Flashcards · H420 · Topic 2

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2.1.1 Cell structure

Resolution (microscopy): The minimum gap that lets two neighbouring points be seen apart; a smaller gap means finer detail.
Artefact: A feature of an image produced by preparation that was not in the living cell.
Differential staining: Using stains that are taken up differently by different structures or cell types (for example the Gram stain separates Gram-positive, purple, from Gram-negative, red, bacteria).
Why do electron microscopes resolve more detail than light microscopes?: The electron beam has a shorter wavelength than visible light. Magnifying beyond the resolution limit adds no detail.
TEM vs SEM: TEM: electrons pass through an ultra-thin section; monochrome 2D image of internal ultrastructure; highest resolution. SEM: electrons scanned over the surface; monochrome image with a 3D appearance. Both need a vacuum, so no living specimens.
A scale bar 20 mm long represents 200 nm. What is the magnification?: 20 mm = 20 000 000 nm. Magnification = 20 000 000 ÷ 200 = ×100 000.
One graticule division is 2.5 µm with the ×10 objective. What is it with the ×40 objective?: The image is four times larger, so one division = 2.5 ÷ 4 = 0.625 µm.
Route of a secreted protein through a cell: DNA in the nucleus → mRNA through a nuclear pore → ribosome on the rough ER → vesicle → Golgi (modifies and packages) → secretory vesicle → fuses with the plasma membrane → exocytosis. Mitochondria supply ATP.
Cytoskeleton and its roles: A network of protein fibres and tubules in the cytoplasm. Roles: mechanical strength, transport within the cell, and cell movement.
Prokaryotic vs eukaryotic cells: Prokaryote: no nucleus; circular DNA not with histones; 70S ribosomes; no membrane-bound organelles; peptidoglycan wall; often plasmids. Eukaryote: nucleus; linear DNA with histones; 80S ribosomes; membrane-bound organelles.
Cilia vs flagella: Both are projections containing microtubules. Cilia move fluid over a cell surface; flagella move the whole cell.
Rough ER vs smooth ER: Rough ER: cisternae covered with ribosomes; folds and processes proteins. Smooth ER: tubes without ribosomes; makes lipids.

2.1.2 Biological molecules

Hydrogen bond (between molecules): A weak electrostatic attraction linking a δ+ hydrogen on one molecule to a δ− oxygen or nitrogen on another.
Properties of water and the roles they give: Polar: solvent. Cohesion: continuous column in xylem. High latent heat of vaporisation: cooling by sweating and transpiration. High specific heat capacity: stable habitat temperature. Ice less dense than water: ice floats and insulates.
Disaccharides and their monomers: Maltose: glucose + glucose. Sucrose: glucose + fructose. Lactose: glucose + galactose. All are C₁₂H₂₂O₁₁ (Mr 342), formed by condensation forming a glycosidic bond.
Starch and glycogen as stores: Starch: insoluble, so no osmotic effect; compact; hydrolysed to glucose when needed. Glycogen: very branched with many ends, so fast hydrolysis; compact; in liver and muscle.
Cellulose structure and function: β-glucose joined by β-1,4 glycosidic bonds into straight chains. Hydrogen bonds between chains form microfibrils, so the wall is strong and resists bursting.
Triglyceride vs phospholipid vs cholesterol: Triglyceride: glycerol + 3 fatty acids (3 ester bonds); energy store, insulation. Phospholipid: glycerol + 2 fatty acids + phosphate; hydrophilic head, hydrophobic tails; membrane bilayer. Cholesterol: four-ring steroid; regulates membrane fluidity and stability.
Elements in biological molecules: Carbohydrates and lipids: C, H, O. Proteins: C, H, O, N and usually S. Nucleic acids: C, H, O, N, P.
Bonds that hold tertiary structure: Hydrogen bonds (weak, broken by heat); ionic bonds between oppositely charged R groups (affected by pH); disulfide bonds between cysteine residues (covalent); hydrophobic interactions between non-polar R groups.
Globular vs fibrous proteins, with examples: Globular: compact, usually soluble, metabolic roles (haemoglobin, amylase, insulin). Fibrous: long strands, insoluble, structural roles (collagen, keratin, elastin).
Why is haemoglobin a conjugated protein?: It has prosthetic groups: four polypeptides, each with a haem group containing Fe²⁺ that binds oxygen.
Roles of Ca²⁺, Na⁺, K⁺ and H⁺: Ca²⁺: muscle contraction, bone strength. Na⁺: nerve impulses, co-transport of glucose. K⁺: nerve impulse recovery, stomatal opening. H⁺: pH, proton gradients for ATP synthesis.
Roles of NO₃⁻, PO₄³⁻ and HCO₃⁻: NO₃⁻: used by plants to make amino acids and nucleotides. PO₄³⁻: part of ATP, nucleotides and phospholipids. HCO₃⁻: carbon dioxide transport and buffering of blood.
Biochemical tests: biuret, iodine, emulsion and Benedict's: Biuret (NaOH then copper(II) sulfate): purple for protein. Iodine: blue-black for starch. Emulsion (ethanol, then water): cloudy white for lipid. Benedict's (heated): green to brick-red for reducing sugar.
Insulin has chains of 21 and 30 amino acids. How many peptide bonds?: (21 − 1) + (30 − 1) = 49 peptide bonds, so 49 water molecules were released when it was made.

