers in water.
- A buffer resists pH change best when the weak acid and its conjugate base are present in roughly equal amounts, near the pKa.
- Osmosis moves water across a semipermeable membrane from low to high solute concentration, setting cell volume.
Organelles and their metabolic role
- **Mitochondrion:** Citric acid cycle, beta-oxidation, oxidative phosphorylation. Has its own DNA.
- **Endoplasmic reticulum:** Rough: protein synthesis. Smooth: lipid synthesis and detoxification.
- **Lysosome:** Acid hydrolases at pH 5. Defects cause storage diseases.
- **Peroxisome:** Very-long-chain fatty acid oxidation, hydrogen peroxide handling by catalase.
NMC competencies in this chapter
- **BI1.1:** Molecular and functional organisation of the cell and its subcellular components
Frequently Asked Questions
Why is the bicarbonate buffer effective if its pKa is far from blood pH?
Its pKa of 6.1 is below the normal pH of 7.4, but the system is open. The lungs blow off carbon dioxide and the kidneys adjust bicarbonate, so the buffer is continually reset rather than being limited by its pKa alone.
What makes the mitochondrion central to metabolism?
It houses the citric acid cycle, fatty acid beta-oxidation and the electron transport chain, so most cellular ATP is produced there. It also carries its own DNA, inherited maternally.
How does the Henderson-Hasselbalch equation help clinically?
It links pH to the ratio of a conjugate base to its weak acid, which is the basis for interpreting acid-base status and understanding how buffers and drug ionisation behave in the body.
Why do lysosomal enzymes need an acidic environment?
Their acid hydrolases are optimally active near pH 5, which the lysosome maintains with proton pumps. This also protects the cytosol, since any leaked enzyme is largely inactive at the neutral cytosolic pH.
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