Biochem exam II

  1. number and classify
    Image Upload 1
    • ketotriose
    • ketone lowest #, either side.  Non-chiral, no L or D.
  2. number and classifyImage Upload 2
    aldoheptose.  D.  Aldehyde is C1
  3. number and classifyImage Upload 3
    ketopentose.  L.  Ketone has lowest number, on C2.
  4. number and classifyImage Upload 4
    aldohexose.  D.  aldehyde is C1, last chiral determines D/L
  5. number and classifyImage Upload 5
    Aldotetrose.  L.  Aldehyde is C1.  last chiral determines name.
  6. Identify, 3-letter abbreviation, facts
    Image Upload 6
    • D-glc
    • D-glucose
    • key metabolite of blood and brain
  7. Identify
    Image Upload 7
    • D-fru
    • D-fructose
    • ketose, fruit sugar and honey, 2x as sweet as table sugar.  5-C ring, ketone.
  8. Identify
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    • D-gal
    • D-galactose
    • C-4 epimer of glucose
    • component of milk sugar
  9. Identify
    Image Upload 9
    • D-man
    • D-mannose
    • C-2 epimer of glucose
    • component of glycoproteins
  10. Identify
    Image Upload 10
    • D-glucose
    • D-glc
  11. Identify
    Image Upload 11
    • L-glucose
    • L-glc
  12. Identify (all parts)
    Image Upload 12
  13. Identify (all parts)
    Image Upload 13
  14. Identify (all parts)
    Image Upload 14
  15. Identify (all parts)
    Image Upload 15
  16. stereoisomers
    • same groups, different arrangement.  Includes enantiomers, diastereomers and epimers.  
    • 2where n=chiral centers
  17. enantiomers
    mirror image isomers.  D vs L if ENTIRE MOLECULE is flipped, all chiral carbons are on opposite sides.
  18. diastereomers
    non-mirror image stereoisomers.  Some (more than one, less than all) chiral carbons are flipped.  2n/2 (this # does not include enantiomers)
  19. epimers
    • subcategory of diastereomer, differs at 1 chiral center.  
    • Mannose is C-2 epimer of glucose.  Galactose is C-4 epimer of glucose.
  20. catalyst
    • decrease activation energy to speed up reactions
    • not changed or used up in reactions (restored if changed intra)
    • all enzymes are catalysts, not all catalysts are enzymes.
  21. enzymes vs nonbiological catalysts
    • enzymes are much more specific (stereospecific)
    • catalyze only one/few specific reactions
    • function under MILD conditions (pH, temp, [salt], aqueous solvents)
    • most biological catalysts are proteins (except ribozymes)
  22. cofactors
    • additional component of enzymes required for activity
    • inorganic metal ions, organic compounds (coenzymes) like metabolites (ATP, SAM, UDP-glucose) or derivatives of water-soluble vitamins (NAD+, FAD)
  23. prosthetic group
    • a cofactor covalently, permanently attached to a protein/enzyme.  
    • FAD
  24. holoenzyme
    enzyme plus prosthetic group
  25. apoenzyme
    enzyme without prosthetic group
  26. oxidoreductases
    catalyze redox reactions.
  27. transferase
    transfer an intact group from one molecule to another
  28. hydrolase
    • hydrolyze bonds (split single bonds via H2O)
    • One substrate HAS to be H2O
  29. lyases
    • cleave C-C, C-O, C-N without hydrolysis or redox.
    • removal of water to form double bond
    • addition of water to double bond
    • A + H2O --> B = hydration (NOT B+C)
    • when in doubt, it's a lyase
  30. isomerase
    • interconversion of isomers
    • includes racemases, which interconvert enantiomers to equilibrium (not always 50/50)
  31. ligase
    • enzyme that joins two molecules in reaction coupled to ATP cleavage
    • Requires a source of energy (ATP, GTP, etc)
  32. enzyme effect on equilibrium
    • NONE
    • enzymes lower activation energy of transition state, no effect on equilibrium or ΔG
  33. a small decrease in ΔG± due to presence of catalyst causes
    large increase in rate
  34. Correct model of enzyme-substrate interaction
    • modified lock and key model
    • fits transition state, optimized weak interactions
  35. lock and key model
    • substrate fits to enzyme like lock/key.  
    • Garbage
    • would stabilize ES and never make product
    • negative catalyst
  36. induced fit model
    • enzyme changes conformation as substrate binds, creating active site that fits S
    • Happens sometimes.
  37. modified lock and key
    • fits transition state (bent metal rod)
    • optimizes weak interactions
  38. specificity pocket
    fold on an enzyme where the substrate goes, specifically interacts with substrate.
  39. basis of specificity of enzymes is
    weak interactions between E and S
  40. 4 ways that weak interactions contribute to catalysis
    • bond (steric) strain (enzyme destabilizes S and pushes towards TS)
    • entropy reduction (correct positioning of functional groups on reactants to increase productive collisions)
    • desolvation (weak interactions to stabilizing H2O replaced by enzyme, removes barrier to rx)
    • electrostatic effects (active site repels S but not TS)
  41. why are enzymes so large?
    multiple weak interactions (tertiary structure) at sites distant from catalytic site
  42. Limits to enzyme activity
    • narrow pH (R groups pKa)
    • narrow temp
  43. why do enzymes have pH optima?
    state changes at different pHs.  Different bonds and charges form.  Could fail to interact with substrate or not even fold properly
  44. why do enzymes have temperature optimum?
