Complete IB Biology SL Revision Guide (Topics 1-6)

Foundations of Cell Biology and Theory

The study of biology at the cellular level is governed by the Cell Theory, which consists of three foundational statements that must be mastered verbatim: first, all living organisms are composed of one or more cells; second, the cell is the basic unit of life; and third, all cells come from pre-existing cells (expressed in Latin as Omnis cellula e cellula). A critical distinction in the study of life is that viruses are categorically not cells and are not considered living organisms because they cannot reproduce independently. Consequently, viruses do not support the cell theory. There are notable exceptions to the cell theory that students must recognize: giant algae, such as Acetabularia, which exists as a single giant cell, and skeletal muscle fibres, which are multinucleate, meaning they contain multiple nuclei within a single continuous membrane.

Prokaryotic and Eukaryotic Cell Structures

Cells are classified into two primary categories based on their internal complexity. Prokaryotes, such as bacteria and archaea, lack a membrane-bound nucleus and instead contain their DNA in a nucleoid region. Their DNA is circular and exists freely in the cytoplasm. Prokaryotic ribosomes are the smaller $70\text{S}$ type, and these cells lack membrane-bound organelles altogether. Their cell walls are composed of peptidoglycan, and they typically range in size from $1 - 10\text{µm}$. In contrast, Eukaryotes (animals, plants, fungi, and protists) possess a true nucleus with a nuclear envelope and linear DNA associated with proteins called histones. They contain larger $80\text{S}$ ribosomes and a variety of membrane-bound organelles, including mitochondria, the endoplasmic reticulum, and the Golgi apparatus. Eukaryotic cell walls vary: plants use cellulose, fungi use chitin, while animal cells have no cell wall. These cells are significantly larger, measuring between $10 - 100\text{µm}$. Despite these differences, both types share four essential features: ribosomes, DNA, a cell membrane, and cytoplasm. The distinction between $70\text{S}$ and $80\text{S}$ ribosomes is medically significant, as it allows antibiotics to target bacterial protein synthesis without damaging human cells.

The Fluid Mosaic Model and Membrane Transport

The structure of the cell membrane is best described by the Fluid Mosaic Model. The membrane consists of a phospholipid bilayer where hydrophilic (water-loving) heads face the watery environment inside and outside the cell, while hydrophobic (water-fearing) tails face inward. This arrangement is spontaneous and self-sealing. The term "fluid" refers to the ability of phospholipids and proteins to move laterally within the membrane, while "mosaic" refers to the scattered pattern of various proteins. Integral proteins span the entire bilayer and serve as channel or carrier proteins for transport. Peripheral proteins are attached only to the surface and are central to cell signaling. Cholesterol is embedded between phospholipids to stabilize fluidity, preventing the membrane from becoming too rigid in the cold or too fluid in the heat. Glycoproteins, which are proteins with carbohydrate chains, are vital for cell recognition, receptor sites, and the immune response.

Membrane transport occurs through several mechanisms. Simple diffusion involves the passive movement of small, nonpolar molecules like $O_2$, $CO_2$, and lipids from high to low concentration. Facilitated diffusion also moves molecules down a concentration gradient (high to low) but requires channel or carrier proteins for polar molecules and ions like glucose, $Na^+$, and $K^+$. Osmosis is strictly defined as the movement of water molecules across a selectively permeable membrane from a region of higher water potential to a region of lower water potential; it may utilize aquaporins for efficiency. Active transport is the only method that requires energy in the form of $ATP$ to move ions or molecules against their concentration gradient (low to high), exemplified by the $Na^+/K^+$ pump. Large-scale transport involves endocytosis, where the membrane engulfs particles to bring them into the cell (e.g., phagocytosis of bacteria), and exocytosis, where vesicles fuse with the membrane to release large molecules like neurotransmitters.

Cellular Division via Mitosis and the Cell Cycle

Mitosis is the process of nuclear division that results in two genetically identical diploid daughter cells, used for growth, repair, and asexual reproduction. It consists of four main stages: Prophase, Metaphase, Anaphase, and Telophase. During Prophase, chromosomes condense, the nuclear envelope breaks down, and spindle fibres form from centrioles. In Metaphase, chromosomes align at the equator (the metaphase plate) and spindle fibres attach to the centromeres. Anaphase occurs when sister chromatids are pulled to opposite poles as spindle fibres shorten, elongating the cell. Finally, in Telophase, nuclear envelopes reform, chromosomes decondense, and cytokinesis begins to divide the cytoplasm into two cells. Students must distinguish mitosis from meiosis, the latter of which produces four genetically different haploid cells used exclusively for the production of gametes.

