Water and Carbon: The Chemical Basis of Life (Chapter 2 Study Notes)

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Water and Carbon: The Chemical Basis of Life

Introduction to Chemical Evolution

Chemical evolution is the leading explanation for the origin of life on Earth. It describes the formation of increasingly complex carbon-containing substances, eventually leading to molecules capable of self-replication. This process marks the transition from chemical to biological evolution, after which evolution by natural selection took over. The descendants of the original molecule became metabolically active, acquired membranes, and fulfilled the five characteristics of life.

Chemical evolution: Formation of complex molecules from simpler substances.
Biological evolution: Process by which living organisms evolve via natural selection.

Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution

Basic Atomic Structure

Atoms consist of a nucleus (protons: +1 charge; neutrons: neutral) surrounded by electrons (-1 charge).
Atoms are electrically neutral when protons equal electrons.
Elements consist of only one type of atom, defined by their atomic number (number of protons).
Mass number = number of protons + neutrons.
Dalton (Da): Unit of atomic mass; 1 Da = mass of one proton or neutron.
Isotopes: Atoms of the same element with different numbers of neutrons (different masses).
Atomic weight: Average mass of all isotopes, weighted by abundance.
Radioactive isotopes: Unstable isotopes that decay over time.

Most abundant elements in living cells: C, H, N, O, P, S (over 99% of atoms in the body).

Electron Arrangement and Chemical Behavior

Electrons occupy orbitals (regions around the nucleus); each orbital holds up to two electrons.
Orbitals are grouped into electron shells (energy levels), numbered 1, 2, 3, etc.
Electrons fill the innermost shells first.
The valence shell is the outermost shell; electrons here are called valence electrons.
The number of unpaired valence electrons determines an atom's valence (bonding capacity).

Chemical Bonds

Atoms are most stable when their valence shells are full.
Chemical bonds fill valence shells by sharing or transferring electrons.
Covalent bonds: Atoms share unpaired valence electrons; the resulting group is a molecule.
Example: Two hydrogen atoms share electrons to form H2.

Nonpolar and Polar Covalent Bonds

Electronegativity: The strength with which an atom pulls electrons toward itself; increases up and to the right on the periodic table.
Nonpolar covalent bond: Electrons are shared equally (e.g., C–H bond).
Polar covalent bond: Electrons are shared unequally, resulting in partial charges (e.g., O–H bond in water).
Partial charges are denoted as δ− (more electronegative atom) and δ+ (less electronegative atom).

Ionic Bonds and Ions

Ionic bond: Electrons are completely transferred from one atom to another, creating ions.
Cation: Atom loses electron(s), becomes positively charged.
Anion: Atom gains electron(s), becomes negatively charged.
The degree of electron sharing forms a continuum: nonpolar covalent → polar covalent → ionic.

Simple Molecules and Molecular Representation

The number of unpaired electrons determines the number of bonds an atom can form.
Atoms with more than one unpaired electron can form double or triple bonds.
Molecular formulas show the types and numbers of atoms (e.g., H2O, CH4).
Structural formulas show how atoms are bonded.
Ball-and-stick and space-filling models show 3D geometry.

Properties of Water and the Early Oceans

Water as the Basis of Life

About 75% of a cell is water.
Water is an excellent solvent: substances (solutes) dissolve in it to form solutions, increasing the likelihood of chemical reactions.

Unique Properties of Water

Water's structure: small size, bent shape, highly polar covalent bonds, overall polarity.
Oxygen atom has a partial negative charge; hydrogen atoms have partial positive charges.
Water molecules form hydrogen bonds with each other and with polar solutes.
Hydrophilic molecules (ions, polar molecules) dissolve in water; hydrophobic molecules (nonpolar) do not.
Hydrophobic molecules cluster together via hydrophobic interactions and van der Waals interactions.

Water in Acid-Base Reactions

Chemical reactions involve breaking and forming bonds; written as equations (e.g., H2O ⇌ H+ + OH−).
Water can dissociate into hydrogen ions (H+) and hydroxide ions (OH−).
In solution, H+ associates with H2O to form hydronium ions (H3O+).
Acids donate protons (increase H3O+); bases accept protons (decrease H3O+).

Measuring Proton Concentration: pH

Mole: 6.022 × 1023 particles; mass of one mole equals atomic/molecular weight in grams.
Molarity (M): Moles of solute per liter of solution.
pH: Logarithmic measure of proton concentration:
Acids: pH < 7; Bases: pH > 7; Neutral: pH = 7.
Buffers minimize changes in pH, maintaining homeostasis.

Life is Carbon-Based

Carbon's Role in Biological Molecules

Carbon forms four covalent bonds, allowing for a vast diversity of molecular shapes and sizes.
Organic compounds: Molecules containing carbon bonded to other elements.
Carbon skeletons can be linear, branched, or ring-shaped.

Functional Groups in Organic Molecules

Functional groups containing H, N, O, P, S confer specific chemical properties.
Amino groups: Act as bases (accept protons).
Carboxyl groups: Act as acids (donate protons).
Hydroxyl groups: Act as weak acids.
Phosphate groups: Carry negative charges.
Sulfhydryl groups: Form disulfide bonds, stabilizing protein structure.

Macromolecules and Polymerization

Macromolecules: Large molecules made of smaller subunits (monomers).
Polymerization: Monomers join via condensation reactions (loss of water); broken by hydrolysis (addition of water).
Hydrolysis increases entropy and is energetically favorable; polymerization requires high monomer concentration.
Macromolecules (proteins, nucleic acids, carbohydrates) may have formed early in chemical evolution.

Table: Comparison of Bond Types

Bond Type	Electron Sharing	Example
Nonpolar Covalent	Equal	H2, CH4
Polar Covalent	Unequal	H2O, NH3
Ionic	Transferred	NaCl

Additional info: These notes synthesize and expand upon the provided lecture slides and textbook excerpts, ensuring coverage of all foundational concepts in Chapter 2 relevant to water, carbon, and the chemical basis of life.