    • too low and collisions decrease, lowering reaction rate too much
    • too high and protein denatures (except thermophiles)
  45. why do living organisms need catalysts?
    need high heat for reactions, would cook ourselves
  46. acid-base catalysis
    • transfer of proton can help stabilize or unstabilize intermediate, pushing rx toward S or P.  
    • transition state is unstable charged intermediate.  
    • can be general or specialized
  47. general acid-base catalysis
    • Ionizable R group on enzyme is the H+ acceptor/donor
    • MORE EFFICIENT than specific due to correct placement
  48. specific acid-base catalysis
    • OH- or H3O+ are the H+ acceptor/donor.  No ionizable R group involved.  
    • less efficient than general acid/base
  49. covalent catalysis
    covalent E-S intermediate via nucleophilic attack (chymotrypsin), ES splits to form E and P
  50. metal-ion catalysis
    • ionic interaction between E-M and S
    • Redox reaction with metal
  51. discuss chymotrypsin reaction mechanism.
    • very small molecule, illustrates TS stabilization, covalent catalysis, general acid and general base catalysis.  Catalytic triad (ser-195, his-57, asp-102) in active site.
    • peptide binds active site of enzyme
    • his-57 acts as general base catalyst, removes H+ from ser-195, aided by asp-102 (stabilizes + charge on his)
    • ser-195 acts as nucleophile, attacks carbonyl of peptide bond (covalent catalysis)
    • tetrahedral TS is charged/unstable
    • stabilized by oxyanion hole (H-bonds to 2 amide N-H--gly and ser)
    • peptide bond cleaved as his-57 donates H+ (from ser) to amino group (general acid catalyst)
    • H2O acts as nucleophile, attacks carbonyl causing a second tetrahedral TS (his-57 takes H+, general base catalyst)
    • ester link to enzyme is cleaved to regenerate enzyme, O returns to make double bond, releases ser, his donates H+ to ser (general acid catalyst)
  52. chymotrypsin molecule
    • very small
    • 3 S-S linked chains (A, B, C), once all one but cleaved post-S-S-bond
    • hydrophobic pocket including tyr
    • contains catalytic triad (ser-195, his-57, asp-102) in active site
  53. which steps in reaction of chymotrypsin contribute to ΔGB?
    H-bonding with groups in oxyanion hole (at tetrahedral intermediate, 2x)
  54. hexokinase
    • catalyses: 
    • glucose + Mg2+·ATP→glucose 6-P + Mg2+·ADP
    • illustrates induced fit
    • must bind with both ATP and Glucose, NOT H2O, conformational change on glucose binding to make active
    • prevents enzyme from being wasteful ATP-ase
  55. enzyme kinetics
    the study of rates of enzyme catalyzed reactions
  56. applications of enzyme kinetics
    • clinical diagnosis (elevated serum enzyme levels indicate disease state)
    • pharmacology (drug design, enzyme inhibitors)
    • research (deduce catalytic mechanisms)
  57. isozymes
    different proteins catalyze same reaction
  58. Michaelis-Menten Equation
    v0=Vmax[S] / Km + [S]
  59. 2 phases of the curve on a michaelis-menten kinetic enzyme
    • S < Km, linear
    • S > Km, plateau
    • hyperbolic
  60. conditions for substrate saturation curve/michaelis-menten kinetics
    • E+S ⇆ ES ⇆ E+P
    • 2 step rx where 1st is rapid and second is rate determining
    • only one substrate
    • raes measured at STEADY STATE (rate of formation of ES = rate of breakdown of ES)
    • must be measured VERY EARLY for v0, so [S] and P are realitively stable/constant
    • because step 2 is slower, v0 = k2[ES]
  61. steady state in michaelis-menten
    rate of formation of ES = rate of breakdown of ES
  62. michaelis-menten when Vmax= v0
    all active sites are bound to S
  63. Vmax occurs in Michaelis-Menten when
    • enzyme is saturated with S
    • max v0 achievable for rx under assay conditions
    • at S below Vmax, enzyme is in the process of loading up with S
  64. If at [S] between 0 and the one that gives v0 = Vmax, add S, which way does equilibrium shift?
  65. If add enough S to rx between 0 and Vmax, equilibrium shifts to ______ and have ______% ES.  Rx then depends on _____.  This occurs on the graph at ________.
    • Right
    • 100%
    • [E]
    • plateau/asymptote
  66. Km
    • Michaelis constant.  Substrate concentration at which v0 = 1/2 Vmax
    • measured in M/mM/μM etc.
    • measure of AFFINITY (if second step is slow)
  67. lower Km means
    higher affinity for substrate (if second step is slow enough)
  68. Michaelis-Menten:
    what fraction of enzyme molecules are bound to S at v0 = 1/2 Vmax?
