Chapter 2: The Chemical Basis of Life - Water & Carbon

Page 1: Chemical Basis of Life

Chapter 2 BY111: The Chemical Basis of Life: Water & Carbon.

Page 2: Essential Elements

Four elements make up $96\%$ of all matter in organisms: Hydrogen, Oxygen, Carbon, and Nitrogen. Core concept: form follows function.

Page 3: Basic Atomic Structure

• Protons: Positively ($+$) charged particles located in the nucleus.

• Neutrons: Neutral particles located in the nucleus.

• Electrons: Negatively ($-$) charged particles in orbitals surrounding the nucleus.

Page 4: Atomic Number

• Atomic Number: The characteristic number of protons in an atom's nucleus.

• Atoms with the same atomic number share chemical properties and belong to the same element (e.g., Helium ${}_2^4\text{He}$ has an atomic number of $2$).

Page 5: Isotopes and Mass Number

• Isotopes: Forms of an element with different numbers of neutrons.

• Mass Number: Total number of protons plus neutrons of the most common isotope.

Page 6: Atomic Notation

Atomic notation displays the mass number (protons + neutrons) above the atomic number (protons) beside the atomic symbol.

Page 7: Subatomic Particle Calculations

For Carbon (${}_6^{12}\text{C}$):

• Atomic number $6 = 6\text{ protons} = 6\text{ electrons}$.

• Mass number $12 = \text{protons} + \text{neutrons}$.

• Number of neutrons: $12 - 6 = 6$.

Page 8: Valence Shells

• Valence: The number of unpaired electrons in an atom's outer electron shell.

• Determines chemical bonding potential.

Page 9: Chemical Bonding

• Atoms are most stable when each electron orbital is filled.

• Covalent Bond: Unpaired valence electrons are shared by both nuclei.

• Ionic Bond: Electrons are transferred completely from one atom to another.

Page 10: Covalent Bonding in Hydrogen

Two hydrogen atoms share unpaired valence electrons to form a molecular hydrogen ($\text{H}_2$) covalent bond.

Page 11: Covalent Bonding in Water and Oxygen

• Two oxygen atoms covalently bond to form oxygen gas ($\text{O}_2$).

• One oxygen atom covalently bonds with two hydrogen atoms to form water ($\text{H}_2\text{O}$).

Page 12: Polar vs Nonpolar Covalent Bonds

• Nonpolar Covalent Bond: Electrons are shared equally between atoms (e.g., $\text{H}_2$).

• Polar Covalent Bond: Electrons are shared unequally due to differences in electronegativity, creating partial charges ($\delta^-$ on Oxygen, $\delta^+$ on Hydrogen in $\text{H}_2\text{O}$).

Page 13: Ions and Ionic Bonds

• Ion: An atom or molecule carrying a charge.

• Cation: Positively charged atom formed by losing an electron.

• Anion: Negatively charged atom formed by gaining an electron.

• Ionic Bond: Electrostatic attraction between oppositely charged ions.

Page 14: Formation of Sodium Chloride

• Sodium loses an electron to form cation $\text{Na}^+$.

• Chlorine gains an electron to form anion $\text{Cl}^-$.

• Electrostatic attraction forms a table salt ($\text{NaCl}$) crystal.

Page 15: Chemical Bonding Spectrum

Chemical bonds exist on a continuum: Nonpolar covalent (equal sharing) $\rightarrow$ Polar covalent (partial charges) $\rightarrow$ Ionic (full charge transfer).

Page 16: Covalent Bond Types

• Single Bonds: e.g., $\text{H}_2\text{O}$, $\text{NH}_3$, $\text{CH}_4$

• Double Bonds: e.g., $\text{CO}_2$

• Triple Bonds: e.g., $\text{N}_2$

Page 17: Molecular Representation Models

Molecules are represented using molecular formulas, structural formulas, ball-and-stick models, and space-filling models.

Page 18: Water Solvency and Electronegativity

• Water is an effective solvent due to polar covalent bonds.

• Electronegativity order: \text{O} > \text{N} > \text{C} = \text{H}.

• Electronegativity increases with proton number and decreases with electron shielding.

Page 19: Hydrogen Bonding in Water

Polarity allows hydrogen bonds to form between partial positive hydrogen atoms and partial negative oxygen atoms of neighboring water molecules.

Page 20: Hydrophilic Interactions

• Hydrophilic: Ions and polar molecules that interact with water's partial charges and remain in solution.

Page 21: Dissolution of Ionic Compounds

Water dissolves ionic crystals such as $\text{NaCl}$ by surrounding individual $\text{Na}^+$ and $\text{Cl}^-$ ions through charge interactions.

Page 22: Hydrophobic Interactions

• Hydrophobic: Uncharged, nonpolar compounds that do not dissolve in water.

Page 23: Structural Attributes of Water

Water's unique features stem from its small size, bent shape, highly polar covalent bonds, and overall polarity.

Page 24: Properties of Water

Key properties driven by hydrogen bonding:

• Cohesion and adhesion

• Lower density as a solid than liquid

• High capacity for energy absorption

Page 25: Cohesion, Adhesion, and Surface Tension

• Cohesion: Binding between like molecules (water to itself), producing high surface tension.

