BIOchem exam 3 (ALL CARDS)

Phototrophs

Obtain free energy from sunlight

Chemotrophs

obtain free energy through the oxidation of carbon fuels

mechanical work, active transport, synthesis of macromolecules

living organisms require an input of free energy to do what?

metabolism

composed of many interconnected reactions

catabolism

the breakdown of complex
molecules in living organisms to form
simpler ones, together with the release of
energy
• Usually involves oxidation
• Produces energy in biologically useful
forms (ATP and ion gradients)

Anabolism

the set of metabolic
pathways that construct bigger molecules
from smaller units.

reduced

—molecules are energy rich

oxidized

— molecules are energy poor

First stage of catabolism

Large molecules in food are broken into smaller units. This is a preparation stage; no useful energy is captured

Second stage of catabolism

Small molecules are degraded to a few simple units that play a central role in metabolism. Most of molecules are converted into acetyl CoA. Some ATP is generated (small amount)

Third stage of catabolism

ATP is produced from the complete oxidation of acetyl CoA (citric acid cycle + oxidative phosphorylation).

ATP

universal currency of free energy

Hydrolysis of ATP

Thermodynamically unfavorable reactions can be driven by favorable reactions, which is ——- in many cases

reactions must be specific, the pathway in total must be thermodynamically favorable (specific and favorable)

n order to construct a metabolic pathway, two criteria must be met:

ATP

What type of molecule is this?

two phosphoanhydride linkages

ATP is an energy-rich molecule because its triphosphate unit has —-

higher, lower

Phosphate can be transferred from compounds with
—- ΔG’ to those with —- ΔG’.

D

Which of the following molecule(s) have a higher phosphoryl-transfer
potential than ATP?
A.Phosphoenolpyruvate
B.creatine phosphate
C.1,3-bisphosphoglycerate
D.All of the above

Phosphoenolpyruvate(PEP), creatine phosphate, 1,3- bisphosphoglycerate(1,3BPG)

What molecules have higher higher phosphoryl-transfer potential than ATP?

creatine phosphate

can regenerate ATP from ADP, allowing a short burst of activity as in a sprint

Activated carriers

small molecules carrying activated functional groups that can be donated to another molecule

ATP

Activated carrier of phosphate groups

Coenzyme A

activated carrier of two- carbon fragments (acyl groups)

NAD+ FAD

Activated carriers of electrons for fuel oxidation

NADPH

Activated carriers of electrons for the synthesis of biomolecules

Fuels

Reduced organic compounds serve as —-from which electrons can be stripped off during oxidation.

NADP+ and NAD+

The reactive site is the same in —-

NAD and NADP

Common redox cofactors

These are commonly called pyridine nucleotides.
• They can dissociate from the enzyme after the
reaction.
• In a typical biological oxidation reaction, hydride
from an alcohol is transferred to NAD+, giving
NADH.

Acetyl CoA

an important donor of acyl groups.
• feeding two-carbon units into
metabolic pathways
• synthesis of fatty acids

(HS is the reactive group)

Stage 1 of glycolysis

(preparatory stage) traps glucose in the cell and modifies it so that it can be cleaved into a pair of phosphorylated 3-carbon compounds

Stage 2 of glycolysis

oxidizes the 3-carbon compounds to pyruvate while generating 2 molecules of ATP

cytosol, phosphorylated

All 10 glycolytic enzymes are in the —-. all 10 intermediates are —— compounds of six or three carbons

Glycolysis

a universal process. One molecule of glucose is oxidized to 2 molecules of pyruvate. Useful biological energy conserved as 2 molecules of ATP and 2 of NADH

b

Glucose is a hydrophilic molecule that enters cells through glucose transporters,
from extracellular space where concentration of glucose is high into cytoplasm
where concentration of glucose is low.
What type of transport is this?
A.Simple diffusion
B.Facilitated diffusion
C.Simport
D.Antiport
E.Primary active transport

Step one: phosphorylation of glucose

reaction is irreversible inside cell

Glucose — hexokinase— Glucose 6- Phosphate

glucose

Starting material for step1 Phosphorylation of glucose

hexokinase

Enzyme for step1 Phosphorylation of glucose

Glucose-6 phosphate

Final product of step1 Phosphorylation of glucose

two lobes separated

Hexokinase in the absence of glucose

two lobes of the enzyme come together

Hexokinase after the binding of glucose

b

How glucose is different from fructose?
A. Glucose is a hexose, fructose is a pentose
B. Glucose is an aldose, fructose is a ketose
C. Glucose major form is cyclic, fructose is mostly linear
D. Glucose is predominantly in a D-form, fructose is predominantly in L-form
E. Glucose can be used as a fuel in our body, fructose cannot