  69. Michaelis-Menten:
    What fraction of enzyme molecules are bound to S at v0 = 1/10 Vmax?
  70. Michaelis-Menten:
    what fraction of enzyme molecules are bound to S at S=Km?
  71. An enzyme has 1 binding site that can bind 3 different substrates.  Which substrate binds most tightly?  Which has greatest Vmax?
    A.  2 x 10-3M
    B.  7 x 10-2M
    C.  6 x 10-4M
    • Most tightly is C, lowest Km.  
    • Can't tell who has highest Vmax, NO DIRECT RELATIONSHIP.
  72. If the Vmax = 50 μmol/min and Km = 3.0 mM, what is v0 when S = 3.0 mM?
    • 25. μmol/min
    • v0 = vmax [S] / Km + [S]
  73. If the Vmax = 50 μmol/min and Km = 3.0 mM, what is v0 when S = 300. mM?
    • 50. μmol/min
    • v0 = Vmax [S] / Km + [S]
  74. If the Vmax = 50 μmol/min and Km = 3.0 mM, what is v0 when S = 2.0 mM?
    • 20. μmol/min
    • v0 = vmax [S] / Km + [S]
  75. If the Vmax = 50 μmol/min and Km = 3.0 mM, what is [S] when v0 = 1/4 Vmax?
    • (1/4)(50 μmol/min) = 50μmol/min·[S] 3.0mM + [S]
    • 37.5 mM·μmol/min + 12.5 μmol/min·[S] = 50μmol/min·[S]
    • 37.5mM·μmol/min = 37.5μmol/min·[S]
    • [S] = 1.0 mM
  76. Vmax on a graph occurs
    at plateau.  Asymptotically approaches Vmax
  77. S at 1/2 Vmax =
  78. determine Vmax and Km from a graph
    • asymptote approaches Vmax
    • where Vmax/2 = y, Km = x
  79. determine Vmax and Km from a data table
    • check if [S] corresponding to 1/2 Vmax is given.  If not, use an (x,y) pair on LINEAR portion, plug into equation.  
    • y=v0, x=[S]
  80. determine Vmax and Km from M-M equation and data table
    • estimate Vmax from table (asymptote)
    • select any (S, v0) coordinate pair away from plateau
    • plug into MM equation and solve for Km
  81. determine Vmax and Km from a Lineweaver-Burk plot
    • y intercept = 1/Vmax, so Vmax = 1/b
    • x intercept = -1/Km, so Km = -1/x intercept
  82. determine Vmax and Km from a Lineweaver-Burk equation
    • Vmax = 1/b
    • slope = Km/Vmax
    • Km = m/b
    • line equation = 1/v0 = Km/Vmax·1/[S] + 1/Vmax
  83. Lineweaver-Burk Plot
    • 1/v0 x 1/[S]
    • used when you run enzyme assay to measure how much enzyme is present (start with saturation numbers so v0 = Vmax)
  84. turnover number
    • # molecules of substrate converted to product by 1 molecule of saturated enzyme  /  time
    • kcat
    • measured in inverse time
  85. kcat
    • # molecules of substrate converted to product by 1 molecule of saturated enzyme  /  time
    • measured in inverse time
    • turnover number
  86. specificity constant
    • kcat/Km (measured in inverse concentration times inverse time)  M-1sec-1
    • significant predictor of catalytic efficiency in vivo.
  87. enzyme inhibitors
    • a compound that binds to an enzyme specifically and decreases its activity without disrupting its structure (not a denaturant)
    • Irreversible, 2 types: transition state analogs, suicide inactivators
    • Reversible, 3 types: competitive, noncompetitive, uncompetitive
  88. Competitive inhibitor
    • reversible, binds via noncovalent
    • binds to active site, COMPETES with substrate
    • can be overcome at high [S]
    • E  + S ⇆ ES ⇆ EP
    • EI
  89. Competitive: What direction does reaction shift as a result?
  90. Competitive: What effect does enzyme/shift have on amount of S bound to E?
    decreases, uses up
  91. Competitive: what direction does reaction shift if S is added?
    right.  With infinite substrate will still reach 100% saturation/equilibrium
  92. Competitive: What is the effect of a competitive inhibitor on Vmax?
    none.  Vmax occurs when all enzyme is bound to substrate.  Unconnected to inhibitor.  Inhibitor just prevents from REACHING Vmax
  93. Competitive: What is the effect of a competitive inhibitor on Km?
    • increased.  It now takes more S to reach 1/2 Vmax
    • Enzyme appears to have less affinity
  94. Is the concentration at which S is saturating greater than, less than or the same in the presence of a competitive inhibitor compared to the absense?
  95. Image Upload 16
    competitive inhibitor
  96. Image Upload 17
  97. Image Upload 18
  98. noncompetitive inhibitor
    • binds reversibly to non-substrate site of enzyme, can bind to E or ES
    • unchanged by increasing substrate
    •      E  + S  ⇄    ES
    • +I ⇅               ⇅+I
    •      EI + S   ⇄   ESI    ←inactive
  99. noncompetitive inhibitor: effect at Vmax
    decreases, can't be overcome by increasing substrate
  100. noncompetitive inhibitor: predict effect at Km
    • none
    • Equilibrium is unchanged--same amount of substrate is necessary, just Vmax has changed
  101. Explain why most competitive inhibitors have structures similar to the substrate for the enzyme they inhibit whereas most noncompetitive inhibitors do not
    Competitive bind at same site, fool enzyme.  Noncompetitive bind at a different site.
