Biology chapter 2: the chemistry of biology

Importance of Chemistry

  • Chemistry is important and this lecture will introduce some basic topics.
  • Focus will be on the molecular level of organization.

Elements and Atoms

  • The periodic table contains all sorts of different elements found in the environment.
  • Molecules are made up of atoms.
  • Atoms are made up of subatomic structures: protons, neutrons, and electrons.

Subatomic Particles

  • Protons: Positive charge
  • Neutrons: Neutral charge
  • Electrons: Negative charge
  • Charge interactions determine how elements and atoms come together to form molecules.

Matter

  • Matter: Substances that have mass and weight and take up space.
  • An atom is an example of a single element.

Elements in Life

  • Life is composed of a limited set of elements; not everything on the periodic table is required.

Periodic Table

  • Different atoms have different atomic weights.
  • Hydrogen (H) is the smallest element.
  • Helium (He) is the next smallest.
  • Important elements for life:

Key Elements for Organic Molecules

  • Hydrogen: Critical, cells are loosely a bag of water.
  • Oxygen: Critical, cells are loosely a bag of water. Water is H_2O.
  • Carbon: All organic molecules contain carbon.
  • Nitrogen: Found in all proteins (amino acids) and nucleic acids (genetic material).
  • Sulfur: Found in certain proteins or amino acids.
  • Phosphorus: Important component of genetic material (DNA and RNA) and cell membranes (phospholipids).

Additional Elements

  • Peach-colored elements: Mineral-type things needed for life (salts, minerals).
  • Examples: Sodium (Na), magnesium (Mg), potassium (K), calcium (Ca), manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn), silicone (Si), chloride (Cl).
  • These are more trace elements.

Atomic Structure

  • Atoms have a nucleus containing:
    • Positively charged protons
    • Neutrally charged neutrons
  • Negatively charged electrons circle the nucleus.
  • Electrons are important in molecule formation through the sharing of electrons.

Chemical Composition of the Body

  • Oxygen (O): 65% of body mass
  • Hydrogen (H): 10% of body mass
  • Carbon (C): 18% of body mass
  • Nitrogen (N): 3% of body mass
  • Calcium (Ca), Phosphorus (P), Potassium (K), etc., are also important.

Vitamins and Minerals

  • Iodine: Important for metabolism.
  • Iron: Hemoglobin carries oxygen; deficiency leads to anemia.
  • Iodine deficiency: Can cause goiter (enlarged thyroid gland).
  • Multivitamins can be used as supplements to a natural food diet.
  • Many additives in processed foods function as preservatives or provide microdoses of vitamins.

Atoms and Compounds

  • Some atoms can form molecules on their own (e.g., O_2).
  • Molecules with different types of atoms form compounds (e.g., H_2O).
  • Compounds: Different atoms mixed in a ratio.

Examples of Compounds

  • Water (H_2O): Two hydrogen atoms for every oxygen atom.
  • Sodium chloride (NaCl): Table salt, one-to-one ratio of sodium and chloride.
  • Environmental oxygen: O_2 gas.
  • Hydrogen gas: H_2

Subatomic Particles Revisited

  • Protons: Positive charge, atomic weight of one.
  • Neutrons: Neutral charge, atomic weight of one.
  • Electrons: Negative charge, very small mass (not included in molecular weight).

Key Terminology

  • Atom
  • Molecule
  • Compound
  • Element
  • Subatomic particles: proton, neutron, and electron

Atomic Structure Details

  • Nucleus: Contains positively charged protons and neutrally charged neutrons (where mass exists).
  • Electrons circle the nucleus in orbitals (electron cloud).

Elements Defined

  • Element: A substance made up of only one type of atom.
  • Example: Oxygen (O_2) is an element made of two oxygen atoms.

Differences in Atoms and Elements

  • Atoms and elements differ in the number of protons, neutrons, and electrons.
  • Hydrogen: One proton and one electron.
  • Helium: Two protons and two electrons.
  • Carbon: Six protons and six neutrons.

