Intro to Metabolism (Ch. 8)

Question 1

Define metabolism

Answer 1

The totality of an organism’s chemical reactions

Question 2

Distinguish between catabolic pathways and anabolic pathways

Answer 2

Catabolic pathways are degradative processes that release energy by breaking down complex molecules into simpler compounds. Ex.: Cellular respiration

Anabolic pahtways consume energy to build complicated molecules from simpler ones. Also called biosynthetic pahtways. Ex.: Synthesis of an amino acid from simpler molecules or of a protein from amino acids.

Question 3

What are the forms of energy?

Answer 3

• Kinetic energy is the energy of motion
  
  • includes heat or thermal energy – kinetic energy associated with the random movement of atoms or molecules
  • light is a type of energy that can do work, like powering photosynthesis
• Potential energy is energy of location or structure
  
  • like water behind a dam
  • Chemical energy refers to potential energy available for release in a chemical reaction
    *

Question 4

What is the first law of thermodynamics?

Answer 4

Conservation of energy.

The first law of thermodynamics is that the energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed.

Question 5

What is the second law of thermodynamics?

Answer 5

Every energy transfer/transformation increases the entropy of the universe.

During every reaction or energy transfer/transformation, some energy is lost and makes the universe slightly more disordered.

Another formulation: *For a process to occur spontaneously, it must increase the entropy of the universe. *

Question 6

Define entropy

Answer 6

Entropy is a measure or disorder or randomness.

Question 7

What is a spontaneous process?

Answer 7

A spontaneous process is one that can occur without an input of energy. It is energetically favorable. Not necessarily instantaneous.

Question 8

Define the Gibbs free energy of a system. What does free energy mean?

Answer 8

Free energy is the portion of a system’s energy that can perform work with the temperature and pressure are uniform through the system. It is like potential energy.

∆G = ∆H - T∆S

∆G = free energy

∆H = change in the system’s enthalpy

T = Temperature

∆S = change in system’s entropy

Question 9

Define enthalpy for biological systems

Answer 9

In biological systems, enthalpy is equivalent to total energy

Question 10

How do we use ∆G to predict a process’s spontanaeity?

Answer 10

If ∆G is negative, the process is spontaneous.

Question 11

Under what circumstances – according to the equation for Gibbs free energy – is a reaction spontaneous? Also state the equation for Gibbs free energy.

Answer 11

∆G = ∆H - T∆S

∆G < 0 when:

• ∆H < 0 (change total energy is negative, i.e. the system gives up enthalpy and H decreases)

or

• T∆S must be positive (the system gives up order and S increases)

or

1. both

Question 12

Why do biologists care about processes’ spontanaeity (re: Gibbs free energy)?

Answer 12

Because spontaneous processes can be harnessed to do work.

Question 13

Describe Gibbs free energy in terms of initial/final states.

Answer 13

∆G = G_final - G_initial

When a process involves a loss of free energy during the change from initial to final state, ∆G is negative.

Question 14

Describe Gibbs free energy in terms of instability

Answer 14

∆G is like a measure of a system’s instability – it’s tendency to change to a more stable state. Unstable (higher G) tend to change in such a way that they become more stable (lower G) – i.e. ∆G < 0.

Question 15

What is an exergonic vs. an endergonic reaction?

Answer 15

Exergonic - energy outward. Releases free energy. Spontaneous.

Endergonic - energy inward. Absorbs free energy from surroudings. Non-spontaneous

Question 16

What kinds of work does a cell do?

Answer 16

• Chemical work
• Transport work
• Mechanical work

Question 17

What is chemical work?

Answer 17

The pushing of endergonic reactions that would not occur spontaneously

Question 18

What is transport work?

Answer 18

Pumping substances across membranes against the direction of spontaneous movement

Question 19

Mechanical work

Answer 19

For instance, beating cilia, contracting muscle cells, and moving chromosomes during cellular reproduction.

Question 20

What is energy coupling?

Answer 20

Energy coupling is a way cells manage their energy resources to do work. They use an exergonic process to drive an endergonic one.

