Principles of Biochemistry 12 |Glycolysis| Class Notes |HarvardX

Glycolysis

digraph{ rankdir = "UD"

subgraph cluster_0{
hexo1 [label = “”, shape = hexagon, width = 1, height = .8]
node [style=filled,color=white];
label = “Glucose”;
color = “white”;
labeljust=l
labelloc=b
}

subgraph cluster_1{
hexo2 [label = “”, shape = hexagon, width = 1, height = .8]
node [style=filled,color=white];
label = “Glucose-6-phosphate”;
URL=“https://www.bing.com”;
subgraph C{
rank = same
P1 -> hexo2 [dir = none, headport = “nw”, arrowhead =“none”]
}
color = “white”;
labeljust=l
labelloc=b
}

subgraph cluster_2{
hexo3 [label = “”, shape = hexagon, width = 1, height = .8]
node [style=filled,color=white];
label = “Fructose-6-phosphate”;
URL=“https://www.bing.com”;
subgraph C{
rank = same
P2 -> hexo3 [dir = none, headport = “nw”, arrowhead =“none”]
}
color = “white”;
labeljust=l
labelloc=b
}

subgraph cluster_3{
hexo4 [label = “”, shape = hexagon, width = 1, height = .8]
node [style=filled,color=white];
label = “Fructose-1,6-phosphate”;
URL=“https://www.bing.com”;
subgraph C{
rank = same
P3 -> hexo4 [dir = none, headport = “nw”, arrowhead =“none”]
hexo4 -> P4 [dir = none, arrowhead =“none”]
}
color = “white”;
labeljust=l
labelloc=b
}

ATP1 [label=“ATP”]
ADP1 [label=“ADP”]
ATP2 [label=“ATP”]
ADP2 [label=“ADP”]
ATP3 [label=“ATP”, color=“salmon”, style=“filled”]
ADP3 [label=“ADP”]
ATP4 [label=“ATP”, color=“salmon”, style=“filled”]
ADP4 [label=“ADP”]
P1 [label=“”, shape = circle, color= “cyan3”, height = 0.3, width = 0.3]
P2 [label=“”, shape = circle, color= “cyan3”, height = 0.3, width = 0.3]
P3 [label=“”, shape = circle, color= “cyan3”, height = 0.3, width = 0.3]
P4 [label=“”, shape = circle, color= “cyan3”, height = 0.3, width = 0.3]
NAD1 [label = “Pi, NAD+”]
NADH1 [label = “H+, NADH”, color=“salmon”, style=“filled”]
BSG [label = “1,3-\nBisphosphoglycerate”, shape = underline]
Phos [label = “3-Phosphoglycerate”, shape = underline]
Pho2 [label = “2-Phosphoglycerate”, shape = underline]
Phoe [label = “Phosphoenol-\npyruvate”, shape = underline]
Pyru [label = “Pyruvate”, shape = underline]

mm1 [label = “Hexokinase” , shape = box, color = “coral”, fontcolor = “coral”]
mm2 [label = “Phosphoglucose\nisomerase” , shape = box, color = “coral”, fontcolor = “coral”]
mm3 [label = “Phospho\nFructokinase” , shape = box, color = “coral”, fontcolor = “coral”]
mm4 [label = “Aldolase” , shape = none, color = “coral”, fontcolor = “coral”]
mm5 [label = “Triose\nphosphate\nisomerase” , shape = box, color = “coral”]
mm6 [label = “” , shape = none, width = 0, height = 0]
mm7 [label = “Phosphoglycerate\nkinase” , shape = box, color = “coral”, fontcolor = “coral”]
mm8 [label = “Phosphoglycerate\nMutase” , shape = box, color = “coral”, fontcolor = “coral”]
mm9 [label = “Enolase” , shape = box, color = “coral”, fontcolor = “coral”]
mm10 [label = “Pyruvate\nkinase”, shape= box, color = “coral”, fontcolor = “coral”]

hexo1 -> mm1 [dir = none , color = “deeppink”]
mm1 -> hexo2 [ color = “deeppink”]
hexo2 -> mm2 [dir = none , color = “deeppink”]
mm2 -> hexo3 [ color = “deeppink”]
hexo3 -> mm3 [dir = none , color = “deeppink”]
mm3 -> hexo4 [ color = “deeppink”]
hexo4 -> mm4 [dir = none , color = “deeppink”]
mm4 -> GAP [color = “deeppink”]
DHAP -> mm4 [dir = back , color = “deeppink”]
DHAP -> mm5 [dir = back , color = “deeppink”, headport = w]
mm5 -> GAP [color = “deeppink”, tailport = e]
GAP -> mm6 [dir = back , color = “deeppink”]
mm6 -> BSG [color = “deeppink”]
NAD1 -> mm6 [dir = none , tailport = w, headport = n, style = dashed]
mm6 -> NADH1 [tailport = n, headport = w, style = dashed]
BSG -> mm7 [dir = back, color = “deeppink”]
mm7 -> Phos [color = “deeppink”]
Phos -> mm8 [dir = back, color = “deeppink”]
mm8 -> Pho2 [color = “deeppink”]
Pho2 -> mm9 [dir = back, color = “deeppink”]
mm9 -> Phoe [color = “deeppink”]
H2O -> mm9 [dir = back, color = “deeppink”]
Phoe -> mm10 [dir = back, color = “deeppink”]
mm10 -> Pyru [color = “deeppink”]

subgraph A{
rank = same
ATP1 -> mm1 [dir = none , color = “blue”]
mm1 -> ADP1 [color = “blue”]
}
subgraph B{
rank = same
ATP2 -> mm3 [dir = none , color = “blue”]
mm3 -> ADP2 [color = “blue”]
}
subgraph BB{
rank = same
ADP3 -> mm7 [dir = none , color = “blue”]
mm7 -> ATP3 [color = “blue”]
}
subgraph BC{
rank = same
ADP4 -> mm10 [dir = none , color = “blue”]
mm10 -> ATP4 [color = “blue”]
}

subgraph C{
rank = same
mm4
DHAP [label= “Dihydroxyacetone\nphosphate”, shape = underline]
GAP [label= “Glyceraldehyde\n3-phosphate”, shape = underline]
}
subgraph D {
rank = same
NADH1
mm6
}
subgraph E {
rank = same
H2O
mm9
}
}