  102. Uncompetitive inhibitors
    • bind reversibly to ES but NOT to E.
    • Increasing substrate concentration doesn't displace enzyme
    • E + S⇄ES
    •         +I⇅
    •           ESI
  103. Uncompetitive inhibitors: predict effect at Vmax
    • decreased
    • Uses up ES, so Equilibrium shifts to the right
  104. Uncompetitive inhibitors: predict effect on Km
    • decreased
    • need less substrate to get to 100% ES.  Looks like affinity has increased
  105. Irreversible Inhibitors
    • form covalent or VERY stable noncovalent with amino acid side chain on enzyme.  Does not come back off.  Permanent inactivation
    • drugs
    • Can be used as affinity labels in research, transition state analogs or suicide inactivators
  106. affinity labels
    irreversible inhibitors, used in research to identify crucial amino acids at active site.
  107. transition state analogs
    • irreversible inhibitor that mimics transition state, not substrate.  
    • modified lock and key ensures extremely tight binding, potent inhibitor
  108. suicide inactivators
    • irreversible inhibitors, mechanism based inactivators).  
    • activated during enzyme reaction, participates during initial steps like substrate, specific to 1 enzyme/site. Few side effects.
  109. 5 strategies to regulate enzyme activity
    • Self Regulation
    • Isozymes
    • allosterism
    • covalent modification
    • proteolytic activation
  110. Self-Regulation
    • When [S] in cell is near Km.  High [S] = high reaction rate, [S] stays stable within a narrow range
    • low [S] = low reaction rate.
  111. Regulatory enzymes
    • regulate an entire metabolic pathway
    • catalyze irreversible steps in pathway (large Keq or very exergonic)
    • activity increases or decreases in response to metabolic concentration
    • catalyse 1st committed step in pathway
  112. Committed step
    place where a metabolic pathway has no more branches, exists only to make the one final product. Where regualatory enzyme catalyzes
  113. Allosteric regulatory enzymes
    • exist in 2 conformations
    • binds substrate noncovalently at active site
    • regulatory/allosteric site binds effectors noncovalently
    • have quaternary structure and exhibit cooperative kinetics (binding one makes others more able to bind)
    • effector can decrease or increase activity
  114. allosteric
    "other shape".  Exists in multiple conformations
  115. effectors
    modulators that bind noncovalently to alter enzyme activity, changing Vmax or affinity.  Can be positive or negative
  116. cooperative kinetics
    • different from michaelas-menten
    • one subunit binding makes next subunit change shape, become more or less likely to bind
    • can be negative or positive change
  117. homotropic effector
    when the substrate is the effector that causes cooperative kinetics in an allosteric enzyme, as in hemoglobin
  118. heterotrophic effector
    • when the substrate is not the effector that causes cooperative kinetics in an allosteric enzyme.  
    • Can increase or decrease enzyme activity by changing Vmax or K0.5 (one or the other)
    • rarely similar to S or P (end products or intermediates of metabolic pathway--feedback loop
  119. negative effectors
    inhibitors.  Binding of effector causes allosteric change to less active conformation, decreases activity
  120. positive effectors
    activators.  Binding of effector causes allosteric change to more active conformation, increases activity.
  121. name an allosteric protein that is not an enzyme.
    what is the homotrophic effector?  What are the heterotrophic effectors (2)?  Are they positive or negative?
    • hemoglobin. 
    • oxygen
    • 2-3-BPG and protons
    • negative, stabilize T-state
  122. Discuss differences and similarities between oxygen binding sites on Hb and the active site on allosteric enzymes
    • similarities: cause shift to more active form/conformational change.  Functional binding sites that allow enzyme to function.  
    • differences: enzyme catalyzes reaction, Hb does not have a catalytic site, releases substrate unchanged
  123. structure of allosteric enzymes
    must have quaternary structure.  Subunits may be identical or different , symmetrically arranged.  If same, each subunit has separate catalytic sites and regulatory sites.
  124. saturation curve of cooperative kinetics is
  125. [S]0.5 and/or K0.5 are seen in
    cooperative kinetics, where vo=1/2 Vmax = K0.5
  126. feedback inhibition
    product or intermediate turns loop off at committed step.
  127. R state
    More active state of allosteric enzyme, does not necessarily mean relaxed.  Preferentially binds and is stabilized by activators and substrate, makes more R.
  128. T state
    Less active state of allosteric enzyme, does not necessarily mean taut.  Preferentially binds and is stabilized by inhibitors, makes more T.
  129. concerted model of allosteric bonding
    S binding to 1 subunit switches all subunits to R, increases affinity for S and increases activity
  130. Sequential model of allosteric bonding
    • S binding to one subunit changes only that subunit.  Hybrid "T-R" in dimer.  
