BIO181_Ch2_S25

Chapter 2: The Chemistry of Life

Elements - Components of Matter

• Elements: The basic building blocks of matter, cannot be broken down into simpler substances.

  • Major Elements (96%): Include carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

  • Mineral Elements (<4%): Elements such as calcium (Ca), potassium (K), etc.

  • Trace Elements (0.01%): Essential in minute quantities (e.g., iron (Fe), iodine (I)).

• Periodic Table Overview:

  • Divided into metals (left side) and nonmetals (right side) marked by the red staircase in the table.

Atoms - Single Elemental Units

• Atom Structure:

  • Composed of a nucleus surrounded by electron shells.

  • Example: Carbon atom

    • 6 protons (p+), 6 electrons (e-), 6 neutrons (n°).

Filling Electron Orbitals

• Electron Configuration:

  • 1st shell: holds 2 electrons

  • 2nd shell: holds 8 electrons

  • 3rd shell: can hold up to 18, but generally satisfied with 8.

• Chlorine: has seven valence electrons, indicating its reactivity.

Covalent Bonding – Sharing of Electron Pairs

• Bond Formation:

  • Hydrogen atoms each donate their single electron, leading to a bond.

  • Each atom respects the duet rule when they combine to form H2.

Nonpolar vs. Polar Covalent Bonds

• Nonpolar Covalent Bond: The electrons are shared equally; example: H₂ molecule.

• Polar Covalent Bond: Electrons spend more time closer to the more electronegative atom; example: H₂O (water).

Multiple Covalent Bonds

• Elements such as carbon can form multiple covalent bonds to satisfy their electron requirements.

Hydrogen Bonding and Surface Tension

• Hydrogen Bonds: Weak attractions between polar molecules, such as H₂O.

• Surface Tension: Caused by hydrogen bonds, leading water to form droplets and facilitating its unique properties.

Ionic Bonds

• Form from electron transfer between metals and nonmetals, creating charged ions that attract.

Helpful Vocabulary

• Solvent: Fluid in which substances dissolve (water in biological systems).

• Solute: Substance that gets dissolved (can be hydrophilic or hydrophobic).

• Solution: Combination of solvent and solute.

Ionic Molecules

• In ionic compounds like NaCl, ions attract water, allowing for biological reactions.

Polar and Nonpolar Covalent Compounds

• Polar Covalent Compounds: Have unequal distribution of charges (e.g., CO, polar ends make them solvable in water).

• Nonpolar Covalent Compounds: No charge separation makes them insoluble in water (e.g., methane, CH₄).

Potential Energy and Kinetic Energy

• Potential Energy: Stored energy (e.g., a stationary object).

• Kinetic Energy: Energy of motion (e.g., a moving object).

• Chemical Bonds: Bonds contain potential energy, which is released during reactions.

Classes of Chemical Reactions

• Dehydration Synthesis: Building larger molecules by removing water.

• Hydrolysis: Breaking down molecules by adding water.

• Anabolic (Synthesis): A + B → AB

• Catabolic (Breakdown): AB → A + B

• Exchange Reaction: AB + CD → AC + BD

Activation Energy

• Concept: Energy required to initiate a reaction.

  • Requires energy input to reach a transition state; energy decreases as reactants convert to products.

The Effect of Enzymes on Activation Energy

• Enzymes: Lower activation energy needed for reactions, enabling faster reactions.

Enzyme-Substrate Interaction

1. Substrates approach the enzyme.

2. Binding causes a shape change in both the enzyme and the substrate.

3. Transition state formation leads to product creation.

4. Products are released.

The Behavior of Acids and Bases in Water

• Dissociation of water leads to equal H+ and OH- in pure water.

• Acids: Increase the H+ concentration (e.g., HCl).

• Bases: Decrease the H+ concentration (e.g., NaHCO3).

The pH Scale

• Ranges from 0 (acidic) to 14 (basic); a logarithmic scale indicating H+ ion concentration.

Carbohydrates - Monosaccharides

• Types of Sugars:

  • Pentoses: 5-carbon sugars (e.g., ribose).

  • Hexoses: 6-carbon sugars (e.g., glucose).

• Isomers: Different structural forms of glucose.

Carbohydrates - Disaccharides

• Formed via dehydration synthesis of two monosaccharides (e.g., sucrose from glucose and fructose).

Carbohydrates - Polysaccharides

• Long chains of monosaccharides (e.g., starch, cellulose) that serve as energy storage or structural components.

Proteins - Monomers (Amino Acids)

• Composed of amino acids, with unique properties determined by R groups.

Proteins - Dipeptides

• Formed by linking two amino acids with a peptide bond through dehydration synthesis.

Levels of Protein Structure

1. Primary: Sequence of amino acids.

2. Secondary: Alpha helices or beta-pleated sheets via hydrogen bonding.

3. Tertiary: 3D shape due to interactions between R groups.

4. Quaternary: Assembly of multiple polypeptide chains.

Nucleic Acids - Monomers (Nucleotides)

• Consist of a nitrogenous base, pentose sugar, and phosphate group (e.g., DNA and RNA components).

ATP - A Nucleic Acid

• Structure: Composed of ribose, adenine, and phosphate groups; ATP is the primary energy carrier in cells.

Lipids - Hydrophobic Organic Molecules

• Includes saturated (no double bonds), monounsaturated (one double bond), and polyunsaturated (multiple double bonds) fatty acids.

Lipids - Triglycerides

• Glycerol linked to three fatty acids through dehydration synthesis, serving as long-term energy storage.

Lipids - Phospholipids

• Composed of a hydrophilic head and hydrophobic tails, forming cell membranes.

Lipids - Steroids

• Characterized by a four-ring structure; cholesterol is a significant steroid in cellular functions.