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Matter
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
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Atoms
the smallest unit of matter that retains the properties of an element
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Atomic number
– The number of protons in the element
– Written as a subscript to the lower left of the atomic symbol
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Mass number
– 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
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Isotopes
- 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
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Examples of isotopes
• 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
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Radioactive Isotopes
- • 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
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Detecting radioactive isotopes
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
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Chemical Bonds
Chemical bonds
– Interactions between valence electrons of atoms
– Result in completing the valence shell
• Examples
- – Covalent- sharing valence electrons
- – Ionic- transferring valence electrons
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Covalent bonds
- • 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
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Polar Covalent Bonds
- • 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•
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Polar covalent bonds in a water molecule
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Polar vs. Non-polar covalent bonds
- • 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
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Ionic Bonds
- • 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
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Hydrogen bonds
- • 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
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Van der Waals
• 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)
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Molecular shape
• 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
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