biochem501 import: unit 2

what bonds are oxidized to make energy

CH and CC

cells obtain most of their energy by...

oxidation reactions, but not by direct reaction with O2

Thermodynamics

how much energy is released as a reaction proceeds towards equilibrium

does a - delta G mean the reaction proceeds to the right or left

right (exergonic reaction)

does a + delta G mean the reaction proceeds to the right or left

left (endergonic)

what does a delta G of zero mean

at equilibrium

what does delta H stand for

enthalpy change

-difference in bond energies between reactants and products

- delta h

exothermic: reaction releases heat, more stable bonds formed

*contributes to a favorable (-) delta G

+ delta h

endothermic: heat input, less stable bonds are formed as heat is absorbed by the reaction

what does delta s stand for

entropy change; change in randomness of a reaction

-more randomness (+ delta S)= more favorable (-) delta G

if Keq is < 1, what is delta G

positive, reverse reaction is favored

if Keq is > 1 what is delta G

negative, forward reaction is favored

what is responsible for the high energy of ATP

repulsion of negatively charged O's

how does ATP provide energy

through group transfers, not by direct hydrolysis

-group transfer energizes the recipient; coupling to ATP breakdown renders amine formation favorable

what kind of compounds do many key reactions of metabolism use

high energy phosphate compounds

what is produced after first part of glycolysis

two 3 C sugars

what is produced after the second part of glycolysis

two pyruvates

what is the first stage of glycolysis called?

preparatory

enzyme for step 1 of glycolysis

hexokinase

what happens in the hexokinase reaction

add phosphate to 6 C sugar to make glucose-6-P

is glucose phosphorylation coupled to ATP breakdown

yes

what is the source of the phosphate group in the hexokinase reaction

ATP from enzyme active site

enzyme for step 2 of glycolysis

phosphohexose isomerase

what does the phosphohexose isomerase do

interconvert glucose 6P and fructose 6P

Is the phosphohexose isomerase reaction reversible or irreversible?

reversible; rearrangement of molecules

is the phosphohexose isomerase reaction driven towards glucose or fructose? why?

fructose because fructose is used up in the reaction

is the hexokinase reaction reversible or irreversible?

irreversible

enzyme for step 3 of glycolysis

phosphofructokinase

is the phosphofructokinase reaction reversible or irreversible

irreversible

is ATP a substrate or inhibitor in the phosphofructokinase reaction? why?

both because it binds to active site AND separate allosteric site

enzyme for step 4 of glycolysis

aldolase

what does the aldolase reaction do?

break 6 C sugars into 2x 3 C sugars

enzyme for step 5 of glycolysis

triose phosphate isomerase

what does the triose phosphate isomerase do

interconverts two sugars

what is the second stage of glycolysis called?

payoff stage

what two molecules have high phosphate group transfer potential

PEP and 1,3-biphosphoglycerate

enzyme for step 6 of glycolysis

dehydrogenase

what happens in step 6 of glycolysis

glyceraldehyde 3 P is oxidized into 1,3-biphosphoglycerate

what step is the ONLY redox reaction of glycolysis

step 6

how is the energy of oxidatio preserved in step 6 of glycolysis

in the phosphate bond and NADH

is NAD+ the oxidized or reduced form?

oxidized

is NADH the oxidizer or reduced form?

reduced

enzyme for step 7 of glycolysis

phosphoglycerate kinase

what step of glycolysis is there the first payoff? what is the payoff?

7. ATP

what happens in step 7 of glycolysis

1,3 BPG phosphate group is taken off and added to ADP to make ATP

enzyme for step 8 of glycolysis

phosphoglycerate mutase

what happens in step 8 of glycolysis

the molecule is rearranged so the phosphate is in a high energy state

what happens in step 9 of glycolysis

phosphoenolpyruvate is formed. H2O is removed to create its C=C

is step 10 of glycolysis irreversible or reversible?

irreversible

what step has the second payoff in glycolysis. what is the payoff?

10. ATP

what does the regulatory logic say

points of regulation are typically via enzymes that catalyze irreversible steps

what is it called when the pyruvate is turned back into glucose

gluconeogenesis

what is the rate determining step of glycolysis

the phosphofructokinase reaction

does high levels of ATP or fatty acid inhibit or stimulate PFK1

inhibit

do high levels of AMP or ADP inhibit or stimulate PFK1

stimulate

How many pyruvate molecules are made from 1 glucose molecule?