Molecular Foundations: DNA Structure and Semi-Conservative Replication

DNA is a double helix composed of two antiparallel strands, where one runs from the $5\text{'}$ to $3\text{'}$ direction and the other from $3\text{'}$ to $5\text{'}$. Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base. Fundamental base-pairing rules dictate that Adenine pairs with Thymine via $2$ hydrogen bonds, while Guanine pairs with Cytosine via $3$ hydrogen bonds; the $G-C$ bond is considered stronger due to this additional bond. This differs from RNA, which contains ribose sugar, Uracil instead of Thymine, and is single-stranded. The width of the helix is kept constant because purines ($A, G$), which have double-ring structures, always pair with pyrimidines ($C, T, U$), which have single-ring structures.

DNA replication is semi-conservative, meaning each new DNA molecule contains one original strand and one new strand. The process involves several enzymes: Helicase unwinds and unzips the double helix by breaking hydrogen bonds at the replication fork. Primase adds a short RNA primer to provide a starting point. DNA polymerase reads the template strand from $3\text{'}$ to $5\text{'}$ and builds the new strand in the $5\text{'}$ to $3\text{'}$ direction by adding complementary free nucleotides. Because DNA polymerase only works in one direction, the lagging strand is synthesized in short fragments called Okazaki fragments, which are subsequently joined by the enzyme Ligase.

Protein Synthesis: Transcription, RNA Processing, and Translation

Protein synthesis occurs in two major stages. Transcription takes place in the nucleus, where RNA polymerase uses the DNA template strand (read $3\text{→}5$) to build a messenger RNA ($mRNA$) strand (built $5\text{→}3$). In eukaryotes, pre-$mRNA$ undergoes RNA processing where spliceosomes remove non-coding introns and join coding exons. Translation occurs at the ribosomes, where the $mRNA$ is read in triplets called codons. Each codon corresponds to a specific amino acid. For instance, $AUG$ is the start codon that codes for methionine. Transfer RNA ($tRNA$) molecules carry specific amino acids to the ribosome, guided by a complementary anticodon that binds to the $mRNA$ codon. Peptide bonds form between amino acids until a stop codon ($UAA, UAG, UGA$) is reached, terminating the process. The genetic code is universal, meaning every organism uses the same codons for the same amino acids, providing evidence for a common ancestor. It is also degenerate, meaning multiple codons can code for the same amino acid, which provides a buffer against the harmful effects of mutations.

Enzyme Kinetics and Metabolic Regulation

Enzymes act as biological catalysts through the Induced Fit Model, where the active site is flexible and changes shape slightly to mould around the substrate to form an enzyme-substrate complex. Several factors influence enzyme activity: an increase in temperature increases kinetic energy and collisions until the optimum temperature is reached, beyond which denaturation occurs. Changes in $pH$ alter the ionization of amino acids in the active site; for example, pepsin requires a $pH$ of approximately $2$, while trypsin requires a $pH$ of around $8$. Increasing substrate concentration increases the rate of reaction until the enzyme becomes saturated, at which point the enzyme itself becomes the limiting factor. Inhibition can be competitive, where a molecule similar in shape to the substrate blocks the active site and can be overcome by adding more substrate, or non-competitive, where an inhibitor binds to an allosteric site. This change to the allosteric site alters the active site's shape so the substrate can no longer bind, a process that is often irreversible and cannot be overcome by adding more substrate.

Cellular Respiration and Energy Production

Respiration is the process of generating energy in the form of $ATP$. Aerobic respiration requires oxygen and produces a high yield of $36 - 38\text{ ATP}$ per glucose molecule. It starts with glycolysis in the cytoplasm, then proceeds to the Krebs cycle in the mitochondrial matrix, and ends with the Electron Transport Chain ($ETC$) on the inner mitochondrial membrane (cristae). The cristae provide a large surface area for $ATP$ synthase, which uses a $H^+$ ion gradient to generate $ATP$ through chemiosmosis. Anaerobic respiration occurs in the cytoplasm and yields only $2\text{ ATP}$. In animals, glucose is converted to lactic acid, while in yeast, fermentation converts glucose to ethanol and $CO_2$.