Step 2: Phosphohexose Isomerization

this reaction proceeds in either direction

Glucose 6- phosphate —- phosphohexose isomerase — Fructose 6-phosphate

glucose-6 phosphate

Starting product of Step 2: Phosphohexose Isomerization

phosphohexose isomerase

enzyme of Step 2: Phosphohexose Isomerization

fructose 6-phosphate

final product of Step 2: Phosphohexose Isomerization

Step 3: 2nd Priming Phosphorylation

First committed step of glycolysis; second irreversible step

• activity increased when ATP is low, and/or ADP and AMP
  are high;
  • Enzyme is inhibited when cell has plenty of ATP

Fructose 6-phosphate- phosphofructokinase-1(PFK-1)—Fructose 1,6-biphosphate

Fructose 6-phosphate

starting material of Step 3: 2nd Priming Phosphorylation

phosphofructokinase-1 (PFK-1)

enzyme of Step 3: 2nd Priming Phosphorylation

fructose 1,6-biphosphate

final product of Step 3: 2nd Priming Phosphorylation

Step 4: Aldol Cleavage of F-1,6-bP

This reaction is thermodynamically unfavorable/reversible.
Product (GAP) concentration is kept low to pull reaction forward.

fructose 1,6-biphosphate—aldolase— dihydroxyacetone phosphate and glyceraldehyde 3-phosphate

fructose 1,6-biphosphate

Starting material of Step 4: Aldol Cleavage of F-1,6-bP (this gets cut in half)

aldolase

enzyme of Step 4: Aldol Cleavage of F-1,6-bP

dihydroxyacetone phosphate and glyceraldehyde 3-phosphate

final products of Step 4: Aldol Cleavage of F-1,6-bP

Step 5: Triose Phosphate Interconversion

Dihydroxyacetone phosphate— triose phosphate isomerase— glyceraldehyde 3-phosphate

dihydroxyacetone phosphate

Starting material of Step 5: Triose Phosphate Interconversion

triose phosphate isomerase

enzyme for Step 5: Triose Phosphate Interconversion

glyceraldehyde 3-phosphate

final product of Step 5: Triose Phosphate Interconversion

payoff phase

The energy gain comes from the —- of glycolysis (steps 6-10)

glucose carbons in GAP

fructose 1,6-biphosphate, dihydroxyacetone phosphate, glyceraldehyde 3-phosphate

Step 6: Oxidation of GAP by Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

First energy conserving reaction of glycolysis

Carbon 1 is oxidized

• A high-energy phosphate
compound generated
• Inorganic phosphate is
incorporated
• Oxidation of aldehyde with
NAD+ gives NADH
• The amount of NAD+ in a cell is
far smaller than the amount of
glucose metabolized in a few
minutes. NADH formed in this
step should be continuously
reoxidized and recycled.

Glyceraldehyde 3-phopshate and inorganic phosphate

Starting material for Step 6: Oxidation of GAP by
Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

Glyceraldehyde 3-phosphate dehydrogenase

enzyme for Step 6: Oxidation of GAP by Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

1,3-biphosphoglycerate (1,3 BPG)

Final product of Step 6: Oxidation of GAP by Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

Step 7: 1st Production of ATP

Makes 1 ATP

1,3-bisphosphoglycerate —-Phosphoglycerate kinase—-ATP and 3-phosphoglycerate

1,3-bisphosphoglycerate (1,3 BPG)

starting material of Step 7: 1st Production of ATP

a high-energy compound. It can donate the phosphate group to ADP to make ATP

Phosphoglycerate kinase

Enzyme for Step 7: 1st production of ATP

is named for the reverse reaction. Like all enzymes, it catalyzes the reaction in both directions. Reverse reaction takes place in gluconeogenesis.

