Transcript Biochemistry: A Short Course

Glycolysis: Energy
Generation Without
an Oxygen
Requirement
Glucose Biofuel Prominence:
Low-reactive ring-form
minimizes protein glycosylation
Glycolysis: A Three
Step Process
• Glucose trapping and
destabilization (priming)
•Three carbon unit generation
(cleaving)
• Energy generation
Induced Fit in
Hexokinase
Glucose induces a
large enzyme
conformational
change
Substrate-induced cleft
closing prevents ATP hydrolysis
Kinases require a divalent metal ion
What function does Mg+2 play in hexokinase?
Hexokinase Closed Around Substrates
What
mechanisms
of catalysis
are
operative?
Hexokinase Reaction Mechanism
What is the Nu:, electrophile, and leaving
group in this reaction?
Phosphoglucose
Isomerase:
Aldose to
Ketose
Conversion
Phosphoglucose Isomerase (PGI) G6P
Conversion via Acid-Base Catalysis
PGI Reaction Mechanism
Phosphoglucose Isomerase (PGI) G6P
Conversion via Acid-Base Catalysis
Base catalyzed
bond formation
Phosphoglucose Isomerase (PGI) G6P
Conversion via Acid-Base Catalysis
Acid catalyzed
ketal formation
Phosphoglucose Isomerase (PGI) G6P
Conversion via Acid-Base Catalysis
Base catalyzes ring closure
H+
Phosphofructokinase: Trapping the
Fructose Isomer
What is the mechanism for this reaction?
Glycolysis Stage I: Glucose Trapping
and Destabilization (priming)
Six Carbon Sugar Cleaved to Two
Three Carbon Units
What is the bond to be cleaved?
Which alcohol becomes an aldehyde?
Haworth and Fischer Projections
Equivalency
The functional group that is down in a Haworth
projection is positioned how in a Fischer
structure?
Aldolase Reaction Mechanism
Aldolase
Fructose-1,6-bisphosphate binds to the aldolase
enzyme for covalent catalysis
Aldolase Reaction Mechanism
What is lost when the Schiff base forms?
Aldolase Reaction Mechanism
Aldolase Rxn Mechanism
Compare and contrast a Schiff base with a
carbonyl group.
Aldolase Reaction Mechanism
What is the process for Schiff base to carbonyl
conversion?
Aldolase Reaction Mechanism
H2O
Aldolase cleaves FBP into GAP and DHAP
Triose Phosphate Isomerase (TIM)
Reversible and driven towards GAP due to product depletion
Which previous glycolytic step is similar to TIM?
Triose Phosphate Isomerase
Reaction Mechanism
Glycolysis: Step #5
Triose Phosphate Isomerase
TIM- or α,β-barrel
with 8 parallel βstrands surrounded
by 8 α-helices.
DHAP conversion to GAP
necessary to proceed
through glycolysis
Stoichiometry: Stages 1-2 of Glycolysis
Two ATPs are initially
invested.
One glucose is
metabolized into two
GAP molecules.
Road
Map for
Energy
Harvest
(Stage 3)
Glyceraldehyde-3-Phosphate
Dehydrogenase: Covalent Catalysis
Glyceraldehyde-3-Phosphate
Dehydrogenase: a 2 Step Process
What amino acid will serve as a nucleophile to
form a thioester?
Glyceraldehyde-3-Phosphate
Dehydrogenase:
Reaction
Mechanism
Glyceraldehyde-3-Phosphate
Dehydrogenase: Catalysis Energetics
Hypothetical reaction with no coupling
Actual coupled reaction
Phosphoglycerate Kinase
What is the Nu:, electrophile and leaving group for
this reaction? (hint: consider hexokinase in
reverse)
Glycolysis: the Three Final Steps
Pyruvate Kinase
What is the Nu:, electrophile and leaving group for
this reaction? (hint: consider phosphoglycerate
kinase)
Glycolysis Energetic
Enzyme
1near
∆G°ʹ
∆G
(kcal/mol) (kcal/mol)
equilibrium means that ∆G is about zero
What is the relationship between ∆G and ∆G°ʹ?
When can ∆G and ∆G°ʹ diverge?
Regulating Glycolysis: A Pictorial Analogue
• Water represents
metabolite flux
• Water amount in
flask represents
intermediate
abundance
• Flasks connections
are enzymes
• Vertical drop represents
decrease in free energy
ΔG° = height difference between flask bottoms
ΔG = height difference between water levels
Alternative Fates for Pyruvate
Anaerobic Recycling of
NADH for Glycolysis
Microbial Recycling of
NADH for Glycolysis
Pathogenic Obligate Anaerobes
Starting and Ending Point for
Fermentation Not Always Same
Chapter 16, Problems 1-12