Biochem exam 1

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Biochem exam 1
2012-05-28 23:54:16
Biochem exam

biochem exam 1
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  1. Proteins are the machines that perform
    most of the functions in our cells
  2. The seven major examples of proteins are
    Hemoglobin, Trypsin, Insulin, Immunoglobulin (antibodies), Myosin, Keratin and Opsin.
  3. Hemoglobin is the main protein found in
  4. Hemoglobin's function is to
    bind oxygen and helps blood carry oxygen from your lungs to your tissues.
  5. The type of function that hemoglobin does is
  6. Trypsin is an enzyme secreted from
    the pancreas into your small intestine.
  7. Trypsin is a type of
  8. The function of trypsin is to
    digest food proteins.
  9. Insulin is a hormone secreted from
    the pancreas into your blood stream.
  10. Insulin is secreted when you eat a meal, shortly after a meal, when
    blood glucose levels are high.
  11. The function of insulin is to
    stimulate cells to convert excess glucose into energy storage molecules such as glycogen.
  12. Immunoglobulin are proteins which bind to the surfaces of
    foreign objects such as viruses or bacteria.
  13. Immunoglobulin are used for
  14. The function of the immunoglobulin is to
    identify foreign objects as targets for attack by the immune system.
  15. Myosin is one of the major proteins involved in
    muscle contraction.
  16. Myosin is involved with
  17. Keratin provides
  18. Keratin forms
    fibers in hair.
  19. Opsin is one of your
    optical (vision) proteins
  20. The function of Opsin is to
    bind the pigment named retinal which is derived from vitamin A
  21. When the retinal pigment is struck by a photon, it changes its own shape and the shape of the protein opsin which binds it, ultimately
    triggering a nerve impulse to the vision processing portion of your brain.
  22. Many different kinds of functions can be achieved by proteins because we have
    many different chemical types of amino acids for construction of proteins AND because we have many different folded three-dimensional geometries for proteins.
  23. Proteins are constructed by
    linking amino acids into long chains.
  24. There are ___ different types of amino acids used to construct proteins.
  25. 19 of the amino acids have the structure consisting
    of a central carbon atom attached to four groups.
  26. The four groups that are attached to the central carbon in the amino acids are
    an NH2 amino group, a COOH carboxylic acid group, a hydrogen atom and an additional group called the sidechain of the amino acid.
  27. The _______ group and ___________ group of the amino acid structure, give the amino acid its name.
    amino and carboxylic acid
  28. The amino acid sidechain varies in _________ from one type of amino acid to another.
  29. The structure of the 1 amino acid that is different from the 19 amino acids is that
    the sidechain forms two chemical bonds to the rest of the molecule, attaching both to the central carbon and to the N of the amino group.
  30. The side chains in the figure extend towards the
    right side of each structure.
  31. The amino acid side chains can have something as simple as __________ or as complex as a _____________.
    a simple hydrogen or functional group.
  32. Proteins chains are created by joining
    amino acids to each other.
  33. The word "condensation" means
    two objects are coming together to from one object; Two objects are condensing to a smaller space.
  34. In many condensation reactions, _____________ is also produced
    a molecule of water
  35. "R" is a symbol used to denote
    any sidechain
  36. In the condensation reaction, the carboxyl group of one amino acid joins with
    the amino group of another amino acid
  37. In the condensation reaction, the carboxyl group of one amino acid joins with the amino group of another amino acid to form
    a substituted amide group.
  38. Carboxylic acid + amine =
  39. The condensation reaction produces an amide where one of the H's on the N is substituted by
    a carbon going to another part of the molecule.
  40. The resulting chain of a condensation reaction retains
    one NH3+ amino end and one COO- carboxyl end.
  41. The direction of the sequence is standardly written beginning at
    the NH3+ end.
  42. A longer chain of amino acids is constructed by
    further condensation reactions.
  43. Individual amino acids are called
  44. A chain of amino acids are called
  45. Proteins are called heteropolymers because they
    are constructed from different types of amino acids
  46. Starch is a homopolymer because
    all the units used to construct it are the same.
  47. A homopolymer is a polymer in which all the units used to construct it are the
  48. A heteropolymer is a polymer in which all the units used to construct it are
  49. Proteins are long chains that can contain up to several hundred
    amino acids.
  50. The amino acid groups in proteins occur in a specific sequence dictated by
    information encoded in the genes of the organism producing protein.
  51. Proteins are originally synthesized as
    linear chains.
  52. Proteins do not remain in linear chains in
    solution .
  53. Proteins are capable of folding themselves into
    elegant, 3-d shapes without external help.
  54. Proteins can fold into (2 types)
    helices or sheets
  55. Proteins that are folded into helices are usually aligned
    in an antiparallel manner
  56. The components that make up a sheet of proteins are called
    strands of sheet.
  57. A protein can mix helices and sheets
  58. The two major uses of nucleic acid is that of
    storing genetic information and storing chemical energy.
