Molecules, Bonds, and Water

• Biochemistry is the study of chemistry of living organisms.
• General Chemistry - Pt. 1

  • element = substance that cannot be broken down chemically into another substance
  • cells in our bodies are made of the same six elements:
  • carbon
  • hydrogen
  • oxygen
  • nitrogen
  • phosphorus
  • sulfer
  • These six elements can be represented in the acronym CHNOPS
• General Chemistry - Pt. 2

  • Atom = smallest unit of an element that still has all the properties of that element.
  • An atom has three subatomic particles
  • proton: + charge
  • electron: - charge
  • neutron: no charge
  • neutrons & protons are in the nucleus
  • electrons move in energy levels (orbitials) - they are in constant motion around the nucleus
  • 1st ring - 2 electrons
  • 2nd ring - 8 electrons
  • 3rd ring - 8 electrons
• General Chemistry - Pt. 3

  • Compound = more than one type of atom combined in set ratio
  • Ex: water = H2O & salt = NaCI
• General Chemistry - Pt. 4

  • Molecules: the smallest unit of a compound that can be divided and still have chemical properties of the compound
  • H2O = one molecule of water
  • O2 gas -> exception for a compound
• General Chemistry - Pt. 5

  • Symbols & formulas:
  • chemicals symbols -> shows the symbol for an atom
  • H = Hydrogen
  • chemical formulas -> show the number & kind of atoms in one molecule
  • H2O = water
  • Subscripts -> the number of each kind of atoms in a molecule
  • the "2" in H2O
  • 2 H2O -> presents two whole water molecules
• Chemical Bonds in Reactions - Pt. 1

  • Atom bond (join) together to form compounds
  • Ionic Bond
  • Definition of ions:
  • Positive (+) ions
  • Atoms with a + charge because they have lost electrons
  • Ex. Sodium (Na) gives up an electron and becomes Na+
  • Negative (-) Ions
  • Atoms with a - charge because they have gained electrons
• Chemical Bonds in Reactions - Pt. 2

  • An ionic bond is formed by attraction between oppositely charged ions
  • one atom transfers an electron to another atom in order to fill the outer orbital
  • the two atoms are now ions and are attracted to each other
  • Example:
  • Na+ gives its one outer e- to CI to become an NA+ ion
  • When CI takes the e- it becomes CI-
  • Na+ and CI- attracts and bond together forming NaCI (salt)

  
• Chemical Bonds in Reactions - Pt. 3

  • Covalent Bond:
  • Two or more atoms share electrons to fill their outer orbitals
  • Shared electrons move around the orbitals of both atoms.

  
• Chemical Bonds in Reactions - Pt. 4

  • Types of Covalent Bonds
  • Polar Covalent Bonds
  • electrons are not shared equally between atom
  • one side of the molecule has a slight + charge and the other side a slight - charge
  • this charge different is called polarity
  • water is polar: the O side is - and the H side is +
  • Because water is highly polar, it can pull other polar molecules apart. dissolving them. This makes water an excellent solvent in the human body. dissolving substances like sugars and salt in the blood for transport through the body.
• Chemical Bonds in Reactions - Pt. 5

  • Types of Covalent Bonds
  • Non-polar Covalent Bonds
  • electrons are shared equally (no polarity)
  • this property causes these molecules to repel water (which is polar)
  • Ex: oils & fats
• Chemical Bonds in Reactions - Pt. 6

  • Types of Covalent Bonds
  • Hydrogen Bond
  • Polar molecules form attractions between the slightly positive H atom of one molecule and the slightly negative atom on another molecule
  • Ex: water and another water
• Chemical Bonds in Reactions - Pt. 7

  • Acids, Bases, and Buffers
  • Water can react with compounds that dissolve to release ions (H+ or OH-)
  • These are called acids or bases
  • The concentrations of H+ and OH- that are formed are measured on a scaled called a pH scale
• Chemical Bonds in Reactions - Pt. 8

  • Acids, Bases, and Buffers
  • Acids: when they dissolve, they release H+ to a solution of water
  • ex: hydrochloric acid (HCI)
  • HCI -> H+ + CI-
  • Acids are 0-7 on the pH scale
• Chemical Bonds in Reactions - Pt. 9

  • Acids, Bases, and Buffers
  • Bases: when they dissolve, they add OH- to a solution of water
  • Ex: sodium hydroxide (NaOH)
  • NaOH -> Na+ + OH-
  • Bases are 7-14 on the pH scale
  • If the number of -OH and H+ are equal, then the solution is neutral and water has been made! H+ plus OH- is HOH (water!)
  • water has a pH of 7
• Chemical Bonds in Reactions - Pt. 10

  • Acids, Bases, and Buffers
  • Buffers
  • Cells need ideal H+ and OH- concentrations to order to maintain homeostasis
  • The pH of the fluids within most cells in the human body must be between 6.5-7.5
  • If the pH is lower or higher, it will affect the chemical reactions that take place within the cells.
• Chemical Bonds in Reactions - Pt. 11

  • Acids, Bases, and Buffers
  • Buffers
  • Buffers are weak acids or bases that react to prevent sudden changes in pH.
  • They donate or remove H+ or OH- to ensure optimal blood pH when there are fluctuations.
  • You have many natural buffers in your blood to maintain blood pH when there are fluctuations.
  • ex. activities like exercise can make blood acidic