Comprehensive CAPS Life Sciences Study Notes
DNA - The Code of Life
- There are two types of nucleic acids: DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid).
- Location and roles:
- DNA: located on chromosomes in the nucleus; forms the genes.
- RNA: formed in the nucleus but functions mainly in the cytoplasm.
- Structure of nucleic acids:
- Nitrogenous bases come in two groups: purines (adenine A, guanine G) and pyrimidines (cytosine C, thymine T in DNA; cytosine C, uracil U in RNA).
- Complementarity:
- Cytosine pairs with guanine (C ≡ G).
- Adenine pairs with thymine in DNA (A ≡ T); in RNA, adenine pairs with uracil (A ≡ U).
- DNA base pairing is held together by weak hydrogen bonds; double helix model proposed by Watson & Crick (1953).
- Nucleotides are the monomers of both DNA and RNA.
- Each nucleotide consists of:
- NB: nitrogenous base
- S: sugar (deoxyribose in DNA; ribose in RNA)
- P: phosphate
- Location of DNA:
- Nuclear DNA forms chromosomes within the nucleus; together with proteins, these form chromatin.
- Extra-nuclear DNA found in chloroplasts (chloroplast DNA, ctDNA) and mitochondria (mitochondrial DNA, mtDNA).
- DNA replication (before cell division): where identical copies of DNA are made.
- Occurs during interphase (before mitosis and meiosis).
- Process (summary):
- The double helix unwinds.
- Hydrogen bonds break; strands unzip.
- Each original strand serves as a template to form a new strand.
- Free nucleotides attach to the template by complementary base pairing (A↔T, C↔G).
- Two identical DNA molecules form, each composed of one original strand and one new strand.
- Enzymes control replication.
- RNA types and structure:
- There are three main types of RNA:
- Ribosomal RNA (rRNA): found in ribosomes in the cytoplasm.
- Messenger RNA (mRNA): produced in the nucleus, exits to cytoplasm to be translated.
- Transfer RNA (tRNA): found in cytoplasm; brings amino acids to ribosome.
- RNA is typically single-stranded; sugar is ribose (not deoxyribose); thymine replaced by uracil (U).
- Similarities & differences between DNA and RNA:
- Similarities:
- Both have sugar–phosphate backbones and nitrogenous bases.
- Both participate in protein synthesis.
- Differences:
- DNA: double-stranded, uses deoxyribose, contains thymine; DNA’s location is nucleus/mitochondria/chloroplasts; DNA replication stores genetic information across generations.
- RNA: single-stranded, uses ribose, contains uracil; functions in transcription and translation.
- DNA replication (details you should know):
- Before cell division, DNA replicates to ensure each daughter cell receives an identical set of chromosomes.
- Conceptually the process creates two genetically identical DNA molecules, each with one original strand and one new strand.
- Protein synthesis (central dogma overview):
- Transcription: DNA → mRNA in the nucleus.
- Translation: mRNA → protein in the cytoplasm at the ribosome; tRNA brings amino acids matching mRNA codons; amino acids linked by peptide bonds to form a protein.
- Codons on mRNA are read in triplets; a codon specifies an amino acid; anticodons on tRNA pair with codons to deliver the correct amino acids.
- DNA profiling (forensic genetics):
- How it works: patterns of DNA fragments are visualized on a profile; a DNA profile is used to identify individuals by comparing with known DNA.
- Uses include: diagnosing inherited disorders; criminal identification; establishing paternity; tracing siblings separated at birth; identifying remains.
- Limitations/ethical issues:
- Small DNA samples may not be unique to an individual.
- Private labs may lack uniform testing standards/quality controls.
- Human interpretation can introduce error.
- Profiling can be expensive.
- Potential for revealing sensitive information (e.g., HIV status) and face prejudice.
- Key terms (glossary-style recap):
- Nucleotide, Nucleic acid, Chromosome, Chromatin, Extra-nuclear DNA, Codon, Anticodon, Template, Replication, Transcription, Translation, DNA profile.
- Quick connections to foundational principles:
- Genetic information flow from DNA to RNA to protein underlies all cellular function.
- Complementarity ensures accurate copying and expression of genes.