    • Increases likelihood of adjacent subunits undergoing change, so still cooperative
    • intermediate states have intermediate levels of activity, so fine-tuned
  131. allosteric enzymes with heterologous subunits
    • cataylic (C) subunit has substrate binding site
    • regulatory (R) subunit has heterotrophic effector sites
    • binding of positive heterotrophic effector causes conformational change in R subunit that goes to C subunit and increases activity (usually increases affinity)
  132. Covalent modification as regulation
    • Enzyme exists as more or less active (2 states), conversion is covalent.  
    • Most common is addition of Pi to Ser-OH
  133. How can phosphorylation of one side chain alter catalytic activity
    • covalent modification, changes polarity and bulk.  Can alter folding/tertiary structure/conformation, changing salt bridges and activity.  
    • substrate can be attracted or repelled by new charge in the way, may need OH or PO4 to bind.  Catalytic activity may be based on OH or PO4, nucleophile/electrophile
  134. glycogen metabolism is regulated in which way?
    • covalent, phosphorylated.  
    • Only one side active at a time (phosphate activates one side and inhibits the other) to avoid futile cycle.
  135. compared to allosterism, covalent modification as regulation is _________
    • slower (make and break covalent bonds is slower)
    • amplifiable (cascade of reactions, initial activates cascade, can grow exponentially)
  136. proteolytic enzyme activation
    • zymogens require splicing to work, irreversible.
    • Helps restrict time and location of enzyme activity
  137. zymogen
    • inactive precurser of an enzyme
    • N-terminal extension (signal sequence) that that tags the enzyme for secretion.  Cleaved co-translationally.
  138. why is it important for proteases and peptidases (trypsin and chymotrypsin) to be made as zymogens and have proteolytic activation?
    Need to delay activation so they don't eat the cell.
  139. what protects stomach and gut lining from being digested after chymotrypsin and trypsin proteases are activated?
    mucus.  Proteins in bilayer aren't exposed due to mucus lining and glycocalyx.  Chains of sugars hang into lumen and block peptide bond.
  140. Proteases have a limited half-life in the stomach and intestine.  Explain
    can't be reversed, always stay active after activation, so much be INactivated.  Pepsin by pH in intestine, or natural small inhibitors that live in intestine for permanent inhibition.
  141. Pro- or -gen indicates
    • inactive form
    • prothrombin, fibrinogen
  142. Pre- indicates
    precursor, secretion.  N-terminal signal sequence on a zymogen, sends out for secretion.
  143. hemiacetal
    • OH
    • R - C - O - R' = (aldehyde + alcohol)
    •      H
    • Closes ring in glc monosaccharide, causes alpha/beta
  144. most stable ring size
    6-membered pyranose ring (includes O)
  145. alpha anomer of glc means
    OH on the bottom of C1
  146. beta anomer of glc means
    OH on the top of C1
  147. mutarotation
    interconversion between alpha and beta forms in a ring.  Exist in equilibrium, change frequently
  148. anomeric carbon
    carbon in the ring attached to O and OH, C1 in ring, causes alpha or beta
  149. anomer
    isomers that differ in configuration only about the anomeric carbon
  150. The most stable sugar and why
    D-glc, beta anomer in chair formation.  Has 109.5 bond angles and EVERY OH is equatorial.  So body runs on glucose.
  151. Explain why the C-2 and C-3 OHs in glc have little tendency to add across the carbonyl
    bond angles are too loose or too tight.  C5 is 109.5, just right.
  152. hemiketals
    • OH
    • R-C-O-R'    ketone + alcohol
    •    R"
    • closes ring in fructose, makes furanose.  Ring is more stable than chain, 5-ring rather than 6 due to enzyme
  153. How to find the anomeric carbon
    Look at the O in the ring.  Next to it, the C with OH attached.
  154. oxidation of a primary alcohol makes a
  155. oxidation of a secondary alcohol makes a
  156. oxidation of an aldehyde makes a
    carboxylic acid
  157. Oxidation of a tertiary alcohol makes a
    doesn't happen because no H on C.
  158. ________ is a good test for reducing sugars which tells us
    • oxidation.  Monosacc and some oligosacc can be oxidized under mild conditions
    • alpha OH ketone is in equilibrium and can be oxidized so aldoses and ketoses with free carbonyls are reducing sugars (blood glucose monitors)
  159. Reducing sugars
    • monosaccharides or oligosaccharides that can be oxidized under mild conditions
    • when alpha ketone is in equilib with aldehyde and can be oxidized.  Aldoses and ketoses with free carbonyls are reducing sugars
  160. If glucose oxidase is stereospecific for beta-D-glc (64% of total blood sugar) who can it be used to test for TOTAL blood glc?
    Le chatelier shift.  Keep removing product and eventually you get all.
  161. oxidized sugars become
    sugar acids
  162. Reduced sugars become
    sugar alcohols, no longer a sugar.
