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biochem final review
chapter review questions from chapters 17-21 and supplemental chapter
103
Biochemistry
Undergraduate 4
12/13/2012

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Term
Energenic barrier that prevents glycolysis from simply running in reverse to synthesize glucose (gluconeogenesis)
Definition
  • highly endergonic in reverse under cell conditions
Term
Energenic cost of overcoming endergonic barrier in gluconeogenesis
Definition
  • 6 NTP molecules
Term
Lactate
Definition
  • readily converted into pyruvate
Term
Pyruvate carboxylase
Definition
  • generates oxaloacetate
Term
acetyl CoA
Definition
  • required for pyruvate carboxylase activity
Term
Phosphoenolpyruvate carboxykinase
Definition
  • generates a high-phosphoryl-transfer-potential compound
Term
glycerol
Definition
  • readily converted into DHAP
Term
fructose 1,6-bisphosphatase
Definition
  • gluconeogenic counterpart of PFK
Term
glucose 6-phosphate
Definition
  • found predominantly in the liver
Term
Rxns of glycolysis are not reversible under intracellular conditions
Definition
  • formation of pyruvate and ATP by pyruvate kinase
  • formation of fructose 1,6-BP by PFK
  • hexokinase catalyzing formation of glucose 6-phosphate
Term
bypasses formation of pyruvate and ATP by pyruvate kinase in gluconeogenesis
Definition
  • formation of PEP from oxaloacetate & GTP by PEP carboxykinase
Term
bypasses formation of F 1,6-BP from fructose 6-phosphate by PFK
Definition
catalyzing of conversion of fructose 1,6-BP to fructose 6-phosphate by fructose 1,6 Bisphosphatase
Term
bypasses hexokinase catalyzed formation of glucose 6-phosphate
Definition
  • glucose 6-phosphatase (only in liver)
Term
gluconeogenesis takes place during intense exercise, why synthesize gluscose at the same time it is needed to generate energy
Definition
  • example of interorgan cooperation, muscle creates lactate and is released into the blood stream, taken up by liver and converted to glucose in gluconeogenesis and released back into blood to be taken up by muscles for energy
Term
liver is primarily gluconeogenic, muscle is glycolytic, why the division of labor
Definition
  • lactic acid is a stong acid, therefore can't accumulate in the blood or muscle, liver removes it and transforms it into glucose and releases it into blood or stores it as glycogen for later use
Term
effect on ability to use glucose as energy if mutation inactivated glucose 6-phosphatase in liver
Definition
  • glucose produced would not be able to be released into blood, therefore tissue would only have dietary glucose to rely on
Term
why is the lack of glucose 6-phosphate activity good in brain and muscle
Definition
  • glucose is the primary source of energy for these tissues and the enzyme would cause the cells to release thier glucose
Term
Number of NTP molecules to synthesize one molecule of glucose from two molecules of pyruvate
Definition
  • 6 NTP: 4 ATP & 2 GTP
Term
Number of NADH molecules to synthesize one molecule of glucose from two molecules of pyruvate
Definition
  • 2 NADH molecules
Term
reciprocal regulation of gluconeogenesis & glycolysis; gluconeogenesis side
Definition
  • enzymes in both cycles act as control points
  • activated by: citrate, acetyl CoA
  • inhibited by : F 2,6-BP, ADP, AMP
Term
reciprocal regulation of gluconeogenesis & glycolysis; glycolysis side
Definition
  • enzymes in both cylcles act as control points
  • activated by: F 2,6-BP, AMP, F 1,6-PB
  • inhibited by: ATP, alanine, citrate, protons
Term
which conditions increase activity of the glycolytic pathway
Definition
  • increase in AMP
  • increase in F 2,6-BP
  • increase in insulin
  • fed
Term
which conditions increase the activity of gluconeogenic pathway
Definition
  • increase in ATP
  • increase in citrate
  • increase in acetyl CoA
  • increase in glucagon
  • fasting
Term
predict effects on pace of glycolysis for loss of allosteric site for ATP in PFK
Definition
  • increased pace
Term
predict effects on pace of glycolysis for loss of citrate binding site on PFK
Definition
  • increased pace
Term
predict effects on pace of glycolysis for loss of phosphotase domain controling level of F 2,6-BP
Definition
  • increased pace
Term
predict effects on pace of glycolysis for loss of binding site for F 1,6-BP in pyruvate kinase
Definition
  • decreased pace
Term
factor the additional high-phophoryl-transfer compounds alter the equilibrium constant of gluconeogenesis
Definition
  • addition of 4 high-phosphoryl-transfer potential compounds change the equilibrium constant by 1032 which make the conversion of pyruvate into glucose thermodynamically feasible
Term
rxn that links glycolysis and the citric acid cycle
Definition
  • pyruvate + CoA + NAD+ yields acetyl CoA +NADH + H+ +CO2
