Module 1 Unit 2

Question 1

What is metabolism?

Answer 1

The totality of an organism’s chemical reactions

Question 2

What is a metabolic pathway?

Answer 2

• • involve the stepwise modification of a reactant/s into a product
• • Each step of the pathway is catalyzed by a specific enzyme

Question 3

What are catabolic pathways?

Answer 3

• • Catabolic pathways release energy by breaking down complex molecules into simpler compounds
• • ex: cellular respiration

Question 4

What are anabolic pathways?

Answer 4

• • synthesize more complex organic molecules using the energy derived from catabolic pathways.y to build complicated molecules from simpler ones; they are sometimes called biosynthetic pathways
• • ex. photosynthesis, synthesis of proteins from amino acids

Question 5

What is energy?

Answer 5

• • the capacity to cause change (the ability to re-arrange a collection of matter)
• • measured in calories (Intake needs to balance expenditure)

Question 6

What is kinetic energy?

Answer 6

• • the relative motion of objects

- - Moving objects can perform work by imparting motion to other matter

Question 7

What is thermal energy and heat?

Answer 7

• • Thermal energy is kinetic energy associated with the random movement of atoms or molecules
• • thermal energy transferred from one object to another is called heat

Question 8

What is potential energy?

Answer 8

• • energy that matter possesses because of its location or structure (energy that is not kinetic, but static)
• -

Question 9

What is chemical energy?

Answer 9

• • the potential energy available for release in a chemical reaction
• • catabolic pathways release energy by breaking down complex molecules

Question 10

What is metabolic rate and what is it affected by?

Answer 10

-- Metabolic rate is a measure of energy use
(Regulated by enzymes)
-- Affected by
> Age
> Genetics
> Sex
> Exercise habits
> Nutritional status

Question 11

What is thermodynamics?

Answer 11

• • The study of the energy transformations that occur in a collection of matter
• • Scientists use the word system to denote the matter under study, and they refer to the rest of the universe (everything outside the system) as the surroundings (the universe is equivalent to the “system” plus its “surroundings”)
• • A completely isolated system is unable to exchange either energy or matter with its surroundings (ex. thermos bottle)
• • In an open system, energy and matter can be transferred between the system and its surroundings (ex. organisms are open systems because they absorb light energy or chemical energy from the environment and then release heat and metabolic waste products to the environment)

Question 12

What is the first law of thermodynamics?

Answer 12

• • energy in the universe is constant; energy can be transferred and transformed, but it cannot be created or destroyed
• • aka principle of conservation of energy
• • ex. plants transforms sunlight to chemical energy, not create it

Question 13

What is the second law of thermodynamics?

Answer 13

• • energy conversions increase the disorder of the universe (entropy) and also generates local increases in order (islands in the entropy)
• • organisms can’t simply recycle their energy over and over again because during every energy transfer or transformation, some energy becomes unavailable to do work (thermal energy released as heat); A consequence of the loss of usable energy as heat to the surroundings is that each energy transfer or transformation makes the universe more disordered
• • disorder is how dispersed the energy is in a system, and how many different energy levels are present
• • Scientists use a quantity called entropy as a measure of disorder, or randomness (The more randomly arranged a collection of matter is, the greater its entropy)

Question 14

What is a spontaneous process?

Answer 14

– if a given process, by itself, leads to an increase in entropy, that process can proceed without requiring an input of energy (energetically favourable)
– releases energy when proceeding in the forward direction
– Starch is more complex, ordered arrangement of
atoms than a simple sugar (requires energy to happen) -nonspontaneous
– Breakdown favoured by 2nd law (less ordered, but does not require energy, instead releases it) -spontaneous since the release of heat increases entropy

Question 15

What is a non-spontaneous process?

Answer 15

• • A process that, on its own, leads to a decrease in entropy is said to be non-spontaneous: It will happen only if energy is supplied
• -For instance, we know that water flows downhill spontaneously but moves uphill only with an input of energy (such as when a machine pumps the water against gravity). When water falls downhilll, some energy is inevitably lost as heat, increasing entropy in the surroundings, so usage of energy ensures that a nonspontaneous process also leads to an increase in the entropy of the universe as a whole

Question 16

What is free energy?

