chapter 8

Word Roots:

cata- = down

ana- = up

kinet- = movement

therm- = heat

ex- = out

endo- = within

allo- = different

AIM: How is matter and energy transformed?

Chapter 8 – An Introduction to Metabolism

Metabolism• The sum of an organism’s chemical reactions

• Molecules being altered in a series of steps resulting in a product

Enzyme 1 Enzyme 2 Enzyme 3

Chemical Reactions

A DCB

•Catabolism

•Anabolism



Energy•Kinetic

•Potential

•Thermal

•Chemical

ffden-2.phys.uaf.edu

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Thermodynamics – the study of the energy transformations that occur in a collection of matter.

The laws that govern energy

The 1st law of thermodynamics-Energy cannot be created or destroyed. It can only change forms.-Conservation of EnergyWhat does that tell you about the total energy in the

universe?It is always the same.



The 2nd law of thermodynamics- With EVERY transfer of energy a bit is leaked to the surroundings (you can never transfer 100% of the energy) and in turn the universe ALWAYS becomes more disordered over time.

The question is, what does “disordered” mean?

Physical disintegration of a systems organized structure

Chapter 8 - An Introduction to Metabolism

AIM: Explain “energy” and how it behaves.AIM: How is matter and energy transformed?


Disorder

Fill it with gasoline and start using it. The chemical PE of the gas will be transferred to the engine as it gets burned causing the engine to move and rotate, which will transfer KE to the wheels. As you drive you are transferring KE to the air and the road as friction. All along, what is happening to your car?


AIM: Explain “energy” and how it behaves.

- DNA will mutate as we are hit with UV light (energy transfer).



Disorder


AIM: Explain “energy” and how it behaves.

DisorderCheetah converting chemical energy stored in food to kinetic energy in muscle contractions to run, disorder added to surroundings in the form of heat and by-products of metabolism



Figure 8.3

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

(b)

Heat co2

H2O+



The 2nd law of thermodynamics

- With EVERY transfer or transformation increases the entropy of the universe

Entropy

-The terms we use to measure disorder. -The greater the entropy, the greater the disorder (the further away we are from the desired state).

Figure 8.3

First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).

(a)

Chemicalenergy

Figure 8.3

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

(b)

Heat co2

H2O+



Summary



How are we [life]able to be so ordered?

•Organisms create order using energy.

•Energy flows into the ecosystem as light (via anabolism) and leaves as heat (via catabolism)

•Disorder of the universe increases.

Now let’s talk about life (think of humans). What do we define as ordered?

AIM: Describe chemical reactions in terms of “energy”.


Endergonic Reactions• Reactions that require energy to happen (need something to accelerate them)

ADP + Pi ATP The synthesis of ATP

6CO2 + 6H2O C6H12O6 + 6O2 photosynthesis

-Absorbs free energy from its surroundings

-Stores free energy in its molecules

Fig 5.3A


AIM: Describe chemical reactions in terms of “energy”

endergonic



Chapter 8 - An Introduction to MetabolismAIM: Describe chemical reactions in terms of “energy”

Energonic reactions are said to be:

NOT spontaneous (they do not spontaneously happen [occur by themselves] – they NEED an input of

energy)




Exergonic Reactions• Reactions that transfers energy away (gives off energy)

ATP ADP + Pi Hydrolysis of ATP

C6H12O6 + 6O2 6CO2 + 6H2O cellular respiration

-Both of these reactions will occur without the input of outside energy (other than activation energy)


Fig 5.3B


exergonic




Exergonic reactions are said to be:

Spontaneous (they do spontaneously happen [occur by themselves] – no energy input required)





How can we describe the energy in substances that is available to accelerate matter (do work)?

This available energy is called FREE ENERGY(energy that if free – meaning available – to accelerate matter)

Free energy = Gibbs Free Energy = G


Let’s go back now and look at endergonic and exergonic reactions with Free Energy (G) in mind…



Endergonic Reactions


Reactions that require energy to happen (need something to accelerate them):

ADP + Pi ATP The synthesis of ATP

ΔG = +7.3 kcal/mol

ΔG = the change in (Δ) free energy (G) as you go from reactants to products

Therefore:1. The product (ATP) has more AVAILABLE energy than the reactants (ADP and P). Every mole of ATP has 7.3 kcal more available energy than a mole of ADP and P.

2. A +ΔG tells you the reactions is endergonic and therefore NOT SPONTANEOUS



Endergonic Reactions


How about photosynthesis? What do you know for sure about ΔG?

