AP BIO UNIT 3 - Topics 1, 2, 3, 4: Enzyme Structure, Enzyme Catalysis, Environmental Impacts on Enzyme Function, Cellular Energy

Metabolism, Metabolic Pathways, Energy, Laws of Thermodynamics, Free Energy, Cells and Energy, ATP, Regeneration of ATP, Rates of Metabolic Reaction, Enzymes, Enzyme Structure and Function, Effects on Enzymes, Enzyme Cofactors and Inhibitors, Regulation of Chemical Reactions, Allosteric Regulation, Feedback Inhibition

What is metabolism?

All of the chemical reactions in an organism

What are metabolic pathways?

Series of chemical reaction that either build complex molecules or break down complex molecules

What are the 2 types of metabolic pathways?

Catabolic and anabolic pathways

What are catabolic pathways?

Pathways that release energy by breaking down complex molecules into simpler compounds

What are anabolic pathways?

Pathways that consume energy to build complicated molecules from simpler compounds

What is energy?

Ability to do work

Why do organisms need energy?

To survive and function

What results in a loss of energy flow within organisms?

Results in death

What is kinetic energy?

Energy associated with motion

What is thermal energy?

Energy associated with the movement of atoms or molecules

What is potential energy?

Stored energy

What is chemical energy?

Potential energy available for release in a chemical reaction

What are thermodynamics?

Study of energy transformations in matter

What do the laws of thermodynamics apply to?

The universe as a whole

What is the 1st law of thermodynamics?

Energy cannot be created or destroyed, only transferred or transformed

What is the 2nd law of thermodynamics?

● Energy transformation increases the entropy of the universe.

● During energy transfers or transformations, some energy is unstable and often lost as heat.

What is entropy?

Disorder

What happens when energy is transferred?

More entropy (disorder) is created

Why do scientists use free energy?

● Determine the likelihood of reactions in organisms or,

● If the reactions are energetically favourable.

Which formula is this?

△G = △H - T△S

Change in free energy

What does △H represent?

Change in total energy

What does T represent?

Absolute temperature (K)

What does △S represent?

Change in entropy

What do free energy change of reactions determine?

Whether or not the reaction occurs spontaneously (no outside input of energy is required)

Based on free energy changes, what can chemical reactions be classified as?

Exergonic or endergonic

What are exergonic reactions?

Reactions that release energy

What is an example of an exergonic reaction?

Cellular respiration (ATP!)

What are the characteristics of exergonic reactions?

△G < 0

Reaction is spontaneous

What are endergonic reactions?

Reactions that absorb energy

What is an example of an endergonic reaction?

Photosynthesis (the sun!)

What are the characteristics of endergonic reactions?

● △G > 0

● Reaction is not spontaneous

● Absorbs free energy 

Living cells have a constant flow of ________ in and out of the membrane.

Materials

Cells are not at __________.

Equilibrium

What are the 3 kinds of work?

Mechanical, transport, chemical

What is mechanical work?

Movement

What are some biological examples of mechanical work?

● Beating of cilia

● Movement of chromosomes

● Contraction of muscle cells

What is transport work?

Pumping substances across membranes against spontaneous movement

What are examples of transport work?

● Active Transport

● Passive Transport

● Diffusion

What is chemical work?

Synthesis of molecules

What is an example of chemical work?

Building polymers from monomers (macromolecules)

What is ATP?

Molecule that organisms use as a source of energy to perform work

What does ATP stand for?

Adenosine triphosphate

How does ATP power cellular work?

● ATP couples exergonic reactions to endergonic reactions.

● ATP -> ADP

How do organisms obtain energy?

● By breaking the bond between the 2nd and 3rd phosphate in a hydrolysis reaction.

● Organisms use this energy for cellular work.

● ATP -> ADP

What is phosphorylation?

The released phosphate moves to another molecule to give energy

How does the regeneration of ATP happen?

● ADP can be regenerated to ATP via the ATP cycle.

● Uses energy from exergonic processes.

● ADP -> ATP

What do the laws of thermodynamics tell us?

If a reaction is spontaneous

What do the laws of thermodynamics not describe?

Rate of reaction

Why would it be impossible for cells to utilize slow reactions?

● Some spontaneous reactions move so slowly it would be impossible for cells to utilize them efficiently.

● The hydrolysis of sucrose to glucose would take nearly 1000 years to happen spontaneously.