Principles of Genetics and Inheritance

Genetics is built upon specific terminology: a gene is a heritable factor and DNA sequence that codes for a polypeptide; an allele is a specific form of a gene differing by only a few bases at the same locus (position) on a chromosome. A dominant allele expresses its phenotype in both homozygous and heterozygous states, while a recessive allele only expresses when two copies are present. The genotype refers to the specific alleles an organism has ($BB, Bb, bb$), whereas the phenotype is the observable characteristic. Codominance occurs when both alleles are expressed simultaneously, such as in the $ABO$ blood group system ($I^A$ and $I^B$ producing blood type $AB$).

Meiosis and the Generation of Genetic Variation

Meiosis involves two divisions resulting in four non-identical haploid daughter cells. It is the core of sexual reproduction in the testes and ovaries. Genetic variation is generated through three main mechanisms: crossing over in Prophase I at chiasmata, where homologous chromosomes exchange segments; independent assortment in Metaphase I, where homologous pairs are oriented randomly; and random fertilization, the principle that any sperm can fertilise any egg. This contrasts with mitosis, which involves only one division and maintains the diploid ($2n$) state.

Patterns of Inheritance and Mutational Impacts

Monohybrid inheritance is analyzed using Punnett squares, which require defining a key for dominant and recessive alleles, identifying parental genotypes, and calculating genotype and phenotype ratios. A test cross involves breeding an individual with a dominant phenotype but unknown genotype with a homozygous recessive individual to determine if the parent is heterozygous. Sex-linked traits are those located on the $X$ chromosome. Males ($XY$) are more frequently affected by recessive $X$-linked conditions like red-green colour blindness and haemophilia A because they only possess one $X$ chromosome; if they inherit the recessive allele, they must express the trait. Females ($XX$) can be carriers ($X^H X^h$) without showing symptoms.

Mutations can be substitution-based or frameshift-based. Substitution replaces one base and can be silent (no effect), missense (changing one amino acid), or nonsense (creating an early stop codon). Frameshift mutations (insertions or deletions) are typically more harmful as they shift the reading frame for all subsequent codons, usually resulting in a non-functional protein. Down Syndrome, or Trisomy 21, is caused by non-disjunction during meiosis, where chromosomes fail to separate, leading to a gamete with an extra copy of chromosome $21$. The frequency of this event increases with maternal age.

Ecological Relationships and Energy Flow

Ecology organizes life into hierarchies: a species is a group of organisms that can interbreed and produce fertile offspring; a population is a group of the same species in the same area; a community is all populations of different species interacting in an area; and an ecosystem includes these communities plus the abiotic environment. Autotrophs (producers) create organic molecules from inorganic sources, while heterotrophs (consumers) ingest organic molecules. Heterotrophs are further divided into detritivores, which ingest dead organic matter for internal digestion (e.g., earthworms), and saprotrophs, which secrete enzymes externally onto dead matter before absorbing products (e.g., fungi).

Energy flow follows the 10\text{%} Rule: only about 10\text{%} of energy is transferred between trophic levels, while 90\text{%} is lost as heat from respiration, movement, growth, or undigested faeces. This limits food chain length. Pyramids of energy are always upright because energy is lost at each level, whereas pyramids of numbers or biomass can sometimes be inverted.

Biogeochemical Cycles: Nitrogen and Carbon

The nitrogen cycle involves five essential processes. Nitrogen fixation converts atmospheric $N_2$ into ammonium ($NH_4^+$) via bacteria like Rhizobium (in legume root nodules) or Azotobacter. Nitrification converts ammonium to nitrites ($NO_2^-$) and then nitrates ($NO_3^-$) in oxygenated soil. Assimilation is the absorption of nitrates by plant roots for protein and nucleic acid synthesis. Ammonification is the release of ammonium from dead matter by decomposers. Denitrification converts nitrates back into $N_2$ in anaerobic, waterlogged conditions. The carbon cycle involves photosynthesis (removing $CO_2$), respiration (returning $CO_2$), combustion, decomposition, and fossilization.

Population Dynamics and Growth Models

Populations show different growth patterns. J-curves represent theoretical exponential growth without limiting factors. S-curves (sigmoid growth) show initial slow growth, exponential growth, and eventual stabilization at the carrying capacity ($K$) due to limiting factors. Density-dependent factors, such as disease, competition, and predation, increase in impact as density rises. Density-independent factors, like natural disasters or extreme temperatures, affect populations regardless of size.