  163. esterification
    alcohol + acid = ester
  164. carboxylate ester
    • esterification
    • ROH + RC(OH)=O   RC(OR)=O + H2O
    • alcohol + carboxylic acid = carboxylic acid ester + water
  165. phosphate ester
    • sugar phosphate
    • ROH + HO-(O-)P(=O)-O= RO(O-)P(=O-) + H2O
    • alcohol + phosphoric acid = phosphate ester + water
  166. How does sugar get phosphorylated?
    phosphate transferred from ATP by kinase (phosphoryl group transfer) to sugar.
  167. amino sugars
    • amino group replaces one hydroxyl group
    • usually happens at C-2, don't have to indicate at this location.  
    • glucosamine, galactosamine, etc.
    • amino can be acetylated (NH - C=O - CH3)
  168. glcNAC
    • N-acetylglucosamine
    • glc with C-2 amine instead of OH, bonded to C=O-CH3
    • important in extracellular matrix and bacterial cell wall
  169. acetal formation
    • reaction that links monosaccharides to form disaccharides and polysaccharides
    • hemiacetal/hemiketal + alcohol = acetal with dehydration synthesis
    • R-CH(OR')-OR"
  170. O-glycoside
    bond based on anomeric C's hydroxyl group.  Once methylated it is locked and can't mutarotate any more.  Non-reducing sugar
  171. N-glycoside
    • when anomeric carbon hydroxyl group bonds to a nitrogen of another molecule
    • That makes nucleotides
  172. difference between maltose and cellbiose, and what they are
    • maltose: glc(alpha 1->4)glc (alpha or beta anomer)
    • cellbiose: glc(beta 1->4)glc (alpha or beta anomer)
  173. sucrose
    • glc (alpha1--> beta2) fru
    • non-reducing (anomerics are both linked, fru is backwards)
    • transport of sugar in plants
  174. maltose
    • alpha glycoside (beta is cellobiose)
    • glc (alpha1-->4)glc
    • product of starch and glycogen breakdown
  175. cellobiose
    • beta-glycoside (alpha is maltose)
    • glc (beta1-->4)glc
    • breakdown product of cellulose
  176. lactose
    • beta-glycoside
    • gal (beta 1-->4) glc
    • milk sugar
  177. how do you tell what is a reducing vs nonreducing sugar?
    anomeric C is reducing end.  If both anomerics are attached is a nonreducing sugar.  If both C1's are linked.
  178. polysaccharides
    • polymers of monosaccharides joined via acetal links
    • length varies
    • can be branched
  179. homopolysaccharides
    same sugar over and over
  180. heteropolysaccharides
    different sugars
  181. storage polysaccharides
    starch (plants, glc(a1-->4)glc).  Amylose or amylopectin, glycogen
  182. starch
    • storage form of glc in plants
    • storage homopolysaccharide
    • glc(a1->4)glc
    • amylose (straight chain) and amylopectin (branches, larger)
  183. amylose
    starch, storage homopolysaccharide.  glc(a1-->6)glc
  184. amylopectin
    • glc(a1>6)glc, branches, larger than amylose
    • Branches = 1 reducing end and many non.  Stores glc as a polymer (prevents high osmolarity)
    • helical conformation (not alpha helix) is compact for storage
  185. glycogen
    • storage form of glc in animals (muscles and liver)
    • like amylopectin but MORE BRANCHED and smaller, so more dense
    • 1 reducing and many nonreducing ends
  186. what is the product when a cotton shirt is hydrolyzed?
  187. why do concentrated solutions of stong acids "burn" holes in cotton clothing?
    hydrolyze fibers.  Acid is a catalyst for hydrolysis, gving more stable transition state for hydrolysis
  188. structural homopolysaccharides
    • cellulose, chitin
    • B1->4 glycositic link fully extended, alternate rings flip
    • high tensile strength with H-bonds between chains
    • roughage, not digestible (beta-linked polysaccharides)
  189. cellulose
    • structural homopolysaccharide in plant cell walls
    • glc in beta(1->4 link)
  190. chitin
    structural homopolysaccharide in exoskeletons of arthropods
  191. difference between cellulose and chitin
    glucose vs glcNAC
  192. beta linked polysaccharides
    • B1->4 glycositic link fully extended, alternate rings flip
    • high tensile strength with H-bonds between chains
    • roughage, not digestible (good for diet)
  193. structual heteropolysaccharides
    2 or more dif monomeric units.  Extracellular support, so beta linkage
  194. peptidoglycans
    • component of bacterial cell wall
    • structural heteropolysaccharides
    • cause gram +/- (lipopolysaccharide coat on -)
    • alternating glcNAc(B1-->4)murNAc
    • cleaved by lysozyme (tears)
    • crosslinked by peptides for strength
  195. glycosaminoglycans
    • structural heteropolysaccharide
    • major component of ground, extracellular in bone
    • linear copolymers of Beta-linked
    • control water content of connective tissue by binding water
  196. What effect does substituting a COOH or NAc for OH have on the polarity of the molecule
    increases, because now charged
  197. What effect does substituting a COOH or NAc for OH have on the ability of the molecule to H-bond water
    increases, more places to bond.
  198. What effect does substituting a COOH or NAc for OH have on the water solubility
    increased, more polar
  199. hyaluronic acid
    • glycosaminoglycan. 