6CO2 + 6H2O C6H12O6 + 6O2

ΔG = +686 kcal/mol

Therefore, every mole of Glucose has 686 kcal more energy than a mole of water and CO2 (oxygen doesn’t have any free energy to speak of as the electrons are held quite tightly).

You know that photosynthesis doesn’t happen without an input of energy to get those electrons to move from water to CO2 and therefore if you input energy the products should have more available energy than the reactants…ΔG will be positive.





Reverse an Endergonic Rx What do you get?

ADP + Pi ATP(endergonic)

ATP ADP + Pi(exergonic)

reverse it




AIM: Describe chemical reactions in terms of “energy”What about if we reverse these reactions in terms of free energy?

ATP ADP + Pi Hydrolysis of ATP

ADP + Pi ATP Dehydration synthesis of ATP

ΔG = +7.3 kcal/mol

ΔG = -7.3 kcal/mol

You simply reverse the sign of ΔG since the products (ADP and P) will now have less available energy than the reactant (ATP).

A -ΔG tells us that energy is lost and this reaction is exergonic and therefore SPONTANEOUS.




Exergonic Endergonic

Spontaneous?

ΔG (+ or -)

Available Energy of products compared to reactants

Free Energy change (ΔG)

YES

NoNegative (-)

Positive (+)Products have less

energyProducts have more energy





What is the sign for ΔG in each case?

ΔG is negative since both involve the release of energy and are spontaneous

How is free energy change ΔG calculated?

ΔG = ΔH – TΔS

Free Energy – the portion of an organism’s energy that can do work.

Enthalpy – a measure of heat energy.

Temperature – in Kelvin (formula assumes constant temperature)

Entropy – the measure of disorder.





ΔG = ΔH - TΔS

ΔH = change in enthalpy or change in total internal energy over the course of the reaction.

1. You can think of it like “heat”a. A negative ΔH (-ΔH) means that “heat energy” is lost by the reactants

b. A positive ΔH (+ΔH) means that “heat energy” is gained by the reactants

- Would this promote a spontaneous reactions (-ΔG)?Yes, energy being released

- Would this promote a spontaneous reactions (-ΔG)?No, requires energy

One must focus calculate two components…ΔH and ΔS, and know the temperature (T):



Fig 8.5



ΔG = ΔH - TΔS

ΔS = change in entropy (measure of disorder) over the course of the reaction.

b. A negative ΔS (-ΔS) means that disorder is decreased or the products are more ordered

a. A positive ΔS (+ΔS) means that disorder is increased or the products are more disordered

- Would this promote a spontaneous reactions?No

- Would this promote a spontaneous reactions?Yes



•When the value of ΔG is negative then the system has lost free energy.

•This is favored by cells

•In order for ΔG to be negative the system must either:

•give up enthalpy – lose heat – (H must decrease)

•give up order (TΔS must increase – disorder is favored)

•Both (H must decrease and S must increase)

•Losing Free Energy is favored by the universe

• - ΔG is “spontaneous”

• +ΔG is “non-spontaneous”



Free energy = measure of system stability•High G – unstable system

•Low G – stable system

•Change in G (ΔG) can drive work.

•Max stability – equilibrium – G is lowest

•Change from equilibrium has a +ΔG and is not favored in closed systems

•However, living things are open systems and generally do not reach equilibrium

•Systems naturally favor moving high ΔG to lower ΔG



Equilibrium & Metabolism•Reactions in closed systems usually reach equilibrium

•Reactions in open systems usually do not

•Cells harness these ‘downhill’ reactions to do work.

•“Downhill” = exergonic

•A cell that has reached metabolic equilibrium is DEAD





Cells can perform 3 kinds of work:

•Mechanical: ex: cilia beating

•Transport: ex: pumping substances

•Chemical: ex: synthesis

How does one get anendergonic process to occur?

If something needs to lose energy, what kind of reaction will that be?An exergonic reaction.

Therefore, an exergonic reaction will be required to make and endergonic reaction proceed.

•Energy coupling: energy released by an exergonic reaction in a cell will be used to power a “coupled” endergonic one



Energy Coupling

This is called:

• ATP - Adenosine Triphosphate

•5-carbon sugar

•Nitrogenous base: adenine

•3 identical functional groups

Mutual repulsion creates high - ΔG



ATP + H2O ADP + Pi

•ΔG = -7.3 kcal/mol

•‘High’ energy bonds result from interactions between phosphate groups – compressed spring.

•Creating ADP is an exergonic reaction: lowers free energy





•Hydrolysis of ATP decreases ΔG and creates heat.

•Enzymes couple ATP hydrolysis (an exergonic reaction) with endergonic reactions.

