Notes: Basic Chemistry in Biology | BIO 101 Thomas University
Atomic Structure and Electron Configuration
Life is composed of matter; periodic trends and basic chemistry principles underpin biology.
The most common elements in living organisms are oxygen (O), Nitrogen (N), Hydrogen (H), and Carbon (C).
Nucleus: the atom's center, containing protons and neutrons; a dense region.
Outer region: electrons orbit the nucleus.
Subatomic particles: Protons (p), Neutrons (n), Electrons (e).
Bohr model (early model): protons are in the nucleus and electrons orbit in circular paths at specific distances from the nucleus.
Orbits are called electron shells or energy shells.
Electron occupancy: electrons normally exist in the lowest available energy shell; fill orbitals closest to the nucleus first, then farther away (1n, 2n, 3n, etc.).
The 2n and 3n shells hold 8 electrons.
Valence shell: the most stable configuration occurs when a shell is filled.
Group 18 (noble gases) have full electron shells.
Isotopes, Radioisotopes, and Radiometric Dating
Isotopes are atoms with the same number of protons but different numbers of neutrons.
Radioisotopes emit neutrons (N), protons (P), and electrons (E).
Radiometric dating takes advantage of this natural phenomenon; carbon-14 is a widely used example for dating.
This dating method allows estimation of the ages of archaeological and geological samples.
Chemical Reactions
Chemical reactions (Rx) are changes in the distribution of energy between atoms or changes in electron arrangements.
Reactants: substances at the start of a reaction.
Products: substances at the end of a reaction.
Catalase can be shown at the arrow of a reaction as an example of an enzyme-catalyzed process.
Reversible reactions: can proceed in both forward and reverse directions.
Irreversible reactions: proceed predominantly in one direction.
Chemical Bonds and Molecular Structure
Chemical bonds are attractive forces that link atoms together to form molecules.
Covalent bonds: electrons are shared between atoms; two or more atoms bond to form a molecule.
Example: H and O share electrons to form H2O; water is formed by covalent bonds.
Polar vs Nonpolar covalent bonds:
Nonpolar covalent: electrons shared EQUALLY between atoms (e.g., CH4).
Polar covalent: electrons shared UNEQUALLY, with one nucleus attracting electrons more strongly (e.g., water, H2O).
Water is polar and typically adopts a bent geometry; O is more electronegative and becomes partially negative, while H is partially positive.
Ionic bonds: metals lose electrons and nonmetals gain electrons to achieve an octet;it involves the transfer of electrons.
Hydrogen bonds: attractive interactions between a hydrogen atom bound to a highly electronegative atom (partial positive) and the lone pair on another electronegative atom (partial negative); common between water molecules.
Bond strength hierarchy: Covalent bonds are strongest, followed by ionic bonds, then hydrogen bonds (which form transiently).
Water as a central biological solvent:
Water makes up about 60-70% of the human body.
Water is a polar molecule and forms hydrogen bonds.
Water is the universal solvent.
Water-related properties:
Cohesion: water molecules stick to one another.
Adhesion: water interacts with surfaces and proteins.
High surface tension.
High heat capacity: helps stabilize large bodies of water and contributes to homeostasis in organisms.
Bodies of water tend to freeze from the top down.
Water and Hydrogen Bonding
Hydrogen bonds become relatively static when water is in a solid form (ice) and arrange into a lattice-like structure.
Ice is less dense than liquid water due to the open lattice, so ice floats.
Water’s polarity and hydrogen bonding underlie many of its life-supporting properties: solvating capability, heat capacity, and chemical reactivity.
Solutions, pH, and Buffers
A solution is a solute dissolved in a solvent; aqueous solutions are dissolved in water.
pH of blood: typically between 7.35 and 7.45.
pH indicates the acidity or alkalinity of a solution.
pH is defined as the negative base-10 logarithm of the hydrogen ion concentration:
Example: the base-10 logarithm of 1 × 10^{-7} is -7, and the negative of that number is 7, which corresponds to a neutral pH of 7. This illustrates how the pH scale works, with values below 7 indicating acidity and values above 7 indicating alkalinity.
Neutral solution has pH = 7; acidic solutions have pH < 7; basic (alkaline) solutions have pH > 7.
Buffers maintain internal solutions of organisms at near-neutral pH, helping resist drastic changes in pH.