Biology: Cells, Plants and Human Body

Cell organelles and functions

Eukaryotic cells contain membrane-bound organelles, and each one has a specific job. Exam questions usually ask which organelle performs a given function, so you should learn the main role of each organelle and the features that distinguish it from others.

• Endoplasmic reticulum (ER) — a network of membranous tubules and sacs that is continuous with the outer membrane of the nuclear envelope. It forms channels that move materials through the cytoplasm and nucleus. Rough ER carries ribosomes, while smooth ER lacks them and is the main site of lipid and steroid synthesis. e.g. A cell that cannot make lipids may have a defective smooth ER, not defective ribosomes.
• Ribosomes — sites of protein synthesis. They do not transport materials.
• Golgi bodies — modify, sort and package molecules. They do not synthesise lipids themselves.
• Mitochondria — sites of aerobic respiration and ATP production. ATP is made by oxidative phosphorylation, in which the enzyme ATP synthase, embedded in the inner membrane, uses the proton gradient to form ATP. The matrix holds Krebs cycle enzymes, but ATP synthase is not located there.
• Lysosomes — contain hydrolytic enzymes such as proteases, lipases and nucleases that work best at acidic pH. They break down macromolecules and worn-out organelles.
• Plastids — double-membrane organelles of plant cells. Chloroplasts carry out photosynthesis, chromoplasts contain pigments, and leucoplasts are colourless storage plastids. Leucoplasts include amyloplasts (starch), elaioplasts (oils) and proteinoplasts (proteins).
• Vacuoles — a mature plant cell often has a large central vacuole that can occupy up to about 90% of the cell volume, and its turgor pressure gives the cell rigidity. Food vacuoles in Amoeba take part in digestion. Animal cells also contain vacuoles, although these are usually smaller and more numerous, so the claim that they are absent is false.
• Cell membrane and cell wall — every cell is bounded by a plasma membrane. Plant cells have an additional cell wall made of cellulose, fungal walls are made of chitin, and bacterial walls are made of peptidoglycan. Animal cells have no cell wall and are surrounded by an extracellular matrix of glycoproteins. Therefore the cell wall is not present in all living cells.
• Prokaryotes and eukaryotes — prokaryotes lack a membrane-bound nucleus; their DNA lies in a nucleoid region, and they have 70S ribosomes. Membrane-bound organelles such as mitochondria occur only in eukaryotic cells.
• Semi-autonomous organelles — mitochondria and chloroplasts carry their own circular DNA and 70S ribosomes, which supports the endosymbiotic theory. The ER, Golgi bodies, cytoskeleton, nucleolus and cell wall do not have their own DNA and ribosomes.
• Plasma membrane — based on the fluid mosaic model, it consists of a phospholipid bilayer, proteins and cholesterol. Cholesterol helps regulate membrane fluidity, so a description that omits any one of these three components is incomplete.

Photosynthesis and respiration

Photosynthesis and respiration are complementary processes. Photosynthesis stores light energy as chemical energy in carbohydrate, and respiration releases that energy for the cell's work.

• Photosynthesis basics — in the light reaction, water is split by photolysis at photosystem II, releasing oxygen, protons and electrons. Light drives this splitting indirectly through excitation of photosystem II and electron transport. In the Calvin cycle, carbon dioxide is reduced, not oxidised, to form carbohydrate.
• Requirements — photosynthesis needs chlorophyll to absorb light, carbon dioxide as the carbon source and water as the source of electrons and hydrogen. Oxygen is a by-product, so it is not a requirement.
• Gas linkage — oxygen released by photosynthesis is used by aerobic respiration to oxidise glucose and release energy as ATP.
• Glycolysis — takes place in the cytoplasm and splits one glucose molecule (C_6H_{12}O_6) into two pyruvate molecules (C_3H_4O_3). It gives a net gain of 2 ATP and 2 NADH. Carbon dioxide is released later, in the mitochondrial Krebs cycle, not in glycolysis.
• Fermentation — an anaerobic pathway that regenerates NAD⁺ so glycolysis can continue. In yeast, pyruvate is converted to acetaldehyde and CO_2, and acetaldehyde is reduced to ethanol. The products are ATP, CO_2 and ethanol. Lactic acid fermentation occurs in muscle cells and some bacteria instead.
• Solar energy capture — green plants absorb only about 1% of the incident solar radiation for photosynthesis, which is a small fraction of the total sunlight.
• Leaf colour — chlorophyll absorbs mainly red and blue light and reflects green light, which is why most leaves appear green.

