Biology: Cells, Human Body and Living Organisms

Cell structure and organelles

The cell is the basic structural and functional unit of all living organisms. Cells are divided into prokaryotic cells, such as bacteria, which lack a membrane-bound nucleus and membrane-bound organelles, and eukaryotic cells, which have a true nucleus and organelles such as mitochondria, Golgi bodies and the endoplasmic reticulum. Every cell is bounded by a plasma membrane. According to the fluid mosaic model, this membrane is a bilayer of amphipathic phospholipid molecules in which proteins are embedded or attached, and cholesterol is interspersed among the phospholipids in animal cells. The membrane is flexible and selectively permeable, so it regulates the passage of substances, and its flexibility allows the cell to engulf particles by endocytosis such as phagocytosis.

Not every cell has a cell wall. Bacteria have a peptidoglycan wall, plant cells have a cellulose wall, and fungi have a chitin wall, whereas animal cells, including human cells, are bounded only by the plasma membrane. Diatoms, which are algae, have a silica wall. Tapeworms, being animals, have no cell wall.

Organelles have specific functions. Mitochondria carry out cellular respiration, chloroplasts carry out photosynthesis, ribosomes synthesise proteins, and the rough endoplasmic reticulum, which is studded with ribosomes, is involved in the transport of the proteins made on its surface. Confusing these functions is a common error in exams. Microbodies are small single-membrane organelles found in both plant and animal cells, and they contain enzymes such as catalase, which breaks down hydrogen peroxide (H_2O_2), and various oxidases.

Mitochondria and plastids are semi-autonomous organelles. Each contains its own circular DNA and ribosomes that resemble those of bacteria. This observation supports the endosymbiotic theory, which holds that these organelles originated from free-living prokaryotes. Golgi bodies, the endoplasmic reticulum, lysosomes and vacuoles have no DNA or ribosomes of their own.

Genetic material is distributed differently in cells. In a plant cell, RNA is present in the nucleus, the cytoplasm, mitochondria, chloroplasts and ribosomes, because ribosomes are composed of ribosomal RNA and proteins. Chromosomes are made of DNA tightly associated with proteins, which in eukaryotes are mainly histones that package the DNA. Bacteria lack a nuclear membrane, and their single circular DNA molecule lies in an irregular, membraneless region called the nucleoid. Prokaryotes possess free 70S ribosomes in the cytoplasm for protein synthesis, but they lack mitochondria and Golgi bodies, which occur only in eukaryotes.

• Nucleoid — the membraneless region of a bacterial cell where the DNA is concentrated. 예) The nucleoid of E. coli contains one circular chromosome and no nuclear envelope.
• Semi-autonomous organelle — an organelle that carries its own DNA and ribosomes but depends on the host cell for most proteins. 예) Chloroplasts are semi-autonomous organelles found in green plant cells.
• Microbody — a small organelle bounded by a single membrane that contains oxidative enzymes. 예) Peroxisomes are a common type of microbody.
• Endosymbiotic theory — the hypothesis that mitochondria and plastids evolved from engulfed prokaryotes. 예) The bacteria-like ribosomes in mitochondria support this theory.

Human nutrition and metabolism

The human diet supplies carbohydrates, proteins, fats, vitamins and minerals. A deficiency of one of these nutrients produces a characteristic disorder, and exam questions usually test the link between a specific nutrient and its deficiency disease.

Kwashiorkor is a severe form of protein-energy malnutrition that affects mainly children. It results from a lack of dietary protein and is marked by oedema and a swollen abdomen. Protein metabolism is the main source of urea. Amino acids are deaminated, which removes the amino group as ammonia. In the liver, ammonia is converted into urea through the urea cycle and excreted by the kidneys. Carbohydrates and lipids contain no nitrogen and therefore cannot produce urea.

Iron is an essential component of haemoglobin, the oxygen-carrying protein of red blood cells. Iron deficiency reduces haemoglobin synthesis and causes anaemia. Scurvy is due to a lack of vitamin C, rickets to a lack of vitamin D, and cholera is a bacterial infection rather than a nutritional disorder.

Excess energy is stored as fat in adipose tissue, which is a specialised connective tissue. Its cells, called adipocytes, store triglycerides in large lipid droplets. This stored fat is the body's main long-term energy reserve and also provides insulation and cushioning. Red blood cells, muscle tissue and epithelial tissue are not the principal fat stores.