- Mutations and DNA profiling underpin evolution, genetic disorders, forensic science, and medical diagnostics.
Meiosis
- Meiosis overview:
- Meiosis is the division of a germ cell into four haploid gametes, each with half the chromosome number of the parent.
- Occurs during gametogenesis (gamete formation).
- In many organisms meiosis occurs after fertilization in others (bread mould example).
- Phases (Meiosis I and II):
- Meiosis I (reduction division):
- Interphase: DNA replication; chromosomes duplicate; each chromosome has two sister chromatids.
- Prophase I: homologous chromosomes pair up (synapsis) forming bivalents; crossing-over occurs (exchange of genetic material).
- Metaphase I: homologous pairs align randomly at the equator (random orientation).
- Anaphase I: homologous chromosomes (each still double-stranded) are pulled to opposite poles; sister chromatids stay together.
- Telophase I: two new nuclei form; cytoplasm divides to produce two haploid cells; chromosomes still double-stranded.
- Meiosis II (equational division):
- Prophase II: nuclear membrane dissolves; chromosomes condense.
- Metaphase II: chromosomes align singly along the equator.
- Anaphase II: sister chromatids are pulled apart to opposite poles.
- Telophase II: four haploid cells form; each has half the original chromosome number; cells are genetically different.
- Significance of meiosis:
- Produces haploid gametes, maintaining chromosome number across generations after fertilization (diploid zygote formed by fertilization becomes diploid again).
- Crossing over and Random arrangement of chromosomes during metaphase I & II introduce genetic variation, increasing genetic diversity in offspring.
- Abnormal meiosis:
- Non-disjunction can occur during Anaphase I or II, leading to aneuploidy or polyploidy.
- Aneuploidy: gamete has an abnormal number of chromosomes.
- Polyploidy: gamete has extra chromosome sets.
- Examples discussed:
- Down syndrome: trisomy 21 (47 chromosomes); often due to non-disjunction.
- Karyotyping is used to detect abnormal chromosome numbers.
- Terminology you should recall:
- Homologous chromosomes, bivalent, chiasma, spindle fibers, centromere, diploid (2n), haploid (n).
- Connections to real-world relevance:
- Genetic variation from meiosis is a cornerstone of evolution and diversity.
- Abnormal meiosis informs clinical genetics, prenatal screening, and diagnosis.
Reproduction in Vertebrates (Overview) / Human Reproduction
- Reproduction strategies:
- External fertilisation: fertilization occurs outside the female's body; water is required for transport and to prevent drying; many offspring produced to offset high mortality.
- Internal fertilisation: fertilization occurs inside the female; common in terrestrial species; fewer offspring but higher survival rate.
- Modes of development:
- Ovipary: eggs laid outside body; development may be fertilized internally or after laying.
- Ovovivipary: eggs fertilized internally but hatch inside the mother; young are relatively developed when born.
- Vivipary: young develop inside the uterus with nutrients from the mother via placenta; live birth.
- Amniotic egg and extra-embryonic membranes (in birds/reptiles):
- Amnion: encloses amniotic cavity with amniotic fluid for cushioning.
- Chorion: facilitates gas exchange.
- Allantois: stores waste; participates in gas exchange.
- Yolk sac: provides nutrition.
- Precocial vs Altricial development (birds):
- Precocial: hatchlings are relatively well-developed, eyes open, can move/feed themselves; examples include finches, canaries, crows, swallows, mynahs.
- Altricial: hatchlings are helpless, eyes closed, need parental care; most passerines and many seabirds fall into this category.
- About 60% of bird species are altricial.
- Parental care: strategies include nest-building, guarding eggs, provisioning food, or internal gestation with placental nourishment (viviparity in mammals).
- Amniotic egg vs mammalian pregnancy:
- Amniotic eggs are common in reptiles and birds; eggs have shells that reduce dehydration; membranes (amniotic, chorion, allantois, yolk sac) support embryo.
- In mammals, embryos are nourished via placenta; most mammals are viviparous.
- Human reproductive anatomy (summary):
- Male: testes (seminiferous tubules), sertoli cells (nurse developing sperm), Leydig cells (testosterone production), epididymis (sperm maturation and storage), vas deferens, seminal vesicles, prostate, Cowper’s glands; penis delivers sperm via urethra.
