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Biochemistry 1 FUNDAMENTALS Atoms and Molecules

Atlantic University School

Of Medicine

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Number Nomenclatures # Grams Prefix Log 10 1000 (1x10E3) Kg 3 1  (1x10E0) g 0 0.001 (1x10E-3) mg -3 0.000001 (1x10E-6) ug -6 1x10E-9 ng -9 1x10E-12 pg -12

Concentration in liquids Molar (M) [x] M = mol/Liter Consider M, mM, uM, nM, pM, etc

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Summary •  Symbols and Formulas. Symbols based on names have been

assigned to every element. Most consist of a single capital letter followed by a lower case letter. A few consist of a single capital letter. Temporary 3-letter symbols have been assigned to elements for which names have yet to be agreed upon. Compounds are represented by formulas made up of elemental symbols. The number of atoms of each element in a molecule is shown by subscripts.

•  Masses of Atoms and Molecules. Because of limitations of early weighing devices, the actual masses of individual atoms could not be determined. However, techniques were used at allowed relative or comparative masses of atoms to be measured. Relative masses called atomic weights have been assigned to each element, and are tabulated in the periodic table. The units used are atomic mass units or amu. Relative masses for molecules, called molecular weights, are determined by adding together the atomic weights of the atoms making up the molecules.

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•  Inside the Atom. Atoms are made up of numerous smaller particles, of which the most important to chemical studies are the proton, neutron, and electron. positively charged protons and neutral neutrons each have a relative mass of 1 amu, and are located in the nuclei of atoms. Negatively charged electrons with a mass of 1/1840 amu are located outside the nuclei of atoms.

•  Isotopes. Most elements in their neutral state are made up of more than one kind of atom. These different kinds of atoms of a specific element are called Isotopes and differ from one another only In the number of neutrons in their nuclei. A symbolism based on atomic number, mass number, and elemental symbol is used for specific Isotopes.

•  Isotopes and Atomic Weights. The atomic weights measured for elements are average weights that depend upon the percent of masses of the isotopes In the naturally occurring element. if the isotope percent abundances and isotopic masses are known for an element, its atomic weight can be calculated.

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•  Counting By Weighing. The assignment of relative masses to atoms and molecules makes It possible to weigh out samples of elements or compounds such that the numerical relationships between number of atoms or molecules in the samples are known. This leads to calculations in which combining masses of elements can be used to determine formulas for compounds formed.

•  The Mole. An extension of the counting by weighing idea leads to the mole concept In which the number of atoms in a specific sample of an element is determined. The sample size used Is a mass in grams equal to the atomic weight of the element. The number of atoms (called Avogadro's number) is, to 3 significant figures, 6.02 x 10 to the 23 power. Use of the mole concept allows useful factors to be determined for use in factor-unit calculations.

•  The Mole and Chemical Formulas. The mole concept when applied to molecular formulas gives numerous relationships which yield useful factors for factor-unit calculations.

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Formative Assessment

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Question 1

•  Atomic symbols for the elements are derived from either their greek or latin names. True False

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•  False

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Question 2

•  Determine the formula weight for calcium carbonate, CaCO3, in amu. 68.09 100.09 124.11 204.27

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•  100.09

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Question 3

•  How many electrons are in a hydride ion if it has a charge of -1? 0 1 2 3

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•  2

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Question 4

•  How many neutrons are found in the nucleus of a 37Cl atom? 17 18 20 37

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•  20

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Question 5

•  For isotopes to be of the same element, they must have different atomic masses. True False

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•  True

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Question 6

•  How many atoms are contained in a sample of water that weighs 9.008 grams Not enough information 1/2 of Avogadro's number Avogadros' number 1.5 of Avogadro's number

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•  1/2 of Avogadro's number

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Question 7

•  A mole of hydrogen gas contains the same number of atoms as a mole of fluorine gas. True False

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•  True

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Question 8

•  How many moles of aluminum are contained in 27.00 g of Al(OH)3? 0.346 0.614 1.000 1.038

•  Do this at Home for tomorrow

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Ibuprophen (NSAID) C13H18O2 FW = ?

Fever, Pain, Dysmenorrhea Inflammatory diseases rheumatoid arthritis

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Ibuprophen (NSAID) C13H18O2 206.29 MW FW AMU Daltons g/mol 400-1200 mg per dose 5 liters blood volume M = ? Fever,

Pain, Dysmenorrhea Inflammatory diseases rheumatoid arthritis

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Ibuprophen (NSAID) C13H18O2 206.29 MW FW AMU Daltons g/mol 400-1200 mg per dose 5 liters blood volume 1mM concentration in blood

Fever, Pain, Dysmenorrhea Inflammatory diseases rheumatoid arthritis

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Prostaglandin H2 Synthetase Cyclooxygenase 2 ~70Kd K-AMU Kg/mol Gastric Mucosa Kidneys Upregulated in many cancers

Arachadonic acid -> Prostaglandin

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Prostaglandin

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Prostaglandin H2 Synthetase Cyclooxygenase 2 Activity inhibited by NSAID COX 2 Ka = 1 pM [Ibuprofen] = 1mM Why so much drug?

Arachadonic acid -> Prostaglandin

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The end

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Moles Al(OH3)

•  0.346