  59. DNA is a type of polymer that stores genetic information in the form of
    a double helix
  60. The information the DNA stores is replicated when
    cells divide
  61. The process of using DNA information to synthesize proteins includes an intermediate step in which
    a single polymeric strand of messenger RNA (mRNA) is produced.
  62. RNA stands for
    ribonucleic acid
  63. The function type of mRNA is that of
  64. DNA stands for
    deoxyribonucleic acid
  65. The individual monomer units of nucleic acids are called
  66. ATP stands for
    adenosine triphosphate
  67. ATP is a small monomer (nucleotide) that releases a lot of
  68. ATP releases a lot of energy when
    one of the three phosphate groups is cleaved away from it.
  69. Nucleic acid polymers are constructed from monomeric units called
  70. A ribonucleotide consists of
    a 5 carbon sugar ribose, a phosphate group attached to carbon 5' of the sugar and a base attached at the 1' carbon.
  71. Ribonucleotides are joined together to make
  72. Deoxyribonucleotides have the same structure as Ribonucleotides except
    an oxygen atom at the 2' position.
  73. Deoxyribonucleotides are used to construct
  74. There are four different types of ________ which make up RNA polymers.
  75. The bases that are attached to the C1 on the ribonucleotides are analogous to
    the sidechains in amino acids and differ in each of the four types of nucleotides.
  76. Nucleotides A and G have _______________ sidechains
    large double ring groups
  77. Nucleotides U and C have __________ sidechains
    small one-ring
  78. Numbered positions in the sugar ring are marked by
    primes (')
  79. Numbered positions in _____ have no primes
  80. All ___________ will either have a :N (a nitrogen w/ 3 bonds and a lone pair) or NH.
  81. NH in nucleotides is a hydrogen bond
  82. :N in nucleotides is a hydrogen bond
  83. In DNA, the sidechains of A, G and C are the same as found in
  84. The fourth type of sidechain in DNA is
  85. T is like U in RNA with the exception that
    there is an extra methyl group at position 5.
  86. The direction to the RNA polymer is from the
    5' end of the nucleotide to the 3' end of the nucleotide.
  87. Nucleotides are joined together by a
    condensation reaction to form polynucleotide chains
  88. Polynucleotide polymers are
  89. There are four different type of monomers of DNA, they are
    (dA, dC, dT and dG)
  90. Ignoring the sidechains of the nucleotide leaves the rest of the polymer, called
    the backbone.
  91. ____________are like ribs sticking out of a spine, and the spine is the backbone
  92. _________ nucleotides are not polymers (it's units are different)
  93. A polymer is a chain of units with
    identical or very similar structures.
  94. DNA is a polymer because
    it is a chain of nucleotides
  95. A and T pair together for DNA by
    a bond between :N and NH and a bond between :O and NH (two hydrogen bonds)
  96. G and C pair together for DNA by
    two bonds between :N and NH and a bond between :O and NH (three hydrogen bonds)
  97. The A and T pair cannot have a third hydrogen bond between the third hydrogen and the carbonyl
    because they are too far apart.
  98. The third hydrogen of the AT pair is considered to be part of a nonpolar C-H bond thus lacking
    a positive charge.
  99. The third hydrogen of the AT pair is not likely to donate a hydrogen because
    it lacks a positive charge.
  100. A complements
  101. C complements
  102. A (in RNA) complements
  103. The primary function of DNA is to provide a mechanism for duplicating genetic information when a cell divides so
    a copy can be incorporated into each of the resultant daughter cells.
  104. During replication, the two strands of the original DNA molecule
  105. During replication, two new strands are synthesized to
    complement the two old strands from the original DNA molecule.
  106. During transcription, DNA partially unwinds to
    expose the sidechains of each DNA strand.
  107. In transcription the lower DNA strand functions as a temporary template (blueprint) for
    constructing a complementary RNA strand called messenger RNA.
  108. The newly synthesized mRNA from the transcription is single
  109. The newly synthesized mRNA from the transcription has the same sequence as the top DNA from the original except
    the T is replaced with U.
  110. When U replaces the T after transcription this means that
    the ribonucleotides replace the deoxyribonucleotides.
  111. The mRNA eventually binds to
  112. When mRNA binds to ribosomes, the information in mRNA is used to make
    a protein during translation.
  113. Each group of three nucleotides on mRNA codes for
    one amino acid in the protein being synthesized by the ribosome.
  114. The correspondence between the nucleic acid triplet and its corresponding amino acid is called
    the genetic code.
  115. tRNA are attached to amino acids and bind to the mRNA in the ribosome during translation of the mRNA sequence.
  116. Genetically coded biopolymers are heteropolymers of
    long specific sequences and well-defined lengths.
  117. Most industrial polymers are simple homopolymers of random variable length or are heteropolymers comprised of a small variety of types of monomeric units that join together in relatively
    random sequences and lengths.
