Essential Concepts in Chemistry and Biology

Posted on Jun 24, 2025 in Human Biology

Thermodynamics Fundamentals

The first law of thermodynamics establishes the notion of internal energy for a thermodynamic system. All energy transfers must be accounted for to ensure strict conservation of the total energy of a thermodynamic system and its surroundings. This law states that energy can be neither created nor destroyed; however, energy can change forms and flow from one place to another. The total energy of an isolated system remains constant.

The second law of thermodynamics states that the entropy of the universe always increases in the course of every spontaneous (natural) change. In other words, over time, differences in temperature, pressure, and density tend to even out.

Key Thermodynamic Terms

  • Enthalpy: The energy content of a process (chemical, thermodynamic, mechanical, etc.) that can be recovered. It is also described as useful energy.
  • Entropy: The energy content of a process (chemical, thermodynamic, mechanical, etc.) that cannot be recovered. It is also described as chaos or disorder.

Atomic Structure and Radioisotopes

An atom is defined by its atomic number (also known as the proton number), which is the number of protons found in the nucleus. This number is identical to the charge number of the nucleus and is conventionally represented by the symbol Z.

A radioisotope is a version of a chemical element that has an unstable nucleus and emits radiation during its decay to a stable form.

Chemical Bonds Explained

Bonds hold atoms and molecules of substances together, determining their structure and properties.

Ionic Bonds

Ionic bonds form when two atoms have a large difference in electronegativity. Electronegativity is the quantitative representation of an atom’s ability to attract an electron to itself. It depends on an element’s tendency to form negative ions in a molecule. Conversely, if an element forms positive ions in a molecule, it is electropositive.

Covalent Bonds

Covalent bonds form when two atoms have a very small (nearly insignificant) difference in electronegativity. There is usually a direct correlation between positive and negative ions, meaning that because they share electrons, the atoms balance. Covalent bonds are typically strong due to this direct sharing.

Polar Covalent Bonds

Polar covalent bonds fall between ionic and covalent bonds. They induce dipole-dipole interactions, where one atom becomes slightly negative and the other slightly positive. This slight change in charge is not large enough to classify it entirely as an ion; they are simply considered slightly positive or slightly negative. Polar covalent bonds often indicate polar molecules, which are likely to bond with other polar molecules but are unlikely to bond with non-polar molecules.

Hydrogen Bonds

Hydrogen bonds only form between hydrogen and oxygen (O), nitrogen (N), or fluorine (F). These bonds are very specific and lead to certain molecules having special properties. Hydrogen bonding sometimes results in the non-hydrogen element (oxygen, for example) having a lone pair of electrons on the atom, making it polar. Lone pairs of electrons are non-bonding electrons that sit in twos (pairs) on the central atom of the compound. Water, for example, exhibits hydrogen bonding and polarity as a result of its bonding.

Understanding Chemical Mixtures

A mixture combines two or more substances that are not chemically bonded.

Solutions

A solution is a homogeneous mixture of one substance dissolved in another, so the properties are uniform throughout. A solution is composed of a solute (the substance being dissolved) and a solvent (the part of the solution that does the dissolving). The solute is of molecular size.

Colloids

A colloid is a type of mixture intermediate between a homogeneous mixture (also called a solution) and a heterogeneous mixture, with properties also intermediate between the two. The particles in a colloid can be solid, liquid, or gas bubbles. The medium they are suspended in can also be a solid, liquid, or gas. Colloids may be colored or translucent because of the Tyndall effect, which is the scattering of light by particles in the colloid. Colloid particles may be seen in a beam of light, such as dust in air in a “shaft” of sunlight. Emulsions are an example of colloids composed of tiny particles suspended in another immiscible (unmixable) material. An emulsion is a suspension of two liquids that usually do not mix together; these liquids are said to be immiscible.

Suspensions

A suspension is a mixture between two substances, one of which is finely divided and dispersed in the other. Common suspensions include sand in water, dust in air, and droplets of oil in air. Particles in a suspension are larger than those in a solution; they are visible under a microscope and can often be seen with the naked eye. Particles in a suspension will settle out if the suspension is allowed to stand undisturbed. Many particles of a suspension can be separated through a filter.

Redox Reactions: Electron Transfer

Redox (reduction-oxidation) reactions include all chemical reactions in which atoms have their oxidation state changed. This means redox reactions involve the transfer of electrons between species.

  • Oxidation: The loss of electrons or an increase in oxidation state by a molecule, atom, or ion.
  • Reduction: The gain of electrons or a decrease in oxidation state by a molecule, atom, or ion.

