Exam #1
Biology 113
Name: ___KEY KEY KEY KEY KEY KEY KEY KEY___
The following are from Chapter 2 (5 questions):
(1) What is an emergent property? Give an example.
A: An emergent property is one that is not easily predicted from knowledge of properties that don’t occur in bulk; good examples from chemistry are such things as the fact that ice floats and hydrophobic exclusion; from biology you may refer to the organization of chemicals into cells and so on up the numerous levels of biological hierarchy
(2) What kind of bonds make up the salt bridges that are found in the interior of proteins?
A: Ionic bounds (though weakened by the presence of water molecules, hydration shells, competing for access to the full charges).
(3) Which of the following covalent bonds is most polar? (consider only the bond between the atoms shown)
(a) C-C
(b) C-H
(c) C=C
(d) C-N
(e) O=O
(f) H-H
A: (d) C-N. All the rest except C-H are technically not polar and C-H bonds are considered effectively not polar.
(4a—answer either 4a or 4b, NOT BOTH) Describe how energy is stored in a chemical bond such that more obtainable energy may be found in one bond (e.g., nonpolar covalent) versus another (e.g., polar covalent).
A: Obtainable (usable) chemical energy is stored in bonds by orbiting electrons. The farther an electron is from its associated nucleus, the more energy it possesses. The closer an electron is to its associated nucleus, the less energy it possesses. Allowing an electron to fall to a lower, less energetic orbital thus results in a release of energy. In nonpolar covaltent bonds, electrons are shared more or less equally between atoms, and therefore, within a covalent bond, maximally distant from each atom. In polar covalent bonds, one atom is pulling the electron closer to itself, implying that the electrons are no longer maximally distant (i.e., they are closer to one atom than to the other) and therefore are less energetic (as well as imparting a partial negative charge on the pulling atom and a partial positive charge on the atom at the other end of the bond).
(4b—answer either 4a or 4b, NOT BOTH) What does dynamic chemical equilibrium mean?
A: in a dynamic chemical equilibrium reactants are converted to products as fast as products are converted to reactants, thus resulting in no net increase in the concentration of either products or reactants, despite the continual occurrence of chemical reaction
(5) How many valence electrons does the element Carbon have? What is the valence of Carbon? (note that I have asked two questions here so I am looking for two answers)
Carbon has __________ valence electrons; Carbon’s valence is __________
The following are from Chapter 3 (5 questions):
(6) The interaction of water with what substance (other than itself) explains surface tension?
A: Air: Surface tension is an emergent property of water which results from the tendency of water molecules to stick to each other better than they adhere to air molecules
(7) What must be “broken” in order for water molecules to transition from the liquid phase to the gaseous phase (gas state)?
(8) Why does ice float?
A: Ice floats because it contains more hydrogen bonds, on average, than liquid water and (and this is a very important and) hydrogen bonding gives water structure and more unoccupied space between molecules; more space means lower density thus ice has a lower density than water so consequently floats upon water rather than sinking beneath it
(9) Within water, a lowering of surface-to-volume ratios drives forward what biologically important phenomenon?
A: Hydrophobic exclusion; the surface-to-volume ratio of the hydrophobic substance is important—the greater this ratio, the more water molecules must interact with this substance rather than with themselves, and therefore the less energetically favorable the interactions; the most-stable situation is one in which water can maximally hydrogen bond with itself/minimally interact with the hydrophobic substance, hence oil clumps in water into spherical droplets (ignoring such complications as gravity and water’s surface), spherical clumps having much lower surface-to-volume ratios than either less-clumped oil or clumps of any other shape
(10) What do organisms employ to maintain hydrogen ion concentrations in aqueous solutions within well-defined ranges? (looking for simple, general term)
The following are from Chapter 4 (5 questions):
(11) In which molecule are single covalent bonds arrayed in a tetrahedron around a central carbon atom?
(a) COH4
(b) COH2
(c) CO2H2
(d) CO2
(e) None of the above
A: a, COH4, which is an alcohol such that three –H and one –OH is bound to the central Carbon; that’s four single bonds, and they are arrayed as though at the corners of an imaginary tetrahedron
(12) Under what circumstances (i.e., molecular structure) would you expect a carbon-containing compound to display two enantiomeric forms?