  118. The primary energy storage molecule in cells is
  119. Energy storage means
    when a molecule can undergo an extremely favorable reaction characterized by a large negative change in Gibbs free energy (delta-G),
  120. For ATP, cleavage of the molecule into phosphate and adenosine -diphosphate (ADP) is
    extremely favorable.
  121. It would be unfavorable and relatively unlikely for the negative phosphate ion in ATP cleavage to
    diffuse back towards the negatively charged ADP molecule to remake ATP.
  122. The equilibrium for ATP hydrolysis lies in the direction of
    the cleaved products.
  123. The two most popular carbohydrates are
    glucose and starch.
  124. Two examples where carbohydrates play a structural role are
    cellulose and chitin.
  125. Cellulose structural role is that of
    forming the walls of plant cells
  126. Chitin's structural role is that of
    forming the exoskeleton of insects and crustaceans
  127. Another function of ____________ is exhibited by the blood group markers.
  128. The blood group markers are
    type A, type B, type O
  129. Blood group markers are attached to
    the exteriors of red blood cells in humans.
  130. The monomeric units in carbohydrates are called
  131. The first carbon (upper carbon) in aldoses are
    an aldehyde group (CHO)
  132. At any given row the aldose structures differ in their
    configurations (R or S forms) at the chiral carbons in the middle of the chain.
  133. The forms that monosaccharides can have are
    linear forms and cyclic forms
  134. In aldoses the linear form has a carbonyl group (C=O) at the carbon at the top of the molecule whereas the other carbons are attached to
    OH groups (alcohol groups).
  135. In aldoses the linear form has a ____________ at the carbon at the top of the molecule
    carbonyl group (C=O)
  136. Ketoses get their name because they
    contain a ketone group with the C=O positioned at the second carbon from the top.
  137. All other carbon (w/o the C=O) in the ketoses have
    alcohol oxygens (including the carbon at the top)
  138. Carbohydrates derive their name from their overall formula
  139. The representing atoms (carbohydrates) are in a ratio of
    one water per carbon
  140. The "carbo" in carbohydrate stands for
  141. The "Hydrate" in carbohydrate stands for
  142. Glucose's carbon are attached to a _________ and a _________ group which makes it a carbohydrate.
    hydrogen and hydroxyl
  143. The OH group makes small carbohydrates very soluble in water because it is
  144. The human blood groups (A,B,O) consist of
    short polymers of sugars, arranged in a specific sequence and attached to lipids or proteins in the surface of cells.
  145. Human blood groups are attached to
    lipids or proteins in the surface of cells.
  146. The specific sequences of the human blood groups are synthesized by
    a series of enzymes.
  147. The specific sequences of the human blood groups are synthesized by a series of enzymes, each catalyzing one reaction joining
    two specific types of carbohydrate units.
  148. Each of the blood types contains the core sequence
  149. the core sequence Fuc-Gal-Glc is found in the blood of the
    type O person. (universal)
  150. The type-A person has an additional gene
    not found in the type-O person which codes for an enzyme.
  151. The type-A extra gene codes for an enzyme which adds
    an extra sugar GalNAc (N-acetylgalactosamine) at the left end of the H antigen core.
  152. The type B person has a different supplementary gene from type A and O whose corresponding enzyme adds
    a galactose (Gal) at that position.
  153. An AB person has inherited both of those enzymes from
    type A and B .
  154. An AB person has inherited both (type A and B) of those enzymes and therefore has some polymers that are
    fully synthesized as the type-A structure, some that are fully synthesized as the type-B structure, and some that have not yet developed beyond the type-O core structure.
  155. Type A can accept from
    type O and type A
  156. Type B can accept from
    type O and type B
  157. Type O can accept from
    type O
  158. Type AB can accept from
    type A, type B, type AB and type O
  159. Starch is a homopolymer of
  160. Starch is a homopolymer because
    only one type of monomer, namely glucose, is used in its construction.
  161. random variations make starch more similar to
    industrial chemical polymers than to genetically coded biopolymers like DNA and proteins.
  162. ________________ form both homopolymers(starch) and heteropolymers (blood groups).
  163. Cellulose is a homopolymer of
  164. The meshwork of H-bonds in cellulose provides
    rigidity, generating a rigid cell wall in plants.
  165. Lipids are nonpolar molecules which are
    insoluble or only slightly soluble in water
  166. There are ___ major classes of lipids
  167. The two major classes of lipids are
    fatty acids and isoprenes
  168. Two examples of fatty acids is the
    phospholipids used to form the outer membranes of cells and the waxes of honeycombs in beehives.
  169. Examples of lipids from the isoprene class are
    the male sex hormone called testosterone, and the light-absorbing pigment called retinal.
  170. Both the lipid, testosterone and the protein, insulin are
  171. Carbon and hydrogen atoms have similar
  172. C-H bonds are non polar
    (not polar).
  173. C-C bonds are nonpolar since
    the connected atoms are both the same type (C).