Term
enzyme that catalyzes the rxn that links glycolysis to the citric acid cycle
Definition
  • pyruvate dehydrogenase
Term
2 fates that the conversion of a pyruvate into acetyl CoA commits the carbon atoms to
Definition
  • oxidation into citric acid cycle
  • incorporation into lipids
Term
fatty acid breakdown generates large amounts of acetyl CoA, the effect it has on puruvate dehydrogenase complex activity
Definition
  • it will inhibit the activity of the complex
Term
fatty acid breakdown generates large amounts of acetyl CoA, the effect it has on glycolytic activity
Definition
activity will be slowed b/c acetyl CoA is being derived from another source
Term
why no O2 is needed for the CAC  although it is a part of aerobic respiration
Definition
  • CAC depends on supply of NAD+, which is generated from rxn of NADH w/ O2 ,no oxygen to accept e-, CAC will cease to operate
Term
energy source that drives the formation of citrate
Definition
  • hydrolysis of the thioester bond that is present on acetyl CoA.  It is converted to citryl CoA and then hydrolyzed converting to citrate
Term
value of ΔG0l for complete oxidation of acetyl unit of acetyl CoA in CAC
Definition
  • 41 kJmol-1
Term
idea that CAC can be considered a supramolecular enzyme
Definition
  • a catalyst facilitates a chemical rxn w/out itself being permenantly altered, CAC operates in that oxaloacetate binds an acetyl group leading to 2 oxidative decarboxylations of 2 C and is regenerated at the end of the cycle
Term
change in the CAC intermediates after addition of inhibitor malonate
Definition
  • succinate, α-ketoglutarate, and other up stream intermediates will increase in concentration
Term
why malonate is not a substrate for succinate dehydrogenase
Definition
  • only has one methylene group, where as succinate has 2 methylene groups and 2 are required for dehydrogenation
Term
rxn in CAC that results in formation of 1 ATP
Definition
  • rxn catalyzed by succinyl CoA synthetase
Term
oxidizing agent
Definition
  • accepts e- from a donor
Term
reducing agent
Definition
  • donates e- to an acceptor
Term
respiration
Definition
  • an ATP-generating process in which an inorganic compound serves as the final e- acceptor
Term
redox potential
Definition
  • measure of the tendency to accept or donate e-
Term
Electron Transport Chain (ETC)
Definition
  • e- flow from NADH & FADH2 to O2
Term
flavin mononucleotide (FMN)
Definition
  • accepts e- from NADH in complex I
Term
Iron-Sulfur protein
Definition
  • facilitates e- from FMN to CoQ
Term
Coenzyme Q (CoQ)
Definition
  • lipid-soluble e- carrier
Term
cytochrome c
Definition
  • donates e- to complex IV
Term
Q cycle
Definition
funnels e- from a 2 e- carrier to a 1 e- carrier
Term
Superoxide dismutase
Definition
  • converts reactive oxygen species into hydrogen peroxide
Term
catalase
Definition
  • converts hydrogen peroxide into oxygen and water
Term
why CoQ is an effective mobile electron carrier in the ETC
Definition
  • soluble in a hydrophobic environment d/t isoprene units & contains 2 O atoms that can reversibly bind 2 e- & 2 H+ to transition b/t quinone and quinol
Term
reactive oxygen species (ROS)
Definition
  • hydroxyl radical (-OH.)
  • hydrogen peroxide (H2O2)
  • superoxide ion (O2-.)
  • peroxide (O2-)
Term
why ROS are dangerous to cells
Definition
  • react with macromolecules such as proteins, nucleotides, & membranes, disrupting cell structure & function
Term
CAC enzyme the is also a part of ETC
Definition
  • succinate dehydrongenase (complex II, FADH2)
Term
how is descrepancy b/t energy requirements and resources reconciled
Definition
  • ATP is regenerated by oxidative phosphorylation and other ATP generating processes
Term
ATP synthase
Definition
  • converts the proton-motive force into ATP
Term
proton-motive force
Definition
  • composed of a chemical gradient and a charge gradient
Term
electron-transport chain
Definition
  • generates the proton gradient
Term
glycerol 3-phosphate
Definition
  • cytoplasmic NADH to mitochondrial FADH2
Term
malate-aspirtate shuttle
Definition
  • cytoplasmic NADH to mitochondrial NADH
Term
respiratory (acceptor) control
Definition
ADP controls the rate of respiration
Term
uncoupling protein
Definition
  • results in heat instead of ATP
Term
F1 subunit
Definition
  • catalytic subunit
Term
F0 subunit
Definition
proton channel
Term
c ring
Definition
  • a proton merry go round
Term
observation that inhibitors of ATP synthase also lead to inhibition of the ETC
Definition
  • if no ATP then no influx of protons into matrix dissipating gradient, therefore outside eventually becomes so charged that ETC can no longer pump against the gradient
Term
ATP synthase blocked by modification of a single side chain by dicycloheylcarbodiimide, what are the most likely targets of this reagent?