A: Two enantiomers are possible given chirality (a chiral or asymmetric carbon) associated with a central carbon; that is, the carbon is found to four different groups, e.g., –H, –OH, –CH3, and –NH2
(13) Draw the structural formula of a molecule consisting of a carbon atom that has three functional groups: A carbonyl group, a hydroxyl group, and a sulfhydral group (none of which are ionized).
A: Approximately:
OH
|
|
SH
(14) Draw the structural formula of formate, a negatively charged organic ion possessing only a single carbon atom.
A: Approximately:
O-
|
|
H
(15) Draw an uncharged amino group.
A: –NH3
The following are from Chapter 5 (11 questions):
(16) What macromolecule possesses a – phosphate – 5’ – 4’ – 3’ – phosphate – backbone?
A: A nucleic-acid polymer (e.g., DNA or RNA)
(17) Which reaction represents dehydration synthesis:
(a) A-OH + HO-B + H2O à energy + A-O-B
(b) A-O-B à A-OH + HO-B + H2O + energy
(c) A-OH + HO-B + energy à H2O + A-O-B
(d) A-O-B + H2O + energy à A-OH + HO-B
(e) A-OH + HO-B à A-O-B + H2O + energy
A: (c) A-OH + HO-B + energy à H2O + A-O-B
(18) What type of bond connects two monosaccharides to form a disaccharide?
(a) Disaccharide bond
(b) Ester linkage
(c) Glycosidic linkage
(d) Peptide bond
(e) Phosphodiester linkage
(19) What is an oil?
(20) How do phospholipids differ from triacylglycerols? Give two ways that/properties by which these molecules differ.
A: A phospholipid has one fatty acid replaced with a phosphate-containing group and consequently a phospholipid, but not a fat, possesses a hydrophilic end in addition the hydrophobic rest of the molecule
(21) What type of lipid is this molecule?
(22) How many types of amino acids serve as the monomers that make up most naturally occurring proteins?
(23) What is the surface chemistry of a protein determined by? (note: neither amino acids nor functional groups are sufficient answers)
(24) What nucleic acid makes up the chromosomes of most organisms?
(25) What is the role of chaperone proteins in macromolecular formation?
(26) What kind of intermolecular interactions bind a double helix together?
The following are from Chapter 5 (11 questions):
(27) In terms of metabolism, what is energy coupling?
A: Energy coupling means that the energy liberated in catabolic processes is harnessed to drive forward anabolic processes
(28) Net movement away from chemical equilibrium
(a) Is an exergonic process
(b) Is used to produce ATP
(c) Does not occur spontaneously
(d) Powers anabolic processes
(e) None of the above
(29) Give a specific example of an endergonic chemical reaction. Please at least show the atoms involved in the reaction (plus energy) but you may describe or name the molecules involved rather than explicitly presenting the rest of their molecular structure.
A: This could be an example of dehydration synthesis, e.g., the synthesis of maltose from two glucose molecules: G-OH + HO-G + energy à G-O-G + H2O where G-OH is glucose and G-O-G is maltose
(30) Why don’t all spontaneous reactions readily occur?
A: Even spontaneous reactions require an initial input of energy, called activation energy, to drive the reaction forward; the description spontaneous refers to the net gain in free energy that results from the reaction going to completion, not that the reaction is highly likely or that the reactants are highly unstable
(31) What does enzyme specificity refer to?
A: The substrates an enzyme is capable of acting on is typically very limited; thus, only specific substrates are acted upon by a given enzyme, the enzyme is specific in what molecules it can use as substrates
(32) Describe the amino acids found in an enzyme’s active site in terms of the enzyme’s primary structure
A: The amino acids found in the active site of an enzyme are not necessarily found adjacent in terms of the enzyme’s primary structure
(33) To effect catalysis, an enzyme’s __________ can stress the substrate into the transition state.
(34) What is a cofactor?
(35) In general, what must an inhibitor do to impact on the activity of an enzyme?
(a) Bind to an enzyme
(b) Bind to an enzyme’s active site
(c) Denature an enzyme
(d) Modify an enzyme’s primary structure
(e) Salt-out an enzyme
(36) Name a property of an enzyme that must exist for that enzyme to be susceptible to allosteric inhibitors or to cooperativity. That is, in principle not all enzymes are susceptible to these effects. Why not?
(37) Given feedback inhibition, when product is sufficiently plentiful, what happens?
A: With feedback inhibition, sufficiently plentiful product serves to inhibit the enzymes involved production of this product