Lectures 5&6- Glucose and Glycolysis

Question 1

Preparatory phase (not done yet)

Answer 1

-The first phase in glycolysis
-Step 1: Neutral glucose has to be phosphorylated to glucose 6-phosphate by hexokinase and an ATP to enter glycolysis
- So far, we have used up an ATP and not made any
- Once glucose gets phosphorylated, it can’t leave the cell and participate in the glucose transport chain into and out of the cell; its stuck in the cell
- Hexokinase and glucose and ATP follow an induced fit mechanism
Step 2: Glucose 6-phosphate isomerizes into fructose 6-phosphate so it is now a ketone instead of an aldehyde through the isomerase, which converts the straight chain glucose to the straight chain fructose, which of course reforms? the ring conformation, since this is preferred. This occurs through the help of the phosphohexase isomerase enzyme
Step 3: Fructose 1,6 bisphosphate is produced by the reaction of fructose 6-phosphate and ATP catalyzed by phosphofructokinase (PFK-1). This step is a COMMITTED STEP, meaning once we go past this step, we are strongly committed to continuing on with glycolysis, whereas glucose-6P could have been used for a variety of other metabolic pathways.
Step 4: Fructose 1,6 bisphosphate is broken up into an alcohol (dihydroxyacetone phosphate, DHAP) and a ketone (glyceraldehyde-3-phosphate, G3P) by aldolase, performing a reverse aldol condensation.
Step 5: DHAP isomerize to G3P through the help of triose-phosphate isomerase, so we now have two identical G3Ps going into the payoff phase. This isomerization follows the exact same mechanism as the isomerization of glucose to fructose, but it utilizes a different enzyme than glucose. This is an example of different enzymes doing the exact same reaction mechanism but with different substrates. Different enzymes have to be used sometimes because their specificity won’t allow them to recognize these different substrates,

Question 2

Payoff phase

Answer 2

The second phase of glycolysis

• Step 6: Glyceraldehyde 3-phosphate is phosphorylated into 1,3 bisphosphoglycerate by glyceraldehyde 3-phosphate dehydrogenase (GAPDH). In the mechanism that takes place, the first redox reaction of glycolysis occurs, in which the hydride on the carbonyl group of the G3P/Enzyme complex gets removed by NAD+. The full mechanism is explained on a separate piece of paper inserted into my lecture notes.
• Step 7: 1,3 bPG gets hydrolyzed into 3-phosphoglycerate. This reaction has a very negative ∆G°’ (about -49 kJ/mol), which is able to drive the phosphorylation of ADP to ATP when coupled together. This is carried out by phosphoglycerate kinase. This is the step where we produce our FIRST ATP in glycolysis.
• Step 8: 3-phosphoglycerate gets isomerized into 2-phosphoglycerate by phosphoglycerate mutase
• Step 9: 2-phosphoglycerate undergoes tautomerization with help from an enolase to form its enol form, phosphoenolpyruvate, PEP
• Step 10: PEP gets hydrolyzed into pyruvate, allowing ADP to be phosphorylated into ATP in another substrate level phosphorlyation.
• Step 11: Pyruvate tautomerizes into its keto form, pyruvic acid

Question 3

Substrate level phosphorylation

Answer 3

• When a phosphorylated compound that has sufficient energy (its hydrolysis has a large enough negative ∆G°’) to energize the phosphorylation of ADP to ATP

Question 4

Keto-Enol form

Answer 4

G

Question 5

Mutase

Answer 5

• An isomerase that moves groups around to form a different isomer
• Ex: phosphoglycerate mutate isomerizes 3-phosphoglycerate into 2-phosphoglycerate and vice versa

Question 6

Kinase

Answer 6

• Enzymes that phosphorylate things

Question 7

Isomerase

Answer 7

• An enzyme that helps a molecule “isomerize” into a different isomer, Ex: Glu6P—>Fr6P

