Ch2 The Chemical Basis of Life + Start of Ch3

Overview of Lecture Content

  • The lectures cover fundamental concepts in biology, chemistry of life, and properties of water, culminating in protein structure and amino acids.

Last Class Recap

  • Topics Covered:

    • 10 Characteristics of Life

    • Scientific Method:

    • Testing a hypothesis and predicting results before conducting experiments.

    • Eukaryotes vs. Prokaryotes - Unity of Life and Diversity of Life (Evolution by Natural Selection).

    • Key Model System: Humans.

    • Fundamental aspects include:

    • Cells as the basic unit of life.

    • Energy through ATP.

    • Genetic governance via DNA genes.

Lecture #2: The Chemical Basis of Life

  • Chapter 2 Overview

Elements and Their Abundance

  • There are 92 naturally occurring elements; their Earth surface abundance differs from that in living organisms.

  • Elements predominantly found in living organisms: Carbon (C), Nitrogen (N), Oxygen (O), Hydrogen (H).

Basic Atomic Structure

  • Components of Atoms:

    • Protons: Positively charged particles.

    • Neutrons: Neutral particles.

    • Electrons: Negatively charged particles.

  • Protons and neutrons reside in the nucleus of the atom, while electrons travel in orbitals or shells around the nucleus.

  • Diagram Description: Visual representations depict the arrangement of subatomic particles.

Elements: Building Blocks of Chemical Evolution

  • Atomic Number (Z): Number of protons in an atom's nucleus defines the element.

  • Atoms sharing the same atomic number share chemical properties, grouping them into the same element.

  • Mass Number: Total of protons and neutrons.

Electron Arrangement

  • Each electron shell has a capacity limit:

    • 1st shell: up to 2 electrons.

    • 2nd and 3rd shells: up to 8 electrons each.

  • Electron shells fill from innermost to outermost.

Chemical Bonding

  • Atoms are most stable with filled outer shells.

  • Types of Bonds:

    • Covalent Bond: Sharing of valence electrons between atoms.

    • Ionic Bond: Transfer of electrons, leading to oppositely charged ions.

Ions and Ionic Bonds

  • Ion: Charged atom or molecule.

    • Cation: Possesses a positive charge (loss of electron).

    • Anion: Possesses a negative charge (gain of electron).

  • Example: Formation of sodium ion (Na+) and chloride ion (Cl-), forming table salt (NaCl).

Covalent Bonds: Examples

  • Instances of bonds include:

    • Single Covalent Bonds: H2 molecule.

    • Double Bonds: Carbon dioxide (CO2).

    • Triple Bonds: Molecular nitrogen (N2).

Polar vs. Nonpolar Covalent Bonds

  • Electrons may be shared unequally:

    • High Electronegativity: Atoms hold electrons tightly, leading to partial charges.

    • Example: Polar covalent bonds in water (H2O).

The Electron-Sharing Continuum

  • Types of Bonds by Electron Sharing:

    • Nonpolar Covalent Bonds: Equal sharing (e.g., H2).

    • Polar Covalent Bonds: Unequal sharing (e.g., H2O).

    • Ionic Bonds: Complete transfer of electrons (e.g., NaCl).

Molecular Geometry

  • Shape dictated by bond angles in covalent bonds:

    • Examples of molecular shapes: Methane (CH4) and Water (H2O).

Properties of Water

  • Water as an Efficient Solvent:

    • Polar nature facilitates dissolving ions and polar molecules.

    • Hydrogen Bonding: Weak attractions between water molecules and other polar substances.

  • Hydrophilic vs. Hydrophobic:

    • Hydrophilic: ions and polar molecules that interact with water.

    • Hydrophobic: Nonpolar substances that do not dissolve in water, e.g., hydrocarbons.

Unique Properties of Water Due to Hydrogen Bonding

  • Cohesion and Adhesion:

    • Cohesion: Water molecules bond with each other.

    • Adhesion: Water molecules bond with different surfaces (e.g., plastic).

  • Lower density of ice due to molecular structure leads to ice floating.

    • Explanation of water expanding when frozen and resulting crystalline formation in ice.

Water's Thermal Properties

  • High specific heat capacity and heat of vaporization, allowing water to absorb significant heat without temperature change.

The pH Scale and Buffers

  • pH Definition: Concentration of hydrogen ions (H+).

    • Pure water pH = 7

    • Acids: pH < 7

    • Bases: pH > 7

  • Buffer Functionality: Minimizes pH changes by absorbing or releasing H+ ions.

The Importance of Carbon

  • Versatility: Due to four valence electrons, allowing the formation of various molecular structures:

    • Linear chains and rings.

Functional Groups of Carbon Compounds

  • Selection of functional groups:

    • Amino, Carboxyl, Hydroxyl, Carbonyl, Phosphate, and Methyl groups.

    • Each displays unique properties and biological functions in molecules.

  • Properties considered:

    • Polarity, potential to ionize, and reactivity contributing to the chemical diversity of life.

Monomers and Polymers

  • Building blocks of macromolecules:

    • Amino acids (proteins), nucleotides (nucleic acids), simple sugars (carbohydrates).

  • Polymerization: Process to form macromolecules via dehydration reactions (releases water).

  • Hydrolysis: Reverse reaction that involves adding water to break down polymers.

Proteins Overview

  • All proteins are polymers made from 20 unique amino acids.

  • Structure includes:

    • Central carbon connected to an amino group (NH2), carboxyl group (COOH), hydrogen atom, and a variable side chain (R-group).

    • Amino and carboxyl groups ionize at physiological pH.

Amino Acid Diversity

  • Amino acids categorized by property of their R-groups:

    • Nonpolar Side Chains: Hydrophobic properties.

    • Polar Side Chains: Hydrophilic and can form hydrogen bonds.

    • Charged Side Chains: Can form ionic and hydrogen bonds.

R-Group Characteristics

  • Comparison of amino acids by structural and chemical properties affecting protein structure and function.

  • Influence of R-groups on overall protein conformation and biological role.