Chemical Foundation of Life: Chapter 2

Chemical Foundation of Life

• Chapter 2 explores the chemical foundation of life, including atoms, molecules, water, and carbon

Atoms are the Building Blocks of Molecules

• Life is composed of matter.
• Elements are unique forms of matter possessing specific chemical and physical properties.

Elements and the Living World

• Elements cannot be broken down into smaller substances.
• Each element is designated by a chemical symbol, consisting of one or two letters.
• Examples: Sulfur (S) and Calcium (Ca)
• Four most common elements in living organisms:
  • Oxygen (O), approximately 65% in humans, 21% in the atmosphere, and 46% in Earth's crust
  • Carbon (C), approximately 18% in humans, trace amounts in the atmosphere and Earth's crust
  • Hydrogen (H), approximately 10% in humans, trace amounts in the atmosphere, and 0.1% in Earth's crust
  • Nitrogen (N), approximately 3% in humans, 78% in the atmosphere, and trace amounts in Earth's crust
  • Sulfur and Phosphorus are also important elements.

The Structure of the Atom

• Atom refers to the smallest unit of matter that retains all chemical properties of an element.

• Example: gold

• Atoms contain two regions:

  • Nucleus: the atom's center, containing protons and neutrons.
  • Outermost region: electrons orbiting the nucleus.

• Protons, neutrons, and electrons are referred to as subatomic particles.

Key Properties of Sub-Atomic Particles

• Proton: Charge of +1, mass of 1 amu, located in the nucleus
• Neutron: Charge of 0, mass of 1 amu, located in the nucleus
• Electron: Charge of -1, mass of 0 amu, located in orbitals outside the nucleus
• In neutral, uncharged atoms, the number of protons equals the number of electrons.

Atomic Number and Atomic Mass

• Atoms of each element have a specific number of protons and electrons.
• Atomic number: the number of protons
  • Each element has a distinct atomic number
• Mass number: the mass of the atom, equal to the number of protons and neutrons
• The number of neutrons can vary in an element.
• Isotopes: elements with different numbers of neutrons
• Electrons don't need to be included in calculation of mass number.
• To calculate the number of neutrons in an element, subtract the atomic number from the mass number

Atomic Mass vs. Atomic Number

• Carbon has an atomic number (number of protons) of 6.
• Carbon exists in two stable isotopes with mass numbers of 12 and 13, respectively.
• Isotopes differ in the number of neutrons.
• Carbon's atomic mass is approximately 12.11, representing the average mass of all types of carbon atoms.

Electron Shells and the Bohr Model

• Atoms with neutral charges. the number of protons equals the number of electrons the number of electrons equals the atomic number
• Orbitals: electron shells at a specific distance from the nucleus
• Distance is also related to energy levels
• An electron normally exists in the lowest available energy shell
• Electrons fill orbitals closest to the nucleus first, then those further away in order (i.e., 1n fills first, then 2n, then 3n, etc.)

Electrons Filling Their Shells

• Outer shell is known as the valence shell.
• The most stable configuration occurs when the valence shell is filled.

Electrons Filling Their Shells

• The octet rule states that with the exception of the innermost shell (which fills at two electrons), the next two shells are stable when they have eight electrons in their valence shell.

Chemical Reactions

• Element groups in the periodic table are based on how electrons distribute amongst orbitals.
• Chemical reactions are changes in the distribution of electrons between atoms, resulting in shared electrons.

Chemical Reactions

• Reactants: substances used at the beginning of a reaction
• Products: substances formed at the end of the reaction
• 2H₂O₂ → 2H₂O + O₂ with reactants yielding the products

Chemical Reactions Can Be Reversible or Irreversible

• An irreversible reaction proceeds in one direction until all reactants are used up (example: cooking food).
• 2H2O2 → 2H2O + O2
• A reversible reaction converts reactants to products, but some product can be converted back to reactant.
• CO₂ + H₂O ⇄ H₂CO₃

How Do Atoms Bond to Form Molecules?

• Chemical bond: an attractive force that links atoms together to form molecules

Types of Chemical Bonds

• Two principle types of chemical bonds involving the sharing or donation of electrons:
  • Ionic bonds
  • Covalent bonds (single, double, or triple, and categorized as polar or nonpolar)
• Weaker bonds involve attractions without complete sharing or donation of electrons:
  • Hydrogen bonds

Ionic Bonds

• Ionic bond formation: Some atoms lose electrons, while others gain electrons to achieve an octet.
• Sodium (Na) is an example of a cation, which is positively charged.
• Chloride (Cl-) is an example of an anion, which is negatively charged.
• The suffix "-ide" typically indicates anions.

Covalent Bonds

• To achieve the octet rule, electrons can also be shared between atoms.
• When two hydrogens and an oxygen share pairs of electrons via covalent bonds, a water molecule is formed.

