Central Metabolic Pathways

Question 1

common routes to breakdown glucose to pyruvate

Answer 1

glycolysis
pentose phosphate pathway
entner-doudoroff pathway (bacteria only)

Question 2

glycolytic pathway occurs in

Answer 2

cytoplasmic matrix of both pro and eucaryotes

Question 3

enzymes in glycolysis:

Answer 3

Hexokinase: Note in bacteria that hexose kinase is often replaced by the phosphotransferase system in which the phosphate is supplied by PEP.
Isomerase
Phosphofructokinase
Fructose 1,6-bisphosphate aldolase
Triose Phosphate Isomerase
Triose Phosphate Dehydrogenase
Phosphoglycerate Kinase
Mutase
Enolase
Pyruvate kinase

Question 4

Summary of Glycolysis

Answer 4

glucose + 2ADP + 2Pi + 2NAD+

2 pyruvate + 2ATP + 2NADH + 2H+

Question 5

the glycolysis pathway can only be reversed from

Answer 5

PEP to fructose 1,6 bisphosphate

Question 6

phosphofructokinase is replaced by

Answer 6

fructose 1,6 bisphosphatase (in reverse glycolysis)

Question 7

ADP allosterically positively regulates

Answer 7

phosphofructokinase

Question 8

PEP feeds back to negatively regulate

Answer 8

phosphofructokinase

Question 9

pyruvate kinase is positively regulated by

Answer 9

fructose 1,6 bisphosphate

Question 10

AMP allosterically negatively regulates

Answer 10

fructose 1,6 bisphosphate phosphatase

Question 11

fate of NADH

Answer 11

respiration
fermentation
hydrogenase (anaerobic)

Question 12

Pyrococcus furiosus (Archaea-hyperthermophile) has a modified EMP

Answer 12

ferments carbohydrates and peptides to acetate. does not support growth for monosaccharides. maltose. sulfur as an electron sink

Question 13

how pyrococcus furiosus differs in EMB (glycolysis)

Answer 13

1]ADP donates phosphate rather than ATP

2]Glyceraldehyde 3 PO4 is oxidized by glyceraldehyde 3 PO4 ferredoxin oxidoreductase (GAPOR) rather than triose phosphate reductase

3]1,3 phosphoglycerate is not produced and therefore the subsequent atp cannot be formed
4[Pyruvate is oxidized by pyruvate:ferredoxin oxidoreductase rather than pyruvate dehydrogenase (sec 7.3.2) to Acetyl CoA and CO2.
5] Instead of producing a reduced NADH, ferredoxin is reduced and linked to a ferre-NADP+ linked enzyme (ferredoxin NADP oxidoreductase or FNOR). The electrons are then given up to form Hydrogen gas
6} ATP is formed when Acetyl CoA is converted to acetate using acetyl CoA synthetase.

Question 14

Pentose Phosphate Pathway

Answer 14

also called hexose monophosphate pathway
can operate at same time as glycolytic or Entner-Doudoroff pathways
can operate aerobically or anaerobically
an amphibolic pathway

Question 15

three stages of PPP

Answer 15

1) oxidative decarboxylation
2) isomerization
3) Sugar rearrangement

Question 16

oxidative decarboxylation

Answer 16

Steps 1-3
1) glucose-6-phosphate dehydrogenase, 2)Lactonase, 3) 6-Phosphogluconate dehydrogenase
The third step produces the decarboxylation.
Two NADPH’s are produced

Question 17

isomerization

Answer 17

Steps 4-5
Ribulose-5-P is converted to xyulose-5-P and to ribose-5-P
(nucleotide precursor)
xylulose 5 - P to ribulose 5- P to ribose 5 P

Question 18

sugar rearrangement

Answer 18

Steps 6-8
Ketolase,Aldolase, Ketolase
Ketolase is a two carbon transfer
Aldolase is a three carbon transfer
Important sugars are produced such as erythrose for aromatic amino acid synthesis
Glceraldehyde 3 phosphate can enter the second half of glycolysis.

Question 19

Pentose Phosphate Pathway

Answer 19

glucose-6-P + 12NADP+ + 7H2O

6CO2 + 12NADPH + 12H+ Pi

Question 20

Thiobacillus novellas and Brucella abortus does not have a complete EMP or Entner-Doudoroff pathway.

Answer 20

They use Pentose Phosphate pathway and the second half of EMP.

Question 21

The Entner-Doudoroff Pathway

Answer 21

Similar to PPP but differs after 6-P-gluconate producing 2-keto-3-deoxy-6-P-gluconate (KDPG) (instead of the oxidative decarboxylation.
KDPG is split into pyruvate and glyceraldehydes-3-P.
Only a net of 1 ATP is produced (along with a NADH and a NADPH).