Answer 16

– the portion of a system’s energy that can perform work (the difference in potential energy between the products and the reactants) when temperature and pressure are uniform throughout the system, as in a living cells
– The change in free energy, ΔG, of a reaction tells us whether or not the reaction occurs spontaneously (value will depend on conditions such as pH, temperature, and concentrations of reactants and products)
ΔG = ΔH - TΔS
– ΔH symbolizes the change in the system’s enthalpy (in biological systems, equivalent to total energy)
– ΔS is the change in the system’s entropy; and T is the absolute temperature in Kelvin (K) units (K=°C+273).
– negative ΔG are spontaneous; For ΔG to be negative, either ΔH, must be negative (the system gives up enthalpy and H decreases) or TΔS must be positive (the system gives up order and S increases), or both
– When ΔH and TΔS are tallied, ΔG has a negative value (ΔG<0) for all spontaneous processes
– In other words, every spontaneous process decreases the system’s free energy (because it releases energy in a form that cannot do work)

Question 17

What are exergonic reactions?

Answer 17

– release energy, and thus have a negative
ΔG, and occur spontaneously
– The greater the decrease in free energy, the greater the amount of work that can be done
– These reactions release the energy in covalent bonds of the reactants -however, breaking of bonds does not release energy, it requires it; the phrase “energy stored in bonds” is shorthand for the potential energy that can be released when new bonds are formed after the original bonds break, as long as the products are of lower free energy than the reactants
– For each mole (180g) of glucose broken down by respiration, 2870 kJ of energy are made available for work; Because energy must be conserved, the chemical products of respiration store 2870 kJ less free energy per mole than the reactants (free energy released)

Question 18

What are endergonic reactions?

Answer 18

• • one that absorbs free energy from its surroundings
• • Because this kind of reaction essentially stores free energy in molecules (G increases), ΔG is positive
• • Such reactions are nonspontaneous, and the magnitude of ΔG is the quantity of energy required to drive the reaction
• • begin with reactant molecules that contain relatively little potential energy and end with products that contain more potential chemical energy

Question 19

What is energy coupling?

Answer 19

• • A key feature in the way cells manage their energy resources to do work (chemical, transport, mechanical) is energy coupling -the use of energy released from exergonic reactions to drive essential endergonic reactions
• • ATP is responsible for mediating most energy coupling in cells

Question 20

What is ATP?

Answer 20

• • adenosine triphosphate
• • contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups (the triphosphate group) bonded to it

Question 21

How is ATP broken down?

Answer 21

• • Hydrolysis of ATP releases energy by transferring its third phosphate from ATP to some other molecule in a process called phosphorylation, and then becomes adenosine diphosphate, or ADP
• • Most cellular work depends on ATP energizing molecules by phosphorylating them; the recipient molecule with the phosphate group covalently bonded to it is then called a phosphorylated intermediate
• • ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind another molecule
• • all three phosphate groups are negatively charged. These like charges are crowded together and their mutual repulsion contributes to the instability of this region of the ATP molecule (The triphosphate tail of ATP is the chemical equivalent of a compressed spring)
• • the reactants (ATP and water) themselves have high energy relative to the energy of the products (ADP and Pi); The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

Question 22

How is ATP regenerated?

Answer 22

• • regenerated by the addition of phosphate to ADP
• • The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell
• • ATP cycle: energy-yielding (exergonic) processes to the energy-consuming (endergonic) ones; energy released in an exergonic reaction, such as the breakdown of glucose, is used in an endergonic reaction to generate ATP
• • requires free energy to make it (not spontaneous)

Question 23

What is activation energy?

Answer 23

• • the energy required to contort the reactant molecules so the bonds can break
• • think of activation energy as the amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the “downhill” part of the reaction can begin
• • Activation energy is often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings; this accelerates the reactant molecules, so they collide more often and more forcefully and It also agitates the atoms within the molecules, making the breakage of bonds more likely
• • When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition known as the transition state; As the atoms then settle into their new, more stable bonding arrangements, energy is released to the surroundings
• • For some reactions, EA is modest enough that even at room temperature there is sufficient thermal energy for many of the reactant molecules to reach the transition state in a short time however In most cases, EA, is so high and the transition state is reached so rarely that the reaction will hardly proceed at all

Question 24

What is an enzyme?

Answer 24

• • macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction
• • lowering the EA needed for a reaction to begin enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures
• • Do not change ΔG
• • are usually proteins, although some RNA molecules can function as enzymes.
• • Enzymes can lower the EA of reactions, but they cannot change the equilibrium point because they cannot change the net energy output.