•Inorganic phosphate is attached to another molecule

•Creates an intermediate – more reactive

•Exergonic reactions release the energy that power endergonic ones

•Catabolism powers anabolism





(Cell respiration)

Protein synthesis,DNA synthesis,RNA synthesis,Active transport, etc

ATP Regeneration•ADP + Pi ATP + H2O

•Energy comes from catabolism

Interesting facts:

•Muscle cells regenerate 10 million molecules of ATP in 1 second.

•Humans would use their body’s weight in ATP every day if it were not recyclable.





1. Cell Respiration (make fuel - transfer the energy)

2. Biosynthesis

3. Storage

What is the fate of the food you eat?

(exergonic) (endergonic)




AIM: Describe the structure/function of Enzymes.

1. Exergonic reactions like hydrolysis of polymers into monomers are spontaneous, which means they will happen all by themselves without an input of energy. The problem is that they typically happen far too_______ to sustain life.

SLOWLY

PROBLEM:

It would take years for the food you eat to hydrolyze down to monomers without any assistance and it might hydrolyze improperly resulting in molecules you cannot use…



2. The desired chemical reaction may not be the reaction that occurs…



What type of molecule is making all of these anabolic (endergonic) and catabolic (exergonic) reaction happen at a reasonable, life sustaining rate?





Enzymes

2. Speed up SPECIFIC reactions

Enzymes orient the substrates properly for the proper reaction to occur in the proper amount of time…

1. Biological protein catalysts (remember enzymes are proteins)

The reaction would have happened by itself, it just takes too long

AIM: Describe the structure and function of enzymes.




What does this figure depict?

This barrier is a symbol of the activation energy needed. The beans need a bit of starter energy (activation energy) to get them over the barrier before they can fall…

How do enzymes speed up reactions?



Enzymes lower the activation energy

Enzymes catalyze reactions by:



•Providing proper orientation

•Stressing bonds and creating transition states

•Providing favorable microenvironments

•Participating in reaction directly

•Macromolecules are rich in free energy, so decomposition is naturally favored

•EA very high for natural decomposition, enzymes lower EA, allowing reactions to progress more quickly



Substrate Specificity•Enzyme names end in –ase and usually start with some form of the substrate name.

•Substrate: reactant the enzyme acts on



Enzyme examples:-Suscrase-Protease-Lipase-Polymerase

Shape Determines Function•Enzyme + Substrate = Enzyme-substrate Complex

•Active site: enzyme location where substrate can bind

•Uses H-bonds (and ionic occasionally)

•Determined by R-group interactions, such as disulfide bridging in amino acid chain



LOCK and KEY MODEL

Model for how enzymes bind their substrates…

With more and more observations we now that this model does NOT fit the data!

Then what do we observe?





Active site

According to the induced fit model of enzyme catalysis, the substrate initially does not fit perfectly and therefore binds weakly to the active site, but induces or causes a conformational change in the enzyme resulting in a better fit and in turn tighter binding, like clasping your hands.

Induced Fit Model


AIM: Describe the structure/function of Enzymes.AIM: Describe the structure and function of enzymes.


1. Substrate enters active site – induced fit.

2. Substrate held by weak bonds

3. Substrates converted into products.

4. Products are released.

5. Enzyme available to assist next reaction.



Enzymatic Reaction Rates



In what pH and temperature do enzymes work best?

Rate of Enzyme Activity – pH



Rate of Enzyme Activity – Temperature





How does [enzyme]affect Rx rate ?

[enzyme] = enzyme concentration





Imagine that the students in the classroom are enzymes (each student is one enzyme). The reaction being catalyzed is eating a slice of pizza. Assuming that the room is totally filled with pizza (saturated with pizza), what would happen to the rate at which pizza is being eaten if we add more students?

It should increase since more students would mean more pizza is being eaten. Therefore, the more enzyme, the greater the reaction rate assuming there is plenty of substrate – see graph on next slide.





As enzyme concentration increases, reaction rate increases





How does [substrate]affect Rx rate ?

Use the same analogy as before – student is enzyme, pizza eating is reaction.





Similar analogy as before. This time there are 20 students and each student has a maximum rate of eating 1 slice of pizza every 2 minutes. What would the rate be if there was no pizza? As we add pizza to the room, what should happen to the rate? Will the rate keep going up as we saw before?

-If there were no pizza, the rate would be zero. Nothing can be eaten.

-As we add pizza, the rate should start to rise.

-The rate will max out at high substrate concentrations because the students can only eat so fast. I can keep adding more and more pizza, but they are already working as fast as they can, they are saturated. The pizza would just pile up all around them. The rate therefore will max out – see graph on next slide.