An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It acts as an oxidizing agent that, by virtue of accepting electrons, is itself reduced in the process. An electron donor is a chemical entity that donates electrons to another compound. It acts as a reducing agent that, by virtue of donating electrons, is itself oxidized in the process.

Thermodynamic Reactions

An exergonic process is one in which there is a positive flow of energy from the system to the surroundings. This is in contrast with an endergonic process (also called a nonspontaneous reaction or an unfavorable reaction), which is a chemical reaction in which the standard change in free energy is positive, and energy is absorbed. In layman’s terms, the total amount of energy is a loss (it takes more energy to start the reaction than what you get out of it), so the total energy is a negative net result.

Properties and Roles of Water

Water’s Unique Properties

  • Cohesion (Surface Tension): Water is attracted to water.
  • Adhesion: Water is attracted to other substances.

Adhesion and cohesion are water properties that affect every water molecule on Earth and also the interaction of water molecules with molecules of other substances. Essentially, cohesion and adhesion are the “stickiness” that water molecules have for each other and for other substances.

Water is called the universal solvent because more substances dissolve in water than in any other chemical. This has to do with the polarity of each water molecule.

Chemical Reactions Involving Water

  • Dehydration: When two molecules come together to produce water (by bonding OH and H to form H2O).
  • Hydrolysis: The reverse of dehydration, breaking H2O into H and OH, thereby breaking a bond.

Electrolysis of Water

Electrolysis of water is the decomposition of water (H2O) into oxygen (O2) and hydrogen gas (H2) due to an electric current being passed through the water.

Biological Roles of Water

  • Membrane Potential Changes:
    • -75 mV: Polarization
    • -75 mV going to +50 mV: Depolarization
    • +50 mV going to -75 mV: Repolarization
    • -75 mV going to -90 mV: Hyperpolarization
  • Thermoregulation (Thermostat Effect): The high heat of vaporization of water means it takes a lot of heat to vaporize sweat on the body’s surface. The essence of sweating is to cool the body, so it is necessary to extract a great amount of heat to cool a unit volume of water. If the heat of vaporization were low, only a little heat would vaporize the water, requiring more sweating to cool the body. A high heat of vaporization is a guard against dehydration through excessive sweating and ensures enough heat is removed to achieve the body’s thermo-homeostatic effect without sacrificing too much body fluid.
  • Lubrication: Water is used as a lubricant in the human body during digestion. The water in saliva lubricates food, easing its passage to the lower digestive tract. Additionally, water around body parts such as eyeballs, muscles, and joints ensures friction-less movement. Examples include synovial fluid and cushioning between the meninges as cerebrospinal fluid (CSF).
  • pH Homeostasis and Buffering: Water provides an environment for chemical reactions and is needed in many, like hydrolysis for food molecule breakdown. Water also helps regulate heat buildup in cells during chemical reactions; a dehydrated cell experiences increased temperature. Acids produce protons (H+ ions), while bases accept protons or generate OH–. Alternatively, acids may be viewed as electron pair acceptors and bases as electron pair donors. Buffering capacity refers to water’s ability to keep pH stable as acids or bases are added. pH and buffering capacity are intertwined; adding equal volumes of an acid and neutral water rarely results in a pH halfway between. If water has sufficient buffering capacity, it can absorb and neutralize added acid without significantly changing the pH. Conceptually, a buffer acts somewhat like a large sponge: as more acid is added, the “sponge” absorbs it without much pH change. The “sponge’s” capacity is limited; once buffering capacity is used up, pH changes more rapidly as acids are added.

Organic Macromolecules

Carbohydrates

Polysaccharides are long carbohydrate molecules made of monosaccharide units joined by glycosidic bonds. They range in structure from linear to highly branched and are often heterogeneous, with slight modifications of the repeating unit. Depending on their structure, these macromolecules can have distinct properties from their monosaccharide building blocks; they may be amorphous or even insoluble in water.

  • Glycogen: A multibranched polysaccharide that serves as a form of energy storage in animals and fungi. In humans, glycogen is made and stored primarily in liver and muscle cells, functioning as the secondary long-term energy storage (with primary energy stores being fats in adipose tissue).
  • Starch (Amylum): A carbohydrate consisting of a large number of glucose units joined by glycosidic bonds. This polysaccharide is produced by most green plants as an energy store. However, in the Asteraceae family, starch is replaced by the fructan inulin. It is the most common carbohydrate in the human diet and is found in large amounts in staple foods such as potatoes, wheat, maize (corn), rice, and cassava.

Lipids

Lipids are a group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, and phospholipids, among others. The main biological functions of lipids include storing energy, signaling, and acting as structural components of cell membranes.