During intense exercise, muscles may not receive enough oxygen, so glucose is broken down anaerobically. Pyruvic acid is then reduced to lactic acid, which accumulates in the muscle and causes cramps and pain. Carbon dioxide is carried away by the blood and does not cause cramps, and human muscle cells do not produce ethanol.

Bile is an alkaline fluid secreted by the liver and stored in the gall bladder. It contains bile salts and pigments but no digestive enzymes. Bile salts emulsify fats into small droplets, which increases the surface area for lipase action. Bile also neutralises the acidic chyme that comes from the stomach, creating the alkaline pH needed for pancreatic enzymes.

Thyroxine is an iodinated amino acid hormone. The thyroid gland needs dietary iodine to synthesise it, because each thyroxine molecule contains iodine atoms as structural components. Sodium chloride, potassium chloride and cholesterol are not used for this synthesis.

A disaccharide is formed when two monosaccharides join by a condensation reaction with the loss of one water molecule. Maltose consists of two glucose units, and lactose consists of glucose and galactose. Starch and glycogen are polysaccharides, and ribose and xylose are pentose monosaccharides.

• Kwashiorkor — severe protein-energy malnutrition caused mainly by protein deficiency. 예) A child with oedema and a swollen belly may be suffering from kwashiorkor.
• Deamination — removal of the amino group from an amino acid, producing ammonia. 예) Deamination of excess amino acids occurs mainly in the liver.
• Emulsification — breaking large fat globules into small droplets by bile salts. 예) Bile salts make fat digestion faster by emulsifying it.
• Disaccharide — a sugar made of two monosaccharide units. 예) Sucrose is a disaccharide of glucose and fructose.

Human circulatory system

Human blood circulates by double circulation. The pulmonary circuit carries deoxygenated blood from the right side of the heart to the lungs, where it is oxygenated, and returns it to the left side of the heart. The systemic circuit then pumps oxygenated blood from the left side of the heart to the rest of the body. Therefore the left side of the heart always contains oxygenated blood, and the right side contains deoxygenated blood.

Each blood vessel has a specific role. The pulmonary artery carries blood from the heart to the lungs, and the pulmonary vein returns oxygenated blood from the lungs to the heart. Capillaries form the connection between arteries and veins, where exchange of materials occurs. The coronary artery supplies blood to the heart muscle itself.

Blood pressure is written as systolic over diastolic pressure. The systolic value, about 120 mmHg in a normal adult, is the peak pressure produced during ventricular contraction. The diastolic value, about 80 mmHg, is the minimum pressure during ventricular relaxation.

Mature mammalian red blood cells lose their nucleus during development, which leaves more room for haemoglobin and improves oxygen transport. Muscle cells, phagocytic cells and ciliated epithelial cells all retain a nucleus.

Platelets, also called thrombocytes, are cell fragments formed in the bone marrow. At a site of injury they adhere together and release clotting factors and thromboplastin, which start the clotting cascade that forms a clot. Red blood cells, eosinophils and monocytes do not perform this function.

The pulse is felt because each contraction of the left ventricle pushes blood into the aorta, which expands and then recoils. This wave of expansion travels along the elastic walls of the arteries, and it is palpated as the pulse. The heart chambers and valves regulate blood flow, but the pulse itself is produced by the arterial walls.

The ABO system classifies blood by the presence of A and B antigens on red blood cells. This gives four blood types: A (A antigen only), B (B antigen only), AB (both antigens) and O (neither antigen). Genotypes such as AO or BO are not separate blood types, because the O allele is recessive.

• Double circulation — a circulatory system in which blood passes through the heart twice in one complete cycle. 예) In humans, blood goes to the lungs and then to the body through the heart.
• Systolic pressure — the peak arterial pressure during ventricular contraction. 예) A reading of 120 mmHg is the systolic value.
• Thrombocyte — another name for a platelet, which helps in blood clotting. 예) Platelets adhere to a wound and begin clot formation.
• Pulse — the rhythmic expansion of an artery caused by the heartbeat. 예) The radial pulse is felt at the wrist.

Animal classification and phyla

Animals are classified by shared body plans and developmental features. Some animals are free-living, whereas others live as parasites in or on a host. Planaria, a freshwater flatworm, lives independently and feeds on small organisms or dead matter. In contrast, the liver fluke, the filarial worm Wuchereria and the malaria parasite Plasmodium depend on a host for at least part of their life cycle.

The phylum Arthropoda is defined by jointed appendages, and insects belong to this group. Earthworms belong to the phylum Annelida, have a segmented cylindrical body and bilateral symmetry, but they lack jointed legs. Segmentation, cylindrical shape and bilateral symmetry are therefore not reliable features for separating insects from earthworms.

