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42 Cards in this Set
- Front
- Back
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What does an equilibrium constant reflect?
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The extent of chemical reaction or stabliity of noncovalent/weak binding of interacting molecules.
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What is Kd?
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Kd is the dissociation constant, the reciprocal of the equlibrium constant (Keq)
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Are chemical reactionsin a cell at equilibrium?
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No, they are at a steady state
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What is the usual energy source for energy-requiring chemical rxns and binding processes?
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Hydrolysis of high-energey phosphoanhydride bonds in ATP.
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What about C, H, O, N, S and P are good for biological molecules?
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1) nonmetals -> form stable covalent bonds w/ eachother 2) light elements -> strong bonds 3) except hydrogen, they form multiple bonds. C forms 3-dimensional bonds.
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What is a covalent bond?
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The overlapping of two half-filled orbitals. The overlapping forms a new orbital w/ 2 electrons. Sharing may be equal or unequal.
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What kind of delta-G do covalent bonds have
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Large, negative. (Bond dissociation energy = 049 - 119 kcal/mole)
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How strong are covalent bonds
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Very strong.
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What kinds of bonds are required for the formation of stable molecules for life?
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Covalent bonds.
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How are covalent bonds formed in living molecules
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Usually w/ the help of enzymes.
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Do S or P orbitals form stronger bonds?
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P orbitals (which extend out into space along an axis, while s orbitals stay centered around the nucleus)
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If an atom forms two or more covalent bonds using p orbitals, what will the bond angle be?
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They will be at right angles, as p-orbitals exist at right angles to each other. (as in H2S). This may not be the case in every instance d/t the existance of hybrid orbitals.
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What are the two types of covalent bonds?
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Polar and non-polar.
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Describe nonpolar covalent bonds
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They are formed by two atoms of a non-metal. B/c they have the same electronegativity, the electrons are shared equally between them. No partial charges are created. Include X2 and Carbon backbones.
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Describe polar covalent bonds
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Formed by nonmetal atoms that are different. Electronegativities are different (more protons or more shell->more sheilding) -> unequal sharing of electrons -> creation of partial charges in the molecule (dipoles)
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What is the most electronegative element?
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Flourine
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Are molecules with polar bonds polar?
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No, if the bonds are arranged symetrically they may be non-polar.
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What is a dipole?
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a molecule with two regions having opposite full or partial charges
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Describe the orbitals of carbon
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Carbon uses 4 hybrid SP3 orbitals. 1s and 2s are full, and 2px and 2py are half-full. Then one of the 2s electrons goes into 2pz, so both 2s and 2pz can form bonds (total=4). Normally the s bond would be weaker, but what happens is a hybid of one s and three p bonds is formed (sp3). Dissociation engergy = 102 kcal/mole. Can occasionally form an 3 SP2 or 2 SP orbitals (double and tripple bonding)
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What arangement does carbon bind in?
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A tetrahedron (109.5 degree seperation = max bond angle seperation).
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What kind of bonds does N form?
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4 SP3 (one w/ 2 electrons), w/ bond angle 107. Two electrons -> - charge -> basicity (proton receptor)
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What kind of bonds does O form?
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4 SP3 orbitals, w/ 2 filled w/ 2 electrons. Bond angle =105. H2O is polar.
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What kind of bonds does S form?
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2, 4, or 6 covalent bonds. (6=H2SO4)
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What kind of bonds does P form?
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5 covalent bonds (H3PO4).
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What are stereoisomers?
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non-superimposable chimical isomers that have identical covalent structures.
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What are the two classes of stereoisomers?
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Enantiomers are mirror-images. Diastereoisomers are non-mirror image chemical isomers.
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When do we see chirality?
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In asymmetric carbon atoms and mirror-image molecules that are optical isomers or stereoisomers.
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Do different stereoismoers of a molecule have different biological activity?
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yes
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Are amino acids chiral?
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All except glycine.
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Describe the optical activity of chiral compounds
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L rotates light left, D right, and an equal molar mixture does not rotate them.
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What form of amino acids are found in living things?
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Only the L forms.
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Describe differences between single and double bonds
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carbon can rotate freely at a single bond, not a double bond. 84 kcal/mol is needed to break a single bond, 170 kcal/mol. Double bonds are planar.
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What is the advantage of weak bonds?
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That they are weak - they allow biological processes to work (E.g. enzyme-substrate interactions). Weak bonds are reversable, which allows them to be used for regulation in metabolic processes (e.g. as neurotransmitter concentration decreases, it dissociates from the receptor, and action stops.)
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What is key-and-lock theory
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That molecular complementarity permits tight, specific binding of biomolecules. It consists of many weak bonds. The "lock and key" are specific d/t the three-dimensional complementarity of shape and charge b/c weak binding only occurs when the molecules get very close.
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Describe the properties of weak bonds
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1) They can be broken at physiological temps 2) They are relatively unstable 3) They have a short lifetime (avg. a fraction of a second). They are formed and broken constantly. 4) The bond length is longer than covalent bonds. 5) Some weak bonds have no stoichiometry [no ratio of atoms to each other], e.g. Van der waals forces. 6) Weak bonds do not have direction or impose restrictions of the relative orientations of bonded atoms (as in = or tripple bonds) 7) Only form as the bondable atoms randomly approach each other 8) They can be extremely strong collectively.
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What are the four types of weak bonds?
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1) ionic 2) hydrogen 3) van der waals 4) hydrophobic interactions
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Describe ionic bonds
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1) also called electrostatic 2) formed by transfer of valence electron 3) more characteristic of non-organic compounds 4) No directed in space (e.g. no bond angle -> formation of large crystals. 4) Bond dissociation energy = 5 kcal/mole 5) force is inversely proportional to the distance^2.
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Describe hydrogen bonds
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Form in any molecule where dipoles are created. Can form / dipole and ions. Bond dissociation energy = 4.5 kcal/mole. Directional but flexible.
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What determines a substance's solubility in water?
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Its ability to form hydrogen bonds.
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Why are most ionic sustances water soluble?
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B/c the energy of hydration (energy released when H2O bonds formed) exceeds the latice energy (energy released when ions form a crystiline structure). Crystaline ions have a lower entropy than solution.
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What are van der waals forces?
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Forces created by the creation of temporary dipoles which then continue to oscillate. They are the most common weak bond. Bond dissociation energy = 1-2 kcal/mole. Requires large numbers of bonds to make a signficant force (w/ significant surface area). Bond force is proportional to 1/x^7. They can cause cohension b/t nonpolar substances that cannot form hydrogen or ionic bonds.
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What are hydrophobic interactions?
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The tendency of water to exclude nonpolar groups. Water forms cages of hydrogen-bonded molecules around non-polar substances - this is thermodynamically unfavorable (too ordered). As groups of nonpolar substances merge, there are fewer cages and more entropy. Water squeees nonpolar molecules into spontaneously forming aggregates. Actual bonds formed by van der waals. Non stoichiometric. May contribute as much as 50% to antigen/antibody binding.
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