Hormones and their functions

Hormones are chemical messengers secreted into the blood, and each hormone has a characteristic target and function. Learning the source and action of each hormone helps in answering identification questions.

• Estrogen — the principal female sex hormone, secreted mainly by the ovarian follicles. It develops the female secondary sexual characters, such as breast development, fat distribution and growth of the uterus and vagina. Prolactin, oxytocin and progesterone have different roles: prolactin supports milk production, oxytocin controls uterine contraction and milk ejection, and progesterone prepares and maintains the uterus for pregnancy.
• Oral contraceptive pills — contain synthetic estrogen and progestin. Through negative feedback they suppress FSH and LH secretion from the anterior pituitary. Without the LH surge, ovulation is inhibited, so the release of the egg does not occur. The pills do not kill sperm, eggs or the zygote.
• Adrenaline (epinephrine) — secreted by the adrenal medulla during stress or excitement. It increases heart rate and the force of cardiac contraction, which prepares the body for a fight-or-flight response. Insulin regulates blood glucose, melatonin regulates the sleep-wake cycle, and thyroxine regulates basal metabolic rate.
• Thyroxine — a thyroid hormone that contains iodine as a structural component. Iodine is needed for its synthesis, so iodized salt supplies an essential part of the diet. Iodine deficiency leads to goitre.
• Menstrual cycle control — regulated by FSH and LH from the pituitary gland, together with oestrogen and progesterone from the ovary. The prostate is a male gland and plays no role in the female cycle.

Plant tissue differentiation

Plant growth depends on meristems, which are regions of undifferentiated cells that keep dividing. Their daughter cells later become specialised, and the process by which this occurs is central to understanding plant tissues.

• Differentiation — meristematic cells acquire specific structure and function and lose the ability to divide, forming permanent tissues. Cell division only increases the number of cells and does not by itself produce specialised tissues.
• Parenchyma — a simple permanent tissue of thin-walled, living cells, often called the basic packing tissue. It fills the spaces between other tissues and is found in xylem, phloem, cortex and pith. By contrast, collenchyma gives flexible support with unevenly thickened living walls, and sclerenchyma gives rigidity through thick, lignified walls.
• Aerenchyma — in aquatic plants, large air cavities reduce the plant's density and provide buoyancy. These cavities are bounded by thin-walled parenchyma cells, which also store food and gases.
• Secondary growth — increase in girth (thickness) of the stem is produced by lateral meristems, namely the vascular cambium and the cork cambium. Apical meristems at the shoot and root tips increase length, and intercalary meristems add length at the nodes or at the base of leaves, so neither is responsible for increase in girth.

Digestive enzymes and their sources

Each digestive enzyme is secreted by a specific gland or region and acts on a specific food class under specific pH conditions. Identifying the source, substrate and optimum pH of each enzyme is the key to these questions.

• Pepsin — a protein-digesting enzyme secreted by the gastric glands of the stomach wall, mainly by the chief cells, as the inactive precursor pepsinogen. Hydrochloric acid activates it, and it breaks proteins into peptides. Chitinase digests chitin, and amylase digests starch.
• Fat digestion in the small intestine — bile salts from the liver, stored in the gall bladder, emulsify large fat globules into small droplets. Pancreatic lipase then hydrolyses the emulsified fats into fatty acids and glycerol. Bile does not digest fat by itself, and trypsin, amylase and pepsin do not act on fats.
• Pancreatic juice — the exocrine part of the pancreas secretes lipase for fats, amylase for starch and proteases such as trypsin for proteins. Bile is not made by the pancreas, surfactant is produced by the alveolar cells of the lungs, and stomach acid comes from gastric glands.
• Optimum pH — pepsin is strongly acidic in action and works best at about pH 2 in the stomach. Trypsin acts in the slightly alkaline environment of the small intestine, at about pH 8. Neither enzyme works best at neutral or strongly alkaline pH in its own region.

Sexual and asexual reproduction

Reproduction is the biological process by which organisms produce new individuals of their own kind. Asexual reproduction involves a single parent, and its offspring are genetically identical to the parent apart from rare mutations. Examples include binary fission in bacteria, budding in yeast, fragmentation, and vegetative propagation. Sexual reproduction involves the fusion of gametes from two parents. In higher organisms it depends on two linked processes. Meiosis produces haploid gametes with new combinations of genes through independent assortment of chromosomes and crossing over. Fertilization then combines gametes at random to form a zygote with a new genetic makeup.

