Unit 3: Cellular energetics

Activation Energy

This initial energy input, which is later paid back as the reaction proceeds

Transition State

To get the bonds into a state that allows them to break, the molecule must be contorted (deformed, or bent) into an unstable state(this is what it is, a unstable state)

Catalysis

The process of speeding up a reaction by reducing its activation energy

Catalyst

the factor that's added to lower the activation energy

Enzyme

Biological catalysts, proteins that catalyzed particular chemical reactions

• Enzymes are usually proteins, though some ribonucleic acid (RNA) molecules act as enzymes too.

Substrate

To catalyze a reaction, an enzyme will grab on (bind) to one or more reactant molecules.

Active Site

The part of the enzyme where the substrate binds

Induced Fit

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 this

When an enzyme binds to a substrate….

the activation energy lowers, so the reaction speeds up

Regulatory molecules

Enzyme activity may be turned "up" or "down" 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, enzymes needed for specific processes can be kept in the places where they act, ensuring they can find their substrates readily, don't damage the cell, and have the right microenvironment to work well.

Feedback inhibition

Key metabolic enzymes are often inhibited by the end product of the pathway they control (feedback inhibition)

Activators

Molecules that increase the activity of an enzyme

Inhibitors

Molecules that decrease the activity of an enzyme

Non-competitive Inhibitor

the inhibitor doesn't block the substrate from binding to the active site. Instead, it attaches at another site and blocks the enzyme from doing its job. This inhibition is said to be "noncompetitive" because the inhibitor and substrate can both be bound at the same time.

Competitive Inhibitor

Binding to an enzyme and block binding of the substrate, for example, by attaching to the active site.

Noncompetitive rate of reaction vs. Competitive rate of reaction vs. normal enzyme

Allosteric regulation

any form of regulation where the regulatory molecule (an activator or inhibitor) binds to an enzyme someplace other than the active site

Allosteric Site

The place where the regulator binds

Allosteric Activation vs. Allosteric Inhibitation

Cooperitivity

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

Cofactors

non-protein helper molecules

• like iron and magnesium

Coenzymes

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

• like vitamin C

First committed step

first step that’s effectively irreversible

Initial Velocity

the amount of product produced per unit time at the start of the reaction

Saturated

meaning that all available enzyme molecules are already tied up processing substrates

Maximum Velocity

maximum rate of reaction is characteristic of a particular enzyme at a particular concentration