ATP and 3-phosphoglycerate

Final products of Step 7:1st production of ATP

Step 8: Migration of the Phosphate

3-phosphoglycerate—Phosphoglycerate mutase— 2-phosphoglycerate

2,3 BPG formed in this step

3- phosphoglycerate

starting material for Step 8: Migration of the Phosphate

phosphoglycerate mutase

enzyme for Step 8: Migration of the Phosphate

2-phosphoglycerate

final product of Step 8: Migration of the Phosphate

Step 9: Dehydration of 2-PG to PEP

A high energy phosphate compound (PEP) generated

2-phosphoglycerate— enolase— phosphoenolpyruvate

2-phosphoglycerate

starting product of Step 9: Dehydration of 2-PG to PEP

enolase

Enzyme for Step 9: Dehydration of 2-PG to PEP for

phosphoenolpyruvate(PEP)

Final product of Step 9: Dehydration of 2-PG to PEP

Step 10: 2nd Production of ATP

• 2nd substrate-level phosphorylation of
glycolysis
• Pyruvate kinase requires K+ and
Mg++ or Mn++ for activity
• Loss of phosphate from PEP yields an
enol that tautomerizes into ketone
(see next slide)
• Tautomerization effectively lowers the
concentration of the reaction product

phosphoenolpyruvate— pyruvate kinase— ATP and pyruvate

phosphoenolpyruvate(PEP)

Starting material for Step 10: 2nd Production of ATP

Pyruvate kinase

Enzyme for Step 10: 2nd Production of ATP

Pyruvate and ATP

Ending material for Step 10: 2nd Production of ATP

Pyruvate tautomerization

— drives ATP production

drives the reaction toward ATP formation by lowering the concentration of the reaction product (enol form of pyruvate)

b

What is substrate-level phosphorylation?
A. phosphorylation of AMP by ATP
B. ATP synthesis when the phosphate donor is a
substrate with high phosphoryl transfer potential
C. phosphorylation of glycolytic intermediates
D. phosphorylation of ATP coupled to an ion gradient
E. ATP and AMP synthesis from two molecules of ADP

1 glucose, 2 ATP, and 2 NAD+

Glycolysis uses

2 pyruvate, 4 ATP, 2 NADH

glycolysis makes

A

Where does glycolysis take place in the cell?
A. Cytoplasm
B. Mitochondria
C. Bloodstream outside the cells
D. Nucleus
E. Endoplasmic reticulum

Lactic acid fermentation

pyruvate —lactate dehydrogenase—L-lactate

pyruvate

starting material for lactic acid fermentation

lactate dehydrogenase

Enzyme for lactic acid fermentation

l-lactate

final product of lactic acid fermentation

this is dumped out of the cell so the reaction direction is maintained

Ethanol fermentation

Two-step reduction of pyruvate to ethanol
• Humans do not have pyruvate decarboxylase.
• We do express alcohol dehydrogenase for ethanol metabolism, but is largely used in
the reverse reaction.
• CO2 produced in the first step is responsible for:
– carbonation in beer
– dough rising when baking bread

NAD+

The substance that must be regenerated for glycolysis to proceed is ____

glycolysis

Only a small amount of energy available in glucose is captured in —

cellular respiration

is the complete oxidation of organic
fuels to CO2 and H2O in the presence of O2 .
• Cells consume O2 and produce CO2 in this process
• It provides more energy (ATP) from glucose than
glycolysis
• Occurs in three major stages:
1. acetyl CoA production (Chapter 18)
2. citric acid cycle: acetyl CoA oxidation (Chapter 19)
3. electron transfer and oxidative phosphorylation
(Chapters 20-21)

Acetyl CoA

fuel for the citric acid cycle

aerobic

under — conditions pyruvate enters the mitochondria where it is converted into acetyl CoA

mitochondrial matrix

citric acid cycles occurs in the —

inner mitochondrial membrane

oxidative phosphorylation occurs in the —-

pyruvate dehydrogenase complex

catalyst for the conversion of pyruvate to acetyl-CoA

TPP, Lipollysine, FAD, NAD+, CoA-SH

5 co-enzymes required for conversion of pyruvate to Acetyl-CoA

conversion of pyruvate of acetyl-CoA

Net reaction:
– oxidative decarboxylation of pyruvate
– first carbons of glucose to be fully oxidized
• Catalyzed by the pyruvate dehydrogenase complex
– requires 5 coenzymes
– TPP, lipoyllysine, and FAD are prosthetic groups.
– NAD+ and CoA-SH are co-substrates.

prosthetic groups

TPP, Lipoyllysine , FAD