Because every generation carries new combinations of traits, a population contains a wider range of variation. When the environment changes, some individuals are likely to survive, so sexual reproduction supports the long-term survival of a species over evolutionary time.

The chromosome number and DNA content follow a fixed cycle. Meiosis halves the chromosome number and fertilization restores it, so the chromosome number of a species stays constant across generations. The DNA content per nucleus also remains the same between parent and offspring. Halving of DNA content in flowering plants takes place during meiosis in the pollen mother cells of the anther, which produce microspores that develop into pollen grains. Mitotic growth, as in germination, fruit formation, or bud formation, does not halve the DNA.

Common confusions:

• Mitosis vs meiosis — mitosis gives genetically identical diploid cells, whereas meiosis gives haploid gametes with variation. e.g., a root-tip cell divides by mitosis, while a pollen mother cell divides by meiosis.
• Binary fission — an asexual process that produces identical cells, so it is not a source of diversity.
• Conjugation — a genetic exchange found in bacteria and ciliates, not the sexual reproduction of higher organisms.

Biotic and abiotic components of ecosystem

An ecosystem has two kinds of components. Biotic components are living organisms, including producers such as plants, consumers such as animals, and decomposers such as microbes. Abiotic components are non-living physical and chemical factors such as temperature, light, moisture, humidity, salinity, and soil type.

The biotic community consists only of living organisms. Humans are animals, protozoans are microbes, and a bush is a plant, so all of them are biotic. Water is essential for life, but it is non-living and is therefore an abiotic component, not part of the biotic community.

The kind of biotic community that develops in a place depends largely on abiotic factors. Moisture, temperature, salinity, and soil type decide which species can survive in a region. Algae are living photosynthetic organisms, so they are biotic, while temperature, humidity, and moisture are abiotic factors.

The term aquatic community refers to a biotic community living in water. The word aquatic means relating to water, so the presence of water sustains such a community.

Key terms:

• Biotic — relating to living components. e.g., a forest's trees, birds, and fungi together form its biotic part.
• Abiotic — relating to non-living components. e.g., rainfall and soil pH are abiotic factors that shape a grassland.

Parts of the flower (gynoecium)

The gynoecium, or pistil, is the female reproductive part of the flower. It consists of three regions: the stigma, the receptive tip that receives pollen; the style, the stalk that connects the stigma to the ovary; and the ovary, the swollen base that contains the ovules.

After pollen lands on the stigma, the pollen tube grows down through the style, enters the ovary, and reaches the ovule through the micropyle. The correct order of the pathway is therefore stigma, style, ovary.

A flower is unisexual when it bears either stamens or carpels but not both. Papaya produces separate male and female flowers, which may occur on different plants or, in some varieties, on the same plant. Hibiscus, mustard, and sunflower bear bisexual flowers that contain both male and female parts.

After fertilization, the ovary develops into the fruit, and each ovule develops into a seed. The fruit is therefore produced by the ovary and the seed by the ovule.

Key terms:

• Stigma — the sticky receptive surface of the pistil. e.g., pollen grains adhere to the stigma and germinate there.
• Unisexual flower — a flower with only stamens or only carpels. e.g., a male papaya flower has stamens but no functional ovary.

Osmosis and cell lysis in RBC

Osmosis is the net movement of water across a semipermeable membrane from a region of higher water concentration (lower solute concentration) to a region of lower water concentration (higher solute concentration). Water potential is often written as \psi_w = \psi_s + \psi_p, where \psi_s is the solute potential and \psi_p is the pressure potential.

A medium with a lower concentration of water has a higher concentration of solutes, so it is hypertonic to the cell. Water leaves the animal cell by osmosis, and the cell loses water. In a hypotonic medium, water enters the cell. An animal cell has no rigid cell wall, so it swells and may burst, whereas a plant cell becomes turgid.

A plant cell in a hypertonic solution loses water from its vacuole. The protoplast contracts and pulls away from the cell wall, a condition called plasmolysis.

A detergent is different from an osmotic solution. It is a surfactant that dissolves the lipids of the cell membrane, so the membrane ruptures and the cell contents are released. This breakdown is called lysis, and it happens in a detergent solution regardless of osmotic pressure. Animal cells cannot become turgid because they lack a cell wall.

