Origins and Biochemistry of Life: Key Concepts for Exams

Posted on Feb 11, 2026 in Biochemistry

Origins and Composition of Life (Ch. 1, L2)

Origins

  • Earth formed: ~4.54 billion years ago (bya) (textbook consensus).
  • Prebiotic world: before life emerged (~4.5–3.5 bya), the atmosphere contained H₂O, N₂, CO₂, CH₄, NH₃, SO₂, with energy from lightning and UV radiation.
  • First evidence of life: ~3.5 billion years ago.

Composition of life

  • ~70% water.
  • Major dry weight: C, H, O, N (~87%), plus P, S, K, Ca, Mg.

Functional groups (must memorize)

  • Amine (can be protonated at pH 7).
  • Carboxyl (deprotonated at pH 7).
  • Alcohol (–OH).
  • Thiol (–SH).
  • Aldehyde, ketone (carbonyls).
  • Phosphates (often −1 to −2 at pH 7).

Charges at pH 7

  • Positive = protonated amines, guanidinium, protonated imidazole.
  • Negative = carboxylates, phosphates, sulfates.

Early Experiments and Evolution

  • Haldane & Oparin (1930s): proposed the primordial soup idea.
  • Urey–Miller (1953): simulated early Earth conditions and produced amino acids, aldehydes, HCN, CO₂; later repeats produced sugars and bases.
  • Polymers form by condensation (decrease in entropy, −ΔS) and are broken by hydrolysis (increase in entropy, +ΔS).
  • Complementarity: puzzle-piece base pairing enables self-replication.
  • Compartmentation: membranes isolate chemistry and allow selection for faster replicators.
  • Endosymbiosis: mitochondria and chloroplasts originated from engulfed bacteria.

Evolution principles (memorize verbatim if required)

  1. No preset goal.
  2. Requires “sloppiness” (mutation).
  3. Constrained by history.
  4. Ongoing process.

Cells

  • Prokaryotes: 1–10 μm, no nucleus, three common shapes: cocci, bacilli, spirilla.
  • Eukaryotes: 10–100 μm, nucleus and organelles (ER, Golgi, mitochondria, chloroplasts, lysosomes, peroxisomes, cytoskeleton).
  • Thiomargarita namibiensis: giant bacterium, 0.1–0.3 mm (100–300 μm) — visible to the eye and larger than many eukaryotes.
  • Molecular phylogeny: eukaryotes are closest to archaea.

Thermodynamics (L3)

Systems

  • Isolated: no exchange of energy or matter.
  • Closed: energy only exchange.
  • Open: energy and matter exchange. Cells are open systems.

Laws and quantities

  • First Law: Energy is not created or destroyed; ΔE = q − w.
  • Second Law: Entropy (S, disorder) increases for the universe.
  • Enthalpy (H): ΔH < 0 (exothermic) is usually favorable.

Gibbs Free Energy

  • ΔG = ΔH − TΔS.
  • ΔG < 0 = spontaneous (exergonic).
  • ΔG > 0 = non-spontaneous.
  • ΔG = 0 = equilibrium.

Temperature dependence

  • ΔH −, ΔS + → always spontaneous.
  • ΔH −, ΔS − → spontaneous below T = ΔH/ΔS.
  • ΔH +, ΔS + → spontaneous above T = ΔH/ΔS.
  • ΔH +, ΔS − → never spontaneous.

Free energy and equilibrium

  • ΔG = ΔG° + RT ln Q.
  • At equilibrium: ΔG = 0 → ΔG° = −RT ln K.
  • Standard biochemical state: 25 °C, 1 atm, solutes = 1 M, pH 7.

Useful constants

  • R = 8.31 J·K⁻¹·mol⁻¹.
  • RT at 298 K ≈ 2.48 kJ/mol.
  • 2.303RT ≈ 5.71 kJ/mol — shortcut for ΔG° = −2.303RT log10 K.

Entropy Patterns (helps with problem set)

  • Hydrolysis increases S; condensation decreases S.
  • Mixing/dilution increases S.
  • Gas moles: more gas increases S; fewer gas decreases S.
  • Water vs ice at 0 °C: liquid has higher entropy.
  • Colder solids have lower entropy.

Ch. 2 — Water, Acids/Bases, Buffers

Why water matters

Biology happens in water: shapes, interactions, reactions, and participation by H₂O itself.

Life is held together by many weak, reversible interactions (not just covalent bonds): ionic, ion–dipole, dipole–dipole, hydrogen bonds, London dispersion, plus cation–π. Many small forces together stabilize 3D structures.