Evidence for Evolution and the Mechanism of Natural Selection

Evolution is supported by five types of evidence: the fossil record shows transitional forms like Archaeopteryx; selective breeding demonstrates human-directed phenotypic changes; homologous structures like the pentadactyl limb (humerus, radius, ulna, carpals, phalanges) suggest common ancestry; comparative biochemistry shows similarities in DNA and proteins like Cytochrome c; and antibiotic resistance provides real-time proof. Natural selection follows four steps: overproduction (leading to competition), heritable variation, differential survival (survival of the reproductive fit), and a subsequent change in allele frequency over many generations.

Biological Classification and the Origin of Species

Taxonomy follows the hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (mnemonic: Dear King Philip Came Over For Good Soup). Binomial nomenclature uses the Genus species format, such as Homo sapiens. The three domains are Bacteria (prokaryotes with peptidoglycan), Archaea (extremophile prokaryotes), and Eukarya. Allopatric speciation occurs when a geographic barrier separates a population, leading to different selection pressures, mutations, and eventually genetic divergence that prevents the production of fertile offspring. Cladistics uses shared derived characteristics to group organisms into clades.

Human Physiology: Digestion and Nutrient Absorption

Digestion utilizes specific enzymes at optimal conditions: Salivary amylase (starch to maltose, $pH∼7$), Pepsin (proteins to polypeptides, stomach $pH∼2$), Pancreatic amylase (starch to maltose, $pH∼7$), Lipase (lipids to fatty acids, $pH∼7$), Trypsin (polypeptides to peptides, $pH∼8$), and Intestinal maltase (maltose to glucose, $pH∼7$). In the small intestine, glucose and amino acids are absorbed into blood capillaries in the villi, while fatty acids and glycerol are absorbed into lacteals. Villi adaptations include a one-cell thick wall, massive surface area, microvilli, and a rich blood/lymph supply.

The Blood System and Cardiovascular Anatomy

Arteries carry blood away from the heart under high pressure using thick, elastic walls; veins carry blood toward the heart under low pressure using thin walls and valves to prevent backflow. Capillaries are one-cell thick to facilitate exchange. A critical exception is the pulmonary artery (carries deoxygenated blood to lungs) and the pulmonary vein (carries oxygenated blood to heart). The heart's left ventricle has a thicker wall than the right because it must pump blood through the systemic circuit at much higher pressure. The sinoatrial (SA) node acts as the pacemaker.

Defense Against Disease: The Immune System

The immune system has three lines of defense. The first consists of physical and chemical barriers: skin, mucus, cilia, stomach acid ($pH∼2$), and lysozyme in tears. The second line is the non-specific response, featuring phagocytes that ingest pathogens. The third line is the specific immune response where B lymphocytes produce antibodies ($Y$-shaped glycoproteins with specific variable regions) and T lymphocytes destroy infected cells. Vaccines work by introducing antigens to stimulate a primary response and the production of memory cells. Upon real infection, the secondary response is faster and produces more antibodies, clearing the pathogen before symptoms develop.

Gas Exchange and Ventilation Mechanisms

Alveoli are adapted for gas exchange with one-cell thick walls, a moist surface to dissolve gases, massive surface area ($∼70\text{ m}^2$), and a rich capillary network to maintain a concentration gradient. Ventilation involves the diaphragm and intercostal muscles; inhalation occurs when these contract to increase thorax volume and drop pressure, while exhalation occurs as they relax to decrease volume and raise pressure.

Neural Communication and Synaptic Transmission

Neurons transfer impulses from receptors to executors. Synaptic transmission is a chemical, unidirectional process. When an action potential reaches the pre-synaptic knob, calcium ions ($Ca^{2+}$) enter, causing vesicles to fuse with the membrane and release neurotransmitters (e.g., acetylcholine) via exocytosis. The neurotransmitter diffuses across the synaptic cleft and binds to receptors on the post-synaptic membrane, generating a new action potential. Enzymes like acetylcholinesterase then break down the neurotransmitter to prevent continuous stimulation.

Endocrine Control of Blood Glucose and Diabetes

Blood glucose is regulated by the pancreas. When glucose is high, beta cells secrete insulin, causing liver and muscle cells to take up glucose and perform glycogenesis (glucose to glycogen). When glucose is low, alpha cells secrete glucagon, stimulating glycogenolysis (glycogen to glucose). Type 1 Diabetes is an autoimmune destruction of beta cells requiring insulin injections. Type 2 Diabetes is a resistance to insulin linked to obesity and lifestyle, often treated through diet and exercise.