  174. Organic chemicals containing mostly hydrogen and carbon atoms are called
  175. Fatty acids resemble
    hydrocarbon fuels.
  176. words ending in "ate"indicate the
    negative deprotonated form of an acid.
  177. The negative COO- form of the carboxylic acid group in organic compounds also may be given a name ending in
  178. Combustion of natural gas (methane)takes place by reaction
    with oxygen produces water and carbon dioxide.
  179. In water and carbon dioxide , oxygens are able to steal electron density away from the neighboring carbon or hydrogen atoms.
    • If you wanted to convert water and CO2 back into oxygen and methane, which is the reverse reaction, you would have to
    • add energy to the system.
  180. If you wanted to convert water and CO2 back into oxygen and methane, which is the reverse reaction, you would have to add energy to the system because
    that energy would have to do the work of taking away the extra electron density on the partially negative oxygens (oxygens hug onto electrons) in order to restore all the atoms back into neutral nonpolar forms.
  181. The general structure of a phospholipid is generated by starting with
  182. The three carbon triple alcohol is
  183. To make a phospholipid first
    Two fatty acids (R1-COOH and R2 COOH) form esters with two of the alcohol groups in glycerol. The third glycerol OH group then forms an ester to phosphoric acid, which in turn forms another ester bond to an alcohol (X). The final structure has a polar end (the negative phosphate group) and also has two long nonpolar tails (R1 and R2 extending from it.
  184. In an aqueous solution, phospholipids aggregate to form
    lipid bilayers.
  185. A bilayer contains two (bi) layers of
    lipid molecules
  186. lipids do not form homopolymers or heteropolymers because
    the individual lipid molecules are not chemically bonded to each other by covalent bonds
  187. The bilayer in the lipid membrane is better described as
    noncovalent aggregate
  188. The bilayer exists in a fluid state where individual lipids molecules are free to diffuse past other lipid molecules.
  189. The dual polar-nonpolar structure of phospholipids generates
    the biological function of forming membranes to separate solutions and construct cellular and subcellular compartments
  190. Retinal is derived from vitamin A, which in turn is derived from
    the orange-colored pigment beta-carotene found in foods such as carrots.
  191. Retinal is bound to the protein
  192. This lipid-protein complex of retinal and opsin is called
  193. When light is absorbed by the retinal,
    it switches back and forth between the cis and trans configurations at one of its double bonds. (triggers the sensation of vision)
  194. An aldose with three carbons is called
  195. An aldose with four carbons is called
  196. An aldose with five carbons is called
  197. An aldose with six carbons is called
  198. Constitutional isomers are
    isomers that differ in their bonding sequence
  199. Conformations of a molecule involves a rotation of
    the single C-C bond.
  200. When dealing with conformations a molecule can take two forms,
    either staggered or eclipsed
  201. Configurations at the double bond means the molecule is
  202. Configurations at a chiral carbon means the molecule is
  203. Two kinds of stereoisomers are
    Chiral Carbons (R,S) and double bond (cis/trans)
  204. In the staggered conformation of the atom the elements are apart visually at _______ increments
    60 angle increments.
  205. Rotation around a cis/trans molecule is not possible due to
    the double bond.
  206. Rotations around a double bond is not possible because
    the pi cloud formed by overlap of p orbitals would break.
  207. The cis isomer cannot be converted to the trans isomer unless
    covalent bonds are broken and atoms are reattached in new locations.
  208. A chiral carbon (asymmetric) is a carbon with
    four different groups attached to it.
  209. The two systems for naming a pair of enantiomers is the
    R,S system names or the D,L system names.
  210. The R,S system is more _____ than the D, L system
  211. Priorities of chiral carbon groups are ranked by
    atomic weight (Highest weight gets first priority)
  212. The only amino acid where the sidechain has a higher group priority than the backbone carboxyl group is
  213. If 1->2->3-> is clockwise and group 4 is in the back, the configuration is
  214. If 1->2->3-> is counterclockwise and Group 4 is in the back, the configuration is
  215. If 1->2->3 is clockwise and group 4 is in the front, the configuration is
  216. If 1->2->3-> is counterclockwise and group 4 is in the front, the configuration is
  217. A polarimeter is a device for
    analyzing rotation of plane-polarized light by asymmetric molecules.
  218. The polarizer only transmits those waves whose planes are
    oriented in a particular direction
  219. The light leaving the polarizer is called
    plane-polarized light
  220. Plane polarized light can be rotated by
    molecules containing one or more chiral carbons.
  221. Molecules causing rotation in the direction marked "+" are called
    dextrorotatory (d) (to the right)
  222. Molecules causing rotation in the "-" direction are called
    levorotatory (l) (to the left)
  223. R and S enantiomers have _____________ effects.
    equal but opposite
  224. d and l actually describe
    one whole molecule
  225. Glyceraldehyde is a
  226. The molecular of formula of glyceraldehyde is
  227. Before the R,S system was developed, biochemists compared chiral carbons to the carbon found in the center of glyceraldehyde.