Water structure and polarity — solvent powers

  • Water is polar, forms hydrogen bonds, interacts well with charges, and weakens polar/ionic interactions (key for flexibility and reversibility in biomolecules).
  • H-bonding: donor/acceptor patterns include peptide groups, alcohols, carbonyls, and bases. Ice has ~4 H-bonds per H₂O; liquid has fewer, which explains many unusual water properties.

Hydrophobic effect

Water forms an ordered “cage” around nonpolar molecules, causing entropy loss. To minimize that penalty, nonpolar groups cluster and water recovers entropy. Define: “tendency of water to minimize contact with nonpolar substances.”

Amphipathic molecules — micelles and bilayers

Molecules with both polar and nonpolar regions (e.g., fatty acids) self-assemble into micelles or bilayers in water. This underlies membrane formation.

Colligative properties, osmosis, dialysis

  • Colligative properties depend on total solute concentration, not identity.
  • Osmosis: water moves through a semipermeable membrane from lower to higher solute concentration; osmotic pressure is the pressure needed to stop that flow.
  • Dialysis: small solutes diffuse through a membrane; large molecules are retained — used to change buffer or remove salts.

Ionization of water, pH, and pOH (must know cold)

  • Kw = [H⁺][OH⁻] = 10⁻¹⁴ at 25 °C → in pure water [H⁺] = [OH⁻] = 10⁻⁷ M; pH + pOH = 14.
  • pH = −log[H⁺]; pOH = −log[OH⁻]. Quick checks: acidic if [H⁺] > 10⁻⁷ M; basic if < 10⁻⁷ M.

Acids, bases, Ka, pKa

  • Acid donates H⁺; base accepts H⁺; every acid has a conjugate base A⁻.
  • Ka = ([H₃O⁺][A⁻])/[HA]; pKa = −log Ka. Stronger acids → larger Ka → smaller pKa.

Henderson–Hasselbalch, titration curves, buffers

  • Henderson–Hasselbalch: pH = pKa + log([A⁻]/[HA]). Use for buffers and weak acid/base mixtures.
  • At the half-equivalence point of a titration, pH = pKa (the flat buffering region).
  • Buffers are mixtures of a weak acid and its conjugate base that resist pH change; maximum capacity at pKa and effective within ±1 pH unit of pKa.

Chapter 6 — Nucleotides and Nucleic Acids

1) Parts and naming

  • Nucleotide = base + sugar + one or more phosphates (phosphate on the 5′ carbon).
  • Bases: purines (A, G) and pyrimidines (C, T, U); know the ring systems and membership.
  • Nucleoside = base + sugar (no phosphate). Know ribo vs deoxyribo forms.
  • Nucleotide forms when you add phosphate(s). Recognize AMP/ADP/ATP and 3′/5′ positions.

Pro-tip: be able to sketch ATP labels: phosphoester to ribose plus two phosphoanhydride bonds between phosphates.

2) What nucleotides do (beyond DNA/RNA)

  • Building blocks for DNA and RNA; carry free energy (ATP); redox carriers (FAD, NAD⁺/NADH, NADPH); cell signaling and regulation roles.
  • Examples: adenosine acts as an autocoid (affects vessel tone, smooth muscle, heart rate; rises with wakefulness → sleepiness).
  • ATP is the energy currency; FAD (from vitamin B₂) and NAD⁺ participate in redox; NADPH powers biosynthesis.

3) Nucleic acids: how they are built and read

  • Polymers of nucleotides: DNA = deoxyribo, RNA = ribo.
  • Linked by 3′–5′ phosphodiester bonds; sequences are written 5′ → 3′.

4) How Watson and Crick solved DNA

Name-drop: Franklin’s X-ray diffraction (helical repeat), Chargaff’s rules (A=T, G=C), and correct tautomeric forms of bases → complementary H-bonding model that explains replication.

5) DNA structure you can recite in your sleep

  • Two antiparallel strands held by hydrogen bonds between complementary bases.
  • Right-handed helix (B-DNA), with major and minor grooves; bases planar and stacked inside; sugar-phosphate backbone outside; A–T and G–C pairs.
  • Helix stability: base H-bonding, base stacking, and ionic interactions involving phosphates (cation shielding).
  • Key characteristics summary: double helix; antiparallel strands; four bases; planar bases inside; deoxyribose sugar; sugar-phosphate backbone outside; A–T, G–C pairing; major and minor grooves.

6) RNA: differences and folding

  • Usually single-stranded, but can base-pair with itself to form stem-loops; RNAs can fold into complex 3D structures.
  • Quick contrast: DNA (double-stranded, deoxyribose, A/T/G/C, genetic storage) vs RNA (single-stranded, ribose, A/U/G/C, expression and catalytic roles).