- Female: ovaries (ova in follicles; estrogen & progesterone production), Fallopian tubes/oviducts (site of fertilization; carry ovum to uterus), uterus (endometrium thickening for implantation), cervix, vagina; urinary bladder; vulva.
- Gametogenesis:
- Spermatogenesis: occurs in testes; spermatogonia undergo meiosis to form four haploid sperm; several stages with Sertoli cells providing nutrition; SRY gene on Y chromosome influences development.
- Oogenesis: occurs in ovaries; one mature ovum is produced from a follicle after meiosis; cytoplasm is unevenly divided; polar bodies form.
- Menstrual cycle (ovarian and uterine cycles):
- Ovarian cycle: development and release of a Graafian follicle; ovulation around day 14 of a ~28-day cycle; LH surges trigger ovulation; corpus luteum forms after ovulation and secretes progesterone.
- Uterine cycle: endometrium thickens under estrogen and progesterone; if fertilization occurs, corpus luteum maintains pregnancy via progesterone; if not, corpus luteum degenerates; menstruation occurs (~day 28).
- Hormones involved (simplified):
- FSH (pituitary): stimulates follicle development; estrogen rise begins endometrial preparation.
- LH (pituitary): triggers ovulation; forms corpus luteum; progesterone production to maintain pregnancy.
- Estrogen: thickens endometrium; regulates many secondary sexual characteristics.
- Progesterone: maintains endometrial lining and pregnancy; supports gestation.
- Other relevant hormones/proteins: hCG (not always detailed in notes), testosterone in males, prolactin for milk production; oxytocin for childbirth (not deeply elaborated here).
- Contraception (summary of options and mechanisms):
- Barrier methods: condom, female condom, diaphragm, loop/IUD; prevent fertilization/implantation.
- Hormonal methods: pill (oestrogen/progestin) inhibits ovulation; injections (progestin); implants (not detailed here).
- Sterilisation: vasectomy (males) – blocks sperm transport; tubal ligation (females).
- Other: withdrawal method; rhythm (calendar) method; effectiveness varies.
- Fertilisation and implantation:
- Sperm travel through uterus to Fallopian tube; fertilisation occurs when a sperm penetrates an ovum; zygote forms (2n, 46 chromosomes).
- Zygote undergoes mitotic divisions to form blastocyst that implants into the endometrium.
- Placenta forms from chorionic villi and uterine tissue; placenta functions include attachment, nutrient/ gas exchange, waste removal; umbilical cord connects embryo to placenta.
- Amniotic fluid cushions the fetus; amnion surrounds the embryo.
- Placental hormones and pregnancy maintenance:
- Corpus luteum secretes progesterone to maintain pregnancy until placenta takes over.
- Placenta eventually secretes hormones to maintain pregnancy (e.g., progesterone).
- Contraception and public health implications:
- Understanding contraception helps reduce unintended pregnancies; public health strategies include education and access to contraception.
HUMAN REPRODUCTION – Key structural and functional notes
- Process flow (fertilization to implantation to birth):
- Copulation introduces sperm into vagina; sperm travel up through uterus to Fallopian tubes.
- Ovulation releases an ovum from Graafian follicle into Fallopian tube; if sperm fertilizes, zygote forms.
- Zygote divides by mitosis to form a blastocyst; blastocyst implants into uterine endometrium; placenta forms; embryo develops into a fetus; gestation lasts ~9 months.
- Gametogenesis in humans:
- Spermatogenesis: produces millions of sperm; constant production throughout reproductive life in males.
- Oogenesis: produces a single ovum per cycle; cytoplasmic division results in one mature ovum and polar bodies.
- The menstrual and ovarian cycles interplay with hormones to regulate ovulation, endometrium preparation, and menstruation.
- Embryo to fetus: development includes amniotic membranes, placenta, and umbilical cord; exposure to maternal physiology supports growth.
Genetics (Overview and Key Concepts)
- Basic terminology:
- Gene: a DNA segment at a locus that influences a characteristic.
- Alleles: alternative forms of a gene; can be dominant or recessive.
