Study guide: Chemical Foundations of Life

📋 Course Outline

1. Matter, Elements, and Atoms
2. Atomic Structure and Isotopes
3. Electron Shells and Orbitals
4. Chemical Reactions and Bonds
5. Water’s Molecular Properties
6. Water, Acids, Bases, and Buffers
7. Carbon and Hydrocarbon Structures
8. Isomers and Molecular Shape
9. Functional Groups in Biomolecules

📖 1. Matter, Elements, and Atoms

🔑 Key Concepts & Definitions

• Matter: Anything that occupies space and has mass.
• Element: A unique form of matter with specific chemical and physical properties that cannot be broken down into smaller substances.

★ Must-know

• The four most common elements in living organisms are:
  • carbon (C)
  • oxygen (O)
  • hydrogen (H)
  • nitrogen (N)

Further detail

• Each element is designated by a one- or two-letter chemical symbol, such as S for sulfur and Ca for calcium.

• In humans, oxygen makes up 65%, carbon 18%, hydrogen 10%, and nitrogen 3%; in the atmosphere, oxygen makes up 21% and nitrogen 78%, while carbon and hydrogen are trace; in Earth’s crust, oxygen makes up 46%, hydrogen 0.1%, and carbon and nitrogen are trace.

📖 2. Atomic Structure and Isotopes

🔑 Key Concepts & Definitions

• Atom: The smallest unit of matter that retains all the chemical properties of an element.
• Isotopes: Forms of the same element with different numbers of neutrons and therefore different mass numbers.

★ Must-know

• An atom has a central nucleus containing protons and neutrons and an outer region where electrons occupy orbitals.

📌 An element’s atomic number is its number of protons, whereas its approximate atomic mass in amu is the combined mass of its protons and neutrons.

Further detail

• Protons have charge +1, mass about 1 amu, and are in the nucleus; neutrons have charge 0, mass about 1 amu, and are in the nucleus; electrons have charge −1, mass about 0 amu, and occupy orbitals.

• The number of neutrons in an atom can be calculated by subtracting its atomic number from its atomic mass.

💡 Memory Hook

Atomic number counts protons; atomic mass reflects protons plus neutrons.

📖 3. Electron Shells and Orbitals

🔑 Key Concepts & Definitions

• Valence shell: An atom’s outermost electron shell, with a filled shell representing the most stable configuration described in the course.
• Bohr model: An early representation of protons in a nucleus and electrons in circular orbits at specific distances from it.

★ Must-know

• In a neutral atom, the number of electrons equals the number of protons and the atomic number.

• Electrons normally occupy the lowest available energy shell, filling orbitals closest to the nucleus before those farther away.

Further detail

📌 When the first two outer shells are filled, each has eight electrons; group 1 elements can achieve stability by losing an outer electron, while group 17 elements can do so by gaining one electron.

• Electron orbitals are predicted spatial regions around the nucleus, and the s subshell has one spherical orbital while the p subshell has three dumbbell-shaped orbitals.

💡 Memory Hook

Electrons fill the lowest-energy shells first, moving outward from the nucleus.

📖 4. Chemical Reactions and Bonds

🔑 Key Concepts & Definitions

• Chemical reactions: Changes in the distribution of electrons between atoms that convert reactants into products.
• Chemical bond: An attractive force that links atoms together to form molecules.

★ Must-know

• An irreversible reaction proceeds in one direction until its reactants are used up, whereas a reversible reaction allows some products to convert back into reactants.

• Covalent bonds form when atoms share electrons, whereas ionic compounds form when metals lose electrons and nonmetals gain them to achieve an octet.

• Polar covalent bonds share electrons unequally, whereas nonpolar covalent bonds share electrons equally; water is polar and methane is nonpolar.

Further detail

• Hydrogen bonds are attractions between a partially positive hydrogen and a partially negative atom on another molecule, while van der Waals interactions are weak attractions caused by changes in electron density between nearby molecules.

💡 Memory Hook

Covalent bonds share electrons; ionic bonds form when electrons are transferred.

📖 5. Water’s Molecular Properties

🔑 Key Concepts & Definitions

• Heat capacity: Specific heat capacity is the amount of heat one gram of a substance must absorb to raise its temperature by one degree Celsius; water therefore heats and cools slowly.
• Heat of vaporization: Heat of vaporization is the energy required to change one gram of a liquid into a gas, and water has a high heat of vaporization.

★ Must-know

• Water makes up 60–70% of the human body and is essential to life because it is polar and can form hydrogen bonds.

