Biology 180 Chapter 2

Anything that takes up space and has mass.

• Is composed of elements
• – Elements cannot be broken down to substances with different chemical or physical properties
• – 92 Naturally occurring elements
• – 25 elements found in organisms

• 11 Most common found in life

• – 96% of life forms are carbon (C), oxygen (O) , hydrogen (H),nitrogen (N)
• – ~4% of life forms are phosphorus (P), sulfur (S), calcium (Ca),potassium (K), Sodium (Na), Chlorine (Cl), Magnesium (Mg)

• 14 remaining trace elements are only about 0.01% of the mass of life forms

the smallest unit of matter that retains the properties of an element

– The number of protons in the element

– Written as a subscript to the lower left of the atomic symbol

– Approximation of the total mass of an atom

– Nearly equals the mass of the protons plus the neutrons

– Measured in amu (atomic mass units) or Daltons

– Written as a superscript to the upper left of the atomic symbol

• Elements can have isotopes
•    Atoms with the same number of protons but differ in the number of neutrons

• Each isotope of an atom has a different atomic mass.
•       Remember each neutron has a mass of approximately 1 Dalton

• Carbon

• – Carbon –12 is the most common isotope ofcarbon (99% of carbon)
• • It has 6 protons, 6 neutrons, 6 electrons–

• Carbon-13 (1% of carbon)
• • It has 6 protons, 7 neutrons, 6 electrons

• Carbon-14 is used for carbon dating youngfossils (<1% of carbon)
• • It has 6 protons, 8 neutrons, 6 electrons

• • The atomic nucleus of some isotopes can be unstable
• • Release particles and energy as the nucleus decays
• • Results in a change in proton number
• – Therefore the isotope decays into a new element!
• • Some useful isotopes in the field of biology
• – 14C= Used to date fossils
• – 32P= Used to radioactively label DNA
• – 35S=Used to radioactively label proteins in vivo
• – 125I=Used to radioactively label proteins in vitro

Emissions expose photographic film

• Scintillation counter
• – Radioactive sample is placed in scintillation fluid

– Energy released by isotope excites compounds in the fluid

– Fluid flashes and the flashes are quantitated

Chemical bonds

– Interactions between valence electrons of atoms

– Result in completing the valence shell

• Examples

• – Covalent- sharing valence electrons
• – Ionic- transferring valence electrons

• • Nuclei share pairs of electrons
• 1. Single Bond: atoms share 1 pair of electrons

2. Double Bonds: atoms share 2 pairs of electrons

3. Triple Bonds: atoms share 3 pairs of electrons

• • No net charge results
• • Valence shell of each atom completed
• • Strongest bonds in living organisms

• • Electronegativity
• – Sometimes one or more of the atoms shares itselectrons unequally
• – Caused by the attraction of an atom for the electrons ofa covalent bond
• – Results in one atom having the electrons in their spacemore often than the one(s) its sharing with

• • Causes partial charges to form on a molecule
• – Partial negative charge (delta-) occurs on the atom thatdraws the electrons
• – Partial positive charge (delta+) occurs on the other•

• • Non-polar covalent bonds
•   – The atoms in the covalent bond equally share theelectrons
•   – Equal electronegativity
• • Polar covalent bonds
• – The atoms in the covalent bond unequally share the electrons
• – Unequal electronegativity
• – A molecule that has polar covalent bonds is called a polar molecule

Example: water is a polar molecule

• • Transfer of electrons
• – The difference in electronegativity of one atom results in the removal of electrons from the other atom
• • Results in ions
• – Cation is positive
• – Anion is negative
• • Ions are attracted to form ionic compounds
• • Can form a crystal in the absence of water
• – Responsible for strength of minerals like agate andmarble.
• • Can ionize in water
• -Relatively weak in water

• • Forms between molecules
• • 2 electronegative atoms of different molecules are attracted to each other
• – delta- is attracted to the delta+
• •In living systems
• – A delta+ hydrogen is attracted to a delta-
• nitrogen or oxygen

• Forms between molecules

• Momentary positive and negative charges created by random placements of electrons

– causes molecules to attract to each other

• Occurs at very short distances between two atoms

• Very weak chemical bond

– But are additive and important when surfaces are brought very close together (remember the Geckos)

• Weak interactions influence shape of large molecules in living systems

• – Weak interactions in living systems
• - hydrogen,ionic, and van der Waals

• The functioning of a cell and communication between cells relies on“lock and key” interactions between molecules

• – Ex. Receptor and ligands,
• – Ex. Enzymes and substrates