- Genotype: the genetic makeup (e.g., AA, Aa, aa).
- Phenotype: observable trait (e.g., brown eyes).
- Homozygous: two identical alleles (AA or aa).
- Heterozygous: two different alleles (Aa).
- Dominant allele: masks the recessive in a heterozygote.
- Recessive allele: expressed only in homozygous form.
- Modes of inheritance:
- Complete (simple) dominance: one allele completely dominates the other; phenotype reflects dominant allele.
- Incomplete dominance: heterozygote shows an intermediate phenotype (e.g., red x white = pink).
- Codominance: both alleles contribute to phenotype (e.g., AB blood type).
- Multiple alleles: more than two alleles exist for a gene (e.g., blood types IA, IB, i).
- Sex-linked: genes located on sex chromosomes (X-linked phenotypes more common in males when recessive).
- Pedigree analysis basics:
- Used to track inheritance of traits, determine whether a trait is dominant/recessive, and assess carrier status.
- Monohybrid cross: single trait cross; phenotypic ratio in F1 often 3:1 for complete dominance in the F2.
- Dihybrid cross (two traits): expected phenotypic ratio 9:3:3:1 under complete dominance and independent assortment.
- Blood typing and ABO system:
- Alleles: I^A, I^B, i; I^A and I^B are co-dominant; i is recessive to both.
- Genotypes and phenotypes:
- Type A: IAIA or IAi
- Type B: IBIB or IBi
- Type AB: IAIB
- Type O: ii
- Mutations:
- Gene mutations: point mutations (base substitution) and frameshift mutations (insertion/deletion).
- Chromosomal mutations/aberrations: changes in chromosome structure or number; non-disjunction can cause Down syndrome (trisomy 21).
- Effects of mutations can be harmful, neutral, or advantageous; some can be fixed in a population.
- Genetic disorders mentioned (examples): Down syndrome (trisomy 21), Sickle cell anemia (point mutation on chromosome 11), Haemophilia, Albinism, color blindness (often X-linked).
- Genetic technologies:
- Genetic engineering: deliberate modification of organisms using biotechnology.
- Cloning: producing genetically identical organisms.
- Stem cells: potential to differentiate into various tissues; embryonic vs cord blood sources; ethical debates.
- DNA profiling: forensic uses; advantages and limitations discussed earlier.
- Tracing genetic lineage and pedigrees:
- Pedigree diagrams indicate inheritance across generations; symbols show sex and phenotype status; used to infer carrier status and disease risk.
Nervous System and Sense Organs
- Nervous system organization:
- Central nervous system (CNS): brain and spinal cord.
- Peripheral nervous system (PNS): nerves outside CNS; subdivided into the somatic and autonomic systems.
- Neurons and nerve impulses:
- Three neuron types:
- Sensory neurons: carry impulses from receptors to CNS.
- Motor neurons: carry impulses from CNS to effector organs (muscles, glands).
- Interneurons (connector neurons): carry impulses within CNS.
- Neuron structure: dendrites, cell body, nucleus, axon; myelin sheath and neurilemma insulate to speed transmission; impulse travels from dendrites → cell body → axon; synapse (gap) where neurotransmitters cross to next neuron.
- Reflex actions and reflex arc:
- Reflex action: rapid, automatic response to a stimulus.
- Reflex arc components: receptor → sensory neuron → interneuron → motor neuron → effector.
- Example described: knee-jerk reflex; reflex provides quick protective response.
- Sense organs and receptors:
- Eye: structure includes sclera, choroid, retina; cornea, iris, pupil, lens, ciliary body; aqueous and vitreous humours; macula (high cone density); blind spot.
- Ear: outer ear (pinna, ear canal), middle ear (tympanic membrane, ossicles: hammer, anvil, stirrup; Eustachian tube), inner ear (cochlea with organ of Corti; semicircular canals for balance).
- Receptors: light, sound, taste, smell, temperature, pressure, pain, balance, etc.
- Visual system: accommodation and pupil reflexes (pupillary mechanism).
- Common neurological disorders and injuries:
- Alzheimer’s disease; Multiple sclerosis; injuries to brain/spinal cord; effects on memory, balance, and autonomic control.