DNA manipulation and sequencing (memorize)

  • Restriction endonucleases (Type II): recognize 4–8 bp palindromes and cut DNA — core tools for cloning.
  • DNA ligase: covalently links complementary fragments (requires proper ends: 3′ OH and 5′ P).
  • Plasmid vectors: essential elements = restriction sites, selectable marker, origin of replication; typical workflow: cut insert and vector with same restriction enzyme → ligate → transform → select.
  • Sanger (dideoxy) sequencing: ddNTPs terminate chains; components: template, primer, dNTPs, ddNTPs, DNA polymerase.
  • PCR: rapid in vitro amplification when sample is small; used for diagnostics, forensics, paleogenetics.

8) Mini practice (fast mental reps)

  1. Name and classify: U, A, G, C, T → which are purine/pyrimidine? (A, G = purines; C, T, U = pyrimidines.)
  2. ATP bonds: circle the phosphoanhydrides; star the phosphoester to ribose.
  3. Sequence writing: for a strand shown left-to-right, annotate 5′ and 3′ ends and identify 3′–5′ linkages.
  4. Stability: two reasons G–C rich DNA resists melting better: more stacking and 3 H-bonds vs 2.
  5. Chargaff math: If T = 19%, what is G%? (T = 19 → A = 19; G + C = 62 → G = 31%.)

Chapter 3 — Amino Acids, Peptides and Proteins (study-buddy sheet)

Expectations

Draw/recognize the 20 amino acids (names + 3-/1-letter codes); describe side-chain polarity/hydrophobicity/charge; use acid–base behavior; calculate pI of amino acids/oligopeptides; explain peptide vs isopeptide bonds; recognize chirality; know essential vs non-essential amino acids; identify modified amino acids and their functions.

Core facts (must know cold)

  • Amino acids are zwitterions near physiological pH. Typical pKa1 (α-COOH) ≈ 2; pKa2 (α-NH₃⁺) ≈ 9.
  • pI (isoelectric point) = pH where net charge = 0. For a species with two relevant ionizations: pI = 1/2 (pKi + pKj), the two pKa’s that bracket the neutral form.

Classification at ~neutral pH

  • Nonpolar (10): Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Tyr, Pro.
  • Polar, uncharged (5): Ser, Thr, Asn, Gln, Cys.
  • Polar, charged (5): Asp, Glu (negative); His, Lys, Arg (positive).

Side-chain highlights

  • Proline: helix breaker, favors tight turns.
  • Cysteine → cystine: forms disulfide bonds (intra- and interchain).
  • Ser/Thr/Tyr: OH groups can be phosphorylated (regulation sites).
  • D-amino acids: found in bacterial cell walls and some peptide antibiotics.

Numbering and stereochemistry

  • Carbon naming on side chains: α, β, γ, … (know how to count).
  • Most amino acids are chiral; proteins use L-amino acids.
  • Essential amino acids: conceptually know ~9 (sometimes listed as 9 or 10 depending on context).

Peptides and proteins — bonding, naming, direction

  • Peptide bond = condensation amide linkage; chains are linear in principle.
  • Regular peptide vs isopeptide (side-chain amide): learn to spot the difference in drawings.
  • Write/read sequences N→C; use 3-/1-letter codes (e.g., AYDG).
  • Primary structure = amino-acid sequence (example: insulin processing preproinsulin → proinsulin → insulin, with disulfides).

Chapter 3 — Amino Acids, Peptides & Proteins (One Pager)

Exam goals: recognize and draw the 20 amino acids; classify by polarity and charge; predict charge at a given pH; calculate pI; identify linkages (peptide, isopeptide, disulfide, phospho Ser/Thr/Tyr); read and write sequences N→C.

Must know constants and rules

  • Typical pKa’s: α-COOH ≈ 2.0; α-NH₃⁺ ≈ 9.0.
  • pI rule (no ionizable side chain): pI = 1/2 (pKa1 + pKa2) using the two pKa’s that bracket the neutral form.
  • Direction: peptides are written N-terminus → C-terminus.

Classification and location

Nonpolar (hydrophobic): Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Tyr, Pro

Polar, uncharged: Ser, Thr, Asn, Gln, Cys

Polar, charged: (−) Asp, Glu; (+) His, Lys, Arg

Where they live in proteins: hydrophobic residues → core; charged/polar → surface; aromatics often at interfaces.

How to do charge and pI fast

  1. List all ionizable groups (N term, C term, side chains) with pKa’s.
  2. Sort by pKa from low → high.
  3. Walk protonation states across pH to find where net charge = 0.
  4. Average the two pKa’s that border that neutral form → pI.

Quick charged side chains (@ pH ~7)

  • Negative: Asp (β-COO⁻), Glu (γ-COO⁻).
  • Positive: Lys (ε-NH3⁺), Arg (guanidinium⁺), His (imidazolium⁺ when protonated; pKa ~6).