  228. The enantiomeric form of glyceraldehyde which rotates light to the left is called
  229. The arrangement of four groups in d-glyceraldehyde was arbitrarily called
    the capital D arrangement
  230. There are two main classes of sugars,called
    aldoses and ketoses
  231. A sugar with an aldehyde is called
    an aldose
  232. A sugar with a ketone is called
    a ketose
  233. Biochemists do not apply the D,L naming system to the asymmetric carbons in sugars, in the extra H-C-OH units.
  234. The D,L system is applied only to the asymmetric carbon that is
    furthest from the carbonyl group.
  235. The asymmetric carbon in biological sugars always resembles the corresponding carbon in
  236. During photosynthesis, D-glyceraldehyde is the starting compound for
    synthesis of longer sugars.
  237. All biologically occurring aldoses resemble
  238. the shortest biological ketose containing an asymmetric carbon is
  239. All other biological ketoses resemble D-erythrulose by
    inserting a variable number of H-COH units between the D-carbon and the carbonyl group.
  240. for biological sugars, both the aldoses and the ketoses have one particular carbon resembling the
    D-carbon of D-glyceraldehyde.
  241. To find out the total number of forms a compound can have, use the equation
    2^n in which n is the number of chiral carbons.
  242. The first carbon at the top of each aldose structure is not chiral because
    it has only three groups attached.
  243. The last carbon at the bottom of each aldose structure is not chiral because
    it has two identical atoms (H) attached.
  244. Aldotriose has ___ chiral carbon
  245. Aldotetroses has ___ chiral carbon
  246. Aldopentose has ____ chiral carbon
  247. Aldohexoses has ____ chiral carbon
  248. L sugars do not occur
    in biology
  249. In each aldose group there are only ____ non chiral carbon
  250. In each ketose structure there are ____ non chiral carbons
  251. There is one fewer chiral carbon in ketoses than
  252. There are non-chiral ______ groups at the ends of a ketose
  253. A ketotriose has ____ chiral carbon
  254. A ketotetrose has ___ chiral carbon
  255. A ketopentose has ___ chiral carbon
  256. A ketohexose has ____ chiral carbon
  257. The D,L system is used for naming the chiral carbon occurring in
    the backbone of amino acids.
  258. The D,L system is based on the series
    L-glyceraldehyde -> L-serine -> any other L-amino acid
  259. In going from L-glyceraldehyde to the amino acid called L-serine, three groups are in the same position.
    They are -H, -CH2OH, and C=O
  260. The aldehyde C=O in the L-glycaraldehyde changes to a
    carboxyl group C=O in the amino acid
  261. The glyceraldehyde OH group changes to
    an NH2 group in serine.
  262. Glycine lacks an
    asymmetric carbon
  263. The central C in glycine has two identical groups
    (H) attached to it.
  264. Serine has one asymmetric carbon in
    the backbone
  265. The one asymmetric carbon in serine is attached to
    an amino group, a carboxylic acid group, an H, and a sidechain
  266. The naturally occurring form of serine in proteins is
  267. All of the remaining 18 types of amino acids found in proteins in biological organisms have the same configuration in the backbone carbon that is found in serine, so they are also called
    L amino acids.
  268. In going from L-serine to any other L-amino acid, three groups remain the same, but ________ changes to a different sidechain.
    the sidechain -CH2-OH group of serine
  269. The D,L system is only applied to the
    chiral backbone carbon of amino acids.
  270. biological amino acids are ___ at the backbone carbon
  271. biological sugars are ____ at the asymmetric carbon farthest away from the C=O group.
  272. Glycine is neither D nor L, since its backbone carbon has
    two identical H's attached to it.
  273. Cysteine is the one example of an L amino acid which is
  274. Cysteine's sidechain contains a
    sulfur atom with a high atomic Weight
  275. The reason why the older D,L system has persisted in biochemistry is because
    the naturally occurring chiral amino acids are consistently L but are not consistently S.
  276. In helices, the H-bonds join the backbone NH groups to the
    backbone C=O groups.
  277. The configuration of the carbon in the center of the backbone of one amino acid in biologically occurring proteins is
  278. In each amino acid, the spiral generates
    two pairs of eclipsed atoms
  279. The D configuration would not work in amino acids because
    eclipsing two large atoms will lead to unfavorable repulsion between their electron clouds.
  280. In proteins it is important that all amino acids have the same configuration, so these helices can
    form in a stable manner.
  281. the efficient formation of hydrogen bonds (NH to O=C) in the repetitively twisting alpha helix stabilizes
    the folding of many proteins.
  282. The "substrate" is
    the material upon which the enzyme is acting
  283. three points of binding to the enzyme provide
    the minimum requirement for specific discrimination between mirror images
  284. For a chiral substrate molecule having two forms (R and S), only one of those forms will be able to
    make all three potential contacts with the enzyme surface.
