BIOL #06

Question 1

Metabolism

Answer 1

• Metabolism is the totality of chemical reactions that occur within an individual (organism or cell)

• Metabolism is an emergent property of life that arises from interactions between molecules found within cells
- Emergent properties are characteristics that arise with increasing levels within the hierarchy of biological complexity that cannot be predicted based on knowing the constitute parts alone (i.e. the properties cannot be reduced)

Question 2

ATP: Cellular Work

Answer 2

• Cellular work:
– Mechanical work: beating of cilia or flagella, muscle cell contraction.
– Transport work: moving substances across membranes against the direction of passive movement.
– Chemical work: pushing endergonic reactions, which would otherwise not occur spontaneously (e.g. synthesis of polymers from monomers).

Question 3

ATP: Energy-Coupling

Answer 3

• Cells use energy-coupling to do work.
– Energy-coupling refers to the use of exergonic reactions (spontaneous) to drive endergonic reactions (non-spontaneous/energy-requiring).

• ATP is responsible for mediating most energy coupling in cells.
– ATP acts as the immediate source or energy for most cellular work.

Question 4

Phosphorylating

Answer 4

• ATP works by phosphorylating (transferring a phosphate group to) target molecules.
– Hydrolysis of the bond between the two outermost phosphate groups results in formation of ADP and Pi in a highly exergonic reaction.

Question 5

Why does hydrolysis of ATP release so much energy?

Answer 5

– All three phosphate groups are negatively charged
– The electrons associated with the oxygens of the phosphate groups have high potential energy because of their locations (close to other electrons and far away from positive nucleus) – there is mutual repulsion between the crowded electrons, causing instability in this region of ATP.

Question 6

How ATP Drives Endergonic Reactions

Answer 6

• In cells, endergonic (energy-requiring) reactions become exergonic (spontaneous) when the substrates or enzymes involved are phosphorylated (i.e. energy-coupling driven by ATP).
– How does energy-coupling happen? If the ΔG (change in free energy) of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that the coupled reactions are exergonic.

Question 7

ATP: Substrate Phosphorylation

Answer 7

• What does ATP phosphorylation do to target molecules?
– After hydrolysis, the released phosphate group is transferred to a molecule (phosphorylation)
– Phosphorylation usually causes a change in the molecule’s shape and the molecule become more reactive (less stable) than the original molecule

Question 8

ATP: How is it regenerated?

Answer 8

• ATP is a renewable resource that can be regenerated by adding a phosphate group to ADP
• The free energy required to phosphorylate ADP comes from exergonic breakdown reactions in the cell (catabolism)
• The shuttling of inorganic phosphates and energy between chemical reactions is called the ATP cycle
• The regeneration of ATP from ADP and an inorganic phosphate is an endergonic reaction (requires energy)

• Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic process of making ATP
– During cellular respiration, ATP is produced via substratelevel phosphorylation and oxidative phosphorylation
– Plants can use light energy to produce ATP

Question 9

Cellular Respiration: A Catabolic Pathway

Answer 9

• A catabolic pathway involves breaking down molecules into smaller units, which releases energy. An anabolic pathway builds molecules.

• Cellular respiration is a catabolic pathway in which oxygen is consumed as a reactant and ATP is produced from molecules with
high potential energy – often glucose.

• How do catabolic pathways decompose glucose and other organic compounds to release energy?
– Electrons must be transferred during chemical reactions – the relocation of electrons releases energy stored in organic molecules.
– In cellular respiration, the energy released from organic molecules is then used to synthesize ATP.
– These reactions are typically called redox reactions.

Question 10

Redox Reactions

Answer 10

• The transfer of one or more electrons during chemical reactions is referred to as oxidation-reduction (redox) reactions.
• Each electron transferred during redox is usually accompanied by a proton (H+).

Question 11

LEO goes GER

Answer 11

– oxidized molecule (LEO)
• loses an electron (and a proton) and has lower potential energy.
• An oxidized molecule acts an a reducing agent because it causes another molecule to gain an electron when it loses one.

– reduced molecule (GER)
• gains an electron (and a proton) and has higher potential energy.
• A reduced molecule acts as an oxidizing agent because it causes another molecule to lose an electron when it gains one.

Question 12

NAD/NADH: Electron Carrier

Answer 12

• Nicotinamide adenine dinucleotide (NAD) is reduced to form NADH –NAD gains an electron and a proton (H+) to become NADH

• NADH donates electrons to other molecules (i.e. becomes oxidized) and is
thus called an electron carrier and has “reducing power” (i.e. acts as a
reducing agent).

• NADH is important to metabolism – carrying electrons from one reaction
to another.

