Metabolism II

Chapter 6

Overview

• Changes in free energy: G– Exergonic vs. endergonic– Spontaneous vs. not spontaneous

• Chemical reactions in the cell: metabolism– Enyzmes, substrates, etc.

• REDOX reactions (energy flow)• Photosynthesis• TEST

Chemical Reactions in the Cell

• All substances are constantly moving inside the cell

• For a chemical reaction to occur, what has to happen?

– 1: The molecules have to physically collide.– 2: They need to collide at exactly the correct

orientation– 3: They need to have enough energy to push past

the repulsion of their electron clouds

Wrong orientation, not enough

velocityTo overcome the

electron cloud repulsion.

Right orientation, not enough

velocityTo overcome the

electron cloud repulsion.

Right orientation, AND enough

velocityto overcome the electron cloud

repulsion.

A hydrolytic enzyme reaction

Heating up the reaction gives the average molecule more velocity

If these 2 reactants were floating around a cell, it would take a very long time for them to come

together by chance, in exactly the right orientation and with enough velocity…

This is where enzymes come into play.

So what do enzymes do?

They:

1. take care of the orientation

2. Bring them close enough together so they will spontaneously reaction

Back to G• The stored up (potential) energy inside a bond between

two atoms (chemical energy) is released (becomes moving, kinetic energy that is free to do work).

• This is a chemical reaction.• If the reactants have more energy to start with than the

products have after the reaction is finished, is this a positive or negative change in Gibb’s Free Energy?

• It’s negative. We’ve rolled downhill. The products can’t do as much work as the reactants.

• These kinds of reactions, which give off energy, are called “exergonic” reactions. They are also “spontaneous”.

• Can the products still do work?• If they have enough energy left in them, sure• These products can go on to react and create something with even

less energy than they had.• The reaction is still spontaneous, we’re still heading downhill.• This is the idea behind an electron transport chain… a high energy

electron is sent downhill, through a series of organized reactions. • The energy given up by the electron is used to perform work (e.g.

make a new chemical bond).• Remember that some energy is always wasted as heat (2nd law).

There is NEVER 100% efficienciency.• Summary: reactions in which energy is going dowhill are

described as:– Spontaneous– Have a negative change in Gibbs Free Energy– Are Exergonic

So how do we go uphill?• ALL life on earth starts at the same “mountaintop” of energy.

– This is where photosynthesis comes into play (more on that later).• The energy from sunlight is physically captured by an antennae-like structure

inside plant cells, and handed off down the chain.• COUPLIING: Here’s the trick: An exergonic reaction, which GIVES OFF

ENERGY, is coupled to a reaction that REQUIRES energy to happen.– This kinds of reactions build things.– They are NOT spontaneous.

• The “building” reaction uses SOME amount of the energy given off by the exergonic reaction to perform work (the rest of the energy is wasted as heat)

– Example: an exergonic reaction within the electron transport chain donates it’s free energy (that’s it is giving off) to an enzyme, which performs the task of reducing NADP+ (needs electron) to NADPH (has electron, which came from H).

• Another way to go uphill: Build up a concentration gradient (such as a lot of protons), and then let them flow downhill (along their concentration gradient). As they flow, they give off energy, which is used for work (such as building ATP from ADP Pi)

ENERGY FROM AN

EXERGONIC REACTION

ENERGY PROVIDED FOR

AN ENDERGONIC

REACTION(MUSCLE

CONTRACTION)

(+HEAT)

(+HEAT)

Metabolism

• Metabolic Reactions are simply chemical reactions that occur within the cell. Metabolism is the grand sum of all chemical reactions in a cell.

• Metabolic reactions have reactants and products just like any other ordinary chemical reaction.

A B

B C

C D

Reaction #1:

Reaction #2:

Reaction #3:

Reactants Products

E1

E2

E3

• Metabolic reactions have catalysts, just like any other chemical reaction.• Metabolic catalysts happen to be proteins that we call enzymes.

– Reactants in metabolic reactions are called substrates. A substrate is simply a molecule that is acted upon by an Enzyme.

A B

B C

C D

Reaction #1:

Reaction #2:

Reaction #3:

enzyme

Reactants

• What kinds of reactants can there be in metabolic reactions?– Organic Compounds of any kind (proteins,

amino acids, fatty acids, sugars, nucleic acids, etc.)

– Inorganic atoms and molecules (e.g. H2, O2, H2O, etc.)

– Ions (H+, OH-, PO4-, etc.)

Enzymes• An enzyme is simply a protein, a polypeptide

chain (one or more!) folded up into a 3D structure.

• It’s the name of the class of proteins we give to those that function as catalysts.

• RNA can sometimes function as a catalyst as well. We call these “ribozymes”.

• Anything that is acted upon by an enzyme, we call a substrate. Substrate is just another word for “reactant”.

Echoes of Taxonomy: Classes vs. Names…….

Metabolic Pathways• Metabolic Pathways are chemical reactions linked together for the purposes of creating a final product.• They are linear. Think of it as an assembly line.

