Biochemistry Crash Course - Biochem Made Simple

Show how the Hershey-Chase experiment proves nucleic acids carry information, using radiolabeled phosphorus and sulfur to distinguish DNA from protein in phages.

Explore the structure of nucleic acids, detailing the nucleotide components sugar, base, and phosphate, and how DNA and RNA differ, base pairing, and polymer formation.

Explore the naming conventions of nucleosides and nucleotides, distinguish phosphodiester and phosphoanhydride bonds, and understand how sugar, base, and phosphate combine to form DNA and RNA building blocks.

Discover how nucleotide polymerization builds DNA and RNA backbones through dehydration to form phosphodiester bonds, and how five prime to three prime directionality guides reading.

DNA remains stable to store information, while RNA is unstable to serve as a transient messenger. The central dogma shows DNA encodes RNA, and RNA makes proteins.

Explain the secondary structures of nucleic acids, focusing on the beta DNA helix, major and minor grooves, and base pairing rules A–T and G–C, plus RNA U substitutions.

Use UV spectroscopy to detect DNA and RNA by absorbance at 260 and 280, estimate concentration and purity via Beer-Lambert law, and discuss melting with GC content.

Explore how pH and pKa govern amino acid charge, detailing ionizable N-termini and C-termini, Henderson-Hasselbalch concepts, and predicting charge shifts across pH values.

Explore the 20 amino acids, their hydrophobic, polar, and charged side chains, with structures and pKa values to memorize, plus conservative substitutions and primary sequence concepts.

Learn to determine the overall charge of a polypeptide at pH 7, pH 1, and pH 14 by evaluating n- and c- termini and ionizable side chains using pKa values.

Explore how the alpha helix, a right-handed secondary structure, forms via backbone hydrogen bonds with 3.6 residues per turn, with R groups projecting outward to yield hydrophilic, or amphipathic variants.

Explore beta sheets, a key secondary structure built from multiple strands connected by loops, stabilized by backbone hydrogen bonds; distinguish parallel and antiparallel arrangements and their hydrogen-bond patterns.

Examine how the tertiary structure folds a single polypeptide under polarity, charge, and hydrophobicity to yield a globular protein, guided by R-group interactions, salt bridges, and motifs.

Explore tertiary structure, disulfide bonds between cysteines, cystine linkages, and the role of prosthetic groups like heme in converting apoproteins (hemoglobin) to holoproteins for oxygen transport.

Learn quaternary structure, where multiple distinct polypeptide subunits form functional proteins, and apply homo versus hetero naming (dimer, tetramer, hexamer) with attention to interfaces, disulfide bonds, polarity, and hydrophobicity.

Explore how non-covalent binding enables protein-ligand interactions and signaling, and how kd quantifies binding strength. See how pH shifts kd and affects binding in proteins like hemoglobin and myoglobin.

Compare myoglobin and hemoglobin as oxygen binding proteins. Myoglobin stores oxygen in muscle as a single polypeptide, while hemoglobin transports four oxygens via a quaternary heterotetramer with heme and histidines.

Learn how myoglobin, a monomer oxygen storage protein, binds oxygen at high concentrations and releases it in emergencies. Understand its KD, binding curves, and contrast with hemoglobin’s quaternary structure.

Describe how hemoglobin's alpha and beta subunits form a tetramer with hemes binding four oxygen molecules for transport from lungs to tissues, and how cooperativity yields a sigmoidal binding curve.

Demonstrates allosteric effects in hemoglobin, showing how 2,3-BPG, a negative hetero allosteric effector, stabilizes the T state and modulates oxygen binding; explains pH-driven shifts between T and R states.

Explore how hemoglobin uses cooperativity and allostery, with pH-dependent two three BPG binding and the Bohr effect, to release oxygen in tissues and bind it in the lungs.

Introduce enzymes as biological catalysts and proteins that speed up reactions by lowering activation energy, enabling both breakdown and synthesis; many are ATP powered to drive uphill reactions.

Enzymes reduce activation energy by stabilizing transition states, desolvation, and aligning substrates for productive collisions, while enabling covalent catalysis and alternative reaction pathways.

Explore enzyme kinetics using the Michaelis-Menten framework, defining Km as the substrate concentration yielding half of Vmax and contrasting it with KD as an affinity metric, with a carpenter analogy.

Explore competitive inhibition of enzymes, where inhibitors mimic substrates to block the active site, raise apparent Km, and keep Vmax unchanged while increasing substrate over inhibitor.