  285. The compound containing the L form of phenylalanine tastes
  286. the D amino acid tastes
  287. Aspartame is the active ingredient in the commercial artificial sweetener called
  288. Thalidomide caused birth defects via
    the mirror image.
  289. Most seashells are
  290. All biological enzymes' catalysts are
  291. Since all biological enzymes' catalysts are asymmetric ________ is possible
  292. Aconitase is an asymmetric catalyst which acts upon a symmetric substrate (citrate) and converts it into a
    specific diastereomer.
  293. an enzyme or hormone receptor can distinguish between R and S forms
    of asymmetric organic molecules
  294. an asymmetric enzyme surface can convert a symmetric reactant into
    a specific asymmetric product
  295. In an XYZZ molecule one of the Z groups can join with X and Y to give three-point attachment to an enzyme surface, but the other Z group can not reach its
    complementary site on the enzyme surface when X and Y are bound to the protein.
  296. S (symmetric) + E (asymmetric) =
    ES (asymmetric)
  297. In the asymmetric ES complex, the Z group which points towards the ceiling could be chemically converted into something else (W), giving a
    specific WXYZ' enantiomer
  298. the Z' group could be modified to generate
    an asymmetric product.
  299. In the actual enzyme-citrate complex, All four chemical groups attached to the central C
    are bound by the enzyme, so the protein can act differently on the two CH2-COO- groups
  300. pH =
    -log [H+]
  301. [H+] =
  302. A relationship linking [H+] and [OH-] is
    [ H+] x [ OH- ] = 10^-14 M2
  303. -pH =
  304. 10-pH=
  305. Strong acids and bases completely
    dissociate in aqueous solution.
  306. Weak acids and bases only partially
  307. there is an equilibrium between the
    protonated and the deprotonated forms.
  308. The protonated form, which can donate an H+ to solution, is called the
    conjugate acid
  309. The deprotonated form, which can bind an H+ and thereby lower the [H+] in solution, is called the
    conjugate base.
  310. The equilibrium reactions, written from left to right, represent
    dissociation of H+ from the molecule.
  311. the equilibrium constant is given by
    the ratio of products divided by reactants.
  312. a large Ka means strong net dissociation producing
    lots of H+ and therefore a large numerator.
  313. Further to the right =
    more dissociation
  314. pKa =
  315. Ka =
  316. The minus sign causes a large Ka to correlate with a
    small pKa.
  317. The strongest acids have the largest ___ and the smallest ___.
    largest ka - smallest pKa
  318. Hydrogen is in column
  319. Carbon is in column
  320. Nitrogen is in column
  321. Phosphorus is in column
  322. Oxygen is in column
  323. Sulfur is in column
  324. The three ionized atoms in bio-organic molecules are
    N+, O- and S-
  325. S appears directly below O in the periodic table so it
    behaves similar in a manner to O
  326. Positive N has __ electrons
  327. Neutral N has ___ electrons
  328. Neutral O (or S) has ___ electrons
  329. Negative O (or S) has ___ electrons
  330. low pH = mostly _______ form
  331. scientist = the cause, molecule =
    the effect
  332. The henderson-hasselbalch equation is
    pKa= log(prot.)/(deprot) + pH
  333. "low pH" means a number that is lower than
    the pKa
  334. the difference term is given by
    (pKa - pH).
  335. Acetic acid has the simplest
    titration curve
  336. To titrate is to cause
    one H+ ion to dissociate
  337. The pKa is the pH at the
    midpoint of a titration curve
  338. the slightest creation or consumption of H+ or OH- by biomolecules or living cells can easily
    alter the pH of that water
  339. We use buffered solutions in the laboratory to maintain
    reactions at a relatively constant pH
  340. The pKa value of acetic acid is
  341. The titration curve of phosphoric acid is like three of
    the acetic acid titration curves strung together in a row.
  342. The three phosphoric acid midpoints occur at
    .5, 1.5 and 2.5
  343. The three pKa values for the phosphorus acid titration is
    2.1, 6.9 and 12.4
  344. Titrations go from fully protonated, to
    fully deprotonated
  345. Glycine is the smallest
    amino acid
  346. The sidechain of glycine is
    a single H atom
  347. Glycine has two titratable groups,
    one of which is negatively charged under certain condition and one of which may be positively charged.
  348. the low pH form at the extreme left side is the
    fully protonated form
  349. The fully protonated forms of amino and carboxyl groups are positive ___ and neutral ____
    NH3+ and COOH
  350. Glycine is net +1 at
    low pH
  351. The fully deprotonated form of glycine occurs
    at the right
  352. The deprotonated form of glycine includes deprotonated neutral ___ and deprotonated negative ____
    NH2 and COO-
  353. The charge of the glycine molecule changes from net ___ on the left, to net __ in the middle, to net __ on the right.
