biochem e3l1 glycolysis

glycolysis:

1. Starting product = glucose

2. End product = pyruvate

3. E in = 2 ATP

4. E out = 4 ATP + 1 NADH

5. Location = cytoplasm

6. Fed v. fasted state

1. Starting product = glucose

2. End product = pyruvate

3. ATP in =

4. ATP out =

5. Location = cytoplasm

6. Fed v. fasted

   1. Fed state = actively breaking down glucose into pyruvate

   2. Fasted state = gluconeogenesis making glucose

glycolysis:

1. equation

2. what E is captured

3. NADH =

   1. source of ATP?

1. equation = glucose +2NAD+2ADP+2P → 2pyruvate+2NADH+2ATP+2H20

2. E captured by synthesis of ATP and NADH

3. NADH = e- carrier

   1. pushes e-’s into mitochondrial matrix

   2. in the ETC, NADH ATP

NADH (nicotinamide adenine dinucleotide):

1. what is it

   1. how does it do that

   2. what does it do in biological rxns

2. how does it yield ATP 2 steps

3. how many e- does it carry/as what

4. 2 forms = ox/red

   1. what is the + stand for?

5. where are the 2 forms found

   1. why?

1. NADH = e- carrier

   1. carries 2 e- as a hydride ion

   2. soluble coenzyme in oxidation reactions

2. 2 steps to ATP

   1. pushes e-’s into mitochondrial matrix

   2. in the ETC, NADH ATP

3. 2 forms (+ stands for oxidized form, not the charge)

   1. NAD+ = oxidized

      1. mostly cytosol

   2. NADH = reduced

      1. mostly mitochondria

4. NADH is high E, so it inhibits the glycolytic pathway when its in high concentration in the cytoplasm bc cell doesn’t need it to pick up e- to make more E

5. NADH kept in mitochondria bc its used for ETC

1. 2 reasons phosphorylation is useful in general (last exam)

2. 3 reasons for phosphorylated intermediates in glycolysis

1. in general

   1. coupling ATP hydrolysis (favorable) w/ unfavorable

   2. Phosphate useful as good leaving group to add groups onto other mCs bc it is unstable

2. phosphorylated intermediates

   1. keeps intermediates inside cell to maintain high catalytic turnover (P- is neg charged)

   2. substrate level phosphorylation = Pi (inorganic phosphate) will be transferred to ADP

   3. enzymatic handles = good leaving groups

1. goal of preparatory phase =

2. preparatory phase structure change =

1. preparatory phase = input a little ATP to get more ATP later

2. 6C aldose (glucose) → 6C ketose (fructose) w/ 2 phosphates

Glycolysis step 1:

1. rxn?

2. ATP used?

3. enzyme?

4. cofactor?

5. reversible?

6. # isozymes?

7. glucokinase?

   1. affinity for glucose and Km?

   2. why?

1. glucose → glucose 6-phosphate

2. 1 ATP —> 1 ADP

3. enzyme = hexokinase

4. cofactor = Mg2+

1. humans have 4 isozymes of hexokinase

   1. isozymes = similar structure enzymes (products of diff genes) that catalyze the same reactions

   2. glucokinase = isozyme that carries out step 1 in liver

      1. low affinity, high Km

      2. liver responsible for sending glucose to brain so it needs to be low affinity to let go (not self consuming)

Glycolysis Step 1 hexokinase Rxn:

1. 2 steps rxn

2. what is the cell doing

3. group transfer or hydrolysis

1. rxn

   1. C6 OH of glucose attacks gamma phosphate of ATP

   2. bound Mg2+ stabilizes - charge in transition state

2. 1st priming rxn = Cell investing E to initiate glycolysis

3. group transfer NOT hydrolysis

Glycolysis step 2:

1. rxn?

2. enzyme

3. cofactor

4. reversible?

5. involves?

6. how guarantee go forward?

1. rxn = isomeration of G6P to F6P

   1. isomeration = glucose switch to fructose

2. enzyme =

3. cofactor

4. reversible?

5. involves ring opening

   1. ring converted to linear

   2. recircularizes into ketone

6. Low DG so remove product fast to drive

glycolysis step 3:

1. what is it

2. enzyme

3. ATP?

4. reversible

5. why special

1. what is it

2. enzyme = PFK-1 phosphofructokinase-1

3. ATP → ADP

4. irreversible

5. why specialspecial bc:

   1. 2nd priming steo

   2. 1st committed step= point of no return

   3. point of regulation, ATP = negative feedback

Glycolysis step 4:

1. what is it

2. enzyme

3. ATP?

4. why special

5. how move forward despite large DG? why?

