Comprehensive Biology Review: From Molecular Basics to Systems Physiology

Structural Sequence of the Human Body

The organizational hierarchy of the human body follows a specific structural sequence from the smallest units of matter to the entire organism. The human body is composed of a group of systems. Each system consists of a group of organs. Each organ consists of a group of tissues. Each tissue consists of a group of cells. Each cell consists of a group of organelles. Each organelle consists of a group of molecules. Each molecule consists of a group of atoms.

Molecular Composition of Living Organisms

Cells of living organisms are composed of two primary types of molecules: organic and inorganic. Organic molecules are large-sized molecules that contain mainly carbon ($C$) and hydrogen ($H$) atoms. Examples include carbohydrates, lipids, nucleic acids, and proteins. Inorganic molecules are molecules that often do not contain a carbon ($C$) atom. Examples include water ($H_2O$) and mineral salts such as sodium chloride ($NaCl$).

Polymers are biological macromolecules formed by the combination of small-sized molecules called monomers. This occurs through a process called polymerization. Polymerization is defined as the process by which monomers are combined together to form a polymer. Major biological polymers include carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

Carbohydrates are biological macromolecules (polymers) made up of smaller molecules (monomers) called monosaccharides. This group includes sugars, starches, and fibers. Carbohydrates are classified into two main categories: simple sugars and complex sugars.

Simple sugars consist of monosaccharides and disaccharides. Monosaccharides include glucose, fructose, galactose, and ribose. Disaccharides, which are formed by the union of two monosaccharides, include lactose, maltose, and sucrose. Complex sugars, also known as polysaccharides, include starch, cellulose, and glycogen.

Lipids

Lipids are biological macromolecules (polymers) made up of smaller molecules (monomers) called fatty acids. They consist of a heterogeneous group of compounds. Lipids are classified into three types: simple lipids, complex lipids, and derivative lipids.

Simple lipids include oils, fats, and waxes. Complex lipids include phospholipids, which are major components of cell membranes. Derivative lipids are produced through the hydrolysis of simple and complex lipids and include cholesterol and certain hormones.

Proteins

Proteins are biological macromolecules (polymers) made up of many smaller molecules (monomers) called amino acids. Chemically, they consist of carbon ($C$), hydrogen ($H$), oxygen ($O$), and nitrogen ($N$) atoms.

An amino acid is the structural unit of protein. It consists of a central carbon atom attached to a hydrogen atom, two functional groups—a basic amino group ($NH_2$) and an acidic carboxyl group ($COOH$)—and a terminal alkyl group ($R$). The alkyl group ($R$) differs from one amino acid to another and therefore determines the specific type of amino acid.

Proteins are formed from repeated units of amino acids linked together by peptide bonds. A peptide bond originates between the carboxyl group ($COOH$) of one amino acid and the amino group ($NH_2$) of another amino acid. This formation involves the removal of a water molecule ($H_2O$), specifically the $OH^{-}$ group from the carboxyl group and the $H^{+}$ ion from the amino group.

Proteins are classified based on the substances involved in their structure into simple proteins and conjugated proteins. Simple proteins consist only of amino acids; an example is albumin ($C, H, O, N$). Conjugated proteins consist of amino acids linked with other elements. Examples include chromatin ($C, H, O, N, P$), casein ($C, H, O, N, P$), thyroxine ($C, H, O, N, I$), and hemoglobin ($C, H, O, N, Fe$).

Nucleic Acids

Nucleic acids are biological macromolecules (polymers) made up of many smaller molecules (monomers) called nucleotides. They consist of carbon ($C$), hydrogen ($H$), oxygen ($O$), nitrogen ($N$), and phosphorus ($P$) atoms. The nucleotide is the basic building unit and consists of three components.

The first component is a pentose sugar containing five carbon atoms. There are two types: deoxyribose sugar, found in DNA, and ribose sugar, found in RNA. The second component is a phosphate group ($PO_4$) which attaches to the carbon atom number $5$ ($C_5$) of the sugar molecule via a covalent bond. The third component is a nitrogenous base which attaches to the carbon atom number $1$ ($C_1$) of the sugar molecule via a covalent bond.

There are five nitrogenous bases: Adenine ($A$), Guanine ($G$), Cytosine ($C$), Thymine ($T$), and Uracil ($U$). DNA (deoxyribonucleic acid) contains Deoxyribose sugar, the bases $A, G, T, C$, consists of two strands, and is located inside the nucleus as part of the chromosome structure. RNA (ribonucleic acid) contains Ribose sugar, the bases $A, G, U, C$, consists of a single strand, and is transcribed from DNA in the nucleus before transferring to the cytoplasm.