    +1, 0, -1
  354. it is favorable for COOH to deprotonate in the glycine titration because
    The COO- form is resonance stabilized
  355. In the glycine titration, the COO- form deprotonates before the
    NH3+ group deprotonates
  356. The isoelectric point is the point in when a molecule's net charge
    is zero.
  357. You have poor buffering when the molecule is
    isoelectric (net charge = 0)
  358. Good buffering corresponds to a
    small slope which represents a small change in pH
  359. Bad buffering corresponds to a
    large slope which represents a large change in pH
  360. Adding H+ on a titration chart is the equivalent to
    moving from left to right in the chart
  361. When CO2 dissolves in water, it combines with H2O to form
    carbonic acid (H2CO3)
  362. Carbonic acid dissociates into
    bicarbonate (HCO3-) and H+
  363. Any process which adds CO2 to the system or removes CO2 from the system causes
    a shift in the equilibrium in the direction consistent with Le Chatelier's principle.
  364. For the lungs, Depleting CO2 at the right of the diagram causes the series of reactions to shift towards the right to replenish the lost CO2. (lowers the H+ concentration)
  365. In the lungs, the pH of the blood rises
  366. In the muscles, metabolism converts glucose (C6 H12 O6) into
    CO2 and H2O.
  367. In the muscles, Adding CO2 to the right of the diagram causes
    a shift in the series of reactions towards the other end, the left of the diagram.
  368. In the muscles, the pH is
  369. Lung blood pH =
  370. Muscle blood pH =
  371. the "large" muscles or lungs are the cause, and the molecules experience the
  372. The enzyme that converts one isomer into another isomer is called
  373. The active site of the isomerase enzyme includes a
    carboxylate anion on the left side and an NH+ group on the right side
  374. A catalyst is neither consumed nor created by the
    overall reaction in which it takes part.
  375. anion exchange chromatography is a procedure used for
    separating molecules having different net negative charges
  376. In anion exchange chromatography, the column contains
    functional groups which are positive. (column binds negative anions)
  377. In anion exchange chromatography, A mixture of biological anions is loaded onto the top of the column where they are bound by
    the positively charged resin.
  378. In anion exchange chromatography, The column is rinsed with
    a NaCl (salt) solution, starting with dilute salt and gradually progressing to concentrated salt.
  379. In anion exchange chromatography, The Cl- in the NaCl solution starts binding to the column, competing with the negative biolo
    gical anions for the positive sites on the resin.
  380. In anion exchange chromatography, The Cl- anion and the biological anion then
    exchange positions.
  381. In anion exchange chromatography, the excess Cl- sticks to the column and the biological molecule
    • reenters the solution
    • In anion exchange chromatography, The most weakly bound biological anion, having the smallest net negative charge, will be competed
    • by dilute Cl- and will elute (exit) first from the column.
  382. In anion exchange chromatography, The most strongly bound biological anion, having the largest net negative charge, will require
    high competing [Cl-] to loosen up from the column.
  383. In anion exchange chromatography, The most negatively charged biological anion will elute
  384. The forms of nucleic acids which occur in biological samples have different numbers of
    negative phosphate groups attached
  385. AMP =
    adenomonophosphate (1 phosphate group)
  386. ADP =
    adenodiphosphate (2 phosphate group)
  387. ATP =
    adenotriphosphate (3 phosphate group)
  388. The order of elution of adenosine, AMP, ADP, and ATP is in the order of their
    net negative charge
  389. The order of elution of adenosine is in the order of their net negative charge because
    the more negative molecules bind more tightly to the positive column and require higher concentrations of negative Cl- to compete with them for the positive sites on the column.
  390. A phosphate OH group deprotonates to O- at pH
  391. The "acid" in a nucleic acid nucleotide is a
    phosphate group
  392. dATP is an energy storage molecule because it contains
    mutually repelling charged groups
  393. The three phosphate groups in deoxy ATP are
    connected to each other
  394. Base pairing in DNA employs a strategy of complementary
    sizes and H-bond properties
  395. Large double rings pair with
    small single rings
  396. NH donors pair with with
    N: or O: acceptors.
  397. The type of biomolecule with naturally occuring examples of both homopolymers and heteropolymers is
  398. A class of structures where we have NOT seen examples of a network of H-bonds within the biomolecule itself is
  399. Lipids are mostly nonpolar
  400. Lipids are nonpolar and aggregate in
  401. Phospholipids form
    membrane bilayers
  402. Of the four types of biomolecules, one of them does not form polymers. This type is
  403. Conversion of mRNA into a protein is called
  404. Formula is mostly CH2 = nonpolar hydrocarbon chain makes it a
    fatty acid
  405. Myosin is a
  406. Mysoin is a homo/hetero polymer?
  407. Oxidation of a fatty acid during metabolism converts
    nonpolar bonds to polar bonds, and releases heat
  408. Phosphates are components of
    membrane lipids and nucleic acids
  409. A reaction joining two amino acids together creates
    an amide plus water
  410. Colored pigments frequently have conjugated
    pi cloud systems
  411. The effect of absorption of light on the pigment retinal is
    a change in configuration at a C=C double bond
  412. The structural origin of the rigidity of cellulose is
    hydrogen bonding
  413. Every nucleotide in RNA contains a ___ component
  414. The term which describes the reaction given below : amino acid + amino acid -> polymer + water
  415. A linear aldose begins with an aldehyde group, ends with a -CH2-OH group, and has H-C-OH carbons in between. The chiral carbon(s) include the
    H-C-OH carbons
  416. When citric acid is bound to the enzyme aconitase, the two -CH2-COOH groups attached to the central carbon atom have ___ probabilities of interacting with groups on the enzyme.