Question 21

What is ATP? Describe its structure.

Answer 21

adenosine triphosphate. ATP has ribose with the nitrogenous base adenine and a chain of three phosphate groups bonded to it.

Question 22

Describe the hydrolysis of ATP. What are its effects? How does it work?

Answer 22

Hydrolysis breaks the bonds between ATP’s phosphate groups.

Adding a water molecule breaks off a molecule of inorganic phosphate (HOPO₃^2-) and leaves the ATP, which is now adenosine diphosphate (ADP).

Question 23

Is ATP hydrolysis exergonic of endergonic? How much energy does it release?

Answer 23

Exergonic.

Question 24

Why does ATP release so much energy when an inorganic phosphate group is broken off during hydrolysis?

Answer 24

Because all three phosphate groups are negatively charged. These like charges are crowded, and their mutual repulsion makes the ATP molecule unstable. The triphosphate tail is like a compressed spring.

Question 25

How could you use ATP hydrolysis to couple an enzymatic reaction?

Answer 25

If ∆G of a particular endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that, overall, the coupled reactions are exergonic. Usually, this means you have to couple the phosphate group to some other group, the covalently bonded phosphorylated intermediate.

Question 26

Which two forms of cell work are most driven by ATP hydrolysis?

Answer 26

* Mechanical work - * Transport work - ATP hydrolysis changes the protein's shape and, often, its binding ability.

Question 27

What is a phosphorylated intermediate? Why are they important? How do they work?

Answer 27

A phosphorylated intermediate is some molecule that receives a phosphate group from ATP, which are covalently bonded. Forming phosphorylated intermediates is the key to coupling exergonic/endergonic reactions. Phosphorylated intermediates are less stable than the unphosphorylated molecule.

Question 28

How do you prepare ADP for use again?

Answer 28

You rephosphorylate ADP using energy from other catabolism. Then it can be hydrolized again.

Question 29

What is an enzyme?

Answer 29

An enzyme is a large protein that acts as a catalyst - a chemical agent that speeds up a reaction without being consumed.

Question 30

What is activation energy?

Answer 30

Free energy of activation is the initial energy required to contort reactant molecules so that the bonds can break

Question 31

How do enzymes affect reactions in terms of E_a?

Answer 31

Enzymes lower E_a (but keep Gibbs free energy the same)

Question 32

What is the active site of an enzyme?

Answer 32

The one part of the enzyme molecule that actually binds to the substrate.

Question 33

What is induced fit?

Answer 33

Induced fit is the effect that occurs when a substrate enters the active site -- the enzyme changes shape slightly and makes the substrate fit even more closely, like a clasping handshake.

Question 34

What environmental factors affect the activty of an enzyme?

Answer 34

* Temperature - higher temp increases activity up to a point until enzyme is denatured * pH - there is an optimal pH for activity * Cofactors - nonprotein helpers that bind to enzymes * Inhibitors - chemicals that stop the action of an enzyme

Question 35

What are the types of inhibitors of enzyme activity?

Answer 35

Competitive and noncompetitive

Question 36

What do you call a case where a protein's function at one site is affected by the binding of a regulatory molecule to a separate site?

Answer 36

allosteric regulation

Question 37

What is allosteric regulation? What effect does it have on activity?

Answer 37

When an enzyme's function is regulated by a regulatory molecule that binds to a separate site on an enzyme. It can inhibit or stimulate activity.

Question 38

Describe most enzymes that are allosterically regulated

Answer 38

* Typically 2+ subunits, each with its own active site * Complex oscillates between catalytically active and inactive shapes

Question 39

Describe allosteric cooperativity. How does it work and what is its effect?

Answer 39

Allosteric cooperativity is when a substrate molecule binding to one active site sets all the other active sites in "active" mode, increasing catalytic activity. It amplifies the response of enzymes to substrates: one substrate molecule primes an enzyme to act on other substrate molecules more readily.

Question 40

What is feedback inhibition?

Answer 40

Feedback inhibition is a mode of metabolic controll wherein a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway. When end product concentration gets high enough, it binds to the original enzyme and production stops.