2.1.3 Nucleotides and nucleic acids

DNA nucleotides vs RNA nucleotides: DNA: deoxyribose; bases A, T, C, G. RNA: ribose; bases A, U, C, G. Each nucleotide is a five-carbon sugar, a phosphate and a nitrogen-containing base.
Purines vs pyrimidines: Purines have two rings: adenine and guanine. Pyrimidines have one ring: cytosine, thymine and uracil. Each base pair is one purine + one pyrimidine, so the helix width is constant.
How many phosphodiester bonds are in a 30 base-pair DNA fragment?: Each strand of 30 nucleotides has 29 bonds, so 2 × 29 = 58 phosphodiester bonds.
ADP vs ATP: Both are phosphorylated nucleotides with ribose and adenine. ADP has 2 phosphates; ATP has 3. ATP + water → ADP + Pi releases energy (hydrolysis).
Structure of DNA: Two antiparallel polynucleotides with a sugar-phosphate backbone outside and bases inside, joined by complementary base pairs (A–T two hydrogen bonds, G–C three), twisted into a double helix.
Purpose of each step in DNA precipitation: Detergent dissolves membrane phospholipids, releasing DNA. Salt masks the negative phosphate charges so DNA clumps. Protease digests proteins bound to DNA. Ice-cold ethanol: DNA is insoluble and precipitates at the boundary.
Roles of helicase and DNA polymerase in replication: Helicase breaks hydrogen bonds between bases and unwinds the helix so both strands act as templates. DNA polymerase forms phosphodiester bonds between free nucleotides, adding them to the 3′ end of the new strand.
Semi-conservative replication and the ¹⁵N/¹⁴N evidence: Each new molecule has one original and one new strand. Bacteria grown in ¹⁵N then moved to ¹⁴N give all hybrid DNA after one generation, then half hybrid, half light. Conservative replication would give no hybrid band.
Spontaneous mutation: A random change in the base sequence that arises during replication without a mutagen, for example a wrong nucleotide being incorporated.
Features of the genetic code: Triplet (three bases per amino acid); non-overlapping (each base read in one codon only); degenerate (most amino acids have more than one codon); universal (same in virtually all organisms).
Transcription in order: RNA polymerase binds at the gene and breaks hydrogen bonds to expose the template strand. Free RNA nucleotides pair with it by complementary base pairing, and RNA polymerase forms phosphodiester bonds. mRNA leaves the nucleus through a nuclear pore.
Translation in order: The small ribosomal subunit binds mRNA at AUG. tRNA anticodons pair with codons, two at a time, bringing specific amino acids that are joined by peptide bonds. The ribosome moves one codon along until a stop codon releases the polypeptide.
mRNA vs tRNA vs rRNA: mRNA: single-stranded copy of a gene carrying codons. tRNA: clover-leaf, anticodon at one end, a specific amino acid at the other. rRNA: with proteins forms the ribosome subunits and helps form peptide bonds.
An mRNA coding region is 1260 bases long, including the stop codon. How many amino acids?: 1260 ÷ 3 = 420 codons. Subtract 1 for the stop codon: 419 amino acids.

