Water and Carbon: The Chemical Basis of Life

Water and Carbon: The Chemical Basis of Life

• Life on Earth relies heavily upon fundamental chemical principles
• Chemical evolution is a leading explanation for the origin of life, involving the formation of complex carbon-containing molecules
• This process eventually led to self-replicating molecules, transitioning life from chemical to biological evolution
• Biological evolution then took over, where the original molecule multiplied, and the descendants became metabolically active, acquired a membrane, and fulfilled the five basic characteristics of life
• 96% of matter in organisms consists of four types of atoms: hydrogen, carbon, nitrogen, and oxygen
• Chemical evolution involved the transition from simple substances to complex structures in living cells
• Understanding the physical structures of hydrogen, carbon, nitrogen, and oxygen atoms is key
• The structures of simple molecules like water and carbon dioxide are fundamental building blocks
• Atoms consist of a nucleus with protons and neutrons surrounded by orbiting electrons

Basic Atomic Structure

• The nucleus is made up of positively charged protons and electrically neutral neutrons
• Electrons orbit the nucleus, carrying a negative charge
• Atoms are electrically neutral because the positive charge of protons is balanced by the negative charge of electrons
• The nucleus is significantly smaller than the overall size of the atom

Understanding Elements

• Elements are made up of only one type of atom
• Each element has a unique atomic number, which is equal to the number of protons in the nucleus of its atom. It is written as a subscript before the element symbol.
• The mass number is the sum of protons plus neutrons in an atom

Atoms are tiny, so how do we weigh them?

• The mass of a proton and neutron is one dalton (Da)
• The mass of an electron is negligible
• The mass number is equal to the mass of an atom in Daltons
• Isotopes are forms of an element with differing numbers of neutrons and therefore different masses
• The atomic weight of an element is the average mass of all naturally occurring isotopes of that element, taking into account their abundance

Weight of molecules in grams

• One mole of an element or molecule is equal to 6.022 x 10²³ atoms or molecules
• The atomic weight of an element can be expressed in grams
• Molecular weight is the sum of the atomic weights of all the atoms in a molecule, and molecular weight of a molecule expressed in grams

The Atomic Structure of the First 18 Elements

• Key elements (C, H, N, O, P, and S) make up over 99% of atoms in the body
• Electrons orbit the nucleus in specific regions called orbitals
• Orbitals are grouped into electron shells
• Shells are numbered (1,2,3) with lower numbers being closer to the nucleus
• Each shell holds a specific number of electrons, first filling the innermost shells
• Electrons in the outermost shell are valence electrons, which determine the chemical behavior of the atom, and participating in chemical bonds

Atomic Structure and Electron Shells

• The arrangement of electrons around the nucleus is crucial in determining an element's chemical behavior
• Electrons orbit atomic nuclei in specific regions called orbitals.
• Orbitals are grouped into electron shells (1, 2, 3, etc.) which correspond to different distances from the nucleus
• Each electron shell contains a specific number of orbitals, each holding a maximum of two electrons
• Electrons first fill the innermost shells before filling outer shells

Covalent Bonding Holding Molecules Together By Sharing Electrons

• Atoms achieve stability by forming covalent bonds, sharing electrons
• Hydrogen atoms, for example, each have one unpaired electron, enabling sharing with other hydrogen atoms to obtain a stable valence shell
• Covalent bonds involve the sharing of electrons between atoms, which creates a stable arrangement and increases stability

Electrons in Covalent Bonds are Not Always Shared Equally

• In some cases, electrons are shared equally between atoms forming a nonpolar covalent bond(like in the hydrogen molecule H₂)
• In other cases, electrons are shared unevenly with one atom pulling the electron more strongly than the other, forming a polar covalent bond (like in the water molecule H₂O)
• Electronegativity refers to the ability of an atom to attract electrons towards itself within a covalent bond.

Nonpolar vs Polar Covalent Bonds

• In nonpolar covalent bonds, electrons are shared equally between atoms and the structure of the molecule is symmetric in nature (example: C-H bond)
• In polar covalent bonds, electrons are shared unequally; the electrons spend more time closer to the atom with higher electronegativity (example: O-H bond in a water molecule)

Electronegativity: Strength With which Atoms Pull Electrons Toward Themselves

• Electronegativity is determined by the number of protons and the distance of the valence shell from the nucleus
• Elements with greater numbers of protons and valence shells that are closer to the nucleus would have significantly higher electronegativity
• Electronegativity increases moving up and to the right in the periodic table
• Oxygen has a higher electronegativity than hydrogen; therefore, electrons spend more time near the oxygen atom in a water molecule

Polar Bonds Produce Partial Charges on Atoms

• Due to differing electronegativity, polar covalent bonds in water create partial positive charges on hydrogen atoms and a partial negative charge on the oxygen atom
• These partial charges are key to water's unique properties, including its ability to create hydrogen bonds with other molecules

Ionic Bonding

• Ionic bonds form when atoms transfer electrons wholly instead of sharing them
• Transferring electrons gives each of the involved atoms a complete outer shell of electrons, making them more stable
• Loss of an electron results in a positive charge (cation)
• Gain of an electron results in a negative charge (anion)

The Electron-Sharing Continuum

• The type of covalent bond (nonpolar, polar, and ionic) is determined by the difference in electronegativity between atoms

Unpaired Electrons in the Valence Shell Can Participate in Double and Triple Covalent Bonds

• The number of unpaired electrons determines how many bonds an atom can form
• Unpaired electrons can form double or triple bonds, leading to more complex molecular structures