Question 22

role of ED pathway

Answer 22

This is low yield is justified by its niche.
When E. coli is grown on gluconate, three enzymes are induced:
Glucokinase, 6-P-gluconate dehydratase and KDGP aldolase.
The enzymes
The adavantage to the Entner-Doudoroff Pathway is the use of aldonic sugars such as gluconate.

Question 23

yield per glucose molecule in ED

Answer 23

1 atp
1 nadph
1 nadh

Question 24

step 1 of ed

Answer 24

hexose kinase

Question 25

Glycolysis pathway, Pentose Phosphate pathway and Entner-Doudoroff pathway share the same route from

Answer 25

Glyceraldehyde-3 Phosphate to Pyruvate.

The products are 2 ATP’s, 1 NADH and Pyruvate

Question 26

Pyruvate Dehydrogenase (The Transition Step

Answer 26

Converts Pyruvate to Acetyl-CoA

Question 27

enzyme complex in Pyruvate dehydrogenase

Answer 27

TPP, NAD+, FAD, lipoic acid, CoA

Question 28

Pyruvate dehydrogenase allosterically regulated:

Answer 28

Negatively by NADH and Acetyl CoA
Positively by PEP and AMP
AMP is an indication of low ATP
NADH accumulation indicates respiration is slowing

Question 29

irreversible steps in TCA

Answer 29

citrate synthase and alpha ketoglutarate dehydrogenase

Question 30

only membrane bound enzyme in TCA

Answer 30

succiny dehyrogenase

Question 31

in Gram negative,citrate synthase inhibited by

Answer 31

NADH and alpha ketoglutarate

Question 32

in Gram positive, citrate synthase inhibited by

Answer 32

ATP

Question 33

C-1 metabolism lacks

Answer 33

the -ketoglutarate dehydrogenase enzyme.C-1 metabolism instead shows a reductive pathway.

Question 34

TCA in anaerobes require

Answer 34

sulfur or thiosulfate as terminal electron acceptor

Question 35

if sugars are catabolized then waht is used to replenish OAA

Answer 35

pyruvate or PEP

Question 36

TCA enzymes

Answer 36

Citrate synthase (1)
Aconitase (2 & 3)
Isocitrate dehygrogenase (4 & 5)
-ketoglutarate dehydrogenase (6)
Succinate thiokinase (7)
Succinate dehydrogenase (8)
Fumarase (9)
Malate dehydrogenase (10)
Note the numbering is different on the reductive TCA diagram

Question 37

bacterium will either have (to replenish OAA)

Answer 37

pyruvate carboxylase or 
PEP carboxylase(not in animals or fungi)

Question 38

PEP is positively regulated by __________ and negatively regulated by ________

Answer 38

acetyl CoA

aspartate

Question 39

reductive TCA lacks

Answer 39

alpha ketoglutarate dehydrogenase and substitutes fumarate reductase for succinate dehydrogenase

Question 40

Reductive TCA

Answer 40

Succinate thiokinase (6)
Fumarate Reductase instead of Succinate dehydrogenase (7)
Fumarase (8)
Malate dehydrogenase (9)
PEP Carboxylase (10) or pyruvate carboxylase (11) to replace OAA for step 1.
Uses (1) FADH2 and (1) NADH

Question 41

glyoxylate cycle purpose

Answer 41

aerobic bacteria growing on fatty acids or acetate. (catabolism of fatty acids produces acetyl CoA
It is similar to TCA but lacks the decarboxylations.
Instead uses two (2-C) acetyl CoA’s to make (4-C) succinate. This is the value of the pathway, it is a source of carbohydrate (succinate) derived from acetyl CoA metabolism (lipid metabolism)
Glyoxylate is a key 2-C intermediate.

Question 42

Two key enzymes of glyoxylate cycle

Answer 42

isocitrate lyase and malate synthase. the end result is succinate and 1 NADH

Question 43

pyruvate to pep (prokaryotic)

Answer 43

pep sythase or pyruvate phosphate dikinase

Question 44

pyruvate from malate

Answer 44

Malic enzyme is found in mitochondria and bacteria
It is important if TCA intermediates are used for growth (i.e., Glycolysis is not active and for example bacteria are growing on succinate as a carbon source) and only uses PEP carboxykinase (and therefore needs pyruvate as an intermediate for biosynthesis)
There are two forms one that uses NADH and one that uses NADPH
Malate + NAD+  pyruvate + NADH + CO2