• In a water molecule, oxygen attracts shared electrons more strongly than hydrogen, giving oxygen a slight negative charge and hydrogen a slight positive charge; hydrogen can then form a weak bond with the oxygen of an adjacent water molecule.

• Hydrogen bonding creates an ice lattice that makes ice less dense than liquid water, allowing ice to float.

Further detail

📌 Water is liquid when its hydrogen bonds continually form and break, becomes gas when heating gives molecules enough kinetic energy to escape as bonds break, and forms a crystalline solid when cooled.

💡 Memory Hook

Water’s polarity enables hydrogen bonding, which underlies several of its properties.

📖 6. Water, Acids, Bases, and Buffers

🔑 Key Concepts & Definitions

• Solvent: A solvent is the substance in which another substance dissolves; water can dissolve ions and polar molecules, while the dissolved substances are solutes.
• Cohesion: The attraction between water molecules, including their tendency to stick together at the liquid–gas interface through hydrogen bonding.
• Surface tension: A substance’s capacity to withstand rupture when placed under tension or stress, with water’s cohesion contributing to it.
• Adhesion: Adhesion is the attraction between water molecules and other molecules; attraction to glass can make water move up a tube when it exceeds cohesion among the water molecules.

📝 Essential Points

• When sodium chloride dissolves in water, it dissociates into ions that become surrounded by spheres of hydration.

📐 Formula - Water ionizes into equal concentrations of hydrogen and hydroxide ions: $\mathrm{H_2O(l) \rightleftharpoons H^+(aq) + OH^-(aq)}$; in pure water each ion concentration is $1 \times 10^{-7}\,\mathrm{mol/L}$.

💡 Memory Hook

High H⁺ means acidic; high OH⁻ means basic.

📖 7. Carbon and Hydrocarbon Structures

🔑 Key Concepts & Definitions

• pH: pH is the negative base-10 logarithm of the hydrogen-ion concentration, expressed as $\mathrm{pH}=-\log_{10}[\mathrm{H^+}]$.

📝 Essential Points

📌 A neutral solution has pH 7, an acidic solution has pH below 7, and a basic solution has pH above 7; high H⁺ concentration is acidic and high OH⁻ concentration is basic.

• Buffers help maintain an organism’s internal solutions at a near-neutral pH.

📖 8. Isomers and Molecular Shape

🔑 Key Concepts & Definitions

• Hydrocarbons: Hydrocarbons are molecules made of carbon and hydrogen, such as methane, whose covalent bonds store energy that is released when they are burned.

★ Must-know

• Carbon is a key component of proteins, carbohydrates, lipids, and nucleic acids because it can form covalent bonds with up to four different atoms and provide a macromolecular backbone.

Further detail

• Carbon has four electrons in its outer shell and can form four covalent bonds to fill that shell and satisfy the octet rule.

• Methane has a tetrahedral geometry, with its four hydrogen atoms spaced 109.5° apart.

📌 Single bonds in hydrocarbons allow rotation, whereas double bonds do not and lock the atoms on either side in place; single-bonded carbon arrangements are tetrahedral while double-bonded arrangements are planar.

• Carbon can form five- and six-membered closed rings with single or double bonds, and nitrogen can replace carbon in a ring; benzene is an important ring found in some amino acids, cholesterol, and its derivatives.

💡 Memory Hook

Cis places carbons on the same side of a double bond; trans places them on opposite sides.

📖 9. Functional Groups in Biomolecules

🔑 Key Concepts & Definitions

• Isomers: Molecules with the same chemical formula but different arrangements of atoms or different types of bonds between atoms.
• Functional groups: Groups of atoms within a molecule that confer consistent, specific properties on the molecule.

★ Must-know

📌 Structural isomers differ in covalent arrangement, geometric isomers differ in atom arrangement around a double bond, and enantiomers share a formula and bonds but are non-superimposable mirror images.

📌 In a cis configuration, carbons are on the same side of a double bond; in a trans configuration, they are on opposite sides.

• Hydrogen bonds connect the two strands of DNA to form its double-helix structure, which is vital to DNA function.

Further detail

📌 Fatty acids with one or more double bonds are unsaturated, whereas fatty acids with no double bonds are saturated.

• D-alanine and L-alanine are enantiomers, and only L-forms of amino acids are used to make proteins.

• Each of the four types of macromolecules has characteristic functional groups, which can interact with other functional groups through hydrogen bonds.