Protochordates are marine chordates that have a notochord and a coelom and are bilaterally symmetrical, but they never develop a vertebral column. This is what distinguishes them from vertebrates, which possess a vertebral column.

New species are often named after the place where they are found, and the specific epithet of such a species takes the name of that locality. This is a common practice in taxonomy and is useful when questions link a species to a state or region.

Biological classification follows a fixed hierarchy of ranks, from the broadest to the most specific: kingdom, phylum, class, order, family, genus and species. Each rank is nested within the one above it, so a species belongs to a genus, a genus to a family, and so on.

• Free-living organism — an organism that lives independently without depending on a host. 예) Planaria lives freely in clean freshwater.
• Protochordate — a marine chordate with a notochord but no vertebral column. 예) Hemichordates and urochordates are protochordates.
• Arthropoda — the phylum of animals with jointed appendages and an exoskeleton. 예) Insects and spiders belong to Arthropoda.
• Taxonomic hierarchy — the ordered set of ranks used to classify organisms. 예) Phylum comes before class, and class comes before order.

Viruses, antibiotics and vaccines

A virus is an acellular infectious agent made of a nucleic acid enclosed in a protein coat called the capsid. It has no cell wall, no cytoplasm and no independent metabolism, so it reproduces only inside a host cell. The genetic material of a virus can be either DNA or RNA, and this is a key basis of classification. For example, dengue virus is a mosquito-borne flavivirus with a single-stranded RNA genome. Because the genome is the nucleic acid, a mutation in a virus is a heritable change in its nucleotide sequence, not a change in cell size, shape or colour.

An antibiotic kills or inhibits bacteria by acting on processes that are specific to bacteria, such as cell wall synthesis or bacterial protein synthesis. A virus has no cell wall and uses the host cell's biochemical machinery, so an antibiotic has no target in a virus. A vaccine works differently. It introduces a harmless form of a pathogen or its antigen, which stimulates the immune system to produce specific antibodies and memory cells, so that the body responds quickly on later exposure. A vaccine does not act as a physical barrier that blocks the pathogen from entering the body, although the primed immune response neutralises and destroys the agent after it enters.

Vaccines are classified by their production method. Covaxin is an inactivated whole-pathogen vaccine, Sputnik V and Covishield are viral vector vaccines that use a harmless virus to carry the antigen gene, and mRNA vaccines are a separate category. Students should match each vaccine with its platform rather than assume that all modern vaccines are mRNA based.

Key distinctions:

• Antibiotic — a drug effective only against bacteria or other cellular targets. e.g. An antibiotic will not cure a common cold, which is viral.
• Vaccine — a preparation that builds active immunity against a specific pathogen. e.g. A measles vaccine prepares the body to respond to measles virus, not to bacteria.
• Viral vector vaccine — a vaccine in which a harmless virus delivers the antigen gene. e.g. The adenovirus-based platform is a viral vector type.

Modes of nutrition and digestion

Organisms obtain food in several ways. Autotrophs such as green plants synthesise their own glucose from carbon dioxide and water using light energy, a process called photosynthesis, whose overall equation is 6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2. Respiration does the opposite, breaking glucose down to release energy, so it does not produce glucose, and mineral absorption is only the uptake of inorganic ions by roots.

Heterotrophs depend on other organisms for food. Saprophytes absorb dissolved organic matter from dead and decaying material by secreting digestive enzymes onto the substrate. Many fungi such as yeast, mushroom and bread mould digest food outside the body and then absorb the soluble products, a process called extracellular digestion. By contrast, Amoeba and Paramecium ingest food into food vacuoles and digest it inside the cell, which is intracellular digestion. Parasites such as Cuscuta obtain nutrients from a host plant and are not saprophytes.

In humans, the digestive tract is a continuous canal. The small intestine is the longest part, about 6 to 7 metres in an adult, and it is the main site of nutrient absorption. Its inner mucosa bears many finger-like projections called villi, and the epithelial cells on each villus carry microvilli, which greatly increase the surface area for absorption.

Key terms:

• Saprophyte — an organism that feeds on dead organic matter. e.g. A bread mould growing on a stale loaf is a saprophyte.
• Extracellular digestion — digestion outside the cell or body. e.g. A mushroom releases enzymes onto the wood it grows on.
• Villi — finger-like projections of the small intestinal lining. e.g. Villi increase absorptive surface area in the ileum.