Sequence notation and practice

Write/read N→C; e.g., AYDG (Ala Tyr Asp Gly). Be ready to translate 3-letter ↔ 1-letter codes.

Micro practice prompts (flashcards)

  1. Given pKa’s for Lys (ε-NH3⁺ ≈ 10.5), compute its net charge at pH 7.
  2. For Gly (no ionizable side chain): pI ≈ (2.0 + 9.0)/2 = 5.5.

Quick reference: 1-letter codes

A Ala, R Arg, N Asn, D Asp, C Cys, E Glu, Q Gln, G Gly, H His, I Ile, L Leu, K Lys, M Met, F Phe, P Pro, S Ser, T Thr, W Trp, Y Tyr, V Val

Appendix A3A — DNA Manipulation

  • Restriction enzymes (Type II endonucleases) recognize 4–8 bp (often palindromic) sites and cut DNA; core tools for cloning and mapping.
  • DNA ligase covalently links complementary DNA ends (requires 3′ OH and 5′ P).
  • Vectors carry DNA and replicate in hosts: plasmids (manipulation/expression) and bacteriophage vectors (library screening).
  • An endonuclease cleaves a nucleic acid within the polynucleotide strand; an exonuclease cleaves by removing terminal residues.

Appendix A3B — Plasmids and Basic Cloning Workflow

  • Plasmid essentials: (1) restriction sites/multiple cloning site (MCS) (2) selectable marker (e.g., antibiotic resistance) (3) origin of replication.
  • Steps (order matters): cut insert and plasmid with the same restriction enzyme → ligate (ligase, ATP) → transform bacteria → select colonies.
  • The E. coli enzyme used to make complementary copies of single-stranded DNA during sequencing is a fragment of DNA polymerase I.
  • Principle of Sanger sequencing: ddNTPs lack 3′ OH → terminate elongation at specific bases → fragment ladders that report sequence.
  • Five components: template, primer, dNTPs, ddNTPs, DNA polymerase. Read products 5′ → 3′ of the new strand (short → long).

Appendix A4A — What cloning means (in this course)

Cloning here means making many identical copies of a specific DNA segment in a host (the clone can refer to the cell population carrying the vector or to the DNA itself). In suitable hosts (e.g., E. coli, yeast) you can produce large amounts of the DNA, its RNA, and even the protein if proper regulatory elements flank the insert.

Standard approach (four-step sequence)

  1. Generate the DNA fragment of interest — by restriction enzyme digestion, PCR, or chemical synthesis.
  2. Insert the fragment into a vector that has sequences needed for DNA replication.
  3. Introduce the recombinant vector into cells (transformation/infection) so it can replicate in vivo.
  4. Identify/select cells that contain the desired construct.

Vectors you should recognize and their capacities

  • Plasmids (e.g., pUC18) — circular DNAs engineered for cloning; practical insert size ≤ ~10 kbp for many plasmids.
  • Bacteriophage λ vectors — accept up to ~16 kbp inserts by replacing a dispensable central region; package size constraints apply.
  • BACs/YACs — very large inserts (up to hundreds of kbp); YACs mimic yeast chromosomes; BACs replicate at ~1 copy per cell in E. coli.

Making recombinant DNA & why matching sites matter

Restriction fragments with compatible sticky ends from insert and vector anneal by base pairing; DNA ligase covalently seals the sugar–phosphate backbone. Using the same enzyme allows precise excision later.

Selecting the right colonies (blue-white screening + antibiotic selection)

Plate transformation mixtures at low density. Use ampicillin to select for ampR plasmid-bearing cells. Include X-gal: intact lacZ → blue colonies; insert in the MCS within lacZ → white colonies (disrupted β-galactosidase). Only ampR colonies grow; within those, white colonies are likely recombinants.

Appendix A4C — PCR (Polymerase Chain Reaction)

  • When/why: need an answer fast from a limited sample (diagnostics, forensics, paleogenetics).
  • Core cycle: denature → anneal → extend using primers and a thermostable polymerase to exponentially amplify a target region.
  • Outcome: milligrams of a specific fragment in vitro for downstream analysis or cloning.

DNA fingerprinting via STRs (forensic application)

  • STRs = short tandem repeats (2–7 bp repeat units; tetranucleotide sites are common).
  • Each locus has alleles defined by number of repeats; each individual carries two alleles (one from each parent).
  • PCR uses primers to unique flanks around the STR; primers are often fluorescently labeled.
  • Capillary electrophoresis resolves amplicons that differ by 1 repeat; multiplexing uses multiple primer pairs with different dyes.
  • Match probability across loci uses the product rule (multiply independent allele pair frequencies), so matching by chance falls dramatically as you add loci.