Biochemistry Test Questions – Flashcards
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Hydrogen, Carbon, Oxygen, Nitrogen. (most abundant in all organims
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First tier (Four elements make > 99% of all atoms in living systems)
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Calcium, Chlorine, Magnesium Phosphorus, Potassium Sodium, Sulfur. Found in all organisms
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Second Tier
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Cobalt, Copper, Iron, Manganese, Zinc. Present in small amounts in all organisms and essential to life
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Third tier
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Hydrogen, Oxygen, Carbon, Nitrogen, Phosphorous, Sulfur
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The most common atoms in biological systems
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Molecular weight, number of protons, electrons, isotopes
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physical properties
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Valence properties, bonding geometryelectro-negativity
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chemical properties
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(18-64 daltons). carbon dioxide, ammonia, nitrogen, nitrate. (ex: autotrophs are able to use co2 as a precursor to synthesize organic molecules)
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The inorganic precursors
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(50-250 daltons). pyruvate, citrate, succinate, glyceraldehine-3-phosphate, fructose 1-6 biphosphate, 3 phosphoglyceric acid
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types of metabolites
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located inside cells. Metabolites exist in dynamic steady state - they are constantly transformed and reformed.
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metabolites location
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precursors or intermediates in cell metabolism ( which provide a metabolic resource for synthesis of the cell's metabolism. They also function to regulate and control the pace of metabolism.
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metabolites function
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(100-350 daltons). amino acids, nucleotides, monosaccharides, fatty acids, glycerides
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building blocks
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are used to form macromolecules in biological systems
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building blocks function
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(1e^3-1e^5 daltons). proteins, nucleic acids, polysaccharides, lipids
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macromolecules
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A unit used in expressing the molecular weight, equivalent to atomic mass unit.
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dalton
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ribosomes, cytoskelaton, multienzyme complexes
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supramolecular complexes
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macromolecules
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supramolecular complexes are formed from
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Composition, Covalent structure, Bonding and molecular geometry
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Properties of molecules based on several levels of organization
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spherically symmetrical
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S- orbitals are
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distorted ellipsoids with two lobes that join at the nucleus
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P-orbitals are
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as far away from each other as possible
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Electron pairs will assume a position
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bond angles of 104.5° (providing for the maximum spacing between electron pairs)
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The stereochemistry of water
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has a classic tetrahedral arrangement with angles of 109.5° (ch4)
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stereochemistry of methane
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allowing for maximum spacing of electron pairs with angles of 106.75° (nh3)
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stereochemistry of ammonia
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Lone pairs orbitals are shorter and occupy more space than the bonding pair orbitals. This creates more repulsion between a lone pair and a bonding pair compared to repulsion between two bonding pairs. This forces the bonding pairs together slightly which reduces the bond angle from 109.5° to ~107°. This is the same reason why water has bond angles of 104.5°.
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bonding angle repulsion
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It is the complete orbital geometry (bonding and non-bonding)
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Determining shape accurately
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of the valence electrons Each total -1 in net charge
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"Electron clouds"
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When the electronegativity of the atoms is equal, the negative charge of the bonding orbital is equally dispersed between the two atoms.
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covalent bond axis
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FONClBCSHPNaK
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electronegativity
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a bond in which thereis an electric charge gradient along the axis of the bond.
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Polar Covalent Bonds
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significant differences in charge distribution acrossthe O-H covalent bond. (This creates a dipole moment and can cause a molecule to become polar depending on the configuration of the molecule.)
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The difference in electronegativity between hydrogen and Oxygen results in
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Because of the geometry of the molecule and the polar nature of its covalent bonds,water as a whole is a dipole. (, two opposing ends of the molecule have opposing electric charges; a line can be drawn across the compound from one localized charge to its opposite in the other end. )
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Water as a Dipole
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a molecule that exhibits polarity with regards to localized electric charges.
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dipole
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The dipole moment is proportional to both the physical distance between the electrically opposing "poles"and the charge difference. (The dipole moment expresses the magnitude of the molecule'spolarity.)
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dipole moment
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qx=(charge difference ● distance)
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dipole moment: U=
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They are symmetrical molecules. The dipole moments on both sides cancel each other creating no net dipole moment. This makes these molecules non polar.
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Why does Carbon dioxide and P-Dichlorobeneze have a dipole moment of 0 even though there is a charge difference between the atoms?
