Chapter 8 - An Introduction to Metabolism

Question 1

what does an organism metabolism do?

Answer 1

An organism’s metabolism transforms matter and energy and is subject to the laws of thermodynamics

Question 2

what is catabolism?

Answer 2

• break things down
• fueling reactions (breakdown of glucose)
• energy is released
• generate more building blocks for biosynthesis

Question 3

what is anabolism?

Answer 3

• build things up
• the synthesis of complex organic molecules from simpler ones
• requires energy from fueling reactions (usually ATP)

Question 4

what is energy?

Answer 4

the capacity to cause change

Question 5

what are the different forms of energy?

Answer 5

1) thermal
2) kinetic
3) potential
4) chemical: potential energy available for release in a chemical reactions

Question 6

what is thermodynamics?

Answer 6

the study of the energy transformations that occur in a collection of matter

Question 7

what kinds of systems are organism?

Answer 7

open systems!

can exchange energy and matter

Question 8

what is the first law of thermodynamics?

Answer 8

energy can be transferred and transformed but it cannot be created or destroyed (it’s constant)

Question 9

how is energy often lost?

Answer 9

unusable energy is often lost as heat

Question 10

what is the second law of thermodynamics?

Answer 10

every energy transfer or transformation increases the entropy (disorder) of the universe

Question 11

what is a spontaneous reaction?

Answer 11

if a process:
- increases in entropy
- proceeds without requiring an input of energy
means its energetically favorable

things in nature strive for high entropy, low enthalpy

Question 12

what is free energy?

Answer 12

the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system as in a living cell

Question 13

what is ∆H?

Answer 13

change in enthalpy

Question 14

what is ∆S?

Answer 14

change in entropy

Question 15

∆G

Answer 15

The change in free energy (ΔG) during a process is related to the change in enthalpy or change in totally energy (H), change in entropy (S), and temperature in Kelvin (T)

Question 16

when is a reaction spontaneous?

Answer 16

• ∆G
• ∆H
  + ∆S

Question 17

values of ∆G

Answer 17

∆G < 0 spontaneous rxn

∆G > 0 not spontaneous

Question 18

what is an exergonic reaction?

Answer 18

• energy released
• spontaneous
• reactants have higher energy than products
  (ΔG < 0)

Question 19

what is an endergonic reaction?

Answer 19

• energy required
• nonspontaneous
• products have higher energy than reactants
  (ΔG > 0)

Question 20

what is chemical equilibrium?

Answer 20

the rate of the forward reaction equals the rate of the reverse and neither is favored (ΔG = 0)

Question 21

what are the three different kinds of work?

Answer 21

1) chemical work
2) transport work
3) mechanical work

Question 22

what is energy coupling?

Answer 22

the use of an exergonic process to drive an endergonic one

ATP is responsible for mediating most energy coupling in cells and acts as immediate source of energy

Question 23

what is ATP?

Answer 23

adenosine triphosphate

contains: ribose sugar, nitrogenous base adenine, and three phosphate groups

used to make RNA

Question 24

what happens when ATP is hydrolyzed?

Answer 24

bonds between phosphate groups of ATP can be broken by hydrolysis –> a molecules of inorganic HOPO3^-2 leaves the ATP which becomes ADP

ATP + H2O –> ADP + Pi
exergonic reaction: releases 7.3 kcal/mol ATP

releases energy because all three phosphate groups are negatively charged and crowded together = repulsion

Question 25

how does hydrolysis of ATP perform work?

Answer 25

the heat/energy released during ATP hydrolysis is harnessed by the cell’s proteins to perform chemical, transport, and mechanical work

Question 26

when can reactions be coupled?

Answer 26

if the ∆G of an endergonic reaction is less than the amount of energy released by ATP hydrolysis then the two reactions can be couples so that overall the coupled reactions are exergonic

Question 27

what is the phosphorylated intermediate?

Answer 27

the recipient molecule of the phosphate group from hydrolysis of ATP is called the phosphorylated intermediate

more reactive/less stable than the original unphosphorylated molecule

Question 28

transport work and ATP hydrolysis

Answer 28

1) ATP is bound noncovalenty to motor protein
2) ATP is hydrolyzed
3) another ATP molecule can then bind
at each stage the motor protein changes its shape and ability to bind the cytoskeleton resulting in movement of protein along cytoskeleton

Question 29

regeneration of ATP

Answer 29

ATP is renewable: it is regenerated by the addition of a phosphate to ADP (phosphorylation)

ATP synthesis requires energy –> energy required comes from exergonic breakdown reactions (catabolism) in the cell (such as cellular respiration)

Question 30

what is an enzyme?

Answer 30

a macromolecule that acts as a catalyst – most are proteins, some are RNA

not a reactant, they aren’t used up

Question 31

how do enzymes lower the Ea of a reaction?

Answer 31

• Induced fit: binding brings functional groups of the enzyme closer to the substrate and enhances catalysis
• Proper orientation of substrates
• Straining bonds (stabilize transition state)
• Providing favorable environment for the reaction
• Covalently binding the substrate (functional groups participate in reaction)

cannot change ΔG of a reaction*

Question 32

what is a substrate?

Answer 32

the react that an enzyme acts on

enzyme binds to its substrate and forms an enzyme-substrate complex

Question 33

what is the active site?

Answer 33

a restricted region of the enzyme molecule that actually binds to the substrate

the pocket/grove where catalysis occurs

Question 34

How would an enzyme catalyze an endergonic reaction?

Answer 34

By coupling the energy from ATP hydrolysis to the unfavorable reaction

Question 35

what effects enzyme activity?

Answer 35

Temperature and pH

affect the shape and folding (therefore activity)

Question 36

what are cofactors?

Answer 36

many enzymes need these nonprotein helps for catalytic activity

may be bound to enzyme as permanent residents or they may bind loosely and reversibly along with the substrate

usually inorganic: metal atoms in ionic form (Zn+2)
if organic –> cofactors

Question 37

what is a coenzyme?

Answer 37

if a cofactor is an organic molecule it’s referred to as a coenzyme

ex. vitamins, NAD+

Question 38

what are competitive inhibitors?

Answer 38

they reduce the productivity of the enzymes by blocking the substrates from entering the active sights - mimics the shape of the substrate

can be overcome by increasing the concentration of the substrate so that there’s more substrate than inhibitor b/c noncovalent bonds = not strong

Question 39

what are noncompetitive inhibitors?

Answer 39

do not directly compete with the substrate to bind to the enzyme at the active site - instead they impede enzymatic reactions by binding to another part of the enzyme which causes the molecule to change its shape in such a way that the active site becomes less effective at catalyzing the conversion of the substrate to product

nonequivalent bonds - not strong

Question 40

what is allosteric regulation?

Answer 40

the term used to describe any case in which a protein’s function at one site is effected by the binding of a regulatory molecule to a separate site

may result in either inhibition of or stimulation

it’s saying we have a lot of the product to inhibit production, no reason for cell to keep breaking down glucose

Question 41

what is feedback inhibition?

Answer 41

a pathway’s end product acts as an inhibitor of an enzymatic step earlier in the pathway

Question 42

localization of enzymes within the cell

Answer 42

the cell is compartmentalized and cellular structures help bring order to metabolic pathways

teams of enzymes for several steps of a metabolic pathway are assembled into a multi-enzyme complex (some are fixed in location and act as structural components)