21 topics
Biochemistry help for the parts that will not stay memorised
Biochemistry is the course where most students try to memorise glycolysis as ten names and lose the plot by step four. The pathway is far easier held as a shape: two ATP spent up front to trap and destabilise glucose, one six-carbon sugar split into two three-carbon pieces, then four ATP earned back, giving a net of two. Three of those steps are irreversible, and those three are the only ones regulated. That structure survives an exam. A list of enzyme names does not.
Where students get stuck
I still do not know what Km actually is
Km is a concentration, not a rate, and that single fact clears most of the confusion. It is the substrate concentration at which the enzyme is running at half its maximum velocity. Because of that, it works as an inverse measure of affinity: a low Km means the enzyme reaches half speed at very little substrate, so it grips that substrate tightly, while a high Km means it needs a lot of substrate to get going. From there the inhibitor patterns stop needing memorisation. A competitive inhibitor fights for the active site, so more substrate can out-compete it and Vmax is unchanged, but you need more substrate to reach half speed, so Km rises. A non-competitive inhibitor binds elsewhere and effectively removes enzyme molecules from play, so Vmax falls while Km stays put.
The reaction has a positive delta G but the textbook says it happens
You are reading the standard value and applying it to a cell, and those are different numbers. Delta G standard prime assumes every reactant and product sits at one molar, pH 7. A living cell is nowhere near that. The value that decides direction is the actual delta G, which equals delta G standard prime plus RT times the natural log of the mass action ratio, and that ratio depends on real concentrations. The classic example is the aldolase step of glycolysis, thermodynamically unfavourable on paper, which runs forward constantly because the next enzyme consumes its products as fast as they appear and keeps the ratio tiny. Cells drive unfavourable reactions by removing products and by coupling, not by changing thermodynamics.
Amino acid titration curves and pI are guesswork for me
Read the curve as a sequence of separate ionisable groups, each losing a proton in turn as pH rises, and remember that a flat region on the curve means buffering at that group's pKa. Start fully protonated at low pH and count the charge: the carboxyl group is neutral when protonated, negative when not, and the amino group is positive when protonated, neutral when not. The isoelectric point is the pH where net charge is zero, and you find it by averaging the two pKa values that sit either side of the neutral species. For glycine that is the two pKa values you were given. For a side chain that ionises, such as aspartate or lysine, you must first work out where the neutral form lies in the sequence, then average the pKa immediately below and immediately above it.
I cannot keep the electron transport chain and chemiosmosis straight
Separate them into two jobs that happen to be attached. The chain itself is a series of carriers of increasing electron affinity, and electrons fall down that gradient releasing energy at each drop. That energy is not stored as ATP at all. It is used to pump protons out of the mitochondrial matrix, building a gradient that is part concentration and part charge. ATP synthase is a separate machine that lets those protons fall back in and turns that flow into ATP. This is why an uncoupler such as dinitrophenol is lethal and instructive at once: it puts a hole in the membrane so protons leak back without passing through the synthase. The chain keeps running, oxygen is still consumed, the energy comes out as heat, and ATP production collapses.
I mix up which pathways are anabolic and which are catabolic, and where they run
Ask two questions of every pathway: is it building or breaking, and does it spend or make reducing power. Catabolic pathways break large molecules down, release energy, and generate NADH, which then feeds the electron transport chain. Anabolic pathways build, consume energy, and use NADPH rather than NADH as their electron donor. That split is deliberate, since it lets a cell run degradation and synthesis at the same time without one undoing the other. Location follows the same logic. Glycolysis and fatty acid synthesis are cytosolic. The citric acid cycle, beta oxidation and the electron transport chain are mitochondrial. When a question asks why a pathway is compartmentalised, the answer is nearly always regulation or preventing a futile cycle.
What's covered
Biochemistry topics you can work through with a tutor, generate practice on, or turn into flashcards and a study plan.
Chemical foundations
- Water, hydrogen bonding and the hydrophobic effect
- Acids, bases, pKa and buffer systems
- Henderson-Hasselbalch calculations
- Functional groups and biological macromolecules
Proteins and enzymes
- Amino acid structures, charge and titration curves
- Primary through quaternary structure and folding
- Enzyme mechanisms and the transition state
- Michaelis-Menten and Lineweaver-Burk analysis
- Inhibition types and allosteric regulation
Bioenergetics and metabolism
- Free energy, coupling and the ATP cycle
- Glycolysis and gluconeogenesis
- The citric acid cycle and its regulation
- Electron transport and oxidative phosphorylation
- Beta oxidation and fatty acid synthesis
Molecules of storage and signalling
- Carbohydrate structure and glycogen metabolism
- Lipids, membranes and transport proteins
- Nucleotides, DNA and RNA chemistry
- Hormonal control and second messengers
Laboratory methods
- Spectrophotometry and the Beer-Lambert law
- Chromatography and electrophoresis
- Enzyme assays and kinetic data plots
Biochemistry questions
Can it help me read a Lineweaver-Burk plot from my own lab data?
Yes. Share your screen with the spreadsheet or plot open and talk through it. The useful part is the interpretation rather than the arithmetic: lines meeting on the y-axis mean an unchanged Vmax and therefore competitive inhibition, while lines meeting on the x-axis mean an unchanged Km. It will also point out when your low-substrate points are dominating the fit, which is the known weakness of a double reciprocal plot.
Do I have to memorise every enzyme name in glycolysis?
That depends on your instructor, so check your outline rather than guessing. What is almost always assessed is the three irreversible steps, their enzymes and their regulators, because those are the control points and every regulation question lands on them. Learn those cold, learn where ATP is spent and earned, and then let the remaining names attach to structures you can already draw.
Will it do my problem set for me if I ask?
It will not hand over completed answers, and it is fairly stubborn about it. On a kinetics problem it will ask what you think Vmax is from the data before doing anything else. If you are genuinely stuck at midnight, the honest use is to ask it to work one similar problem fully on the whiteboard, then do yours yourself while it watches and corrects the step you get wrong.
I am taking this alongside organic chemistry and drowning. Where do they overlap?
More than most students expect, and using that overlap saves real time. Enzyme mechanisms are organic mechanisms drawn with an active site around them: nucleophilic attack, leaving groups and acid-base catalysis are the same arrows you push in organic. If you can already explain why a carbonyl carbon is electrophilic, several enzyme mechanisms stop being new material and become the same idea in a protein.
Stuck on biochemistry right now?
Talk it through out loud, share your screen, and watch it worked out step by step on a whiteboard.
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