---
title: "Biochemistry & Molecular Biology"
description: "25 topics in Science, in the order they build on each other."
canonical: https://lightmysky.com/learn/science/areas/biochemistry-and-molecular-biology
source: https://lightmysky.com/learn/science/areas/biochemistry-and-molecular-biology.md
retrieved: 2026-09-02
---

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# Biochemistry & Molecular Biology

25 topics in Science, in the order they build on each other.

Page: https://lightmysky.com/learn/science/areas/biochemistry-and-molecular-biology

- [Deriving the Michaelis-Menten Equation from the Steady State](https://lightmysky.com/learn/science/deriving-the-michaelis-menten-equation-from-the-steady-state-mt_BFp0fwZ8_i): Assuming the enzyme-substrate complex is formed and broken down at the same rate turns a scheme of four rate constants into one equation with two measurable constants. Seeing where each constant comes from explains why the Michaelis constant is not a binding constant.
- [Double-Reciprocal Plots and Telling Inhibitor Types Apart](https://lightmysky.com/learn/science/double-reciprocal-plots-and-telling-inhibitor-types-apart-mt_9y397ROu9X): Plotting reciprocals turns a curve into a straight line whose intercepts give the two constants directly. Each inhibition type moves a different intercept, so the plot identifies the mechanism rather than just showing that the rate fell.
- [How Enzymes Lower the Activation Barrier](https://lightmysky.com/learn/science/how-enzymes-lower-the-activation-barrier-mt_uwB5TXF3Nb): Catalysis comes from binding the transition state more tightly than the substrate, helped by holding reactants together, straining bonds and moving protons at the right moment. The enzyme changes the path, never the position of the equilibrium.
- [Protein Folding, Chaperones and What Misfolding Costs](https://lightmysky.com/learn/science/protein-folding-chaperones-and-what-misfolding-costs-mt_n9rlqjbaXK): A chain of amino acids reaches its working shape by burying hydrophobic side chains and settling into the lowest free energy it can find. Chaperones keep partly folded chains apart while that happens, and a chain that ends up in the wrong shape is either recycled or aggregates.
- [Post-translational Modification and Protein Turnover](https://lightmysky.com/learn/science/post-translational-modification-and-protein-turnover-mt_93cxQwxxkh): Most proteins are altered after they are made: phosphate groups, sugars, lipid tails and cleaved segments all change what a protein does. Tagging with ubiquitin sends it to the proteasome, so the amount of a protein is set by degradation as much as by synthesis.
- [Allosteric Enzymes, Cooperativity and the Sigmoid Curve](https://lightmysky.com/learn/science/allosteric-enzymes-cooperativity-and-the-sigmoid-curve-mt_u8f5QLHq-g): Enzymes with several subunits can shift between a low-activity and a high-activity form, so binding at one site changes affinity at the others. The result is an S-shaped response that makes the enzyme act like a switch over a narrow concentration range.
- [Coenzymes, Cofactors and the Chemistry They Supply](https://lightmysky.com/learn/science/coenzymes-cofactors-and-the-chemistry-they-supply-mt_CZ2ytn3SQr): Amino acid side chains cannot do every chemical job, so enzymes recruit metal ions and small organic molecules to carry electrons, groups or single carbons. Many of those helpers are what vitamins are for.
- [Coupled Reactions and Why ATP Is the Cell's Currency](https://lightmysky.com/learn/science/coupled-reactions-and-why-atp-is-the-cells-currency-mt_1yVJRArCow): An unfavourable reaction proceeds when it shares an intermediate with a favourable one, so the two free energy changes add. ATP is used because its hydrolysis releases a useful amount, not the largest amount available.
- [Control Points in Glycolysis and the Committed Step](https://lightmysky.com/learn/science/control-points-in-glycolysis-and-the-committed-step-mt_2vAoKtnmoz): Only a few reactions in a pathway are far from equilibrium, and those are where regulation acts. In glycolysis the committed step responds to signals about how much energy the cell already has, which is why the pathway speeds up when demand rises.
- [Replication Machinery: Origins, Forks and Telomeres](https://lightmysky.com/learn/science/replication-machinery-origins-forks-and-telomeres-mt_v95MJWeV_B): Replication starts at defined origins and runs in both directions, with one strand made continuously and the other in pieces. Because polymerase cannot start a chain or work backwards, linear chromosomes lose a little end sequence each round unless telomerase restores it.
- [DNA Damage and the Repair Pathways That Fix It](https://lightmysky.com/learn/science/dna-damage-and-the-repair-pathways-that-fix-it-mt_r0qipp0YRR): Bases are damaged constantly by chemistry inside the cell and by radiation outside it, and each kind of damage has a repair route matched to it. Proofreading and mismatch repair together cut the error rate of copying by orders of magnitude.
- [Transcription Initiation: Promoters, General Factors and Polymerase Recruitment](https://lightmysky.com/learn/science/transcription-initiation-promoters-general-factors-and-polymerase-recruitment-mt_0Ky-pYgh0Y): Eukaryotic polymerase does not find a promoter alone: general factors assemble on it first and position the enzyme at the start site. The rate of transcription is set mostly at this assembly step.