- Drugs and the nervous system:
- Drugs can stimulate or inhibit neurotransmitter action; effects include memory changes, paranoia, anxiety.
Endocrine System and Homeostasis
- Endocrine system basics:
- Glands: endocrine glands secrete hormones into the bloodstream; exocrine glands have ducts.
- Major glands and hormones (examples):
- Hypothalamus: ADH (vasopressin), regulates pituitary activity.
- Pituitary (hypophysis): TSH, FSH, LH, prolactin, growth hormone.
- Thyroid: thyroxine (T4) – regulates metabolic rate.
- Pancreas: insulin and glucagon – regulate blood glucose.
- Adrenal glands: adrenaline (epinephrine), aldosterone – stress response and salt balance.
- Ovaries: estrogen, progesterone – female development and pregnancy maintenance.
- Testes: testosterone – male development.
- Negative feedback and homeostasis:
- Homeostasis: maintenance of a relatively constant internal environment.
- Negative feedback: a change in a controlled condition triggers a response that counteracts the initial change to restore normal levels (e.g., thyroxine and TSH levels).
- Hormone regulation examples:
- Thyroid axis: low thyroxine → pituitary releases more TSH → thyroid release increases thyroxine; high thyroxine → less TSH → thyroxine production decreases.
- Glucose regulation: high blood glucose → pancreas secretes insulin → lowers glucose; low glucose → glucagon from pancreas raises glucose by converting glycogen to glucose.
- Stress response: adrenaline prepares body for emergency (increases heart rate, blood flow to muscles, dilates bronchi, etc.).
- Diabetes mellitus:
- Type 1: pancreas stops producing insulin; requires insulin injections.
- Type 2: insulin produced but not effectively used; managed via diet, exercise, sometimes medication.
- Hormone vs nervous coordination:
- Hormones are chemical messengers; slower but longer-lasting; act on many targets; can interact.
- Nerves transmit electrical impulses rapidly; specific to particular effectors; fast responses.
- Negative feedback examples in practice:
- ADH controls water re-absorption in kidneys; aldosterone controls Na+ reabsorption; hypothalamus/pituitary regulate many axes.
Homeostasis
- Core idea: maintain stable internal conditions despite environmental changes.
- Osmoregulation and water balance:
- Nephron and ADH regulate water re-absorption; hypothalamus senses osmolality; pituitary secretes ADH accordingly.
- Water balance adjustments result in dilute or concentrated urine depending on needs.
- Thermoregulation:
- Heat loss/gain regulated by vasodilation/vasoconstriction; sweating; hypothalamus acts as thermostat.
- Gas exchange and metabolism:
- Carbon dioxide and oxygen balance tightly regulated by respiratory and circulatory adjustments.
Plant Responses to the Environment
- Plant hormones (growth substances):
- Auxins (IAA): promote tropisms (phototropism and geotropism), promote cell elongation, apical dominance, root development.
- Gibberellins: promote internode elongation, root growth, flowering, leaf aging, stomatal closure during drought.
- Abscisic acid (ABA): dormancy in seeds, dormancy in apical buds, inhibits growth; involved in drought responses.
- Tropisms:
- Phototropism: growth toward light; stems are positively phototropic; roots are negatively phototropic.
- Geotropism: growth in response to gravity; roots are positively geotropic; stems are negatively geotropic.
- Auxin distribution controls bending by stimulating differential growth on sides of plant organs.
- Phototropism mechanism:
- Auxin produced at shoot tips moves downward; uneven distribution causes bending toward light due to differential growth.
- Geotropism mechanism:
- Auxins accumulate on the lower side of horizontally placed roots; differential growth causes downward bending.
- Weed control using plant hormones:
- Hormone-based herbicides rely on auxin analogs to kill targeted weeds while sparing crops.
- Plant defense mechanisms:
- Thorns, chemical secretions, and leaf/fruit defenses protect plants from herbivores and pathogens.
Evolution by Natural Selection
- Evidence for evolution:
- Fossils (paleontology): dating fossils via relative dating and radiometric dating; fossils reveal gradual changes and transitional forms; phylogenetic trees illustrate relationships.
- Homologous structures: similar anatomical plans across species imply common ancestry and adaptive modification.