Plant tissues and meristems

Meristems are regions of continuous cell division in plants. Apical meristems lie at the tips of roots and shoots and lengthen the plant body. Intercalary meristems are small regions of dividing cells located between mature tissues, most commonly at the base of leaves and at the internodes. In grasses the intercalary meristem sits at the base of the leaves, which is why grass can regrow quickly after cutting or grazing.

Xylem is a complex conducting tissue. Its conducting elements, tracheids and vessels, are dead cells with lignified walls, and xylem fibres are dead sclerenchymatous cells that provide mechanical support. The only living component of xylem is xylem parenchyma, which stores food and helps in lateral conduction.

Key distinctions:

• Apical meristem — at the tips of stems and roots, increases length. e.g. The root tip is an apical meristem.
• Intercalary meristem — between mature tissues, at leaf bases and internodes. e.g. The base of a grass leaf.
• Xylem parenchyma — the living cells of xylem. e.g. Cells that store starch in the wood of a tree.

Mendelian inheritance and progeny testing

In a monohybrid cross between a pure tall pea plant (TT) and a short plant (tt), all F_1 offspring are heterozygous Tt and tall. Self-pollination of the F_1 generation gives an F_2 genotypic ratio of 1 TT : 2 Tt : 1 tt, so the phenotypic ratio is 3 tall : 1 short. The ratio of pure tall plants (TT) to short plants (tt) in F_2 is therefore 1:1.

Progeny testing is used to find out the genotype of a plant that shows a dominant trait. Since a tall plant may be TT or Tt, selfing it reveals the genotype. If the plant is heterozygous, short offspring appear in the progeny because the recessive allele is expressed when two copies are inherited. Selfing is therefore a practical test of parental origin and genotype, while cross-pollination with another plant mixes genotypes and does not directly test the plant.

Key points:

• Homozygous dominant — TT, shows dominant trait only. e.g. A TT plant gives only tall progeny when selfed.
• Heterozygous — Tt, carries a hidden recessive allele. e.g. A Tt plant gives about one short plant in four when selfed.
• Progeny testing — inferring genotype from offspring. e.g. Observing the offspring of a tall plant to decide whether it is TT or Tt.

Osmosis and diffusion

Diffusion is the net movement of particles from a region of higher concentration to a region of lower concentration, down a concentration gradient. Osmosis is a special case of diffusion in which water molecules move across a selectively permeable membrane. Osmosis is the net movement of water from a region of higher water concentration (lower solute concentration) to a region of lower water concentration (higher solute concentration), through a semi-permeable membrane that allows water but restricts solutes. A fully permeable membrane lets solutes pass as well, so no sustained osmotic gradient is maintained.

The effect of osmosis on cells depends on the external solution. In an isotonic solution, such as normal saline for human blood, the solute concentration equals that of the cell, so there is no net water movement and the red blood cells keep their normal diameter. In a hypotonic solution, water enters the cell and it swells, and it may burst, while in a hypertonic solution water leaves the cell and it shrinks.

Key terms:

• Isotonic — same solute concentration as the cell. e.g. Normal saline for blood cells.
• Hypotonic — lower solute concentration than the cell, so water enters. e.g. Pure water placed around red blood cells.
• Semi-permeable membrane — allows water but not solute molecules. e.g. A plant cell membrane.

Disease elimination certifications

Public health agencies certify that a disease has been eliminated in a country or region when local transmission has been interrupted and the conditions that would allow reintroduction are controlled. Certification is therefore a formal recognition of elimination, not merely a fall in case numbers.

In India, Goa has been recognised as the first rabies-free state, a status reached through sustained mass dog vaccination and animal birth control. Rabies is a viral zoonotic disease transmitted mainly by the bites of infected animals, especially dogs. Malaria, a protozoan disease, has been certified as eliminated in China by the World Health Organization, which recognises countries that have interrupted local transmission.

Key points:

• Elimination — reduction of a disease to zero local transmission in a defined area. e.g. Certification of a country as malaria-free.
• Eradication — permanent worldwide reduction of a pathogen to zero. e.g. Smallpox is the classic example.
• Rabies — a viral disease that is almost always fatal once symptoms appear. e.g. Dog bites are the main route of transmission to humans.

Energy flow in ecosystems

Energy enters an ecosystem as sunlight, is fixed by producers, and passes from one trophic level to the next. At each transfer only about 10 per cent of the energy is passed on, and the rest is lost mainly as heat through respiration and in unassimilated material. Because the energy available at each higher level becomes progressively smaller, the number of trophic levels in a food chain is limited, usually to four or five.