Question 13

Cellular Respiration as a Redox Reaction

Answer 13

• In cells, glucose is oxidized through a long series of carefully controlled redox reactions. The resulting change in free energy is used to synthesize ATP from ADP and Pi. Together, these reactions comprise cellular respiration.
• The carbon atoms of glucose are oxidized (LEO) to form carbon dioxide, and the oxygen atoms in oxygen are reduced (GER) to form water:

Question 14

Glycolysis

Answer 14

• Glycolysis (“sugar-splitting”), a series of 10 chemical reactions, is the first step in glucose oxidation.
• All of the enzymes needed for glycolysis are found in the cytosol.
• In glycolysis, glucose is broken down into two 3-carbon molecules of pyruvate, and the potential energy released is used to phosphorylate ADP to form ATP.

• Glycolysis consists of two phases:
– an energy investment phase
– an energy payoff phase.

Question 15

Energy Investment Phase

Answer 15

• In energy investment phase (first 
5 reactions):
– two molecules of ATP are consumed
– glucose is phosphorylated twice, 
forming fructose-1,6-bisphosphate.
– No CO2released

Question 16

Substrate-level phosphorylation

Answer 16

– when ATP is produced by the enzyme-catalyzed transfer of a phosphate group from an intermediate substrate to ADP.
– This is how ATP is produced in glycolysis and the citric acid cycle.

Question 17

Feedback Inhibition

Answer 17

• Feedback inhibition occurs when an enzyme in a pathway is inhibited by the product of that pathway.
– ATP can bind allosterically (i.e. outside of active site) to enzymes in the pathway and change their affinities for substrates.
– Cells able to stop glycolytic reactions when ATP is abundant can conserve their stores of glucose for times when ATP is scarce.

Question 18

Mitochondria Membranes

Answer 18

• Mitochondria have both inner and outer membranes.
– interior filled w/layers of sac-like structures called cristae, which are connected to the inner membrane by short tubes.
– The mitochondrial matrix is inside the inner membrane but outside the cristae.

Question 19

Pyruvate Processing

Answer 19

• Pyruvate processing is the second step in glucose oxidation.
– This step is catalyzed by pyruvate dehydrogenase (an enzyme in the
mitochondrial matrix).

• In the presence of O2:
– Pyruvate undergoes a series of reactions that results in a product molecule with high potential energy – acetyl coenzyme A (acetyl CoA).
– During these reactions, another molecule of NADH is synthesized, and one of the carbon atoms in pyruvate is oxidized to CO2.

Question 20

Pyruvate Processing Regulation

Answer 20

• Pyruvate processing is under both positive and negative feedback control.
– Abundant ATP reserves inhibit the enzyme complex.
– Large supplies of reactants, such as pyruvate and NAD+, and low supplies of ATP, stimulate it.

Question 21

The Citric Acid Cycle

Answer 21

• In the third step of glucose oxidation, acetyl CoA (product of pyruvate processing) enters the citric acid cycle, located in the mitochondrial matrix (outside of the cristae).
– Each acetyl CoA is oxidized to two molecules of CO2
.
• The potential energy released from acetyl CoA:
1.Reduces NAD+ to NADH.
2.Reduces flavin adenine dinucleotide (FAD) to FADH2 (another electron carrier).
3.Phosphorylates GDP to form GTP (later converted to ATP).

Question 22

The Substrates of the Citric Acid Cycle

Answer 22

• A series of carboxylic acids is oxidized and recycled in the citric acid cycle.

What makes the citric acid cycle a cycle? The molecule Oxaloacetate reacts with Acetyl CoA to produce Citrate, citrate is then broken down and rearranged until Oxaloacetate is the final product…picking up a new Acetyl CoA…

Question 23

The Citric Acid Cycle Regulation

Answer 23

• Citric acid cycle can be turned off at multiple points via several different mechanisms of feedback inhibition.

Question 24

The Citric Acid Cycle

Answer 24

• The citric acid cycle completes glucose oxidation.
• The cycle starts with acetyl CoA and ends with CO2, releases potential energy, and can slow down when energy supplies are high
• The energy released by oxidation of one acetyl CoA produces 3 NADH, 1 FADH2, and 1 GTP (which is then converted to ATP).

Question 25

Free Energy Changes, NADH, and FADH2

Answer 25

• During glucose oxidation, for each glucose molecule that is oxidized to 6 CO2
– the cell reduces 10 molecules of NAD+
to NADH
– 2 molecules of FAD to FADH2
– and produces 4 molecules of ATP by substrate-level phosphorylation.

• The 4 ATP produced can be used directly for cellular work.
• Most of glucose’s original energy is contained in the electrons transferred to NADH and FADH2, which then carry them to oxygen, the final electron acceptor.