Question 8

Ethanol formation

Answer 8

• Ethanol can be produced from pyruvate by the help of TPP, going through the intermediate Acetaldehyde, and then becoming ethanol though reduction with NADH, restoring some of the NAD+ to be used again in glycolysis

Question 9

Thiamine pyrophosphate

Answer 9

• A cofactor to pyruvate decarboxylase (and probably other enzymes as well)
• It’s “business end” is a thiazodium ring, which is really good at generating a negatively charged carbon, called a carbanion, which is very reactive and can attack pyruvate to form acetaldehyde, which can then be reduced by NADH to give ethanol

Question 10

Pyruvate decarboxylate

Answer 10

• This enzyme is used in the pathway that reduces pyruvate to ethanol and restores some of the NAD+ used in glycolysis
• Used in first step which involves the decarboxylation of pyruvate to acetaldehyde

Question 11

Alcohol dehydrogenase

Answer 11

• This enzyme is used in the pathway that reduces pyruvate to ethanol and restores some of the NAD+ used in glycolysis
• Used in the second step, in which acetaldehyde is reduced by NADH to ethanol, which oxidizes NAD+ to “restock it” for glycolysis

Question 12

Glycogen

Answer 12

G

Question 13

Glycogen phosphorylase

Answer 13

G

Question 14

Phosphoglycomutase

Answer 14

G

Question 15

Fructose 2,6 bisphosphate

Answer 15

• A positive regulator of Phosphofructokinase

Question 16

Pentose phosphate pathway. Draw out structures and know enzyme names for the oxidative phase

Answer 16

• A pathway that converts glucose into ribose
• This is an important pathway b/c ribose is needed in DNA, so it is needed whenever DNA replicates or gets transcribed into RNA
  Oxidative phase
• Step 1: Glucose-6-phosphate is oxidized via dehydrogenation to give 6-phospho-gluco-lower case delta?- lactone with the help of NADP+ getting reduced, and glucose 6-phosphate dehydrogenase catalyzing the reaction
  -Step 2: The lactone is hydrolyzed, breaking the ester bond, to form 6-phospho-gluconate (a linear carboxylic acid?) via the help of lactonase
• Step 3: 6-phospho-gluconate is decarboxylated, and in the process, oxidized via NADP, to give D-Ribulose 5-phosphate. This is done through the enzyme 6-phosphogluconate dehydrogenase
  -Step 4: D-Ribulose 5-phosphate isomerizes to D-Ribose 5-phosphate via phosphopentose isomerase
  In the non-oxidative phase, to go from D-ribulose 5-phosphate to ribose, the principle is that many sugars are made by shuffling 2 and 3 carbon units around with transketolase (2 carbon) and transaldolase (3 carbon).

Question 17

NADP+

Answer 17

• Used in the pentose phosphate pathway to oxidize glucose 6 phosphate into a ribose

Question 18

Ribose 5-p

Answer 18

• Used to make up DNA and RNA?

Question 19

anomer

Answer 19

an epimer that differs in configuration at the acetal/hemiacetal carbon, since that carbon used to be double bond to oxygen and didn’t have a configuration before

Question 20

epimer

Answer 20

a stereoisomer that differs in configuration at any single stereogenic center

Question 21

Warburg Effect

Answer 21

• Observation that most cancer cells predominantly produce energy by a higher rate of glycolysis followed by lactic acid fermentation in the cytosol
• Basically, cancer cells do glycolysis at a higher rate than normal cells

Question 22

Steady state in regards to metabolic pathways

Answer 22

-There is typically a steady state level of ALL molecules as we go through a pathway; molecules are coming into the body through what we eat and are being sent along the pathway step by step as they are being converted into other things like a pipe, kind of

Question 23

What are some examples of regulated glycolytic enzymes?