Molecule's Shape Often Dictates Its Behavior

• The shape of molecules influences their behavior in chemical and biological processes
• Methane has a tetrahedral shape, and water is bent, due to the arrangement of bonds and the repulsive forces between electron pairs

Molecules Can Be Represented Several Ways

• Several representations are used to depict molecules, including molecular formulas, structural formulas, ball-and-stick models, and space-filling models

Properties of Water and the Early Oceans

• Water is an excellent solvent, dissolving many substances, making them more susceptible to chemical reactions
• Properties of water are directly correlated to its unique atomic structure

A Water Can Interact with Other Water Molecules

• Water is a polar molecule, with a partial negative charge on the oxygen atom and partial positive charges on the hydrogen atoms
• Water molecules interact with each other through hydrogen bonds, which are weak electrostatic attractions between the positive hydrogen and negative oxygen of adjacent water molecules

Water Is an Efficient Solvent

• Water's ability to form hydrogen bonds makes it an efficient solvent for polar and charged molecules

Not Everything Dissolves in Water

• Hydrophobic molecules are nonpolar and do not dissolve in water
• Hydrophobic molecules interact with each other through van der Waals interactions to cluster together

Cohesion and Adhesion

• Water molecules exhibit strong cohesive forces (attraction among like molecules) as a result of hydrogen bonds
• Water also exhibits adhesion, the attraction between unlike molecules, such as water molecules and other polar surfaces
• The cohesion and adhesion properties of water have significant implications in a variety of biological and environmental processes

Surface Tension

• Cohesion causes water to have a high surface tension, which means its surface resists external forces that increase its surface area
• Surface tension is the cohesive force at the surface of a liquid

Water Is Denser as a Liquid Than as a Solid

• Water is denser as a liquid than as a solid (ice) because hydrogen bonds between molecules create a relatively open crystalline structure in ice compared to water; as a result, ice floats on water
• This unique property is vital for aquatic ecosystems, preserving life during cold conditions

Water Has a High Capacity for Absorbing Energy

• Water has a high specific heat capacity, meaning it takes more energy to change its temperature
• Many hydrogen bonds in water must break before water molecules can move faster, thus stabilizing temperature changes

The Role of Water in Acid-Base Chemical Reactions

• Chemical reactions involve the breaking and formation of chemical bonds
• Water can dissociate into hydrogen ions (H⁺) and hydroxide ions (OH^-) contributing to the acidity or basicity of a solution
• Chemical equilibrium in water is dynamic, with the rates of reaction proceeding in both directions being relatively balanced

Measuring the Concentration of Protons

• Moles quantify the number of molecules in a sample
• Molarity (M) quantifies the concentration of a solute in a solution; one mole of solute per liter of solution

The Role of Water in Acid-Base Chemical Reactions

• Acids increase hydrogen ion concentration in water.
• Bases decrease hydrogen ion concentration in water

The pH of a Solution in Acid-Base Reactions

• pH is a measure of the concentration of hydrogen ions in a solution
• pH scale ranges from 0 to 14; a lower pH means higher concentration of hydrogen ions
• The pH of most living cells is approximately 7 (neutral)

Chemical Reactions in Aqueous Systems

• Chemical reactions involve the rearrangement of atoms to form different substances
• The expressions or equations for chemical reactions should be balanced (the number of each type of atom on the left side of the equation is equal to the number of atoms on the right side of the equation)

What Makes a Chemical Reaction Spontaneous?

• Spontaneous reactions occur without external influence
• Two factors distinguish spontaneous reactions: whether products have lower potential energy and whether reaction products are less ordered than the reactants

Stanley Miller's Spark-Discharge Experiment in 1953

• A classic experiment demonstrating chemical evolution by simulating early Earth conditions (e.g., heat, electrical charges)
• This experiment produced organic molecules from simple gases, like ammonia and methane
• The results provided evidence for a potential pathway in the creation of life's building blocks from simple precursors

Life Is Carbon Based

• Life on Earth relies heavily on carbon-based molecules
• Carbon atoms can form extensive chains and rings, giving rise to a vast diversity of complex molecules with different functions. This versatility is due to carbon's ability to form up to four covalent bonds.

Functional Groups Define the Chemical Behavior of Organic Molecules

• Functional groups are specific groups of atoms attached to carbon chains that give molecules their particular chemical properties and behaviors
• They influence how molecules function in biological systems

Small Organic Molecules Can Assemble into Large Molecules

• Larger molecules (polymers) are formed from smaller molecules (monomers) through a process known as polymerization
• Polymerization involves linking monomers together, and it is a key step in forming macromolecules like proteins, nucleic acids, and carbohydrates

Polymers can be Extended or Broken Apart

• Polymers can be synthesized or broken down by creating or breaking the covalent bonds that link monomers, a process called condensation (dehydration) reactions, or hydrolysis, respectively
• Polymers are formed via condensation and broken down via hydrolysis.

Small Organic Molecules Can Assemble into Large Molecules cont

• Many polymers, the macromolecules of life, were produced and polymerized from simple monomers in the early environments on Earth
• The dominance of hydrolysis over polymerization in those early environments was key in directing how these organic building block polymers formed

End of Chapter Questions to Practice

• The questions provided are for practice and review for a specific chapter; questions 1, 2, 3, 5, 8, 12 and 16 are for the student to answer, and some questions may require referring to a particular associated case study to obtain the relevant data

This quiz explores the essential chemical principles underlying life on Earth. It covers the processes of chemical evolution, the formation of complex molecules, and the roles of key elements such as hydrogen, carbon, nitrogen, and oxygen. Understanding these concepts is crucial for grasping the transition from chemical to biological evolution.