2

How many ATP formed per 1 glucose molecule?

2

what does the pasteur effect say

yeast consumes more glucose under anaerobic conditions

what are fermentations

ways to generate NAD+ from NADH in anaerobic conditions

when turning pyruvate into lactate, what is oxidized and what is reduced

pyruvate is reduced and NADH is oxidized

where in the mitochondria are the citric acid cycle, fatty acid oxidation and pyruvate oxidation

the matrix

where in the mitochondria is the ATP synthase

the inner membrane

what is lipoic acid in the pyruvate dehydrogenase complex

covalently attached to lysine, facilitates shutting of substrate

what is thiamine pyrophosphate in the pyruvate dehydrogenase complex

component of active site that attacks substrate

step E1 of pyruvate DH mech

decarboxylation, releases a CO2

-active site contains anion derived from TPP, which can attack pyruvate substrate

-this leaves the rest of the substrate covalently bound to the active site of TPP

-NO REDOX/OX yet

-CC bond converted to CH bond only

step E2 of pyruvate DH mech

oxidation, reduce lipoic acid and release Acetyl CoA

-CH can be oxidized by lipoic acid group found on the second unit of the enzyme

-this reduces lipoic acid while oxidizing CH causing the substrate to be transferred to lipoic acid

-cofactor CoA-SH binds to release Acetyl CoA

step E3 of pyruvate DH mech

shuttle e- to NAD+ carrier and enable PDH to go another round

-long sidechain allows for reach to give electron to cofactor FAD to reduce it to FADH2

-this can then pass the electron off to soluble NAD+ to form NADH

what are the two ways that coupling is useful?

1- drives unfavorable reactions by energy of ATP breakdown

2- preserves energy of favorable reactions by coupling to ATP synthesis or the synthesis of other high energy compounds

what are the outputs of the citric acid cycle?

3 NADH, FADH2, 2 CO2 and GTP

what are the inputs of the citric acid cycle?

Acetate of Acetyl-CoA (2 C and 4 reduced bonds)

enzyme for step one of citric acid cycle

citrate synthase

enzyme for step two of citric acid cycle

aconitase

enzyme for step three of citric acid cycle

isocitrate dehydrogenase

enzyme for step four of citric acid cycle

alpha ketoglutarate dehydrogenase

enzyme for step five of citric acid cycle

succinyl coA synthetase

enzyme for step six of citric acid cycle

succinate dehydrogenase

enzyme for step seven of citric acid cycle

fumarase

enzyme for step eight of citric acid cycle

malate dehydrogenase

is the citrate synthetase in step one of the citric acid cycle regulated

yes

what kind of reaction does aconitase do? what does this mean

isomerization, a rearrangement of the molecule

what step of the citric acid cycle is a CO2 released in (first)?

3

what steps of the citric acid cycle involve oxidative decarboxylation

3 and 4

when is GTP formed in the citric acid cycle

step 5

What does succinyl CoA synthetase do?

harvests energy of thiolester by phosphorylation

when is fumarate formed in the citric acid cycle

step 6

when is FADH2 formed in the citric acid cycle

step 6

what does fumarase do

add H2O across C=C bond via a hydration reaction

when is NADH formed in the citric acid cycle

step 8

is step 8 of the citric acid cycle endergonic or exergonic

endergonic

does high ADP activate or attenuate the citric acid cycle

activate

does high ATP activate or attenuate the citric acid cycle

attenuate

what does the Warburg effect say

normal cells produce lactate in anaerobic conditions but cancer cells produce lactate in anaerobic AND aerobic conditions

what are lipases

enzymes that hydroluze fats and allow them to be transported across the mitochondrial membrane

what is the first step of fatty acid oxidation

activation

-fatty acid joined to coenzyme A

-enzymes on outer mitochondrial membrane

what is the second step of fatty acid oxidation

transport

-across inner mitochondrial membrane into matrix

-carnitine carrier system separates cytosolic and mitochondrial pools

what is the third step of fatty acid oxidation

beta oxidation

-conversion of fatty acid into acetyl-coA units in mitochondrial matrix

-4 step process

does the activation step have a + or - delta G

-

what replaces the CoA to transport a fatty acid into the mitochondria

carnitine

what was the findings of the Knoop experiement

fatty acids are broken down by 2 C units and oxidation occurs at the beta C

What type of enzymes typically catalyze redox reactions?

dehydrogenases