14.2 Biochemistry

14.2 Biochemistry on NMAT Chemistry

Biochemistry on CEM NMAT Chemistry sits next to organic chemistry: same atoms and functional groups, now organized into life’s molecules and pathways. Items test structure–function links, enzyme logic, and where ATP/energy flow happens — not memorizing every intermediate of every pathway.

Cross-link: the Biology genetics section (central dogma, transcription, translation) is the same story told from the cell’s side. Chemistry items may ask what bond forms or what vitamin is needed; biology items may ask where in the cell or what mutation does.

Quick frame: Name the macromolecule class → monomer and bond → one cellular job. For pathways: location + net purpose (ATP, reducing power, carbon skeleton) beats intermediate laundry lists.

Carbohydrates

Monomers: monosaccharides (glucose, fructose, galactose; ribose/deoxyribose in nucleic acids).
Disaccharides: sucrose (glucose+fructose), lactose (glucose+galactose), maltose (glucose+glucose) — formed by dehydration (condensation), broken by hydrolysis.
Polysaccharides: starch and glycogen (storage), cellulose (plant structure). Same glucose monomers can yield very different polymers depending on linkage geometry (α vs β is a classic distinction: humans digest starch, not cellulose).

Functions: quick and stored energy; structural roles; recognition markers on cell surfaces (intro level). Reducing-sugar tests (Benedict’s) connect back to free aldehyde/ketone groups in open-chain forms — organic functional-group thinking applied to biomolecules.

Lipids

Not true polymers in the same sense, but a hydrophobic family:

Saturated fatty acids (no C=C) pack tightly → often solid at room temperature; unsaturated (one or more C=C) kink and pack loosely → often liquid oils. Hydrogenation of oils is an applied organic addition reaction in disguise.

Proteins

Monomers: amino acids (amino group + carboxyl group + side chain R on the α-carbon).
Bond: peptide bond (amide linkage) from condensation of –COOH and –NH₂.

Structural levels:

1. Primary — sequence of amino acids (covalent peptide bonds).
2. Secondary — local folding (α-helix, β-sheet) via backbone H-bonds.
3. Tertiary — overall 3D fold (R-group interactions: H-bonds, ionic, hydrophobic, disulfide).
4. Quaternary — multiple polypeptide subunits (e.g., hemoglobin).

Function spectrum: enzymes, transport, structure (collagen), defense (antibodies), signaling, motion. Denaturation (heat, extreme pH, some solvents) disrupts higher-order structure without necessarily breaking the primary sequence — activity is lost when shape is lost.

Nucleic acids

DNA: deoxyribose, bases A/T/G/C, double helix, stores genetic information.
RNA: ribose, bases A/U/G/C, usually single-stranded, roles in mRNA, tRNA, rRNA during protein synthesis.

Nucleotide = sugar + base + phosphate(s). Base-pairing (A–T/U, G–C) and antiparallel strands are the structural rules that make replication and transcription faithful.

Enzymes: lock-and-key, induced fit, rates, cofactors

Enzymes are mostly proteins that catalyze reactions by lowering activation energy; they are not consumed in the net reaction.

Both emphasize specificity. Modern teaching leans induced fit, but either model can appear in stems; choose the option that stresses complementarity and active-site geometry.

Factors affecting rate:

• Temperature: rate rises to an optimum, then falls as the enzyme denatures.
• pH: each enzyme has an optimum (pepsin acidic, many cytosolic enzymes near neutral).
• Substrate concentration: rate rises then plateaus at V_max when enzyme is saturated.
• Enzyme concentration: more enzyme → higher rate if substrate is not limiting.
• Inhibitors: competitive (bind active site; overcome by more substrate) vs noncompetitive (bind elsewhere; change shape; not fully overcome by substrate) at intro depth.

Cofactors: nonprotein helpers. Inorganic ions (Mg²⁺, Fe²⁺, Zn²⁺) or organic coenzymes (often vitamin-derived). Without the needed cofactor, the apoenzyme may be inactive.

Central metabolism overview (purpose-first)

Do not memorize every enzyme name. Own the map:

Anaerobic note: without O₂, ETC backs up; cells may regenerate NAD⁺ via fermentation (lactate in animals; ethanol + CO₂ in yeast) so glycolysis can continue — far less ATP than full aerobic respiration.

Photosynthesis link (if a stem wanders): light reactions make ATP/NADPH and O₂; Calvin cycle fixes CO₂ into sugar — reverse energy story relative to respiration, still intro level.

Protein synthesis — chemistry meets genetics

Recall the central dogma from the Biology genetics section:

DNA → (transcription) mRNA → (translation) polypeptide

Chemistry angles NMAT may probe:

• Peptide bond is an amide; polymers are condensation products.
• Codons are triplets on mRNA; tRNA carries amino acids via ester linkage to the tRNA (advanced detail; recognition of “tRNA brings amino acids” is enough).
• Start codon AUG (Met); stop codons release the chain.
• Mutations: silent / missense / nonsense / frameshift change primary structure and thus can change tertiary fold and enzyme activity — structure–function again.

Vitamins and coenzymes — selected high-yield table

Focus on coenzyme role, not exhaustive deficiency pathology lists.

Water-soluble vs fat-soluble: B vitamins and C tend to need regular intake (excess often excreted); A/D/E/K store in fat (toxicity risk if oversupplemented) — a common classification item.

Integration checklist before you leave this section

1. Glucose polymer with α linkages for storage vs β for cellulose.
2. Phospholipid bilayer = hydrophobic tails in, hydrophilic heads out.
3. Enzyme graph: substrate concentration vs rate levels off at saturation.
4. O₂’s job in aerobic respiration = final electron acceptor, not “making glucose.”
5. Peptide bond = amide; DNA base pairs hold the information layer.

You are ready for NMAT biochemistry when you can: (1) match each macromolecule to monomer, bond, and function, (2) explain enzyme rate curves and competitive vs noncompetitive inhibition in one sentence each, (3) state the purpose and location of glycolysis, Krebs, and ETC, and (4) connect a vitamin to a coenzyme role without memorizing clinical minutiae.