Questions & Discussion

Q: State two features shared by both prokaryotic and eukaryotic cells. [2] ANSWER: Any two of: ribosomes / DNA / cell membrane / cytoplasm. (Both can carry out protein synthesis and cellular respiration.)

Q: Explain why facilitated diffusion does not require ATP. [2] ANSWER: Facilitated diffusion moves molecules DOWN the concentration gradient (high to low) — this is the direction molecules naturally move. No energy input is needed because the molecule moves in its natural direction. ATP is only needed to move molecules AGAINST their gradient (active transport).

Q: Describe what happens to a plant cell placed in a hypertonic solution. [3] ANSWER: Water moves OUT of the cell by osmosis (lower water potential outside) / cell membrane pulls away from cell wall / this is called PLASMOLYSIS / cell becomes flaccid / turgor pressure is lost.

Q: State the role of helicase in DNA replication. [1] ANSWER: Helicase unwinds the double helix / breaks hydrogen bonds between complementary base pairs / separates the two strands to expose them as templates at the replication fork.

Q: Explain the difference between competitive and non-competitive inhibition. [4] ANSWER: Competitive: inhibitor has similar shape to substrate / binds to the active site / competes with substrate for active site / can be overcome by increasing substrate concentration. Non-competitive: inhibitor binds to the allosteric site (not active site) / changes the shape of the active site / substrate cannot bind even if present / adding more substrate does NOT overcome inhibition.

Q: Outline the process of translation. [4] ANSWER: mRNA attaches to ribosome / ribosome reads mRNA in triplets called codons / tRNA with complementary anticodon brings specific amino acid / peptide bond forms between adjacent amino acids / ribosome moves along mRNA one codon at a time / stop codon reached = polypeptide released.

Q: Explain why males are more likely to be affected by X-linked recessive conditions than females. [2] ANSWER: Males only have one X chromosome (XY) so only need ONE copy of the recessive allele to express the trait. Females have two X chromosomes so need TWO copies of the recessive allele to show the trait. Females with one copy are carriers but do not show the condition.

Q: Explain why a deletion mutation is usually more harmful than a substitution mutation. [2] ANSWER: Deletion causes a frameshift — the reading frame is shifted for all codons downstream of the deletion, altering every amino acid from that point onward, usually producing a completely non-functional protein. Substitution only affects ONE codon — may be silent (same amino acid) due to the degenerate nature of the genetic code, or may only alter one amino acid.

Q: Explain why energy transfer between trophic levels is inefficient. [3] ANSWER: Only approximately 10% of energy is transferred between trophic levels. Energy is lost as: heat through cellular respiration (metabolic processes in all organisms) / undigested material passed out as faeces / energy used for movement, growth and reproduction / not all organisms at one trophic level are eaten by the next.

Q: Distinguish between a detritivore and a saprotroph. [2] ANSWER: Detritivore: ingests dead organic matter and digests it internally (intracellular digestion). Example: earthworm. Saprotroph: secretes digestive enzymes EXTERNALLY onto dead organic matter and then absorbs the digested products. Example: fungi or bacteria.

Q: Outline how natural selection can lead to antibiotic resistance in bacteria. [4] ANSWER: Random mutation occurs in some bacteria giving resistance to antibiotic / antibiotic is applied and kills non-resistant bacteria / resistant bacteria survive and are able to reproduce / pass on the resistance allele to their offspring / over generations the resistance allele becomes more frequent in the population / eventually most bacteria in the population are resistant.

Q: Explain how a secondary immune response differs from a primary immune response. [3] ANSWER: Memory cells are produced during the primary immune response / on second exposure to the same antigen, memory cells recognise it immediately / secondary response is FASTER (short lag period) / produces MORE antibodies / at HIGHER concentrations / body clears the infection before it causes disease.

Q: Explain why the left ventricle has a thicker wall than the right ventricle. [2] ANSWER: Left ventricle pumps blood through the systemic circuit — to the entire body — which is a much longer distance requiring much higher pressure. Right ventricle only pumps blood to the lungs (pulmonary circuit) which is a short distance requiring much lower pressure. Thicker muscular wall = more force = higher pressure generated.

Q: Distinguish between Type 1 and Type 2 diabetes. [2] ANSWER: Type 1: autoimmune condition where beta cells are destroyed / no insulin produced / requires insulin injections. Type 2: body cells are resistant to insulin / insulin is produced but cells do not respond / associated with lifestyle / managed with diet and exercise.