Question 25

How do enzymes bind to reactants?

Answer 25

– The reactant an enzyme acts on is referred to as the enzyme’s substrate
enzyme + substrate enzyme-substrate complex enzyme + products
– The reaction catalyzed by each enzyme is very specific
– Only a restricted region of the enzyme molecule actually binds to the substrate called the active site which is typically a pocket or groove on the surface of the enzyme where catalysis occurs
– The specificity of an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate as well as a complementary match between the charged amino acids found in the active site and charged regions of the substrate
– As the substrate enters the active site, the enzyme changes shape slightly due to interactions (H-bonds, ionic bonds) between the substrate’s chemical groups and chemical groups on the side chains of the amino acids that form the active site -makes the active site fit even more snugly around the substrate resulting in an induced fit which enhances ability to catalyze the reaction

Question 26

How do enzymes lower activation energy?

Answer 26

> > As the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition form, stressing and bending critical chemical bonds that must be broken during the reaction; Because EA is proportional to the difficulty of breaking the bonds, distorting the substrate helps it approach the transition state and thus reduces the amount of free energy that must be absorbed to achieve that state
The active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be; For example, if the active site has amino acids with acidic R groups, the active site may be a pocket of low pH in an otherwise neutral cell and the acidic amino acid may facilitate H+ transfer to the substrate as a key step in catalyzing the reaction
Amino acids in the active site directly participate in the chemical reaction (sometimes involves brief covalent bonding between the substrate and the side chain of an amino acid)

Question 27

What determines the rate at which a particular amount of enzyme converts substrate?

Answer 27

• • partly a function of the initial concentration of the substrate; The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules
• • At some point, the concentration of substrate will be high enough that all enzyme molecules have their active sites engaged; the enzyme is said to be saturated, and the rate of the reaction is determined by the speed at which the active site converts substrate
• • When an enzyme population is saturated, the only way to increase the rate of product formation is to add more enzyme

Question 28

How does temperature/pH affect enzyme activity?

Answer 28

> > Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly; Above that temperature, however, the speed of the enzymatic reaction drops sharply because it disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures

• • Without denaturing the enzyme, this optimal temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to the products
• • he optimal pH values for most enzymes fall in the range of pH 6–8

Question 29

What are cofactors/coenzymes?

Answer 29

• • Many enzymes require nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins
• • these cofactors may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate
• • If the cofactor is an organic molecule, it is referred to, more specifically, as a coenzyme (vitamins act as coenzymes are be used to make coenzymes)
• • Both are nonprotein enzyme helpers; but most cofactors are metal ions, and coenzymes are organic molecules that are a specific type of cofactor.

Question 30

What are enzyme inhibitors?

Answer 30

• • chemicals selectively inhibit the action of specific enzymes
• • Sometimes, the inhibitor attaches to the enzyme by covalent bonds, in which case the inhibition is usually irreversible; Many enzyme inhibitors, however, bind to the enzyme by weak interactions, and when this occurs the inhibition is reversible

Question 31

What are competitive inhibitors?

Answer 31

• • reversible inhibitors that resemble the normal substrate molecule and compete for admission into the active site
• • reduce the productivity of enzymes by blocking substrates from entering active sites
• • This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites.

Question 32

What are noncompetitive inhibitors?

Answer 32

• • 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. This interaction causes the enzyme molecule to change its shape in such a way that the active site becomes less effective at catalyzing the conversion of substrate to product.
• • ex. Sarin (binds covalently to the R group on the amino acid serine, which is found in the active site of acetylcholinesterase, an enzyme important in the nervous system)

Question 33

What is allosteric regulation?

Answer 33

• • the term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site; may result in either inhibition or stimulation of an enzyme’s activity
• • most enzymes oscillates between two different shapes, one catalytically active and the other inactive; The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme
• • ATP binds to several catabolic enzymes allosterically, lowering their affinity for substrate and thus inhibiting their activity. ADP, however, functions as an activator of the same enzymes
• • The subunits of an allosteric enzyme fit together in such a way that a shape change in one subunit is transmitted to all others
• • cooperativity: a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites ex. hemoglobin -the binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining binding site

Question 34

What is feedback inhibition?

Answer 34

– the product may act as an inhibitor of one of the enzymes in the pathway that produced it