What are enzymes?

Macromolecules that catalyze reactions by lowering activation energy

What does catalyze mean?

Speed up

How do enzymes work to catalyze chemical reactions?

Decreasing the Activation Energy required to start the reaction. The higher the AE, the slower the reaction will be. (Reference enzyme charts/graphs. The higher peak of the AE is the slower reaction, and is the one likely with out an enzyme.)

What are the characteristics of enzymes?

Not consumed by the reaction.

Type of protein.

End in -ase.

What is a substrate?

The reactant an enzyme acts on

What is an active site?

Area for substrate to bind

Explain the cycle of an enzyme-substrate complex.

1. Active site open

2. Substrates

3. Substrates are held together in active site by weak interactions

4. Substrates converted into products

5. Products released

What is induced fit?

Enzymes will change the shape of their active site to allow the substrate to bind better.

When does induced fit occur?

● Occurs in an enzyme substrate complex.

● Occurs if the substrates don't fit properly when binding to the active site.

What is enzyme catabolism?

Enzyme helps break down complex molecules

What is enzyme anabolism?

Enzyme helps build complex molecules

Why do different factors affect enzymes?

● Enzymes are proteins, which means their 3D shape can be affected by different factors.

● A change in shape means a change in function.

What is the efficiency of enzymes affected by?

Temperature

pH

Chemicals

What are optimal conditions for enzymes?

The conditions (temperature and pH) that allow enzymes to function optimally (at their best)

How does temperature affect enzyme activity?

● Rate of enzyme activity increases with temperature (due to collision) up to a certain point.

● After that point, the enzyme will denature.

Why do enzymes function best at a specific pH?

Being outside a normal pH range can cause hydrogen bonds in the enzyme to break, changing the shape of the enzyme.

What are enzyme cofactors?

● Non protein molecules that assist enzyme function.

● Can be bound loosely or tightly.

What are the types of enzyme cofactors?

● Inorganic cofactors

● Coenzymes (organic cofactors)

What do inorganic cofactors consist of?

Metals

What are holoenzymes?

Enzymes with the cofactor attached

What are coenzymes?

Organic cofactors

What is an example is a coenzyme?

Vitamins

What do enzyme inhibitors do?

Reduce the activity of specific enzymes

What are the types of inhibition?

● Permanent

● Reversible

What is permanent enzyme inhibition?

Inhibitor binds with covalent bonds

What are examples of permanent inhibition?

Toxins and poisons

What is reversible inhibition?

Inhibitor binds with weak interactions

What are the types of enzyme inhibitors?

● Competitive

● Noncompetitive

What are competitive inhibitors?

● Reduce enzyme activity by blocking substrates from binding to the active site.

● Inhibition can be reversed with increased substrate concentrations.

What are noncompetitive inhibitors?

● Bind to an area other than the active site (allosteric site).

● This changes the shape of the active site, preventing substrates from binding.

● Type of allosteric inhibition

What must a cell be able to regulate?

Its metabolic pathways

How do cells regulate their metabolic pathways?

● Control where and when enzymes are active

● Switch genes that code for enzymes on or off

What is allosteric regulation?

Molecules bind (noncovalent interactions) to an allosteric site which changes the shape and function of the active site.

What are the types of allosteric regulation and what causes them?

● Activation (by an allosteric activator)

● Inhibition (by an allosteric inhibitor)

● Cooperativity

What might allosteric regulation result in?

May result in inhibition (by inhibitor) or stimulation (by an activator) of the enzymes activity.

What is an allosteric activator?

Substrate binds to allosteric site and stabilizes the shape of the enzyme so that the active sites remain open

What is an allosteric inhibitor?

Substrate binds to allosteric site and stabilizes the enzyme shape so that the active sites are closed (inactive form)

What is cooperativity?

● Substrate binds to one active site (on an enzyme with more than one active site) which stabilizes the active form.

● Considered allosteric regulation since binding at one site changes the shape of other sites.

What is feedback inhibition?

The end product of a metabolic pathway can act as an inhibitor to an early enzyme in the same pathway.

Explain the steps of feedback inhibition.

1. Substrate

2. Substrate binds to enzyme

3. Intermediate formed

4. Enzyme forms product

5. Product binds to the allosteric site on a different enzyme, making its active site inactive.

-> This prevents or delays the enzyme's activity from making more product when enough has been made.

6. Pathway continues once the product is used up by the cell.