Metabolism

Metabolism is the total of chemical reactions occurring within a living organism. It is divided into catabolism and anabolism. Catabolism is the process of breaking down chemical bonds between atoms of macromolecules to extract the stored chemical energy. An example is the release of energy from glucose oxidation during cellular respiration.

Anabolism is the process of using simple molecules to build up more complex substances through chains of reactions that consume energy. Examples include the synthesis of protein from amino acids and the synthesis of lipids from fatty acids.

Classification of Living Organisms

Living organisms are divided into unicellular and multicellular organisms. Unicellular organisms consist of only one cell that performs all vital activities needed for life; examples include Amoeba, Paramecium, and Bacteria. Multicellular organisms consist of many cells that differentiate and specialize in their functions; examples include humans, whales, and trees.

Cell Structure and Organelles

The cell is composed of the protoplasm (nucleus and cytoplasm) surrounded by the cell wall and cell membrane. The cell wall surrounds the cells of plants, algae, fungi, and some bacteria but is absent in animal cells. It is composed of cellulose fibers and functions to support, protect, and give the cell its shape. It is pitted to allow the passage of water and dissolved substances.

The cell membrane (plasma membrane) surrounds the cytoplasm of both plant and animal cells. It is a thin membrane composed of two layers of fluid phospholipid molecules, protein molecules, and cholesterol molecules. It prevents the protoplasm from spreading outside and organizes the passage of substances to and from the cell.

The cytoplasm is a semi-liquid substance composed mainly of water, organic substances, and inorganic substances, filling the space between the cell membrane and the nucleus. Within the cytoplasm are various organelles.

Ribosomes are responsible for synthesizing protein. The centrosome, located in animal cells (except nerve cells) but absent in plants and algae, plays a vital role in cell division by extending spindle filaments that withdraw chromosomes to the poles. Lysosomes are small vesicles formed by Golgi bodies containing digestive enzymes. They get rid of worn-out organelles and digest large nutrient molecules. White blood cells use lysosomal enzymes to destroy pathogens.

Mitochondria are the main storehouse for respiratory enzymes and energy production. They oxidize nutrients (especially glucose) to release energy, which is stored in ATP (Adenosine Triphosphate) molecules. Vacuoles are membranous sacs used for storing water, nutrients, and wastes. In animal cells, they are small and numerous, while in plant cells, they are gathered into one or more large vacuoles.

Plant Tissues

Plant tissues are classified into simple and compound tissues. Simple tissues include parenchyma, collenchyma, and sclerenchyma. Parenchyma is a living tissue with oval or rounded cells and intercellular spaces for aeration; it contains plastids, stores nutrients like starch, and performs photosynthesis. Collenchyma is a living tissue with rectangular cells thickened by cellulose to provide support and elasticity. Sclerenchyma is a non-living tissue thickened by lignin and cellulose to provide hardness and elasticity.

Compound tissues include xylem and phloem. Xylem consists of vessels, tracheids, and parenchyma cells. Vessels are long tubes where protoplasm and transverse walls have disappeared and internal walls are lignified to transport water and salts. Tracheids are single lignified cells without protoplasm. Phloem consists of sieve tubes and companion cells. Sieve tubes lack nuclei and have perforated sieve plates to allow cytoplasmic threads to pass. Companion cells provide the energy needed for the phloem to transport produced nutrients from leaves to other plant parts.

Animal Tissues

Epithelial tissues cover the outer surface or line internal cavities. Simple epithelial tissues consist of one layer and include squamous (lining blood capillaries and lung alveoli), cuboidal (lining kidney tubules), and columnar (lining the stomach and intestine). Stratified squamous epithelial tissue consists of several layers, such as the skin epidermis.

Muscular tissues consist of muscle fibers capable of contraction and relaxation. Skeletal muscles are striated and voluntary, connected to the skeleton. Cardiac muscles are striated and involuntary, found in the heart wall. Smooth muscles are unstriated and involuntary, located in the digestive canal and blood vessels.

Connective tissues consist of distant cells immersed in an interstitial substance. Connective tissue proper is the most widespread, connecting different body tissues (found in skin dermis and mesentery). Skeletal connective tissue has a solid interstitial substance for support (bones and cartilages). Vascular connective tissue has a fluid interstitial substance to transport food, gases, and waste (blood and lymph).

Nervous tissues consist of neurons that regulate body activities by receiving sensory stimuli and conducting them to the brain and spinal cord, then transmitting motor impulses to effector organs like muscles or glands.

Genetics and Cell Types

A karyotype is the arrangement of chromosomes descendingly according to size and then numerated. In humans, the $23^{rd}$ pair determines sex: $XX$ for females and $XY$ for males. Cells are divided into somatic cells and sex cells (gametes). Somatic cells are diploid ($2n$) and contain two sets of homologous chromosomes. Sex cells are haploid ($n$) and contain one set (half the number) of chromosomes.