Covalent Bonds

• More than one set of electrons can be shared.
• Double bonds, and covalent bonds can occure
• The oxygen atoms in an O2 molecule are joined by double bonds

Polar Bonds-Covalent Bonds

• Polar covalent bonds, electrons are unequally shared by the atoms and attracted more to one nucleus than the other
• Because electrons are not equally distributed around the atoms of the bond, there is an unequal distribution of charge
• Water has polar covalent bonds
• Pole will result if these bonds are charged

Non-Polar Bonds-Covalent Bonds

• Non-polar covalent bonds, electrons are equally shared by the atoms
• Both bond type and molecular shape determine whether a molecule is polar or nonpolar.
• There is no charge resulting from this type of bond

Weaker Bonds and Interactions

• Hydrogen bonds involved interactions between the partial positive charge of hydrogen and the partial negative charge of a more electronegative atom on another molecule.
• Vander Waals interactions are weak attractions or interactions between two or more molecules in close proximity due to changes in electron density

Water

• Most critical molecule for life on earth
• It's polar nature and ability to form hydrogen bonds make it essential

Water - Essential to Life

• Polar molecule and ability to form hydrogen bonds.
• Hydrogen Bonds.

Properties of Water

• The chemical bonds between hydrogen and oxygen in water are polar covalent bonds.

• Oxygen is more electronegative than hydrogen.

  • Oxygen has a slightly negative charge.
  • Hydrogen has a slightly positive charge.

• Hydrogen bond forms between one water molecule to the oxygen of an adjacent water molecule.

Polar and Nonpolar

• Oil and water do not mix
• Oil is hydrophobic, meaning "water-fearing."
• Substances that mix with water and dissolve are hydrophilic, meaning "water-loving."

Hydrogen Bonds and the States of Water

• Liquid: hydrogen bonds are constantly made, broken, and remade.
• Gas: increased kinetic energy causes hydrogen bonds to break, and molecules escape into the air.
• Solid: a crystalline structure is maintained by hydrogen bonds, introducing space between molecules, resulting in less densely packed ice that floats.

Water's Solvent Properties

• Ions and polar molecules can dissolve in water (hydrophilic).
• Water is the solvent.
• The compounds dissolved or mixed in with the water are the solute.
• Solvent + solute dissolve into a solution.

Hydrogen Bonds

• Water can form hydrogen bonds with other polar molecules and ions.
• Dissociation of NaCl in water occurs as atoms break off and form ions.
• When table salt (NaCl) is mixed in water, hydration shells are formed around the ions.

Carbon

• An Essential element of life is Carbon
• Carbon: NH3NotN4Hyt

Carbon is an Essential Atom of Life

• Carbon (C): a key component of macromolecules (proteins, carbohydrates, lipids, and nucleic acids).
• Carbon-containing molecules are known as organic molecules.
• Carbon forms covalent bonds with up to four different atoms.
• Each carbon has four electrons in the outer shell and forms four covalent bonds to "fill" the outer shell.
• This allows it to achieve the octet rule.
• Carbon serves as the backbone for the macromolecules.

Hydrocarbons

• Hydrocarbon = carbon + hydrogen
• Covalent bonds between atoms in hydrocarbons store energy.
• This energy is released when these molecules are burned.
• Hydrocarbons are used as fuel.

Hydrocarbon Chains

• Carbaliphatic molecule refers to Hydrogen Chains
• Carbon forms single bonds with other atoms - shape is tetrahedral
• Carbon double bonds shape is planar, or flat.
• Single bonds, like those found in ethane, are able to rotate while double bonds, like those found in ethene cannot rotate, so the atoms on either side are locked in place.

Hydrocarbon Rings

• Ring and carbon chains are aka Aromatic Hydrocarbons
• Carbon rings can form five and six-membered rings.
• Single or double bonds may connect the carbons in the ring
• Benzene: important hydrocarbon ring, used in some amino acids, cholesterol and its derivatives
• Nitrogen may be substituted for carbon.

Isomers

• Isomers: molecules that have the same chemical formula but differ in placement or arrangement of atoms or types of bonds between atoms
  • Structural isomers: have a different covalent arrangement of atoms
  • Geometric isomers: have a different arrangement of atoms around a double bond
  • Enantiomers: molecules that share chemical formula and bonds but differ in 3D placement of atoms; have mirror images

Trans vs Cis Molecules

• Some long chain hydrocarbons can have one or more double bonds
• Trans configuration - carbons are on opposite sides of double bond
• Cis configuration - carbons on same side of double bond

Enantiomers

• D-alanine and L-alanine: mirror images
• You cannot superimpose these two structures on each other
• Only the L-forms of amino acids are used to make proteins

Functional groups

• Functional groups: groups of atoms within a molecule that confer consistent specific properties to these molecules
• Each of the four types of macromolecules has its own set of characteristic functional groups Functional groups often interact with other functional groups via hydrogen bonds.
• Functional groups participate in chemical reactions

Hydrogen Bonds

• Hydrogen bonds between functional groups helps stabilizes biological molecules and allows them to perform their biological function in relation to DNA structure.