General Biology: Chemistry Foundations (Chapter 2 Study Guide)

Chapter 2: Chemistry in Biology

Atomic Structure

The atom is the fundamental unit of matter, composed of subatomic particles. Understanding atomic structure is essential for grasping chemical interactions in biological systems.

• Atom: The smallest unit of an element, consisting of a nucleus (protons and neutrons) and electrons in orbitals.

• Model: A simplified atom model shows a central nucleus with protons (+) and neutrons (0), surrounded by electron (-) shells.

• Subatomic Particles:

  • Proton: Positively charged particle in the nucleus.

  • Neutron: Neutral particle in the nucleus.

  • Electron: Negatively charged particle in orbitals around the nucleus.

• Atomic Number: Number of protons in the nucleus; defines the element.

• Mass Number: Sum of protons and neutrons in the nucleus.

• Relationship: If you know any two of atomic number, mass number, or number of neutrons, you can calculate the third:

  • Number of neutrons = Mass number - Atomic number

  • Atomic number = Number of protons

• Periodic Table: A chart organizing elements by atomic number and properties. It provides information such as atomic mass, symbol, and electron configuration.

Elements, Compounds, Isotopes, and Ions

Elements and compounds are basic chemical categories, while isotopes and ions are variations of atoms with different properties.

• Element: Pure substance consisting of only one type of atom (e.g., Oxygen).

• Compound: Substance formed by two or more elements chemically bonded (e.g., H2O).

• Isotope: Atoms of the same element with different numbers of neutrons (e.g., Carbon-12 vs. Carbon-14).

• Ion: Atom or molecule with a net electric charge due to loss or gain of electrons (e.g., Na+, Cl-).

• Comparison of Isotopes: Isotopes have the same atomic number but different mass numbers due to varying neutrons. They may have different stability or radioactive properties.

Chemical Bonds

Chemical bonds hold atoms together in molecules and compounds. The type of bond affects molecular properties and biological functions.

• Covalent Bond: Atoms share electron pairs (e.g., in H2O).

• Ionic Bond: One atom transfers electrons to another, forming charged ions that attract (e.g., NaCl).

• Hydrogen Bond: Weak attraction between a hydrogen atom (partially positive) and an electronegative atom (e.g., oxygen in water).

• Example: Water molecules are held together by covalent bonds within the molecule and hydrogen bonds between molecules.

Electron Shells and Valence Electrons

Electron arrangement determines chemical reactivity. The outermost shell (valence shell) is key for bonding.

• Valence Electrons: Electrons in the outer shell; determine bonding behavior.

• Determining Valence Electrons: Use the periodic table group number for main group elements.

Water Molecule Structure and Hydrogen Bonding

Water's molecular structure and hydrogen bonding are central to its unique properties.

• Water Molecule: Two hydrogen atoms covalently bonded to one oxygen atom (H2O).

• Hydrogen Bonds: Form between the partially positive hydrogen of one water molecule and the partially negative oxygen of another.

• Diagram: Three water molecules oriented so that hydrogen bonds connect hydrogen (δ+) to oxygen (δ-) of adjacent molecules.

Emergent Properties of Water

Water exhibits several unique properties due to its polarity and hydrogen bonding, which are vital for life.

• Cohesion: Water molecules stick to each other (surface tension).

• Adhesion: Water molecules stick to other substances (capillary action).

• High Specific Heat: Water resists temperature change, stabilizing environments.

• High Heat of Vaporization: Water absorbs much heat before evaporating.

• Expansion upon Freezing: Ice is less dense than liquid water, so it floats.

• Solvent Properties: Water dissolves many substances due to polarity.

• Examples: Surface tension allows insects to walk on water; capillary action helps plants transport water.

Cohesion vs. Adhesion

Cohesion and adhesion are both effects of hydrogen bonding but differ in their interactions.

• Cohesion: Attraction between water molecules.

• Adhesion: Attraction between water molecules and other materials.

• Example: Water droplets forming beads (cohesion); water climbing up plant vessels (adhesion).

Solutions: Solute, Solvent, and Solution

Solutions are mixtures where substances are evenly distributed.

• Solute: Substance dissolved (e.g., salt).

• Solvent: Substance doing the dissolving (e.g., water).

• Solution: Homogeneous mixture of solute and solvent.

• Example: Saltwater is a solution of salt (solute) in water (solvent).

Hydrophobic vs. Hydrophilic Substances

Chemical properties determine whether substances interact with water.

• Hydrophilic: "Water-loving"; substances that dissolve or mix well with water (e.g., sugars, salts).

• Hydrophobic: "Water-fearing"; substances that do not mix with water (e.g., oils, fats).

• Determination: Polar or charged molecules are hydrophilic; nonpolar molecules are hydrophobic.

Water Dissociation and pH

Water can dissociate into ions, affecting acidity and basicity.

• Dissociation: $H_2O \rightarrow H^+ + OH^-$

• Ions Produced: Hydrogen ion ($H^+$) and hydroxide ion ($OH^-$).

• pH Scale: Measures concentration of $H^+$ ions; ranges from 0 (acidic) to 14 (basic).

• Acid: Substance that increases $H^+$ concentration (pH < 7).

• Base: Substance that decreases $H^+$ concentration (pH > 7).

• pH Units: Each unit change is a tenfold change in $H^+$ concentration.

• Example: pH 5 to pH 3 is a 100-fold increase in $H^+$.

Buffers

Buffers help maintain stable pH in biological systems, which is crucial for proper cellular function.

• Buffer: Substance that minimizes changes in pH by accepting or donating $H^+$ ions.

• Importance: Buffers maintain homeostasis in organisms, protecting against harmful pH fluctuations.

• Example: Blood contains bicarbonate buffer to keep pH near 7.4.

Summary Table: Key Terms and Comparisons

Term	Definition	Example
Element	Pure substance of one type of atom	Oxygen (O)
Compound	Substance of two or more elements bonded	Water (H2O)
Isotope	Same element, different neutrons	Carbon-12 vs. Carbon-14
Ion	Charged atom/molecule	Na+, Cl-
Covalent Bond	Electron sharing	H2O
Ionic Bond	Electron transfer	NaCl
Hydrogen Bond	Weak attraction (H to electronegative atom)	Between water molecules

Additional info: Some context and examples have been expanded for clarity and completeness.