  417. The term configuration applies to ___ .
    R vs. S ; and cis vs. trans
  418. The naming system which is based on a comparison to the standard, glyceraldehyde, is the ___ system.
    D vs. L
  419. D-glyceraldehyde , a 3 carbon sugar with one chiral center, is the building block for longer sugars, so
    its chiral center appears in other biological sugars.
  420. Glycerol and glyceraldehyde each have
    3 carbons
  421. Ibuprofen has one chiral carbon. The most inexpensive way to synthesize it is as a racemic mixture of R and S forms. The % of the ibuprofen molecules in the pill you buy which are physiologically active is
  422. Racemic mixture are always 50/50 because
    Only one of the two enantiomers is physiologically active.
  423. Levo is the root word for
  424. Linear aldose sugars have their aldose group at C-1. The D carbon is always ___ .
    the highest numbered chiral carbon
  425. In chiral amino acids,the L carbon is in the
    backbone (HN-C-carbonyl)
  426. Spark =
    symmetric catalyst
  427. a symmetric catalyst exerts no chiral forces on the reactants, so it
    can't force a specific chiral product.
  428. Except for glycine (which is neither D nor L), the amino acid products produced by passing a spark thru a mixture of NH3, CH4, H2O and H2 are ___ .
    50% L and 50% D
  429. The designations which are based on the rotation of plane-polarized light of a particular wavelength are ___ .
    d and l
  430. A surface marked T-F-M clockwise (thumb/forefinger/middle-finger) would bind the right hand
    better than the left hand (3 contacts vs 2).
  431. The stereospecificity of biological reactions can be demonstrated by considering a model requiring attachment of a substrate to an enzyme at a minimum of ___ points.
  432. If a D amino acid is incorporated into the normal right-handed alpha helix of a protein, then there will be steric conflicts between the ___ .
    sidechain R group and backbone carbonyl O atom
  433. The "a" is for the equilibrium written in the direction of acid dissociation as in
    HA -> H+ plus A-
  434. When describing acid-base equilibria, we speak of the pKa. The "a" stands for
    acid dissociation
  435. The active site of triose phosphate isomerase contains a glutamic acid (Glu) sidechain (HOOC/COO- , pKa=5) and a histidine sidechain (HN+/N:). At pH 7, the glu sidechain initially acts to
    revmove an H+ from the substrate
  436. A molecule of the type (HA -> A- and H+) is best able to resist changes in pH due to either incoming H+ or incoming OH- when
  437. Buffers are composed of ___
    weak acids or bases
  438. An underwater swimmer holds his breath. CO2 from metabolism builds up in the blood. The [H+] ___ during the swim.
  439. H2PO4- can be what in water?
    a conjugate acid or a conjugate base
  440. The sidechain of cysteine exists as SH -> S:- plus H+ , with a pKa of 9. The dominant forms at pH 2 and pH 8 are
    SH (pH 2) ; SH (pH 8)
  441. One "equivalent" of NaOH is
    the amount of NaOH needed to fully titrate one functional group
  442. For the reaction HA -> A- + H+, Ka equals
    Ka = dissociated products/reactants = ([A-]x[H+])/[HA]
  443. One form of the Henderson Hasselbalch equation is (pKa-pH) = log (protonated/deprotonated). True or false : Another form is (pH-pKa) = log (deprotonated/protonated).
  444. The "p" in pH and pKa means
    -log (base 10)
  445. The pH of blood is 7.4, and the pH of stomach gastric juice is 1.4. The blood [H+] is ____ than the gastric juice.
    a million times lower (7.4 - 1.4 = 6 ... 10^6 = a million)
  446. The titration curve for phosphoric acid exhibits three S-shaped curves. The first midpoint (pKa 2.15) corresponds to the reaction
    H3PO4 <=> H2PO4(-1) + H+
  447. A small pKa means a ___ Ka.
  448. In the titration curve for glycine, the simplest amino acid, the structure in the middle of the curve is
  449. The midpoint of a titration curve (reaction HA -> H+ and A-) has HA = A- = 50% of each. This occurs when
    pH = pKa
  450. At pH 4, what are the concentrations of [H+] and [OH-]? 10^-3 M is the notation for 1 mM.
    [H+] = 10^-4 M. [OH-] = 10^-10 M.