- Biogeography: related species cluster geographically; similar environments in different regions host different species.
- Molecular biology and genetics: DNA/protein sequence similarities reflect descent and relatedness.
- Sources of variation:
- Mutations: random changes in DNA sequences; can be point mutations or frameshifts; can be neutral, harmful, or advantageous.
- Meiosis: crossing over and independent assortment generate novel genetic combinations; random fertilisation adds to variation.
- Lamarck vs Darwin:
- Lamarckism: inheritance of acquired characteristics; traits modified by use/disuse are passed to offspring.
- Darwinism: variation arises randomly; natural selection favors advantageous traits; populations accumulate beneficial traits over generations.
- Speciation and evolution:
- Allopatric speciation occurs when geographic barriers separate populations; independent evolution leads to new species.
- Punctuated equilibrium proposes long periods of little change interrupted by rapid evolutionary bursts.
- Human impact on evolution:
- Artificial selection (selective breeding) demonstrates how humans influence trait frequencies.
Human Evolution
- Out of Africa hypothesis:
- Modern humans (Homo sapiens) originated in Africa and migrated to other continents; mitochondrial DNA (mtDNA) studies support a common maternal ancestor in Africa.
- Key fossil evidence and timeline:
- Ardipithecus ramidus (5-4 mya), Australopithecus afarensis (3.9-2.9 mya), Australopithecus africanus (2-2 mya), Homo habilis (~2.2-1.6 mya), Homo erectus (1.5-0.2 mya), Homo sapiens (~200k years ago to present).
- Evolutionary trends observed in fossil record:
- Increase in brain size over time.
- Foramen magnum moved forward indicating bipedalism.
- Reduction in prognathism and dental size (teeth) as diet shifts toward cooked food.
- Brow ridges reduce; cranium becomes more rounded; facial structure becomes flatter.
- Pelvis becomes shorter and wider; spine more curved to support upright walking.
- Phylogenetic relationships:
- Transitional fossils (e.g., Australopithecus sediba) show mosaic traits bridging earlier and later Homo species.
- Modern human origins:
- Mitochondrial DNA and genetic evidence indicate a recent common maternal ancestor (mitochondrial Eve) in Africa.
- Comparative anatomy with African apes:
- Humans differ in cranium size, foramen magnum position, brow ridges, spine curvature, pelvis shape, dentition, and jaw projection.
Human Impact on the Environment
- Climate change & greenhouse effect:
- Greenhouse gases (CO2, methane CH4, water vapour) trap heat and keep Earth warm; excessive greenhouse gas intensities lead to enhanced greenhouse effect and global warming.
- Primary causes: burning fossil fuels, deforestation, agriculture (methane from ruminants, rice paddies, waste decomposition).
- Consequences: increased evaporation, more intense rainfall and flooding, sea-level rise, droughts, more wildfires, biodiversity loss.
- Carbon footprint:
- A measure of total greenhouse gas emissions by individuals, populations, or organizations per year.
- Ozone layer and CFCs:
- Ozone layer absorbs UV radiation; destruction by CFCs threatens skin cancer risk and eye damage; strategies include phasing out CFCs and protecting ozone.
- Deforestation & biodiversity loss:
- Removal of forests reduces carbon sequestration, disrupts habitats, and reduces biodiversity.
- Water quality and availability:
- Dams affect water storage; wetlands purify water; pollution from agriculture and industry degrades water bodies; eutrophication from excess nutrients; heavy metals from mining.
- Waste management:
- Solid waste disposal requires safe landfill design to prevent leachate; recycling reduces energy use and pollution; methane can be captured for energy.
- Food security and GMOs:
- Genetically modified organisms (GMOs) can increase yield, resist pests/drought, improve shelf-life, and alter nutritional content; debates include ethics, safety, and ecological impacts.
- Sustainable practices:
- Reduce/reuse/recycle; switch to renewable energy; protect biodiversity; adopt sustainable farming and land management.
Ethical, Philosophical & Practical Implications
- Genetic engineering and cloning:
- Potential benefits: medical proteins, disease resistance, increased yields.
- Ethical concerns: effects on ecosystem, animal welfare,