Types of Lipids and Related Compounds

  • Triglycerides:
    • Saturated compounds are “saturated” with hydrogen—all available places where hydrogen atoms could be bonded to carbon atoms are occupied.
    • Unsaturated compounds have double bonds (C=C) between carbon atoms, reducing the number of places where hydrogen atoms can bond to carbon atoms.
    • Unsaturated fats have a lower melting point and are more likely to be liquid.
    • Saturated fats have a higher melting point and are more likely to be solid at room temperature.
    • Trans fat: An unsaturated fat with trans-isomer fatty acid(s). Because the term describes the configuration of a double carbon–carbon bond, trans fats are sometimes monounsaturated or polyunsaturated, but never saturated. Trans fats occur during the processing of polyunsaturated fatty acids in food production. In the vegetable and animal kingdoms, fatty acids generally have cis (as opposed to trans) unsaturation.
  • Phospholipids: A class of lipids that are a major component of all cell membranes as they can form lipid bilayers. The ‘head’ is hydrophilic (attracted to water), while the hydrophobic ‘tails’ are repelled by water and are forced to aggregate. The hydrophilic head contains the negatively charged phosphate group and glycerol. The hydrophobic tail usually consists of two long fatty acid hydrocarbon chains.
  • Steroids: A type of organic compound that contains a characteristic arrangement of four cycloalkane rings joined to each other. Examples include the dietary fat cholesterol, the sex hormones estradiol and testosterone, and the anti-inflammatory drug dexamethasone. Cholesterol is required to build and maintain membranes; it modulates membrane fluidity over the range of physiological temperatures. The hydroxyl group on cholesterol interacts with the polar head groups of membrane phospholipids and sphingolipids, while the bulky steroid and hydrocarbon chain are embedded in the membrane, alongside the nonpolar fatty-acid chain of other lipids. Through interaction with phospholipid fatty-acid chains, cholesterol increases membrane packing, which reduces membrane fluidity.
  • Vitamin D: A group of fat-soluble secosteroids responsible for enhancing intestinal absorption of calcium and phosphate. In humans, the most important compounds are vitamin D3 (cholecalciferol) and vitamin D2 (ergocalciferol). Both can be ingested from diet and supplements. The body can also synthesize vitamin D (specifically cholecalciferol) in the skin from cholesterol when sun exposure is adequate (hence its nickname, the “sunshine vitamin”).
  • Cortisol (Hydrocortisone): A steroid hormone, specifically a glucocorticoid, produced by the zona fasciculata of the adrenal cortex. It is released in response to stress and low blood glucocorticoid levels. Its primary functions include increasing blood sugar through gluconeogenesis, suppressing the immune system, and aiding in fat, protein, and carbohydrate metabolism. It also decreases bone formation. Various synthetic forms of cortisol are used to treat a variety of diseases.
  • Bile (Gall): A bitter-tasting, dark green to yellowish-brown fluid produced by the liver of most vertebrates that aids the digestion of lipids in the small intestine. In many species, bile is stored in the gallbladder and discharged into the duodenum when the organism eats. Bile is 85% water, 10% bile salts, 3% mucus and pigments, 1% fats, and 0.7% inorganic salts.
  • Eicosanoids (Icosanoids): Signaling molecules made by oxidation of 20-carbon fatty acids. They exert complex control over many bodily systems, mainly in inflammation or immunity, and as messengers in the central nervous system.
    • Prostaglandins: A group of lipid compounds derived enzymatically from fatty acids.
    • Leukotrienes: A family of eicosanoid inflammatory mediators produced in leukocytes by the oxidation of arachidonic acid by the enzyme arachidonate 5-lipoxygenase.
    • Thromboxane: A member of the eicosanoid family of lipids. The two major thromboxanes are thromboxane A2 and thromboxane B2. The distinguishing feature of thromboxanes is a 6-membered ether-containing ring.
  • Lipoproteins: Biochemical assemblies containing both proteins and lipids, bound to the proteins, which allow fats to move through the water inside and outside cells. The proteins emulsify the lipid molecules.
    • Low-density lipoprotein (LDL): One of the five major groups of lipoproteins that enable transport of multiple different fat molecules, as well as cholesterol, within the water around cells and within the water-based bloodstream.
    • High-density lipoprotein (HDL): One of the five major groups of lipoproteins that enable the transportation of lipids (fats), such as cholesterol and triglycerides, within the water around cells, including the bloodstream.

Vitamins

Vitamins are essential micronutrients your body needs in small amounts for various roles throughout the human body. The fat-soluble vitamins (A, D, E, and K) are stored in the body for long periods and generally pose a greater risk for toxicity when consumed in excess than water-soluble vitamins.

