Metabolism

Question 1

What is metabolism?

Answer 1

All the chemical reactions in an organism, organized in pathways.

Question 2

What are anabolic pathways and how do they function?

Answer 2

Anabolic pathways are biosynthetic processes: they build complex molecules and use energy.

Question 3

Examples of anabolic pathways

Answer 3

Synthesis of sugar from CO2, synthesis of proteins from amino acids.

Question 4

What do anabolic pathways use as energy?

Answer 4

ATP and other high energy molecules like NADH

Question 4

What are catabolic pathways and how do they function?

Answer 4

They are degrative processes: they break down complex molecules by breaking bonds and forming new ones, releasing energy.

Question 5

What type of energy can catabolic pathways form?

Answer 5

ATP

Question 6

Describe the basic steps of a biological pathway. (3)

Answer 6

1. Pathway starts at a substrate 2. Each step/reaction is catalyzed by an enzyme, which are all regulated to balance metabolic supply and demand. 3. Various reactions occur and result in a final product.

Question 7

Are organisms energy transformers? Why/why not?

Answer 7

Yes, because cells change energy from one form to another.

Question 8

What is the first law of thermodynamics?

Answer 8

The conservation of energy; energy is constant.

Question 9

What is the second law of thermodynamics?

Answer 9

Every energy transformation increases the entropy of the universe.

Question 10

What happens to the reaction and energy when entropy is increased?

Answer 10

It is a spontaneous reaction and is energetically favourable.

Question 11

What happens to the reaction and energy when entropy is decreased?

Answer 11

It is a non spontaneous reaction and only occurs when energy is supplied.

Question 12

What is the equation for Gibbs free energy?

Answer 12

deltaG = deltaH - T(deltaS) where dG = gibbs, dH = entropy, T = temp, dS = entropy

Question 13

What happens if dG is negative?

Answer 13

That means that is is an exergonic reaction and a net release a free energy (energy is lost from initial to final). The process is spontaneous and the final state is more stable (less ‘free’ energy).

Question 14

What happens if dG is positive?

Answer 14

It is an endergonic reaction and absorbs free energy, so it is a non-spontaneous process.

Question 15

What are some key characteristics of open systems?

Answer 15

There is a constant flow of materials in and out, it is never at equilibrium and never stops working, so dG is less than 0.

Question 16

Why do products from biological pathways never accumulate?

Answer 16

Because they become reactants in the next step of the pathway.

Question 17

Cells couple energy by using exergonic processes. What does this drive, and what type of energy does it use?

Answer 17

This drives endergonic processes using ATP.

Question 18

What is an exergonic reaction?

Answer 18

A net release of free energy, and it is a spontaneous process where dG < 0.

Question 19

What is an endergonic reaction?

Answer 19

An absorption of free energy; it is non-spontaneous process where dG > 0.

Question 20

What is ATP made of?

Answer 20

ATP is made of a sugar ribose with an nitrogenous base and a three phosphate chain with 3- charges that are close together.

Question 21

There is a triphosphate group attached to ATP with 3- charges. What does this act like, according to physics?

Answer 21

A compressed spring.

Question 22

What type of reaction regenerates ATP?

Answer 22

Energy from exergonic reactions (releases energy)

Question 23

What energy is used to perform work in the cell?

Answer 23

ATP.

Question 24

What is an example of chemical work?

Answer 24

When ATP is used to convert H2O to ADP, a phosphorylated intermediate and energy. ATP + H2O --> ADP + P(i) + energy

Question 25

What is an example of transport work?

Answer 25

ATP is used in active transport to move solutes through the lipid bilayer

Question 26

What is an example of mechanical work?

Answer 26

ATP is used to power motor proteins along the cytoskeletal track

Question 27

Enzymes are catalysts. What does this do for the reaction?

Answer 27

Catalysts speed up reactions without being consumed.

Question 28

How do enzymes speed up reactions?

Answer 28

As catalysts, they can lower the activation energy of a reaction.

Question 29

Can a reaction turn from exo to endergonic (and vice versa)

Answer 29

No, the activation energy can lower, but the dG cannot. It is unaffected by the enzyme.

Question 30

What are the four ways enzymes can lower the activation energy of a reaction?

Answer 30

1. Orientation of enzymes, 2. Stretch substrate & break bonds, 3. Bond to the active site, changing polarity, 4. Amino acids of enzymes can participate in reactions.

Question 31

What is activation energy?

Answer 31

Activation energy is a barrier in a reaction, energy needs to reach a transition state to overcome it.

Question 31

Heat is a form of energy (thermal). Why is adding heat to cells not favourable for the reaction?