Radioactivity and Isotopes

  • Radioactivity: Occurs when there are different proportions of neutrons and protons.
  • Radioisotope: Differentials in protons and neutrons.
  • Example: Radioactive carbon has two additional neutrons.
  • Radioactivity can damage DNA and can become incorporated into the body (e.g., radioactive iodine in the thyroid).

Electron Clouds and Chemical Bonds

  • Molecules form as atoms come together to form molecules. Electron clouds like to be full.
  • Atoms share electrons with neighboring atoms to fill electron clouds.
  • Covalent Chemical Bond: Sharing electrons with another atom forms a strong chemical bond.

Electron Orbitals

  • Limited number of elements go into organic molecules: hydrogen, carbon, nitrogen, and oxygen.
  • Electron shell/orbital: Innermost orbital wants two electrons; the second orbital wants eight electrons.

Electron Sharing

  • Hydrogen: Wants to share its electron.
  • Hydrogen gas: Two hydrogen atoms share electrons for a total of two in the orbital.
  • Carbon: Shares four electrons.
  • Nitrogen: Wants to pick up three electrons.
  • Oxygen: Wants to share two electrons.
  • Atoms want to fill their electron orbitals/shells.

Covalent Bonds

  • Key concept: Covalent bond when you share electrons with another atom; these are strong bonds.
  • Nitrogen wants to share three.
  • Oxygen wants to share two.
  • The number of electrons in the outermost shell determines reactivity.

Stable vs. Reactive Molecules

  • Molecules with full outer shells are stable.
  • If the outer shell is not full, the molecule is reactive.
  • Helium: Naturally has a full shell and is inert.
  • Sharing electrons is important for chemical bonding.
  • Covalent bond is one of the strongest and most important chemical bonds in biology.

Types of Chemical Bonds

  • Covalent bond: Strongest bond we'll discuss atoms share electrons.
  • Ionic and hydrogen bonds: Weaker bonds that can be broken apart more easily.

Ionic Bonds

  • Ionic Bonds: Involve transferring electrons.
  • Sodium Chloride (NaCl): Table salt made of sodium and chloride atoms.

Electron Transfer and Charges

  • Electron Transfer Changes charges.
  • Reduction: Acquiring an electron (reduces charge making it more negative).
  • Oxidation: Giving up an electron (becomes more positive).
  • Opposite charges attract each other (ionic bond).

Example of Ionic Bond Formation

  • Chlorine (Cl): Has seven electrons in its outer shell wants eight.
  • Sodium (Na): Has one electron in its outer shell would like to have eight.
  • Sodium gives up electron in its outer shell (transfers it to chlorine).
  • Chlorine now has a full outer shell, and sodium’s second shell becomes full.

Ionic Bond Charges

  • Sodium gives up a negative charge, becomes positively charged.
  • Chlorine adds a negative charge, becomes negatively charged.
  • Opposite charges attract each other.

Crystal Formation

  • Arrangement of charges forms a crystal.
  • Alternating Pattern: Negatively charged particle, positively charged, negatively charged so on.

Covalent Bonds Details

  • Instead of transferring electrons, covalent bonds involve sharing.
  • Tighest/strongest type of bond that we're going to discuss.

Single vs. Double Bonds

  • Sharing electron: Single Bond
  • Sometimes two shared covalent bonds = Double Covalent Bond: even stronger!
  • Example for double bond: O_2 gas; share two fill both outer layers.

Examples of Covalent Bonds

  • Methane: Carbon has four in its Outer Shell picks up four other separate hydrogens in order to achieve electron sharing.
  • Water: Oxygen shares a pair of electrons from hydrogen molecule.

Charge Distribution in Water

  • Distribution of charge happens!
  • Electronegativity: Stronger Pull electron to Center
  • Nonpolar: Equal pull no distribution of charges.
  • Polar: Molecule with charge distribution.

Hydrogen Bonds

  • Weakest bonds we're going to explore easily break!
  • Molecules with charge distributions create a polar charge between particles.
  • Important for DNA - Easy access to information in DNA because separation/access to nucleic acid is granted easily.