Proteins

The covalent bond between two amino acids is called a peptide bond. When three or more amino acids are linked by peptide bonds, the resulting chain is called a polypeptide. The atoms associated with the peptide bond share electrons unevenly because oxygen attracts electrons more than nitrogen.

Protein Structure Levels

The structure of a protein has at least three levels of organization and can have four levels:

  1. Primary Structure: The linear sequence of amino acids joined by peptide bonds. Each particular polypeptide has its own unique sequence of amino acids.
  2. Secondary Structure: Occurs when the polypeptide takes on a certain orientation in space. Once amino acids are assembled into a polypeptide, the resulting C=O section between amino acids in the chain is polar, having a partially negative charge. Hydrogen bonding is possible between the C=O of one amino acid and the N—H of another amino acid in a polypeptide. Coiling of the chain results in an α (alpha) helix, or a right-handed spiral, and a folding of the chain results in a pleated sheet. Hydrogen bonding between peptide bonds holds the shape in place.
  3. Tertiary Structure: The protein’s final, three-dimensional shape. In enzymes, the polypeptide bends and twists in different ways. In most enzymes, the hydrophobic portions are packed on the inside and the hydrophilic portions are on the outside where they can make contact with water. The tertiary structure of enzymes determines what types of molecules they will interact with. The tertiary shape of a polypeptide is maintained by various types of bonding between the R groups, including covalent, ionic, and hydrogen bonding.
  4. Quaternary Structure: Some proteins have only one polypeptide, while others have more than one, each with its own primary, secondary, and tertiary structures. These separate polypeptides are arranged to give these proteins a fourth level of structure. Hemoglobin is a complex protein with a quaternary structure; many enzymes also have a quaternary structure. Each of the four polypeptides in hemoglobin is tightly associated with a nonprotein heme group, which contains an iron (Fe) atom that binds to oxygen, allowing hemoglobin to transport O2 to tissues.

Protein Functions

  • Support or Structural: Some proteins are structural proteins. Keratin, for example, makes up hair and nails. Collagen lends support to ligaments, tendons, and skin.
    • White collagen fibers contain collagen, a protein that gives them flexibility and strength.
    • Reticular fibers are very thin collagen fibers, highly branched proteins that form delicate supporting networks.
    • Yellow elastic fibers contain elastin, a protein that is not as strong as collagen but is more elastic.
    • Dystrophin is responsible for holding muscle fibers together. Defects in this protein are a leading cause of muscular dystrophy, a disease characterized by the wasting away of muscle tissue.
  • Enzymes: Enzymes bring reactants together and thereby speed chemical reactions in cells. They are specific for one particular type of reaction and typically function at body temperature.
  • Motion: The contractile proteins actin and myosin allow parts of cells to move and cause muscles to contract. Muscle contraction facilitates the movement of animals from place to place.

Examples of protein roles in the body include muscle cells containing actin and myosin, red blood cells containing hemoglobin, and support tissues containing collagen.

Protein Denaturation

When proteins are exposed to extremes in heat and pH, they undergo an irreversible change in shape called denaturation. For example, the addition of vinegar (an acid) to milk causes curdling. Similarly, heating causes coagulation of egg whites, which contain a protein called albumin. Denaturation occurs because the normal bonding between the R groups has been disturbed. Once a protein loses its normal shape, it is no longer able to perform its usual function. Researchers recognize a change in protein shape is responsible for both Alzheimer’s disease and other neurodegenerative conditions.

Enzyme Inhibition

  • Non-competitive inhibition: A type of enzyme inhibition where the inhibitor reduces the activity of the enzyme and binds equally well to the enzyme whether or not it has already bound the substrate.
  • Isosteric: Having the same number of valence electrons in the same configuration but differing in the kinds and numbers of atoms.
  • Allosteric: Of or involving a change in the shape and activity of an enzyme that results from molecular binding with a regulatory substance at a site other than the enzymatically active one.

Membrane Transport Proteins

The permeases are membrane transport proteins, a class of multipass transmembrane proteins that facilitate the diffusion of a specific molecule in or out of the cell by passive transport. In contrast, active transporters couple molecule transmembrane transport with an energy source such as ATP or a favorable ion gradient.

Blood Plasma Components

  • Plasma:
    • 91% of blood plasma is water.
    • Plasma proteins (albumins, globulins, and fibrinogen) are mostly produced by the liver.
    • Plasma proteins maintain osmotic pressure and help regulate pH. Albumins transport other molecules, globulins function in immunity, and prothrombin and fibrinogen enable blood clotting.