Answer 23

• Hexokinase and glucokinase, which phosphorylate glucose and ?
• phosphofructokinase (PFK-1), which phosphorylates fructose
• pyruvate kinase, which phosphorylates pyruvate

Question 24

Isozyme

Answer 24

-Enzymes with identical function but different structure
Ex: hexokinase I, found in all cells, and glucokinase, found in only the liver
- Both phosphorylate glucose

Question 25

lactone

Answer 25

• An internal ring ester

Question 26

Regulation of Hexokinase Isozymes

Answer 26

• Hexokinase I that is found in all cells is not allosterically regulated, and follows typical Michaelis-Menten kinetics
• Glucokinase, found in the liver, is allosterically regulated by glucose, so when not much glucose is around (ex, when fasting), the liver isn’t using it up, but when a lot of glucose is around (ex: after drinking a Big Gulp), it kicks into high gear

Question 27

PFK-1

Answer 27

• Phosphofructokinase
• Is allosterically regulated by multiple molecules
• Is positively regulated by AMP, ADP, and fructose 2,6 bisphosphate, but negatively regulated by ATP and citrate.

Question 28

The _____ acid yields the _____ anion

Answer 28

-ic and -ate

Ex: acetic acid to acetate

Question 29

Glycerol (draw it out)

Answer 29

propane 1,2,3 triol

Question 30

1,3bPG

Answer 30

• 1,3 bisphosphoglycerate
• A molecule that when hydrolyzed, releases enough energy to allow for the formation of ATP from ADP and Pi.
• This is one of those “high energy molecules” that is formed during glycolysis

Question 31

PEP

Answer 31

• Phosphoenoylpyruvate
• A molecule that when hydrolyzed, releases enough energy to allow for the formation of ATP from ADP and Pi.
• This is one of those “high energy molecules” that is formed during glycolysis

Question 32

Restoration of NAD+. Draw out the reactions

Answer 32

• After using NAD+ in glycolysis, reducing it to NADH, we need to regenerate that NAD+ to be able to keep doing glycolysis over and over again to meet the energy needs of the cell
• One way it can be restored is through the reduction of a C=O in pyruvate to a C-OH (giving us lactic acid) through the use of NADH, which gets oxidized to NAD+. This reaction is catalyzed by lactate dehydrogenase (LDH)
• This reaction has a very negative ∆G, and thus goes very far to the right
• Another way to restore the NAD+ is another fermentation reaction with pyruvate. This time, thiamine pyrophosphate (TPP), provides an activated carbon to decarboxylate pyruvate to acetaldehyde, which is then reduced by NADH and alcohol dehydrogenase to form ethanol as our end result.

Question 33

At which steps in glycolysis is NAD+ used?

Answer 33

-Step 6 (Step 1 of payoff phase): glyceraldehyde 3-phosphate gets phosphorylated by glyceraldehyde 3-phosphate dehydrogenase to 1,3 bisphosphoglycerate

Question 34

At which steps in glycolysis is ATP used?

Answer 34

• Step 1 of preparatory phase: Phosphorylation of glucose to glucose-6-phosphate via hexokinase
• Step 3 of preparatory phase: Phosphorylation of fructose-6-phosphate to fructose 1,6 bisphosphate via phosphofructokinase (PFK-1)

Question 35

At which steps in glycolysis is ATP produced?

Answer 35

• Step 7 (Step 2 of payoff phase): 1,3 bisphophoglycerate gets dephosphorylated to give 3-phosphoglycerate and ATP via phosphoglycerate kinase
• Step 10 (Step 5 of payoff phase): Phosphoenolpyruvate gets dephosphorylated to give pyruvate and ATP via pyruvate kinase

Question 36

Draw the structure of acetaldehyde

Answer 36

done

Question 37

Draw out glycolysis, including the structures of each intermediate, the enzyme names, ATP and NAD, etc

Answer 37

done

Question 38

Draw out the NAD+ business end

Answer 38

done

Question 39

Draw out the FMN, FAD business end

Answer 39

done