Topic 3 Notes/Study Guide

QUICK REVIEW!

CHEMICAL REACTIONS: processes that change one set of chemicals (reactants) into another set of chemicals (products)
REACTANTS: the elements or compounds that ENTER into a chemical reaction
PRODUCTS: the elements or compounds CREATED by a chemical reaction

Chemical reactions always involve the breaking of bonds in reactants and the formation of new bonds in products.

ENERGY CHANGES

Energy is released or absorbed whenever chemical bonds form or are broken. Because chemical reactions involve the breaking and forming of bonds they involve changes in energy.

So I bet you're wondering...Ms. Hudson what does this have to do with biology?!?!

Well, in order to stay alive, organisms (living things) need to carry out reactions that require energy. Every organism must have a source of energy to carry out chemical reactions.

ACTIVATION ENERGY

ACTIVATION ENERGY: the energy that's needed to get a reaction started; the energy needed for a reaction to begin.

The higher the activation energy, the slower the chemical reaction will be. Many reactions have such high activation energies that they basically don't proceed at all without an input of energy.

So how do these reactions occur? Well, it's possible to lower the activation energy of a reaction, and thereby increase the reaction rate. How? Keep Reading!

HOW TO INTERPRET GRAPHS...

The peak of each graph represents the energy needed for the reaction to go forward aka the TRANSITION STATE. The difference between this required energy and the energy of the reactants is the ACTIVATION ENERGY.

On a graph the ACTIVATION ENERGY is the amount of energy needed to get the REACTANTS to the TRANSITION STATE (top of the graph).

Enzymes Overview

WHAT IS AN ENZYME?

Some chemical reactions that make life possible are too slow or have activation energies that are too high to make them practical for living tissues...They need a CATALYST!!!

CATALYST: a substance that speeds up the rate of a chemical reaction by lowering the activation energy

ENZYMES: proteins that act as biological catalysts.

Enzymes are very specific. They usually only catalyze one chemical reaction.

- Part of an enzymes name comes from the reaction it catalyzes.
- Fun Fact: Most enzymes end in the suffix "-ase"

Look at the graph to the right. How did the enzyme impact the activation energy of the chemical reaction?!

HOW DO ENZYMES WORK?

Enzymes have an ACTIVE SITE a site where reactants (SUBSTRATES) can be brought together to react. Such a site reduces the energy needed for a reaction.

SUBSTRATES: the reactants of an enzyme-catalyzed reaction

[Step 1] The substrates bind to a site on the enzymes called the ACTIVE SITE.

- The active site and the substrates have a complementary shape.
- The fit is so precise that the active site and substrate are often compared to a lock and key. This is known as the LOCK AND KEY MODEL.
- INDUCED FIT MODEL: an enzyme changes shape slightly when it binds its substrate, resulting in an even tighter fit. This adjustment of the enzyme to snugly fit the substrate is called induced fit.

[Step 2] The enzyme and substrate are bound together by intermolecular forces and form an ENZYME-SUBSTRATE COMPLEX.

[Step 3] The enzyme and substrate remain bound together until the reaction is done. Once the reaction is over, the products of the reaction are released and the enzyme is free to start the process again.

IMPORTANT NOTE:

Enzymes don't change whether a reaction is energy-releasing (exothermic/exergonic) or energy absorbing (endothermic/endergonic). Instead enzymes lower the energy of the TRANSITION STATE. Remember the TRANSITION STATE is the unstable state that reactants must pass through in order to become products. (The transition state is at the top of the "energy hill" in diagrams.)

ENZYMES SPEED UP CHEMICAL REACTIONS BY LOWERING THE ACTIVATION ENERGY!!

Try to identify the following in this GIF:

Substrate

Enzyme

Active Site

Enzyme-Substrate Complex

Products

LOCK AND KEY MODEL vs. INDUCED FIT MODEL

ENZYME REGULATION

Here are some of the ways enzymes can be regulated/controlled...

pH and Temperature - Enzymes have a specific temperature and pH range that they work in; exposing enzymes to a pH or temperature outside of that range will DENATURE the enzymes and cause it to stop functioning
Regulatory Molecules: Enzyme activity may be turned "on" or "off" by activator and inhibitor molecules that bind specifically to the enzyme.
Cofactors: Many enzymes are only active when bound to non-protein helper molecules known as cofactors.
Compartmentalization: Storing enzymes in specific compartments can keep them from doing damage or provide the right conditions for activity.
Feedback inhibition: Key metabolic enzymes are often inhibited by the end product of the pathway they control.