    • major component of synovial fluid and cartilage
    • most abundant glycosaminoglycah in human body
  200. hyaluronidase
    enzyme in pathogenic bacteria (flesh-eating, entry into connective tissue) and in sperm (entry into ovum through zona pellucida).
  201. examples of glycosaminoglycans
    • hyaluronic acid
    • chondroitin sulfate
    • heparin
    • dermatin sulfate
  202. homopolysaccharides composition, linkate ad function
    • same sugar over and over, 1->4, alpha or beta
    • alpha: starch (storage in plants), glycogen (storage in animals)
    • beta: cellulose (structure in plants), chitin (structure in arthropods/yeast/fungi/algae)
  203. heteropolysaccharides
    • peptidoglycans or glycosaminoglycans.
    • 2 or more sugars, extracellular support, Beta
    • peptidoglycan: bacterial cell walls, glcNAc(B1-4)murNAc, cleaved by lysozymes
    • glycosaminoglycans: beta glcNAc or galNAC + glucuronic acid or sulfate ester, bind water and shock absorber/lubricant.  Hyaluronidase (bacteria and sperm), chondroitin sulfate (human), keratin slulfate (human), heparin, dermatin sulfate
  204. glycoconjugates
    conjugates of carbohydrate and another category of macromolecule
  205. proteoglycans
    • glycosaminoglycans attached to protein via O-glycosidic link to ser.  
    • membrane bound or proteoglycan aggregates
  206. proteoglycan aggregates
    found in extracellular matrix of connective, "bottle brush" or "tree"
  207. On what level of structure in cell heirarchy does a proteoglycan aggregate belong?
    supramolecular complex.  Mix of macromolecules
  208. glycoproteins
    • glycoconjugate.  Protein covalently linked to carbohydrate that is not a simple copolymer.  
    • O-glycosidic link to specific ser or thr, etc, galNAc or ga; or N-glycosidic link which links to asp and is glcNAc
  209. oligosaccharide chains in glycoproteins are ____________and _________ than in glycosaminoglycans
    shorter and more complex (more sugars and branches)
  210. functions of carbohydrate on glycoproteins
    stabilizes active conformation, affect folding of nascent protein
  211. where should carb groups be on a folded glycoprotein?
    outside, polar due to OH
  212. glycolipids
    • lipids covalently linked to carb via sphingosine
    • found in lipid bilayer
    • some contain complex oligosacch and are informational
  213. lipopolysaccharides
    • lipids (fatty acid chains) that are covalently linked to carbohydrates
    • found in the outer membrane of gram negative bacteria
    • complex oligosaccharide chains (informational)
    • contribute to antigenicity of bacteria
  214. NTP
    nucleotide triphosphates = energy currency of cell (ATP, GTP, CTP, TTP)
  215. structural component of nucleotides
    • monosaccharide (ribose or deoxyribose)
    • heterocyclic aromatic amine base
    • phosphate
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    Adenine, Purine
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    Ribose (beta anomer)
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    • cytosine
    • pyrimidine
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    deoxy ribose (B form)
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    • Guanine
    • purine
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    • thymine
    • pyrimidine
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    • Uracil
    • pyrimidine
  223. phosphodiester
    • sugar-phosphate bond 
    • monoprotic form (released 2 H) of phosphoric acid
    • RO-(OH)P(OR')=O
    • pKa~1
  224. nucleosides
    Beta-N-glycosides = base + sugar, no P
  225. adenine nucleoside
    adenosine or deoxyadenosine
  226. guanine nucleoside
    guanosine or deoxyguanosine
  227. cytosine nucleoside
    cytidine or deoxy cytidine
  228. uracil nucleoside
  229. thymine nucleoside
  230. NMP
    • nucleoside monophosphates
    • phosphate monoesters (on OH) of nucleosides
    • don't have to label ester bond if 5'
    • (adenosine monophosphate, deoxyguanosine-3'-monophosphate, etc), can be on ANY OH (watch deoxy)
  231. NDP
    • nucleoside diphosphates
    • phosphoric acid anhydride of NMP.  
    • (adenosine-5'-diphosphate vs adenosine-3', 5'-bisphosphate, 2Pi separated)
  232. NTP
    • nucleoside tri phosphates
    • 3 on same (anhydride) = adenosine-5'-triphosphate
    • 3 on dif = adenosine'2',3',5'-trisphosphate
    • function: storage of energy
  233. cyclic nucleotides
    • when phosphate makes a ring, attached to 3' and 5'
    • adenosine 3',5' cyclic monophosphate (cyclic AMP, cAMP)
    • always 3'5'
    • 2nd messengers in hormone response (cAMP = glucagon to increase glucose.  cGMP insulin to decrease glucose)
  234. polynucleotides
    polymers formed by joining nucleotides together via 3'-5'-phosphodiester bonds
  235. amphipathic
    half polar, half nonpolar.  In lipids, small polar head group and large nonpolar tail.  Aka amphiphilic
  236. fatty acids
    • storage lipids.  Straight chain carboxylic acid with long unbranched hydrocarbon tail (even # of C)
    • amphipathic
    • saturated, monounsaturated, polyunsaturated.  Cis in nature (more cis = lower melting point)
  237. monounsaturated fatty acid
    one C=C, cis conformation in nature.  Kink in chain, don't pack as well, lower melting point
  238. saturated fatty acid
    no C=C, highest melting point
  239. polyunsaturated fatty acid
    • more than 1 C=C, cis in nature, don't pack well, lowest melting point
    • Never conjugated, breaks in between double bonds
  240. unsaturated trans fatty acid
    only exists artificially, allows packing like saturated
  241. melting point __________ with chain length and _________ with increasing number of double bonds.  Why?