Allosteric inhibitors bind away from the active site to reduce enzyme activity, lowering Vmax and increasing Km. Cooperativity and tense and relaxed states regulate enzyme function in cells.

Biochemistry crash course explains how kinases add and phosphatases remove phosphate groups to regulate protein activity and binding by changing conformation; phosphorylation can activate or inhibit enzymes and binding proteins.

Introduce lipids as a major biomolecule class, with triacylglycerols, diacylglycerols, and glycerophospholipids. Explain fatty acid naming by chain length and double bonds, with cis/trans and delta notation.

Explore triacylglycerides and diacylglycerides on a glycerol backbone with mixed fatty acids for energy storage; examine glycerophospholipids bearing polar head groups, including phosphatidyl ethanolamine and phosphatidyl serine, in membrane bilayers.

Explore higher lipid structures—micelles, phospholipid bilayers, and steroids like cholesterol; examine hydrophobic effects, water interactions, membrane compartmentalization, and liposome delivery in vaccines.

Explore how membranes regulate fluidity across cold and hot temperatures by fatty acid tail length and double bonds, within the fluid mosaic model and cholesterol regulation.

Explore how molecules move across cell membranes, from diffusion down concentration gradients of gases and water to facilitated diffusion by membrane proteins for larger or charged species.

Explore how membrane proteins enable passive and active transport across membranes, detailing channels, uniporters, symporters, antiporters, primary and secondary transport, ATP-driven conformational changes, including the sodium-potassium pump.

Explore how the sodium potassium pump uses ATP hydrolysis to move three sodium ions out and two potassium ions in, sustaining ion gradients for neuronal depolarization and signaling.

Explore metabolism by contrasting catabolism, the breaking of bonds that releases energy, with anabolism, the building of molecules that requires energy, and their interdependent energy flow.

Explore high energy molecules like ATP and thioesters, and how their hydrolysis releases energy to power anabolic reactions, while NAD+ and FAD shuttle electrons in cellular redox reactions.

Explore how coupling reactions convert unfavorable anabolic steps into favorable ones using ATP hydrolysis and high-energy molecules. Examine delta g, Le Chatelier, and phosphocreatine as energy storage for ATP production.

Explore metabolic pathways, distinguishing upstream and downstream flows, and irreversible commitment steps powered by ATP, with reversible steps governed by reactant concentrations; preview glycolysis, the Krebs cycle, and pyruvate.

Explore how multistep metabolic pathways are controlled by activation and inhibition to maintain cellular homeostasis, focusing on irreversible steps, product and feedback inhibition, and feedforward activation.

Explore anaerobic energy metabolism, glycolysis, and the fate of pyruvate under anaerobic and aerobic conditions, including fermentation to lactate or ethanol and the energy yield differences from glucose.

Trace glycolysis from glucose to pyruvate, revealing the investment and payout phases that net 2 ATP and produce NADH, with key steps like hexokinase and pfk1.

Explore how glycolysis is regulated by hexokinase and phosphofructokinase-1 through glucose-6-phosphate, ATP/ADP, and fructose-1,6-bisphosphate, plus pyruvate kinase allostery, coordinating energy needs.

Learn how fermentation regenerates NAD+ to sustain glycolysis during low oxygen, yielding ethanol in yeast and lactate in mammals, with lactate feeding the heart when oxygen is scarce.

Explore aerobic energy metabolism, tracing glucose from glycolysis to pyruvate dehydrogenase, the citric acid cycle, and the electron transport chain with NAD+/NADH and FAD/FADH2 to 32 ATP per glucose.

Discover how pyruvate dehydrogenase moves pyruvate into the mitochondrial matrix and converts it to acetyl-CoA via oxidative decarboxylation, generating NADH and releasing CO2.

Explore the citric acid cycle in the mitochondrial matrix, tracing how two acetyl-CoA molecules from glucose yield NADH, FADH2, and ATP equivalents through oxidative decarboxylation and energy extraction.

Explore oxidative phosphorylation in mitochondria, where the electron transport chain builds a proton gradient and ATP synthase converts ADP and Pi into ATP using oxygen as the terminal electron acceptor.

Trace aerobic respiration from glycolysis to the citric acid cycle, marking ATP and NADH production, electron carriers like FADH2, and how starting substrates alter total ATP yield.

Learn how decoupling oxidative phosphorylation uncouples proton flow from ATP synthesis, using decouplers like two four DNP, and how brown adipose tissue uses this thermogenesis to burn fuel as heat.