6. ring opening?

5. special bc cleave 6C sugar into 2 3C sugars

6. goes forward bc products quickly removed by next step

   1. dihydroxyacetone phosphate is a ketose so its unstable and quickly converts to aldose

1. what is the mechanism behind the product being removed in step 4

2. how are GAP and DAP numbered (from what #C of glucose)

1. dihydroxyacetone phosphate is a ketose so its unstable and quickly converts to aldose

Key concept:'

1. why does product removal drive a rxn w/ high DG’0 forward?

2. equation?

1. drives rxn forward bc it lowers Q to get a neg DG even w/ a high

glycolysis step 5:

1. what is it

2. enzyme

3. what kind of reaction

4. why DAP converted to GAP?

3. isomerization through enediol intermediate

4. only GAP substrate for next enzyme (

glycolysis step 5:

GAP carbon numbering

1. dihydroxyacetone phosphate flips and becomes an aldose

prep phase

glycolysis step 6:

1. overall rxn

2. 2 involved reactions

   1. loaded gun?

3. first what

4. enzyme named correctly?

1. 1st E yielding step =

   1. NAD+ picked up 2 e- → NADH, which will be used to make ATP later

2. 2 reactions

   1. oxidation of aldehyde w/ NAD+ gives NADH

      1. favorable

   2. phosphorylation yields a high-E product (acyl phosphate on

      1. unfavorable

glycolysis step 6:

1. “loaded gun”

1. phosphorylation yields a high-E product (acyl phosphate on

   1. unfavorable

   2. loaded gun = acyl phosphate hydrolysis has very negative DG’0

glycolysis step 7:

1. why special

2. coupled? why?

3. enzyme named correctly? why?

1. special

   1. 2nd payoff phase

   2. 1st payoff with ATP

   3. substrate level phosphorylation #1

2. steps 6 and 7 are coupled with 1,3 BPG as the common intermediate

   1. 7 has a favorable (-) DG so it can drive step 6 (unfavorable)

1. enzyme should be phosphotase bc it removes a phosphate from sugar (makes ATP from ADP)

   1. discovered in reverse direction hence “kinase”

1. substrate level phosphorylation =

2. oxidative phosphorylation =

1. substrate level phosphorylation = generation of ATP from ADP and reactive chemical intermediates using soluble enzymes

2. oxidative phosphorylation = e- carrier, NADH or FADH2, donate e- to ETC and ATP synthase complex yields ATP

glycolysis step 8:

1. enzyme?

2. advantage of rearranging phosphate group?

1. phosphoglycerate mutase

2. placing Phosphate - charge nearby another O- makes it a better leaving group

glycolysis step 9:

1. type of reaction

2. role of Mg2+?

3. why PEP important?

1. type of reaction

2. part of enolase active site that stabilizes intermediate

3. PEP has high phosphorylation transfer potential compared to 2-phosphoglycerate

glycolysis step 10:

1. why special

2. enzyme correct name?

3. product(s)

4. regulation

5. enzyme requires

6. how many ATP?

1. special

   1. payoff phase

   2. 2nd substrate level phosphorylation

2. enzyme has wrong name should be phosphatase

3. 2 tautomers of pyruvate

   1. enol and keto forms (keto more stable)

4. pyruvate kinase activity, regulated by level of Mg2+

   1. when there is plenty of ATP, Mg ions sequestered by ATP and slows down pyruvate kinase

5. 4 molecules of ATP bc 2 glyceraldehyde mCs

payoff phase

1. how many mCs of ATP did you get from payoff phase

2. in glycolytic pathway, what’s the total amount of ATP you get?

3. in glycolytic pathway, what’s the net amount of ATP you get?

1. 4

2. 4

3. 2

fermentation:

1. what is it

2. reaction after glycolysis

3. why does it happen?

4. when/where does fermentation happen

   1. fed state?

5. why important

6. what if person has LDH mutation?

1. fermentation = extract E but does not use O2 or change NAD+/NADH ratio

2. rxn in pic

3. NAD+ is a necessary reactant for glycolysis to run (step 6). However, running glycolysis full tilt depletes NAD+ stores

4. fermentation happens when you need ATP but have depleted NAD+ and can’t perform glycolytic pathway,

   1. common in muscles during strenuous exercise

   2. can be well fed and have plenty of sugar, NAD+ depletion will still stop glycolysis

5. important bc regenerates NAD+ so glycolysis can run forward again

6. can’t do strenuous activity