    • melting point increases with increased chain length, intermolecular forces (London)
    • melting poing decreases with increased C=C double bonds due to less packing ability, decrease in London forces
    • so saturated are solids at room temp and unsaturated are liquids
  242. water solubility __________ with increasing chain length because
    decreases.  Amphipathic molecules, nonpolar overwhelms polar as gets longer.
  243. Tendency to be oxidized ____________ with more C=C double bonds because
    • increases because they are more chemically reactive--don't need to remove/substitute anything, just can add on
    • Makes rancid
  244. Fats
    • storage lipids, triacylglycerol (triglyceride).  Glycerol ester is backbone, three different fatty acids attached. 
    • Nonpolar, not amphipathic, too many hydrocarbons
    • Very not-oxidized molecule, so good carbon source
  245. fat in diet vs heart disease.  Polyunsaturated, monounsaturated, omega three, trans
    • poly decreases blood cholesterol and heart attack risk (good)
    • mono decreases blood cholesterol without decreasing HDL (better)
    • O-3 decrease all the bad stuff (LDL, triglycerides, blood cholesterol) (best)
    • trans fat increases LDL and decreases HDL, worst
  246. waxes
    fatty acid ester of monohydroxy alcohols, usu fatty acid and alcohol are saturated, both long chains
  247. T or F, fats are more reactive than waxes
    • true.  One ester in wax vs 3 in fats.  Even more nonpolar than fats, even less reactive
    • nonpolar and inert so don't go rancid
    • protective coat and water barrier
  248. glycerophospholipids
    • diacylglycerol (2 fatty acids and one phosphoric acid, ester to glycerol backbone)
    • phosphoric acid is polar head group
    • lipid bilayers in membranes
  249. sphingolipids
    • phopholipid with backbone of sphingosine NOT GLYCEROL (amino alcohol).  Watch for OH bonded to backbone C, amide bond in center link.  Phosphate at bottom, but NOT GLYCEROPHOSPHATE
    • amphipathic.  In plasma membrane and myelin sheath
  250. glycosphingolipids
    • sphingosine backbone + fatty acid and sugar(ceramide) + sugar residue on 3rd with O-glycosidic bond
    • non-reducing (anomeric facing backbone)
    • amphipathic
  251. ceramide
    sphingosine + fatty acid with amide link.  No head group.
  252. cerebroside
    • glycosphingolipid with single monosaccharide.  Always non-reducing
    • lots in nervous system and plasma membrane
  253. gangliosides
    glycosphingolipid with oligosaccharide chain.  Lots in nervous system, plasma membrane, cell surface marker
  254. sterols
    • structural membrane lipids in eukaryotic cells, four fused rings.  Cholesterol.  Amphipathic but not very polar. 
    • keeps membanes fluids, precursor in steroid hormone, bile salts, vitamin D3, etc.
  255. steroids
    • oxidized derivatives of sterols (dif C=C on rings and additions)
    • Include corticosteroids, androgens, estrogens, progesterone, prednisolone and prednisone, bile salts
  256. eicosanoids
    • from arachidonic acid (ring closure, oxidation) at a signal
    • paracrine hormones (very short travel)
    • Include prostglandins, thromboxanes, leukotrienes
  257. Image Upload 26
    cerebroside glycosphingolipid
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    cerebroside glycosphingolipid
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  260. Image Upload 29
    ganglioside glycophospholipid
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    polyunsaturated fat
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    saturated fat
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    saturated fatty acid
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  265. Image Upload 34
  266. Image Upload 35
  267. Image Upload 36
    trans unsaturated fat
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  269. Image Upload 38
  270. Image Upload 39
    unsaturated fatty acid
  271. Beer's Law
    • A=εbc
    • A = absorbance
    • ε = extinction coefficient (constant) 
    • b = pathlength (cm)
    • c = concentration
  272. biuret assay
    • peptide bond + Cu = complex that absorbs
    • all proteins comparable results (not dependant on AA conc)
    • Stable, time not critical
    • not very sensitive
  273. Lowry assay
    • Cu complex forms like biuret, then trp and tyr reduce W and Mo salts, Absorbance
    • very sensitive
    • linear over short range, depends on AA composition
  274. Bradford Assay
    • dye binds to R groups, changes color
    • very sensitive, more than Biuret or Lowry, convenient
    • detergents interfere and composition of AA dependent
  275. Direct Spectrophotometric assay
    • Tyr and Trp absorb at 280
    • fast, nondesctructive so sample is recoverable
    • tyr/trp dependent, intereference from nucleic acid
Card Set
Biochem exam II
biochem test II, enzymes, carbohydrates