Answer 31

Adding heat can cause proteins to denature and it is not controlled so multiple reactions can take place at once.

Question 32

Describe the process of an enzyme binding to a substrate (basic catalytic cycle).

Answer 32

Enzyme + substrate <=> enzyme - substrate complex <=> enzyme + product(s)

Question 33

Can enzymes bind to any substrate? Why/why not?

Answer 33

No, enzymes only recognize their own specific substrate. For instant, maltose cannot bind with sucrase. Only sucrose can bind with sucrase. It depends on the shape and induced fit.

Question 34

Describe the COMPLETE catalytic cycle step by step. (6)

Answer 34

1) Substrates enter active site forming enzyme-substrate complex; enzyme changes shape to fit substrate (induced fit). 2) Substrate held in active site by weak interactions (H-bonds, ionic bonds). 3) Active site lowers activation energy and reaction speeds up. 4) Substrates converted to products - can be more than one product. 5) Products are released. 6) Active site is available for 2 new substrate molecules.

Question 35

What is the active site and its function?

Answer 35

Where the substrates bonds to the enzyme, forming a enzyme - substrate complex. It lowers the activation energy and holds the substrates in place via weak bonding interactions.

Question 36

What are two things that enzyme activity depend on?

Answer 36

Temperature and pH

Question 37

What happens to the rate of reaction at the optimal temperatures and pHs?

Answer 37

The rate of reaction increases.

Question 38

What are the three things that regulate enzyme activities?

Answer 38

1) Gene expression, 2) Intracellular location of enzymes, 3) Stabilizing active/inactive forms

Question 39

How does gene expression regulate enzyme activities?

Answer 39

They express genes as needed - increasing/decreasing amount of enzyme protein produced

Question 40

How does the specific intracellular location of enzymes regulate enzyme activities?

Answer 40

Enzymes that work together are grouped in proteins complexes with specific pathways

Question 41

What are the three types of stabilizing enzymes in their active and inactive forms? (How stabilizing regulates enzyme activities)

Answer 41

1) Allosteric regulation, 2) cooperativity, 3) feedback inhibition

Question 42

Enzymes can oscillate between inactive and active forms. How does allosteric regulation stabilize this so the enzymes stay in either active or inactive?

Answer 42

Allosteric regulation binds activators and inhibitors to active and inactive enzymes respectively to stabilize them.

Question 43

Why is binding regulators (activators, inhibitors) important?

Answer 43

Active vs inactive has an impact on protein function.

Question 44

What are enzymes made of?

Answer 44

Enzymes are proteins made of polypeptide chains which are made up of amino acids.

Question 45

How does the binding of one inhibitor/activator affect the other sites?

Answer 45

The shape of the allosteric enzyme changes for all subunits when one activator/inhibitor is bonded.

Question 46

An inhibitor stabilizes the inactive form of an allosteric enzyme. What does this do to the active site?

Answer 46

It makes it so that the substrate cannot bond because the active site is no longer functional.

Question 47

What does the activator stabilizes on an allosteric enzyme?

Answer 47

Stabilizes active form.

Question 48

What are regulatory sites?

Answer 48

Places where activators and inhibitors can bind (but not the only place).

Question 49

Other than a regulatory site, enzyme inhibitors can bond to active sites. Why is this something that they do?

Answer 49

Inhibitors bond to the active site in place of a substrate to regulate cellular metabolism - competitive inhibition.

Question 50

What is the irreversible cause of inhibitors binding to the active site in place of a substrate?

Answer 50

Strong covalent bonds

Question 51

What is the reversible cause of inhibitors binding to the active site in place of a substrate?

Answer 51

Weak bonds - h-bonds/ionic bonds.

Question 52

What is competitive inhibition?

Answer 52

Inhibitors bind to active site to regulate cellular metabolism and prevent substrate from binding, "competing" with substrate.

Question 53

What is noncompetitive inhibition?

Answer 53

Inhibitors do not bind to active site and change shape of the enzyme instead which leads to less activity but does not block substrate from bonding.

Question 54

What is cooperativity and how does it regulate active/inactive forms in the process of regulating enzyme activities?

Answer 54

One substrate changes all the subunits once bound to active site, leading to an increase in catalytic activity in all sites and amplifies the response.

Question 55

What is feedback inhibition pathway and how does it regulate active/inactive forms in the process of regulating enzyme activities?

Answer 55

A substrate binds to an enzyme, and turns through a whole lotta intermediates and enzymes until it reaches an end product. This end product binds to the allosteric site, so the active site of the original enzyme is no longer able to act as a catalyst. After the product is used up by the enzyme, then the active site becomes available again and the pathway continues.