2.1.4 Enzymes

Lock and key vs induced-fit hypothesis: Lock and key: the substrate fits an active site of exactly complementary shape. Induced fit: the active site changes shape slightly as the substrate binds, giving a closer fit and straining bonds in the substrate, which lowers the activation energy.
Intracellular vs extracellular enzymes: the H420 examples: Intracellular: catalase, inside cells, breaks down toxic hydrogen peroxide to water and oxygen. Extracellular: amylase, secreted (for example in saliva), hydrolyses starch to maltose outside the cell.
How does temperature affect enzyme activity, and what is Q₁₀?: Rising temperature gives molecules more kinetic energy and more successful collisions, so the rate rises to the optimum. Above it, vibrations break hydrogen and ionic bonds in the tertiary structure, the active site changes shape and the enzyme denatures. Q₁₀ = R2 ÷ R1, where R2 is the rate at a temperature 10 °C higher than R1; no units.
How does substrate concentration affect the rate of an enzyme-controlled reaction?: The rate rises as substrate concentration rises, because more enzyme–substrate complexes form. It levels off when all the active sites are occupied; enzyme concentration is then the limiting factor.
Cofactor vs coenzyme vs prosthetic group: Cofactor: a non-protein substance an enzyme needs, such as the chloride ion for amylase. Coenzyme: an organic cofactor, often made from a vitamin (NAD from nicotinamide, vitamin B3). Prosthetic group: a cofactor permanently bound to the enzyme, such as Zn²⁺ in carbonic anhydrase.
Competitive vs non-competitive inhibition: Competitive: similar in shape to the substrate and binds the active site; raising substrate concentration reduces the effect. Non-competitive: binds elsewhere (an allosteric site) and changes the shape of the active site; raising substrate concentration does not overcome it.
End-product inhibition: The final product of a metabolic pathway inhibits an enzyme early in the pathway, usually non-competitively and reversibly, so the product regulates its own production. Example: ATP inhibits phosphofructokinase in glycolysis.
Mechanism of enzyme action, in order: A substrate complementary to the active site (shaped by the tertiary structure) binds, forming an enzyme–substrate complex. The reaction gives an enzyme–product complex, then the products leave and the enzyme is reused. The enzyme lowers the activation energy.
How does pH affect enzyme activity?: Each enzyme has an optimum pH. H⁺ and OH⁻ ions disrupt the ionic and hydrogen bonds holding the tertiary structure and alter charges in the active site, so the substrate binds less well. Extreme pH denatures the enzyme.
PAG4: why measure the initial rate, and how?: Later in the reaction substrate is used up and product builds up, so the rate falls for other reasons. Plot product (for example O₂ volume from catalase) against time and draw a tangent at t = 0; its gradient is the initial rate.

2.1.5 Biological membranes

Roles of membranes within and at the surface of cells: Partially permeable barriers (between the cell and its surroundings, around organelles and within them); sites of chemical reactions (such as the inner mitochondrial membrane and thylakoid membranes); sites of cell communication (cell signalling).
Fluid mosaic model: components and their roles: Phospholipid bilayer: a barrier to polar and charged substances. Cholesterol: regulates fluidity and stability. Channel and carrier proteins: transport. Glycoproteins and glycolipids: cell recognition, signalling and attachment. Membrane-bound receptors: sites where hormones and drugs bind.
How do temperature and organic solvents affect membrane permeability?: Higher temperature gives phospholipids more kinetic energy, so the bilayer becomes more fluid and leaky; high temperatures also denature membrane proteins. Organic solvents such as ethanol dissolve the bilayer. Leakage of pigment from beetroot, measured with a colorimeter, shows the effect.
Facilitated diffusion vs active transport: Facilitated diffusion: passive, down a concentration gradient, through channel or carrier proteins. Active transport: against a concentration gradient, through carrier proteins, using ATP.
Endocytosis vs exocytosis: Endocytosis: the membrane folds around material and pinches off a vesicle to bring it into the cell (phagocytosis for solids, pinocytosis for liquids). Exocytosis: vesicles fuse with the plasma membrane to release their contents. Both need ATP.
Effects of solutions of different water potential on animal and plant cells: Higher water potential outside: water enters by osmosis; animal cells swell and may burst (haemolysis of red blood cells); plant cells become turgid. Lower water potential outside: water leaves; animal cells shrink (crenation); plant cells become flaccid, then plasmolysed.
Osmosis and water potential: Osmosis: net movement of water from a region of higher water potential to a region of lower water potential across a partially permeable membrane. Water potential (ψ, kPa) is 0 for pure water; solutes make it negative.
PAG8: finding the water potential of potato tissue: Blot and weigh equal potato cylinders, leave them in a range of sucrose concentrations for a set time, blot and reweigh. Plot percentage change in mass against concentration: where the line crosses 0 % the solution has the same water potential as the cells.