• Adhesion: Binding between unlike molecules.

• Capillary Action: Result of combined cohesive and adhesive properties.

Page 26: Surface Tension Mechanisms

• Adhesion pulls water upward at solid contact points to form a meniscus.

• Surface cohesion resists upward pull, creating surface tension that supports light objects.

Page 27: Thermal Properties and Density of Water

• Water expands upon freezing, making ice less dense than liquid water.

• High specific heat and high heat of vaporization allow significant energy absorption.

Page 28: pH Scale

Solutions range on a spectrum from Acidic (high proton concentration) to Neutral to Basic (low proton concentration).

Page 29: Chemical Evolution Theory

• Pattern: Complex carbon-containing substances are required for life.

• Process: Simple chemical compounds combined early in Earth's history to form complex carbon molecules.

Page 30: Atmospheric Environments

Early atmospheric environments included volcanic gases: $\text{H}_2\text{O}$ vapor, $\text{CO}_2$, $\text{N}_2$, and possibly $\text{H}_2$ and $\text{CO}$.

Page 31: Hydrothermal Vents

Deep-sea hydrothermal vents provided extreme heat, gases ($\text{CO}_2$, $\text{H}_2$), and catalytic metals (nickel, iron).

Page 32: Chemical Equilibrium and Reactions

• Reversible reaction example: $\text{CO}_2(g) + \text{H}_2\text{O}(l) \rightleftharpoons \text{H}_2\text{CO}_3(aq)$.

• Chemical Equilibrium: Occurs when forward and reverse reaction rates are equal.

• Endothermic: Absorbs heat; Exothermic: Releases heat.

Page 33: Forms of Energy

• Energy: Capacity to do work or supply heat.

• Potential Energy: Stored energy.

• Kinetic Energy: Energy of active motion.

Page 34: Reaction Spontaneity

Spontaneous reactions are determined by:

1. Decreased potential energy in products.

2. Increased entropy/disorder (lower order in products).

Example reaction: $2\,\text{H}_2 + \text{O}_2 \rightarrow 2\,\text{H}_2\text{O}$ releases potential energy as heat and light.

Page 35: Cellular Energy Changes

Combustion / Cellular Respiration reaction:

$\text{C}_6\text{H}_{12}\text{O}_6 + 6\,\text{O}_2 \rightarrow 6\,\text{CO}_2 + 6\,\text{H}_2\text{O} + \text{heat}$

Reactants have high potential energy and order; products have low potential energy and lower order.

Page 36: Pathways of Prebiotic Synthesis

Simple environmental molecules reacted via sunlight or hydrothermal vent catalysis to produce complex molecules like ribose, glycine, acetaldehyde, and acetic acid.

Page 37: Experimental Testing of Chemical Evolution

Miller-Urey spark discharge experiments demonstrated that adding kinetic energy (spark) to simple gases ($\text{CH}_4$, $\text{NH}_3$, $\text{H}_2$, water vapor) yields formaldehyde, hydrogen cyanide, and organic compounds containing $\text{C-C}$ bonds (amino acids).

Page 38: Precursor Synthesis

• Key chemical evolution step: Formation of formaldehyde ($\text{H}_2\text{CO}$ / $\text{CH}_2\text{O}$) and hydrogen cyanide ($\text{HCN}$).

• Reaction: $\text{CO}_2(g) + 2\,\text{H}_2(g) \rightarrow \text{CH}_2\text{O}(g) + \text{H}_2\text{O}(g)$.

Page 39: Free Radical Formation

High-energy photons break unreactive atmospheric molecules into highly reactive free radicals ($\text{H}$, $\text{O}$, $\text{CO}$) with unpaired electrons.

Page 40: Storage of Chemical Energy

Chemical energy is potential energy in bonds. Ancient solar energy was converted into stored chemical energy inside $\text{H}_2\text{CO}$ and $\text{HCN}$.

Page 41: Importance of Carbon

Carbon has $4$ valence electrons and forms up to four covalent bonds, enabling complex molecular shapes essential for chemical evolution.

Page 42: Carbon Chains and Rings

Carbon forms diverse skeletal shapes, including chains (e.g., Octane, $\text{C}_8\text{H}_{18}$) and rings (e.g., Glucose, $\text{C}_6\text{H}_{12}\text{O}_6$).

Page 43: Function of Carbon Skeletons

Carbon atoms furnish the framework that gives organic molecules overall shape, while attached functional groups define reactivity.

Page 44: Six Major Functional Groups

• Amino: Acts as a base; attracts a proton (e.g., Glycine).

• Carboxyl: Acts as an acid; loses a proton (e.g., Acetic acid).

• Carbonyl: Reacts to form larger compounds; found in aldehydes and ketones (e.g., Acetaldehyde, Acetone).

• Hydroxyl: Highly polar; enhances solubility through hydrogen bonding; weak acid (e.g., Ethanol).

• Phosphate: Multi-phosphate links store large chemical energy amounts (e.g., 3-Phosphoglyceric acid).

• Sulfhydryl: Forms disulfide ($\text{S-S}$) bonds to stabilize protein structure (e.g., Cysteine).