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Cofactors: non-protein chemical bound to a protein and required for it to function properly.

ANALOGY: a hammer is a tool used by a construction worker to do their job, while a cofactor is a tool used by a protein to do its job. Cofactor = tool.

1. Inorganic

2. Organic = coenzyme

Two types of cofactors:

Ex. Zn, Mg, Mn, Fe (minerals)

Ex. Vitamins



What protein is this?

This is hemoglobin.

What is the function of this protein?

To carry molecular oxygen (O2) from the lungs to all other cells in the body.

Where is it found?

Inside red blood cells (RBCs)





Amino acids cannot bind to molecular oxygen (O2). How is this accomplished?It must have a cofactor

What cofactor does it have?





Fe

Molecular oxygen

Cofactors 4 Heme cofactors

The iron atom in the center of each heme (orange) can bind a single O2 molecule (red).

AIM: How are enzymes regulated (controlled)?


Enzymes need to be regulated-Enzymes are not always on. -Some have “on/off switches”.

Why is this important? -The cell needs to maintain specific levels of substrates and products (homeostasis).

-We should not waste resources



Inhibiting (turning off) enzymes(This is NOT denaturing)



Competitive inhibitors: compete against the substrate for the active site.



Noncompetitive inhibitors do not compete.

They will bind another part of the enzyme, cause a conformational change in the active site, and the substrate will no longer fit.

Ex: Toxins, Poisons, Antibiotics

•Can inhibit or activate an enzyme

•Ex: ATP can be an inhibitor and ADP can be an activator



Allosteric regulation of Enzymes

Allo – “other” Steric – “relating to the spatial arrangement of atoms in a molecule

- Occurs when a molecule binds to a site of the protein “other” than the active site causing a conformational (steric) change resulting in a functional change.



Allosteric regulation of Enzymes

-Can inhibit or activate an enzyme

-Example: ATP can be an inhibitor and ADP can be an activator

ATP binds allosterically to several catabolic enzymes, inhibiting their activity when there is an accumulation of ATP

What will happen when ATP is being used faster than it is being produced?

Feedback Inhibition

•Pathway is switched off by noncompetitve/competitive inhibition of an enzyme early in a pathway with a product of the pathway



1 2

3

4 5 6

In this example, a series of enzymes will convert substrate A into end product G using six reactions (six enzymes). Remember, this is like a factory line where each worker (enzyme) makes a small change to the substrate to get the end product.

The concentration of G is low now, so what will these enzymes do?

Using inhibition to maintain specific solute concentrations:

1 2

3

4 5 6

TOO MANY!!!!!!STOOOOPPPP!


1 2

3

4 5 6

When the concentration of the product “G” gets too high, it will bind to enzyme 3 and shut it off. “G” will no longer be made. It shut itself off…negative feedback. What will happen when levels of “G” decrease?

“G” will fall off enzyme 3 and production will resume.

What type of inhibitor is “G”?

It is noncompetitive!


1 2

3

4 5 6

This method of inhibition where the product shuts off its own production has a name…

NEGATIVE FEEDBACK


Negative Feedback



When the output of a system goes back (feeds back) and inhibits or turns down (in the negative direction) its own production when it gets too high thereby maintaining a specific concentration.



Positive Feedback When the output of a system goes back (feeds back) and further enhances its own production (in the positive direction) leading to more output and in turn more enhancement and even more output, etc…



Opposite of negative feedback.

Such a condition is considered unstable…



Positive Feedback


Examples:

2. Child Birth contractions – the hormone oxytocin stimulates contraction of the uterus. This will cause the baby to press up against the uterus, which causes more oxytocin release, more contractions, more pushing of the baby.

1. Hypothetical – if your house thermostat worked based on positive feedback, the output (heat) would further activate the thermostat, which would instruct the release of more heat, which would even further activate thermostat, etc…





We will purposely inhibit enzymes…why?

This is how you treat many diseases. You can kill bacteria and viruses is you stop their workers from working by inhibiting them.

If your own proteins are making too much product like too much cholesterol, we can make inhibitors to stop them from working, etc… By controlling the workers you can control what happens in the organism to some degree.



Specific Locations of Enzymes in a Cell•Multi-enzyme complexes: enzymes in a cascade are located near each other, facilitates a chain of reactions

•Enzymes in solution can be separated by membranes

•Enzymes can be incorporated into membranes



chapter 8

Documents

chemical energy

transfer of energy

kinetic energy

energy flows

energy transformations

total energy

endergonic reactions

input of outside energy