Definition
  • it reacts w/ carboxyl groups making aspertate and glutamate side chains the likely targets
Term
how would you use site specific mutagenesis to determine if the residue is essential for proton conduction
Definition
  • Asp 61 of subunit c in F0 subunit would be converted into asparagine by site specific mutagenesis eliminating proton conduction
Term
why mitochondria of muscle cells have more cristae than that of liver cells
Definition
  • muscle cells have greater energy demands therefore require more ATP meaning more sites for oxidative phosphorylation calling for an increase in amount of cristae
Term
why the ETC ceases to operated upon exposing CAC to an inhibitor of ATP-ADP translocase.
Definition
  • ADP and ATP cannot exchange b/t matrix and mitochondria, ATP synthase will halt d/t lack of substrate ADP, proton gradient will increase until ETC can no longer pump against it.
Term
use of proton-motive force other than synthesis of ATP
Definition
  • ATP export from matrix, and phosphate import into matrix
Term
how inhibition of ATP-ADP translocase affects the CAC
Definition
  • ADP can't enter matrix, ETC ceases to function d/t no energy acceptor NADH will build up in matrix inhibiting CAC enzymes
Term
how inhibition of ATP-ADP translocase affects the aerobic glycolysis
Definition
  • glycolysis will stop aerobic function and switch to anaerobic so NADH can be reoxidized into NAD+ by lactate dehydrogenase
Term
lactic acidosis is most common sign of mitochondrial disorders b/c
Definition
  • the means of generating ATP becomes anaerobic glycolysis leading to high levels of lactic acid in the blood
Term
use Chargaff's rule to calculate % of all bases in DNA that is 20% thymine
Definition
  • T-20%, A-20%, G-30%, C-30%
Term
A stand of RNA is 20% U predict the % of remaining bases
Definition
  • can't be predicted b/c single strand nucleic acids are not subject to base-pairing
Term
reason GC and AT are the only base pairs permissible in the double helix
Definition
  • they only form stable H-bonds in this pairing, also 2 purines would be too large to fit inside the double helix while 2 prymidines would be too small to base pair together
Term
why heat denatures or melts DNA in solution
Definition
  • the energy causes the chains to wiggle, disrupting the H bonds b/t base pairs & stacking forces are disrupted as well causing strands to seperate
Term
DNA chains in double helix have opposite polarity means
Definition
  • one end of stand starts w/ a 5l -OH group while the other end is a free 3i -OH group, the 2 strands must run in opposite directions to form double helix therefore they have opposite polarity
Term
with weak forces holding the helix together why is it hard to disrupt
Definition
  • individual H-bonds & stacking forces are weak but there are so many that they are strong accumulatively
Term
reason DNA double helix must be associated with cations, usually Mg2+
Definition
  • negatively charged phophoryl groups would be too much and cause repulsion so cations are needed to counter the charge
Term
3 forms of a double helix
Definition
  • A-DNA
  • B-DNA
  • Z-DNA
Term
A-DNA
Definition
  • shorter, wider, and more dehydrated than B-DNA
Term
B-DNA
Definition
  • most common form of DNA
Term
Z-DNA
Definition
  • left handed form
Term
radioactive materials needed to tag DNA but not RNA
Definition
  • tritiated thymine or tritritiated thymidine
Term
precursors to prepare DNA w/ backbone phophoryl atoms uniformly labeled 32P and position of the radioactive atoms
Definition
  • dATP, dGTP, dCTP, TTP labeled w/ 32P in the innermost α phosphoryl atom
Term
Retrovirus
Definition
  • has RNA as it's genetic material.  The RNA is catalyzed by reverse transcriptase to form DNA
Term
how is the flow of information in a retrovirus different
Definition
  • RNA to DNA vs normal DNA to RNA
Term
Deoxynucleoside triphosphates
Definition
  • activated precursor for DNA polymerase
Term
ribonucleoside triphosphate
Definition
  • activated precursor for RNA polymerase
Term
direction of chain elongation for DNA and RNA polymerases
Definition
  • from 5l to 3l for both
Term
template conservation for DNA and RNA polymerases
Definition
  • DNA-semiconserved
  • RNA-conserved
Term
need of a primer for DNA and RNA polymerases
Definition
  • DNA-needs one
  • RNA-doesnt' need one
Term
mRNA
Definition
  • encodes info that on translation yeilds a protein
Term
rRNA
Definition
  • catalytic component of ribosomes, molecular complexes that synthesize proteins
Term
tRNA
Definition
  • adaptor molecule, capable of binding amino acids & recognizing the corresponding codon,  along with amino acids it is a substrate of ribosomes
Term
why is RNA readily hydrolyzed by alkali and DNA is not
Definition
  • the 2l hydroxyl in RNA acts as an intramolecular nucleophile, in alkaline hydrolysis it forms a 2l to 3l cyclic intermediate
Term
degeneracy of genetic code
Definition
  • more than one codon can encode for the same amino acids
Term
biological benefit of degenerate genetic code
Definition
  • a nucleotide change might yeild a synonym or a codon for an amino acid with similiar chemical properties
Term
relationship b/t number of amino acid codons and frequency of it's presence in proteins
Definition
  • highly abundant amino acids have most codons, least abundant have least condons, allowing for variation in base composition and decreases the likelihood that a substitution will change the encoded amino acid
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