Study guide: Chemical Foundations of Life

📋 Course Outline

1. Elements and Atomic Structure
2. Atomic Mass and Isotopes
3. Electron Shells and Orbitals
4. Reactions and Chemical Bonds
5. Water Polarity and Hydrogen Bonds
6. Water’s Physical and Solvent Properties
7. pH, Acids, Bases, and Buffers
8. Carbon and Hydrocarbon Structures
9. Isomers and Molecular Configuration
10. Functional Groups and Biological Molecules

📖 1. Elements and Atomic Structure

🔑 Key Concepts & Definitions

• Matter: Anything that occupies space and has mass.
• Atom: The smallest unit of matter that retains all the chemical properties of an element.

★ Must-know

• The four most common elements in living organisms are:

  • carbon
  • oxygen
  • hydrogen
  • nitrogen

• An atom has a central nucleus containing protons and neutrons, with electrons in the surrounding outer region.

Further detail

• Protons have a +1 charge and a mass of 1 amu, neutrons have no charge and a mass of 1 amu, and electrons have a −1 charge and a mass of 0 amu; protons and neutrons are in the nucleus, while electrons occupy orbitals.

📖 2. Atomic Mass and Isotopes

🔑 Key Concepts & Definitions

• Atomic number: The number of protons in an atom, and each element has a distinct atomic number.
• Atomic mass: The mass of an atom, approximately equal to the number of protons plus neutrons, and expressed in atomic mass units (amu).
• Isotope: Forms of the same element that have different numbers of neutrons and therefore different mass numbers.

★ Must-know

• The number of neutrons is calculated as $\text{atomic mass} - \text{atomic number}$.

Further detail

• Hydrogen-1 has 0 neutrons, hydrogen-2 has 1 neutron, and hydrogen-3 has 2 neutrons.

• Radiometric dating estimates the age of remains by comparing radioactive isotopes in the sample with relevant reference amounts; carbon-14 decays to nitrogen-14, and carbon dating can date carbon-containing remains less than about 50,000 years old.

💡 Memory Hook

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

📖 3. Electron Shells and Orbitals

🔑 Key Concepts & Definitions

• Valence shell: An atom’s outermost electron shell; a filled valence shell is the most stable configuration.
• Bohr model: An early atomic model that places protons in the nucleus and electrons in circular orbits at specific distances from the nucleus.

★ Must-know

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

• Electrons normally occupy the lowest available energy shell and fill orbitals from the shell nearest the nucleus outward.

Further detail

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

• Electron orbitals are complex spatial distributions predicted by quantum mechanics, and subshells are designated s, p, d, and f.

💡 Memory Hook

Electrons fill the shells nearest the nucleus first.

📖 4. Reactions and Chemical Bonds

🔑 Key Concepts & Definitions

• Chemical reaction: A change in the distribution of electrons between atoms.
• Chemical bond: An attractive force that links atoms together to form molecules.

📝 Essential Points

• Reactants are substances used at the beginning of a reaction, whereas products are substances formed at its end.

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

• A covalent bond forms when atoms share electrons, whereas an ionic compound forms when metals lose electrons and nonmetals gain electrons to achieve an octet.

• A polar covalent bond shares electrons unequally, whereas a nonpolar covalent bond shares them equally; molecular shape and bond type together determine molecular polarity.

💡 Memory Hook

Covalent bonds share electrons; ionic bonds transfer them.

📖 5. Water Polarity and Hydrogen Bonds

🔑 Key Concepts & Definitions

• Hydrogen bond: A weak interaction between the slightly positive hydrogen of one molecule and a slightly negative, more electronegative atom of another molecule.

★ Must-know

• In a water molecule, oxygen attracts the shared electrons more strongly than hydrogen, giving oxygen a slight negative charge and hydrogen a slight positive charge.

Further detail

• Water makes up 60–70% of the human body, and its polarity enables it to form hydrogen bonds.

📌 Ionic and covalent bonds require energy to break, whereas hydrogen bonds and van der Waals interactions are weaker attractions.

💡 Memory Hook

Oxygen attracts shared electrons → water has partial charges → water molecules form hydrogen bonds.

📖 6. Water’s Physical and Solvent Properties

🔑 Key Concepts & Definitions

• Specific heat capacity: The amount of heat one gram of a substance must absorb to raise its temperature by one degree Celsius.
• Heat of vaporization: The energy required to change one gram of a liquid into a gas; water has a high heat of vaporization.
• Cohesion: The attraction between water molecules, including at the liquid–gas interface, where hydrogen bonding helps them stick together.

★ Must-know

• In liquid water, hydrogen bonds are continually made and broken; heating increases molecular kinetic energy until hydrogen bonds break and molecules escape as gas, while cooling allows a crystalline solid structure to form.

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

📌 Water is the solvent, while a substance dissolved or mixed in water is a solute; water can dissolve ions and polar molecules.

Further detail

📌 Adhesion is attraction between water and other molecules, whereas cohesion is attraction among water molecules; adhesion to glass can draw water up a tube.

📖 7. pH, Acids, Bases, and Buffers

★ Must-know

📐 Formula - The pH of a solution is the negative base-10 logarithm of its hydrogen-ion concentration: $\mathrm{pH}=-\log_{10}[\mathrm{H}^+]$.

• Pure water contains equal hydrogen-ion and hydroxide-ion concentrations of $1\times10^{-7}\ \mathrm{mol/L}$, and its pH is 7.

📌 A solution is acidic when its pH is below 7 and basic when its pH is above 7; high hydrogen-ion concentration indicates acidity, while high hydroxide-ion concentration indicates alkalinity.

Further detail

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

💡 Memory Hook

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

📖 8. Carbon and Hydrocarbon Structures

🔑 Key Concepts & Definitions

• Hydrocarbon: A molecule composed of carbon and hydrogen whose covalent bonds store energy that is released when the molecule is burned.

★ Must-know

• Carbon is a key component of these macromolecules:

  • proteins
  • carbohydrates
  • lipids
  • nucleic acids

• Carbon has four electrons in its outer shell and can form four covalent bonds, allowing it to serve as a backbone for macromolecules and satisfy the octet rule.

Further detail

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

📌 Single carbon–carbon bonds can rotate and give a tetrahedral arrangement, whereas double bonds cannot rotate and hold the atoms in a planar arrangement.

📖 9. Isomers and Molecular Configuration

🔑 Key Concepts & Definitions

• Isomer: Molecules with the same chemical formula but different arrangements of atoms or different types of bonds between atoms.

★ Must-know

📌 Structural isomers differ in covalent arrangement, geometric isomers differ in atom arrangement around a double bond, and enantiomers have the same formula and bonds but differ in three-dimensional arrangement as mirror images.

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

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 that cannot be superimposed, and only L-forms of amino acids are used to make proteins.

💡 Memory Hook

Cis places carbons on the same side; trans places them on opposite sides.

📖 10. Functional Groups and Biological Molecules

🔑 Key Concepts & Definitions

• Functional group: A group of atoms within a molecule that confers consistent, specific properties on that molecule.

★ Must-know

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

Further detail

• Each of the four types of macromolecules has its own characteristic functional groups.

• Functional groups often interact with other functional groups through hydrogen bonds.