DENATURE: when a protein loses its shape and can no longer bind substrate; denatured proteins are usually non-functioning

Factors that may affect the active site and enzyme function are temperature and pH. All enzymes have an optimal pH and temperature range. If conditions go outside this range the enzyme may denature (unfold and stop working).

- Temperature: A higher temperature generally makes for higher rates of reaction. However, either increasing or decreasing the temperature outside of a tolerable range can affect chemical bonds in the active site, making them less well-suited to bind substrates. Very high temperatures may cause an enzyme to denature, losing its shape and activity.
- pH: Active site amino acid residues often have acidic or basic properties that are important for catalysis. Changes in pH can affect these residues and make it hard for substrates to bind. Enzymes work best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) can make enzymes denature.

pH

The pH Scale

The pH scale ranges from 0 to 14. The pH scale measures the amount of hydrogen (H+) ions in a solution and compares it to the number of hydroxide ions (OH-). Specifically, it measures the concentration of hydrogen ions in a solution.

At a pH of 7, the concentration of H+ equals the concentration of OH- so the solution is NEUTRAL. Pure water has a pH of 7.

Solutions with a pH below 7 have more H+ ions than OH- ions and are ACIDIC. The lower the pH, the stronger the acid.

Solutions with a pH above 7 have more OH- ions than H+ ions are BASIC. The higher the pH, the stronger the base.

Each step on the pH scale represents a factor of 10. So a solution with a pH of 4 is 10 times more acidic than a solution with a pH of 5.

Fun Fact: We typically think of only acids as burning us, but in truth, both strong acids and strong bases are caustic, which means they can burn us.

Water can react to form ions (positively or negatively charged atoms or molecules). The reaction in which this happens is shown to the right: (The double arrows means it can happen in either direction.)

When this happens the number of positive hydrogen ions produced equals the number of negative hydroxide (OH-) ions produced.

THIS IS WHY WATER IS NEUTRAL!

Acids

An ACID is any compound that forms H+ ions in solution.

Acidic solutions contain higher concentrations of H+ ions than pure water and have a pH below 7.

Strong acids typically have a pH around 1 to 3.

Bases

A BASE is a compound that produces hydroxide (OH-) ions in solution.

Basic, or alkaline solutions contain lower concentrations of H+ ions than pure water and have pH values above 7.

Strong bases typically have a pH of about 11 to 14.

Another name for a basic solution is an ALKALINE solution.

Homeostasis and pH

Organisms have to maintain HOMEOSTASIS (internal balance) with many different factors such as body temperature, hydration levels, oxygen levels, and pH.

There are safeguards that help keep pH balanced. They are called BUFFERS!

Regulatory Molecules

REGULATORY MOLECULES

Enzymes can be regulated by other molecules that either increase or reduce their activity.

ACTIVATORS: molecules that increase the activity of an enzyme

INHIBITORS: molecules that decrease the activity of an enzyme

COMPETITIVE INHIBITORS:

An inhibitor binds to an enzyme and blocks the binding of the substrate, by attaching to the active site. The inhibitor “competes” with the substrate for the enzyme.

NONCOMPETITIVE/ALLOSTERIC INHIBITORS:

The inhibitor doesn't block the substrate from binding to the active site. Instead, it attaches to another site and blocks the enzyme from doing its job. It's "non-competitive" because the inhibitor and substrate can both be bound at the same time.

ALLOSTERIC REGULATION: Any form of regulation where the regulatory molecule (an activator or inhibitor) binds to an enzyme someplace other than the active site.

The place where the regulator binds is called the ALLOSTERIC SITE.

COOPERATIVITY: the substrate itself can serve as an allosteric activator when it binds to one active site, the activity of the other active sites goes up. This is a type of allosteric activator.

Many enzymes don’t work optimally, or even at all unless bound to other non-protein helper molecules called COFACTORS.

COENZYMES are a subset of cofactors that are organic (carbon-based) molecules.

The most common sources of coenzymes are dietary vitamins.

Sources: Prentice Hall Biology, Khan Academy

Enzyme Videos

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