- [Alternative Splicing and One Gene, Many Proteins](https://lightmysky.com/learn/science/alternative-splicing-and-one-gene-many-proteins-mt_xei9v3IIsE): The spliceosome can include or skip particular exons, so one gene yields several related proteins depending on cell type and conditions. Which sites are used is set by regulatory proteins binding near them.
- [Gluconeogenesis and the Reciprocal Regulation of Opposing Pathways](https://lightmysky.com/learn/science/gluconeogenesis-and-the-reciprocal-regulation-of-opposing-pathways-mt_D1MbKcb6Le): Making glucose is not glycolysis run backwards: the three irreversible steps are bypassed by different enzymes, which is what allows separate control. Signals that activate one direction inhibit the other, so the cell avoids running both and wasting ATP.
- [The Citric Acid Cycle as a Hub, and Refilling It](https://lightmysky.com/learn/science/the-citric-acid-cycle-as-a-hub-and-refilling-it-mt_BPPfI-vnab): The cycle both oxidises acetyl groups and supplies carbon skeletons for biosynthesis, so intermediates are constantly withdrawn. Because it is a cycle, those withdrawals stop it unless separate reactions top the intermediates back up.
- [Redox Potentials and the Proton-Motive Force](https://lightmysky.com/learn/science/redox-potentials-and-the-proton-motive-force-mt_lU8kgepFRN): Electrons pass down a chain of carriers arranged in order of their standard potentials, and the energy released at three points is used to move protons out. The gradient stores that energy as both a concentration difference and a voltage.
- [ATP Synthase as a Rotary Machine](https://lightmysky.com/learn/science/atp-synthase-as-a-rotary-machine-mt_PDe3f-FVfD): Protons flowing back through the membrane turn a rotor, and that rotation changes the shape of three catalytic sites in turn so each binds, forms and releases ATP. The step that costs energy is releasing the product, not making the bond.
- [Fatty Acid Oxidation, Ketone Bodies and Choosing a Fuel](https://lightmysky.com/learn/science/fatty-acid-oxidation-ketone-bodies-and-choosing-a-fuel-mt_2GNrC-0ziR): Fatty acids are shortened two carbons at a time, feeding acetyl groups into the cycle and reduced carriers into the chain, which is why fat yields more ATP per carbon than sugar. When carbohydrate runs low the liver converts some of that acetyl into ketone bodies the brain can use.
- [Fluorescent Tagging and Reading a Live-Cell Image](https://lightmysky.com/learn/science/fluorescent-tagging-and-reading-a-live-cell-image-mt_J0toch-ZZ3): Fusing a fluorescent protein to a gene lets a specific protein be watched in a living cell, and antibodies stained with dyes do the same job in fixed cells. Both methods report location and timing, and both can change the thing they measure.
- [Fractionation, Blotting and Pulling Down a Binding Partner](https://lightmysky.com/learn/science/fractionation-blotting-and-pulling-down-a-binding-partner-mt_MRfFQlBIPy): Breaking cells open and spinning them at increasing speeds separates organelles by size and density, and a blot then asks whether a named protein is present in a fraction. Precipitating one protein with an antibody brings its partners with it, which is how binding is tested.
- [The Pentose Phosphate Pathway and Reducing Power for Biosynthesis](https://lightmysky.com/learn/science/the-pentose-phosphate-pathway-and-reducing-power-for-biosynthesis-mt_2p-JnaEaTO): A branch off glycolysis produces the reduced carrier used for building molecules and for defending against oxidative damage, plus the five-carbon sugars needed for nucleotides. The cell adjusts the branch according to whether it needs reducing power, ribose or both.
- [Transamination, Ammonia and the Urea Cycle](https://lightmysky.com/learn/science/transamination-ammonia-and-the-urea-cycle-mt_MFu5uQKyFL): Amino groups are moved onto keto acids rather than released, and only at the end is nitrogen freed as ammonia, which is toxic. The liver converts it into urea in a cycle that costs ATP, and the carbon skeletons left behind enter metabolism elsewhere.
- [Flux Control and Following Atoms with Labelled Substrates](https://lightmysky.com/learn/science/flux-control-and-following-atoms-with-labelled-substrates-mt_PzhsDwD_aW): Control of a pathway is usually shared between several enzymes rather than held by one, and how much each holds can be measured. Feeding a substrate whose atoms are labelled and seeing where they appear is how the routes actually taken are established.
- [Proteomics: Mass Spectra, Quantification and Interaction Maps](https://lightmysky.com/learn/science/proteomics-mass-spectra-quantification-and-interaction-maps-mt_a-8UHB2SFR): Mass spectrometry identifies peptides from mass and fragmentation, and quantification turns spectra into abundances that can be compared between conditions. This stop covers what a proteome measurement misses and how an interaction map is built and misread.
- [Target Validation and Lead Discovery: From a Biological Claim to a Molecule](https://lightmysky.com/learn/science/target-validation-and-lead-discovery-from-a-biological-claim-to-a-molecule-mt_xHWq5Rg85r): A target is worth pursuing only if changing it changes disease and if a molecule can reach it. This stop covers genetic and chemical validation, screening for hits, and the properties a hit has to gain before it counts as a lead.