Biology: The Core - The Chemistry of Life

Matter and Elements

  • Matter: Defined as anything that occupies space and has mass.

  • Elements: Substances that cannot be broken down or transformed chemically into other substances. Each element has its own chemical properties.

    • There are 118 known elements.

    • Out of these, 92 occur naturally.

    • Fewer than 30 elements are found in living cells, notable examples include:

    • Carbon (C)

    • Oxygen (O)

    • Hydrogen (H)

  • Atom: Each element is composed of atoms.

Geology vs Biology

  • Top 8 Elements of Earth’s Crust:

    • Oxygen (O)

    • Silicon (Si)

    • Aluminum (Al)

    • Calcium (Ca)

    • Iron (Fe)

    • Magnesium (Mg)

    • Sodium (Na)

    • Potassium (K)

  • Composition of the Human Body:

    • 99% of the human body is comprised of six key elements:

    • Oxygen (O)

    • Hydrogen (H)

    • Nitrogen (N)

    • Carbon (C)

    • Calcium (Ca)

    • Phosphorus (P)

Atomic Structure

  • Components of Atoms: Atoms consist of protons (positively charged), neutrons (no charge) located in the nucleus, and electrons (negatively charged) that surround the nucleus.

  • Stability of Atoms: Atoms prefer to achieve stability by having a neutral charge.

The Periodic Table

  • The periodic table arranges elements in columns and rows based on their characteristics, providing essential information on how elements interact to form molecules.

  • Most periodic tables include a key or legend to help understand the information they contain.

Atomic Number and Mass

  • Atomic Number: The number of protons in an element.

  • Mass Number: The total number of protons and neutrons in an atom. Examples include:

    • Carbon:

    • Carbon-12: 6 protons, 6 neutrons

    • Nitrogen:

    • Nitrogen-14: 7 protons, 7 neutrons

    • Oxygen:

    • Oxygen-16: 8 protons, 8 neutrons

Isotopes

  • Isotopes: Different forms of the same element that have the same number of protons and electrons but differ in the number of neutrons.

    • Some isotopes are naturally occurring, while others are unstable.

  • Examples of Isotopes:

    • Carbon-12: 6 protons, 6 neutrons

    • Carbon-14: 6 protons, 8 neutrons

  • Radioactive Isotopes: Unstable isotopes that lose subatomic particles to form more stable elements.

Electron Behavior

  • Electron Shells: Distinct energy levels of electrons encircling the nucleus.

  • Valence Shells (Octet Rule):

    • The outermost electron shell of an atom.

    • If the valence shell is full, the atom is stable.

    • If not full, the atom is reactive, indicating that electrons will either be pulled in or away.

Bonding Basics

  • Chemical Bonds: Atoms link together by forming weak or strong electrical attractions that hold them in proximity.

  • Molecules: Stable groups of two or more atoms linked by chemical bonds (e.g., H₂).

  • Compounds: Molecules made up of two or more different elements (e.g., H₂O).

  • Types of Bonds:

    • Ionic bond

    • Covalent bond (both polar and nonpolar)

    • Hydrogen bond

Ionic Bonding

  • Ions: Atoms with an electrical charge due to the lack of a full valence shell.

    • Cations: Positive ions (e.g., Na⁺)

    • Anions: Negative ions (e.g., Cl⁻)

  • Ionic Bonding: The association between ions of opposite charge (e.g., NaCl, table salt).

Covalent Bonds

  • Unlike ionic bonds, covalent bonds involve the sharing of electrons in a mutually stabilizing relationship.

  • Polar Molecules: Molecules with regions having opposite electrical charges (stronger).

  • Non-Polar Molecules: Covalently bonded molecules that are electrically balanced.

Hydrogen Bonding

  • Hydrogen Bonding: Interactions between molecules, significant for the unique bonding of water and the structure of DNA.

  • Example: At room temperature, water would exist as a gas without hydrogen bonding.

Properties of Water

  • Importance of Water:

    • Polar: Allows for various interactions.

    • Stabilizes Temperature: Capable of absorbing and releasing heat energy slowly.

    • Good Solvent: Acts as a universal solvent by breaking ionic bonds and forming spheres around ions due to polarity.

    • Cohesive and Adhesive: Cohesion refers to water molecules' attraction to each other, while adhesion refers to the attraction between water molecules and other substances.

Density of Ice vs Liquid Water

  • Structure of Ice: Water freezes in a lattice structure making ice less dense than liquid water, allowing it to float and insulating animals underneath.

pH Scale

  • pH of a Solution: Measures acidity, ranging from 0 (acidic) to 14 (basic).

  • Each unit change in pH represents a tenfold change in H⁺ ion concentration.

Buffers

  • Buffers: Chemicals that minimize pH changes by accepting ions, helping to stabilize pH levels within cells and during exercise.

Impacts of pH Change

  • Environmental Changes: Rising CO₂ levels lead to increased ocean acidity, impairing marine organisms' ability to build skeletons or shells.

  • Ecosystem Health: Changes in pH can significantly affect ecosystems, especially due to climate change-induced CO₂ level increases.

Carbon-based Life

  • Carbon's Role in Life: All life on Earth is predominantly carbon-based because carbon can bond with up to four other atoms, forming diverse organic compounds.

Carbohydrates

  • Basic Composition of Carbohydrates: Composed of carbon, hydrogen, and oxygen.

  • Types of Carbohydrates:

    • Monosaccharides: Simple sugars converted to glucose for energy production (ATP).

    • Disaccharides: Made of two simple sugars; bonds break to yield glucose.

    • Polysaccharides: Composed of multiple simple sugars, such as starch (converted to glucose), cellulose (fiber, indigestible), and glycogen (energy stored in cells).

Lipids (Fats)

  • Definition of Lipids: Fats that are nonpolar and do not mix with water.

  • Triglycerides: Common dietary lipids consisting of a glycerol backbone and three fatty acid chains.

  • Functions of Lipids:

    • Serve as a fuel source during rest and low-intensity activities.

    • Aid in vitamin absorption.

    • Provide cushioning for vital organs.

Fatty Acid Chains

  • Types of Fatty Acids:

    • Saturated: No double bonds, linked to heart disease.

    • Unsaturated: Contain double bonds, generally healthier.

    • Trans Fats: Unhealthy, chemically created fats.

Protein Structure and Function

  • Proteins: Comprised of amino acid monomers linked by peptide bonds.

  • Diversity of Proteins: 20 different amino acids can form thousands of proteins vital to human structure and function.

  • Denaturation: A change in the protein’s structure due to heat, acids, and bases, leading to loss of function.

Nucleotides and Nucleic Acids

  • Nucleotides: Constitute the building blocks of nucleic acids (DNA or RNA) and the energy compound ATP.

  • Basic Structure of Nucleotides:

    • Phosphate group

    • Pentose sugar

    • Nitrogenous base

  • Nucleic Acids:

    • DNA: Deoxyribonucleic acid storing genetic information.

    • RNA: Ribonucleic acid that assists in translating the genetic code into proteins.

Enzymes

  • Function of Enzymes: Proteins that speed up chemical reactions without being changed themselves, essential for metabolism.

  • Activation Energy: Enzymes function by lowering activation energy, thereby facilitating reactions.

  • Specificity of Enzymes: Each enzyme recognizes a specific substrate (target molecule). Changes in enzyme shape, such as those caused by genetic mutations, can inhibit function, as seen with lactase and lactose intolerance.