A C D

E1 E2 E3

B

Pathway 1

Pathway 1: Reactant = AProduct = DIntermediates = B, C

Reactants, Intermediates, and Products are relative terms particular to a pathway. A is not a reactant.

A is a reactant in Pathway 1

(Where can A come from?)Some other pathway

Reaction 1

Reaction 2

Reaction 3

• A product for one reaction can be used as the reactant for in next.

A C D

E1 E2 E3

B

Pathway 1

What is B in Reaction 1?What is B in Reaction 2?

Reaction 4

• The class of a given molecule depend upon the context in which we are speaking.

A C D

E1 E2 E3

B

Pathway 1

What is B in Reaction 4?

B can now be classified as an INTERMEDIATE

Pathway “Crosstalk”• As alluded to before, substrates and products of one pathway can also be

used as substrates in other pathways.

A C D

E1 E2 E3

B

Pathway 1

E

E4

F

E5

Pathway 2

Challenge QuestionWhat happens if we turn off the gene that codes for the mRNA that makes the polypeptide chain that folds into Enzyme #2 (E2) above?

Pathway “Crosstalk”• As alluded to before, substrates and products of one pathway can also be

used as substrates in other pathways.

A C D

E1 E2 E3

B

Pathway 1

E

E4

F

E5

Pathway 2

AnswerB is used by Enyzme #4; E and F are made, but C and D are not.

(Enzyme 3 is twiddling its zinc fingers).

Pathway “Crosstalk”• What is B considered with respect to Enzyme 1?• With Respect to Enzymes 2 and 4?

A C D

E1 E2 E3

B

Pathway 1

E

E4

F

E5

Pathway 2

B is the Product of Enzyme 1B is the Substrate of Enzyme 2 & 4

Pathway “Crosstalk”• What is B considered with respect to Enzyme 1?• With Respect to Enzymes 2 and 4?

A C D

E1 E2 E3

B

Pathway 1

E

E4

F

E5

Pathway 2

B is the Product of Enzyme 1B is the Substrate of Enzyme 2 & 4

More on Enzymes

• Enzymes bind to the chemical reactants of a reaction and hold them together, so they can react naturally.

• They decrease the required Activation Energy of a reaction.

• Just like any other protein, they are sensitive to changes in the environment– Temperature– pH

Regulating Reactions

• What can affect a metabolic reaction?– Environmental factors (temperature, pH)– Concentration of the Substrates– Concentration of the Enzyme– Concentration of cofactors (also called

coenzymes)– Phosphorylation (gives the enzyme energy

to do work!)– Presence or absence of enzyme inhibitors

Inhibition

• What happens if “F” inhibits Enzyme 4?

A C D

E1 E2 E3

B

Pathway 1

E

E4

F

E5

Pathway 2

B is the Product of Enzyme 1B is the Substrate of Enzyme 2 & 4

Inhibition• Enzymes can be prevented from functioning by having something bind to the

active site that is not the substrate of that given pathway (Competitive Inhibition)

• Enzymes can have something bind to a region other than the active site, that prevents it from functioning. (Noncompetitive Inhibition)

REDOX

• Energy Flows. Starting at sunlight, and ending with water, carbon dioxide, and oxygen.

• What is the mechanism by which energy moves?– Recall that all matter is ultimately surrounded by

electron clouds of some kind (and when they aren’t, the are positively charged and therefore attract electrons).

– Logically, this must mean that energy has to move through these clouds.

• Recall from chapter 2: electrons have a certain amount of energy associated with them.– This describes how far away they are from the

nucleus, and what the shape of their orbital is.– The energy carried by photons. So think of

photons AS energy.– When energy (photons) strikes matter, it is

either absorbed, reflected, or transmitted.

• Reflected: If it’s an energy level our eyes detect, we’ll see it.

• Transmitted: the photon had enough energy to just blow past the atoms and continue going (think of glass, clear plastic, water)

• Absorbed: The electrons in orbit around atoms “catch” the photon. If the electron absorbs enough energy, it can actually escape the atom and leave!– The electron will be attracted by positive charges.– When the electron leaves, it leaves a positive charge. This

positive charge attracts another electron, with less energy.

• Losing an electron is called oxidation.• Gaining an electron is called reduction.• This is how energy flows through a

system.

REDOX• Reduction-Oxidation (REDOX for short) reaction are those chemical

reactions that concern themselves with energy flow. Since energy flows through electrons…

• REDOX reactions concern themselves with the gain and loss of electrons.

• Reduction reactions are ALWAYS coupled with oxidation reactions – the electron had to come from somwhere!

• Electrons are attracted by positive charges. What is the most fundamental unit of positive charge?– A proton

• When a proton is given an electron, what element are we now dealing with?– Hydrogen

• Therefore, redox reactions are also concerned with the gain and loss of hydrogen atoms.

• Photosynthesis: Carbon Dioxide is reduced to form glucose. Water is oxidized to Oxygen. Chapter 7

• Cell Respiration: Glucose is oxidized to carbon dioxide. Oxygen is reduced to water. Chapter 8