Plant Physiology and Nutrition

Nutrition is either autotrophic (producing food internally through chemical reactions) or heterotrophic (obtaining food from other organisms). Molecular movement in plants occurs through various phenomena. Diffusion is the movement of molecules or ions from a high-concentration medium to a low-concentration medium. Osmosis is the passage of water from a high-water concentration (low salt) to a low-water concentration (high salt) through a semi-permeable membrane.

Permeability varies by structure. Cellulose walls are permeable to water and salts. Walls covered by lignin, cutin, or suberin are impermeable. The plasma membrane is semi-permeable (selective permeability), allowing water, controlling salts, and preventing large molecules like sugars and amino acids. Imbibition is the ability of cell walls (especially colloidal particles) to absorb water, swell, and increase in volume.

Digestion and Enzymes

Digestion is the conversion of polymers into monomers by hydrolysis, catalyzed by enzymes. For example, proteins are digested into amino acids, carbohydrates into monosaccharides (glucose), and fats into fatty acids and glycerol. These monomers can then diffuse through cell membranes.

Digestive juices include saliva (containing mucus and amylase/ptyalin), gastric juice (water, $HCl$, and pepsinogen), bile juice (secreted by the liver, devoid of enzymes), pancreatic juice (sodium bicarbonate, amylase, trypsinogen, and lipase), and intestinal juice (peptidases, maltase, sucrase, lactase, and enterokinase). Absorption follows digestion, where nutrients transfer to blood or lymph through villi in the ileum of the small intestine.

Circulatory System Components

Blood vessels include arteries (carrying blood from the heart), veins (carrying blood to the heart), arterioles, venules, and capillaries. Blood consists of four components: plasma, red blood cells (RBCs), white blood cells (WBCs), and platelets.

RBCs are enucleated, biconcave, living about $120$ days, and transport $O_2$ and $CO_2$. An adult male has $4$ to $5$ million cells, and a female has $4$ to $4.5$ million cells. WBCs are nucleated, have no specific shape, live $13$ to $20$ days, and protect the body by attacking microbes and producing antibodies (standard count is $7,000$ cells). Platelets are non-cellular particles living about $10$ days that play a role in blood clotting (standard count is $250,000$).

Respiration and ATP

Gas exchange is the physical process of obtaining oxygen and releasing carbon dioxide. Cellular respiration is the vital process where cells extract energy from food molecules (like glucose) and store it as ATP. Aerobic respiration requires oxygen, occurs in the cytoplasm and mitochondria, and produces $38$ ATP. Anaerobic respiration occurs without oxygen in the cytoplasm and produces only $2$ ATP.

An ATP molecule is built of three subunits: a nitrogenous base (Adenine), a pentose sugar (Ribose), and three phosphate groups. ATP is the universal energy currency; it is easily transferred and releases energy when it changes into ADP (adenosine diphosphate).

Plant Tropism

Tropism is the growth response of a plant toward or away from a stimulus. Auxins (plant hormones) mediate these responses. In the stem, light causes auxins to accumulate on the dark side, stimulating elongation and causing curvature toward the light (positive phototropism). Gravity causes auxins to accumulate on the lower side of a horizontal stem, stimulating elongation and causing upward curvature (negative geotropism).

In the root, light causes auxins to accumulate on the dark side, which inhibits elongation on that side, leading to curvature away from the light (negative phototropism). Gravity causes auxins to accumulate on the lower side of a horizontal root, inhibiting growth there and causing downward curvature (positive geotropism). Roots also show positive hydrotropism, curving toward water.

Nervous System Function

Nerve cells (neurons) are classified into three types. Sensory neurons transmit impulses from receptors to the central nervous system (CNS). Motor neurons transmit impulses from the CNS to effectors (muscles/glands). Connector (intermediate) neurons link the two. A nerve impulse is the message transmitted from sense organs to the brain/spinal cord and then to effectors. Synapses can occur between nerve cells, between a nerve and a gland, or between a nerve and a muscle cell.

Questions & Discussion

What are the types of synapse? Synapses can occur between a nerve cell and another nerve cell, between a nerve cell and a glandular cell, or between a nerve cell and a muscular cell.

What is the difference between simple and conjugated proteins? Simple proteins like albumin consist only of amino acids and the elements $C, H, O, N$. Conjugated proteins involve amino acids linked with other elements, such as Iodine in Thyroxine or Iron in Hemoglobin.

What is the function of the cell wall? The cell wall supports and protects the cell, gives it a characteristic shape, and allows for the easy passage of water and dissolved substances because it is pitted.