Free Energy of Hydrolysis

digraph{ node [shape = plain] edge [dir = none] mm1 [label = "" , shape = none, height = 0, width = 0] mm2 [label = "" , shape = none, height = 0, width = 0] mm3 [label = "" , shape = none, height = 0, width = 0] mm4 [label = "" , shape = none, height = 0, width = 0] mm5 [label = "" , shape = none, height = 0, width = 0]

PEP [label = “Phosphoenolpyruvate\n(PEP)”]
G6P [label = “Glucose-6-phosphate”]
Height [label=“High free energy\nkJ/mol”]
Low [label=“Low free energy\nkJ/mol”]
ATP [shape="star ", color=“salmon”, style=“filled”]

Height-> mm1 [dir = back]
mm1 -> mm2 -> mm3 -> mm4 -> mm5
mm5 -> Low [dir = true]
“-62” -> mm1 -> PEP {rank = same; “-62”; mm1; PEP}
“-30” -> mm3 -> ATP {rank = same; “-30”; mm3; ATP}
“-14” -> mm5 -> G6P {rank = same; “-14”; mm5; G6P}

}

Coupling

$PEP + H_ 2O \longrightarrow Pyruvate + P_ i$
$\ \ \ \ \Delta G^ {\circ} = -62 kJ/mol$

$ADP + P_ i \longrightarrow ATP + H_ 2O$
$\ \ \ \ \Delta G^ {\circ} = +30 kJ/mol$

Since they share the common reactacts, this two reaction could be combined together, which was called coupling

$PEP + ADP \overset{Pyruvate Kinase}{\longrightarrow} Pyruvate + ATP$
$\ \ \ \ \Delta G^ {\circ} = -32 kJ/mol$

Coupling:

1. Common reactacts
2. Catalyzed by one enzyme

Example 1

$PEP + H_ 2O \longrightarrow Pyruvate + P_ i$
$\ \ \ \ \Delta G^ {\circ} = -62 kJ/mol$
$Glucose + P_ i \longrightarrow Glucose^ {_ -} 6 ^{_ -} phosphate + H_ 2O$
$\ \ \ \ \Delta G^ {\circ} = +14 kJ/mol$
The Enzyme were dose not shared by this two reaction
As as result, they can not be coupled

Example 2

$ATP + H_ 2O \longrightarrow ADP + P_ i$
$\ \ \ \ \Delta G^ {\circ} = -30 kJ/mol$
$Glucose + P_ i \longrightarrow Glucose^ {_ -} 6 ^{_ -} phosphate + H_ 2O$
$\ \ \ \ \Delta G^ {\circ} = +14 kJ/mol$

Coupled Reaction:

$Glucose + ATP \overset{hexokinass}{\longrightarrow} Glucose^ {_ -} 6 ^{_ -} phosphate + ADP$
$\ \ \ \ \Delta G^ {\circ} = -16 kJ/mol$

Pyruvate and NADH

digraph{ node [shape ="box"] CO2 [label = "CO2", shape = none, fontcolor="blue"] CO22 [label = "CO2", shape = none, fontcolor="blue"] NADH1 [label = "NADH", shape = none, fontcolor="salmon"] NAD1 [label = "NAD+", shape = none, fontcolor="salmon"] NAD2 [label = "NAD+", shape = none, fontcolor="salmon"] NADH2 [label = "NADH", shape = none, fontcolor="salmon"] AceCoA [label = "Acetyl-CoA"] "Citric acid cycle" [shape = "underline"]

mm1 [label = “” , shape = none, height = 0, width = 0]
mm2 [label = “” , shape = none, height = 0, width = 0]
mm3 [label = “” , shape = none, height = 0, width = 0]
mm4 [label = “” , shape = none, height = 0, width = 0]

Pyruvate -> mm1 [dir= none]
CO2 -> mm1 [dir = back]
mm1 -> AceCoA
AceCoA -> “Citric acid cycle”
Pyruvate -> mm2 [dir= none]
Pyruvate -> mm3 [dir= none]
mm2 -> CO22 [headport=“e”]
mm2 -> Acetaldehyde [label = “Pyruvate\ndecarboxylase”]
Acetaldehyde -> mm4 [dir= none]
mm4 -> Ethanol [label = “Alcohol\ndehydrogenase”]
NADH1 -> mm4 [dir= none, color= “darksalmon”]
mm4 -> NAD1 [color= “darksalmon”]
mm3 -> Lactate [label = “Lactate\ndehydrogenase”]
NADH2 -> mm3 [dir = none; color= “darksalmon”]
mm3 -> NAD2 [color= “darksalmon”]

subgraph cluster_0{
mm1; CO2; AceCoA; “Citric acid cycle”
label = “Aerobic”
{rank=“same”; mm1; CO2}
fontsize = 30
fontcolor = “white”
color = “darksalmon”
style = “filled”
}
subgraph cluster_2{
CO22; mm2
{rank = “same”; mm3; NADH2; NAD2}
Acetaldehyde; Lactate; Ethanol
{rank = “same”; NADH1; NAD1; mm4}
label = “Anaerobic”
fontsize = 30
fontcolor = “white”
color = “deepskyblue3”
style = “filled”
}

}

.