2.1.6 Cell division, cell diversity and cellular organisation

Stages of the cell cycle: Interphase: G1 (growth, proteins and organelles made), S (DNA replicated), G2 (further growth and checks). Then mitosis (the nucleus divides) and cytokinesis (the cytoplasm divides), giving two genetically identical cells.
How is the cell cycle regulated?: Checkpoints check the cell before it moves on: at G1 (cell size, nutrients, DNA damage), at G2 (DNA replicated without damage) and the spindle assembly checkpoint in mitosis (every chromosome attached to the spindle). A cell that fails may repair, leave the cycle (G0) or undergo apoptosis.
Main stages of mitosis: Prophase: chromosomes condense; the nuclear envelope breaks down; centrioles move to the poles and spindle fibres form. Metaphase: chromosomes line up at the equator, attached by their centromeres. Anaphase: centromeres divide; chromatids are pulled to opposite poles. Telophase: nuclear envelopes reform. Cytokinesis: the cell membrane pinches in (animal cells).
Significance of mitosis vs meiosis in life cycles: Mitosis: growth, tissue repair and asexual reproduction in plants, animals and fungi; the cells are genetically identical. Meiosis: makes haploid cells, so the diploid number is restored at fertilisation, and creates genetic variation by crossing over and independent assortment.
Specialised animal cells in H420 and one adaptation of each: Erythrocyte: biconcave, no nucleus, for carrying oxygen. Neutrophil: multilobed nucleus and many lysosomes, for phagocytosis. Squamous epithelial cell: very flat, a short diffusion path. Ciliated epithelial cell: cilia move mucus. Sperm cell: flagellum and many mitochondria.
Specialised plant cells in H420 and one adaptation of each: Palisade cell: many chloroplasts, for photosynthesis. Root hair cell: a long extension giving a large surface area for water and mineral ion uptake. Guard cells: change shape with turgor to open and close the stoma.
Stem cell, and the source of stem cells in plants: An undifferentiated cell that can divide repeatedly and differentiate into specialised cell types, a renewing source of cells. In plants, meristems at root and shoot tips and in the cambium are the stem cells; cambium cells differentiate into xylem and phloem.
Meiosis: what separates in each division?: Meiosis I: homologous pairs line up at the equator and the homologous chromosomes separate (anaphase 1), halving the chromosome number. Meiosis II: centromeres divide and sister chromatids separate (anaphase 2). Result: four genetically different haploid cells.
Homologous chromosomes: A pair of chromosomes, one from each parent, of the same size and shape with the same genes at the same loci, but possibly different alleles.
Erythrocytes and neutrophils from bone marrow stem cells: Both come from the same multipotent stem cells in bone marrow. Erythrocytes fill with haemoglobin and lose the nucleus and most organelles. Neutrophils develop a multilobed nucleus and many lysosomes. Different genes are expressed in each.
How xylem vessels and phloem sieve tubes form from meristem cells: Xylem: cells elongate, walls are lignified, the cells die and end walls break down into continuous tubes. Phloem: sieve tube elements lose the nucleus and most organelles; end walls become sieve plates; companion cells keep a nucleus and many mitochondria.
PAG1: preparing a root tip squash to see mitosis: Cut root tips (meristem), warm in dilute HCl to separate the cells, stain with a DNA stain such as toluidine blue, then squash gently under a coverslip without twisting. Mitotic index = cells in mitosis ÷ total cells counted.