Introduction to metabolism

Question 1

Describe intermediary metabolism.

Answer 1

enzyme catalyzed processes in the cell that extract energy from nutrient molcules and use that energy to construct cellular components.

Question 2

Which type of intermediary metabolism supplies the energy for work?

Answer 2

catabolism

Question 3

What type of intermediary metabolism is used to perform oxidation?

Answer 3

catabolism

Question 4

How can we say that metabolic pathways are irreversible if some of their steps are reversible?

Answer 4

A metabolic pathway is irreversible if it contains even one irreversible step.

Question 5

How do redox potential and free energy relate?

Answer 5

A reaction with positive redox potential will have negative free energy

Question 6

Describe reduction potential.

Answer 6

measure of the affinity of a compound to acquire electrons (become reduced), measured in volts or millivolts

Question 7

Describe thermodynamic coupling.

Answer 7

Using the energy released from a catabolic reaction to fuel a less energetically favorable, anabolic reaction.

Question 8

Why is ATP a high energy bond?

Answer 8

the potential energy difference between the reactant and the product (ADP) is large.

Question 9

Describe the chemistry behind why ATP has a high potential energy.

Answer 9

• charge repulsion: all three PO4 molecules are in close proximity and repel one another. Hydrolysis of ATP relieves some of this stress.
• inorganic phosphate released upon hydrolysis has resonance to stabilize it

Question 10

Describe how the thioester bond is higher in energy than an ester bond.

Answer 10

Oxygen ester is stabilized by resonance, but thioester is not, so thioester has lower stability and thus higher potential energy.

Question 11

Which enzyme keeps pools of ADP, ATP, and AMP in equilibrium?

Answer 11

adenylate kinase

Question 12

Which molecule is most sensitive to energy changes in the cytosol?

Answer 12

AMP

Question 13

What does the free energy of ATP hydrolysis depend on?

Answer 13

The standard free energy, as well as the ratio of ATP, ADP, and inorganic phosphate. More negative free energy indicates that there is more ATP (reactant) in the cell available for hdrolysis.

Question 14

What is the most common covalent modification?

Answer 14

phosphorylation

Question 15

How does phosphorylation modify a protein?

Answer 15

It adds a big bulky and charged molecule which changes the environment of the amino acids around it

Question 16

Name the major mechanisms of metabolic regulation.

Answer 16

1. covalent modification (kinase and phosphatase activities)
2. allosteric regulation (shift in concentration between relaxed and tense state)
3. transcriptional/degradation control

Question 17

What is a common, general allosteric effector?

Answer 17

The product of a certain reaction

Question 18

In what state is insulin released?

Answer 18

fed

Question 19

In what state is glucagon/epinephrine released?

Answer 19

unfed state

Question 20

Describe the type of activity which insulin elicits, and the general pathway.

Answer 20

Phosphatase-type activity.

• Insulin binds receptor tyrosine kinase, causing the dimer to come together and autophosphorylate itself
• allows PIP3 to become phosphorylated which induces the activation of downstream phosphatases.

Question 21

Describe the type of activity which glucagon/epinephrin elicits and the general pathway.

Answer 21

Kinase-type activity

• glucagon binds trimeric G protein, alpha G accepts a GTP, leaves, and activates adenylate cyclase
• adenylate cyclase creates cAMP which activates protein kinase A
• protein kinase A activates phosphorylase kinase

Question 22

Describe homolytic versus heterolyric cleavage, and which type the cell uses

Answer 22

The cell uses heterolytic cleavage because the products are more stable.

• homolytic: products of the cleavage will split an electron pair, giving rise to carbon radicals.
• heterlytic: products will either take or give up the entire electron pair. gives rise to carbanions and carbocations.

Question 23

Difference between nucleophiles and electrophiles when it comes to bond cleavage.

Answer 23

Nucleophiles have the lone pair of electrons, and electrophiles want the lone pair of electrons

Question 24

Name some common nucleophiles.

Answer 24

• negatively charged oxygen
• negatively charged sulfhydryl
• carbanion
• uncharged amine group
• imidazole
• hydroxide ion

Question 25

Name some common electrophiles

Answer 25

• carbonyl carbon
• protonated imine group
• phosphorous of phosphate group
• proton

Question 26

What is the energy source for ox phos?

Answer 26

The downhill flow of electrons, as redox potential gets higher and higher as O2 is approached

Question 27

Reduction potentials are a measure of what?

Answer 27

electron affinity, or electronegativity

Question 28

Oxidants have what type of affinity for electrons?

Answer 28

Oxidants have a high electronegativity, and therefore oxidize reductants.

Question 29

Electrons flow from ____ to _____ (reductants/oxidants)

Answer 29

Electrons flow from reductants to oxidants

Question 30

How is the reducing potential of NADH shuttled across compartments?

Answer 30

• NADH in cytosol reduces OXA to malate, which can enter the mitochondria
• malate is then oxidized back to OXO, regenerating NADH within the mito
• OXO is converted to aspartate which can then pass from mito to cytosol, where the cycle can start again

Question 31

What is the purpose of the TCA?

Answer 31

To transfer electrons from organic substrates (starting with pyruvate) to carrier molecules NAD and FAD.

Question 32

From what is the energy available from redox reactions?

Answer 32

The differernce in the elctron affinity of two different compounds.

Question 33

Coupled redox reactions consist of:

Answer 33

two half reactions:

• an oxidation reaction
• a reduction reaction

Question 34

How are standard reduction potentials determined?

Answer 34

An electrochemical cell is used to measure the relative electron affinity of a test redox pair compared to the hydrogen half reaction. Agar bridge between half cells allows ions to flow and balance the charge to keep electron circuit in tact. Galvanometer connects the two cells and measures the flow of electrons between them.

Question 35

Another name for a half reaction is…

Answer 35

redox pair

Question 36

Where does the Fe-Cu redox reaction take place?

Answer 36

In cytochrome c of the mito inner membrane

Question 37

Describe aerobic respiration in terms of electron flow.

Answer 37

Aerobic respiration is the transfer of electrons from glucose to oxygen to form Co2 and H2o

Question 38

What is the most reduced form of carbon?

Answer 38

methane. electrons are owned all by the carbon and not by the hydrogen atoms

Question 39

What is the most oxidized form of carbon? Why?

Answer 39

carbon dioxide. electros are owned all by the oxygen

Question 40

Describe the reduction of NAD to NADH.

Answer 40

Involves the transfer of a hydride ion (-) which contains two electrons and 1 H, and the relase of a proton into solution.

Question 41

Describe the reduction of FAD to FADH2.

Answer 41

It is reduced by sequential addition of one electron and one proton at a time to give the fully reduced FADH2 product.

Question 42

What do we call enzymes that catalyze redox reactions?

Answer 42

Formally, they are called oxidoreductases, but because most oxidation reactions involve the loss of hydrogen, they are often called dehydrogenases.

Question 43

Why do we get more energy from NADH than from FADH2?

Answer 43

Redox potential difference from NADH to O2 is greater than from FADH2 to O2.