Key terms:

• Hypotonic — having lower solute concentration than the cell. e.g., red blood cells placed in pure water swell and may lyse.
• Plasmolysis — shrinkage of the protoplast away from the cell wall in a hypertonic medium. e.g., a leaf peel in concentrated sugar solution shows plasmolysed cells.

Animal and plant classification groups

Animal and plant groups are defined by shared structural features. Pisces is the class of fishes. Fishes have gills, fins, and a backbone, and they live in water. The dogfish is a cartilaginous fish that belongs to this fish group. The jellyfish belongs to the phylum Cnidaria, the silverfish is a wingless insect, and the starfish belongs to the phylum Echinodermata. None of these three is a fish.

Bryophytes, such as mosses and liverworts, are called the amphibians of the plant kingdom. They grow on land but need a film of water for their male gametes to swim to the egg during fertilization. Their bodies are not differentiated into true roots, stems, and leaves, and they lack vascular tissue. By contrast, thallophytes are algae and fungi with a undifferentiated plant body called a thallus. Pteridophytes are vascular ferns, and gymnosperms are seed plants that do not form fruits.

A species is defined by strong similarity in appearance among its members together with distinctness from other groups. Both similarity within the group and difference from other groups are used to define it.

Key terms:

• Cartilaginous fish — a fish whose skeleton is made of cartilage. e.g., sharks and dogfish belong to this group.
• Thallus — a plant body that is not divided into roots, stems, and leaves. e.g., the body of a filamentous alga.

Double fertilization in angiosperms

In angiosperms, the pollen grain germinates and produces a pollen tube that carries two male gametes into the embryo sac. Double fertilization then occurs. One male gamete fuses with the egg cell to form the diploid zygote, 2n. The second male gamete fuses with the diploid secondary nucleus to form the triploid primary endosperm nucleus, 3n. Neither gamete degenerates; both take part in fertilization.

The sequence in sexual reproduction is egg, then zygote, then embryo, then seed. The zygote develops into the embryo, and the ovule develops into the seed. Within the flower, the ovary develops into the fruit, the ovule into the seed, and the zygote into the embryo.

Key terms:

• Zygote — the diploid cell formed when a male gamete fuses with the egg. e.g., the first cell of the embryo in a maize grain.
• Primary endosperm nucleus — the triploid nucleus that gives rise to the food-storing endosperm.

Prokaryotic cell structure and DNA

Prokaryotes, such as bacteria, lack a membrane-bound nucleus. Their genetic material lies in an irregular region called the nucleoid. Most prokaryotes have a single circular, double-stranded DNA chromosome. Small extra DNA molecules called plasmids are not counted as chromosomes.

Bacterial DNA is described as naked because it is not associated with histone proteins. In eukaryotes, DNA is wrapped around histones to form nucleosomes. The bacterial chromosome is instead compacted by supercoiling and nucleoid-associated proteins.

In eukaryotes, DNA replication takes place during the S phase, when chromatin is decondensed and the DNA is accessible. Chromatin condenses into visible rod-shaped chromosomes during prophase, before division. Prokaryotes divide by binary fission, which is a different process from the mitosis or meiosis of eukaryotes. Therefore the processes of cell division are not the same in the two groups.

Key terms:

• Nucleoid — the region of the bacterial cell where the chromosome is located. e.g., an E. coli cell has its circular chromosome in the nucleoid.
• Naked DNA — DNA not complexed with histones. e.g., bacterial DNA is naked, while human DNA is packed into nucleosomes.

Animal epithelial tissues

Epithelial tissue covers body surfaces and lines internal cavities. Squamous epithelium consists of thin, flat cells that protect surfaces against abrasion or allow passage of substances. Stratified squamous epithelium forms the inner lining of the oesophagus, where it resists the friction of passing food.

Other epithelia are specialized for different roles. Simple columnar epithelium with microvilli lines the small intestine for absorption. Cuboidal epithelium forms the kidney tubules and many gland ducts, and the ducts of salivary glands are lined by cuboidal or columnar cells.

The cornea is the transparent outer covering at the front of the eye. Its outer surface is covered by stratified squamous epithelium, and its inner part consists of collagen fibres and cells, which are proteins arranged in a regular pattern. The cornea contains no blood vessels and gets its oxygen from the air and tears. By contrast, the retina is the light-sensitive layer, and the iris is the muscular diaphragm that controls the pupil.