Unit 4: Bioenergetics, ATP, and Enzymes

Question 1

State the laws of thermodynamics

Answer 1

First: Energy can’t be created or destroyed
Second: Energy transformations always result in an increase in entropy

Question 2

Describe

Entropy

Answer 2

Chaos
Randomness
Unusable energy
The opposite of free energy

Question 3

Describe

Free energy

Answer 3

Measure of instability
Usable energy
The opposite of entropy

Question 4

Explain

ΔG

Answer 4

Changes in free energy that occurs over the course of a chemical reaction
-ΔG = the system (molecules in the reaction) has LOST free energy == exergonic
+ΔG = the system has GAINED free energy == endergonic

Question 5

What is a positive ΔG?

Answer 5

Increase in free energy in a system
More energy in PRODUCTS than REACTANTS
Endergonic == Energy absorbed into system

Question 6

What is negative ΔG?

Answer 6

Decrease in free energy in a system
More energy in REACTANTS than PRODUCTS
Exergonic == Energy released into environment

Question 7

Define / briefly describe

Spontaneous

Answer 7

Exergonic
Reactions that are energetically favorable

NOT THE SAME AS “FAST”!!!

Question 8

How can endergonic reactions happen?

Answer 8

Endergonic reactions REQUIRE energy from another source
Often “coupled” with exergonic reactions
So long as exergonic reaction RELEASES more energy than endergonic ABSORBS, the pair of reactions will still be possible

Question 9

What are the types of activities cells do that require energy?

Answer 9

Chemical work: Coupling an exergonic reaction with an endergonic one to allow the endergonic reaction to happen
Transport: Establishing concentration gradients (which increases order / decreases entropy)
Mechanical: Moving cell parts / cytoskeleton

Question 10

Describe

Energy coupling

Answer 10

Pairing of an exergonic reaction (releases energy!) with an endergonic one (which couldn’t happen without an input of energy from environment)

Question 11

What is this molecule?

Answer 11

Adenosine triphosphate (ATP)

Question 12

What is this part of ATP called?

Answer 12

A phosphate group

Specifically, the third phosphate, which is broken off when ATP -> ADP

Question 13

What is this part of ATP called?

Answer 13

Phosphate

This is the 2nd phosphate (counting from sugar); still present in ADP

Question 14

What is this part of ATP called?

Answer 14

Ribose
Reminder: Nucleotides contain a pentose / 5-carbon sugar, which is ribose here

Question 15

What is this part of ATP called?

Answer 15

Adenine
Reminder: Nucleotides contain a nitrogenous base, which is adenine here

Question 16

What is this part of ATP called?

Answer 16

Adenosine
(Ribose + Adenine)

Question 17

How is ATP “used”?

Answer 17

ATP → ADP + Pi
The last phosphate breaks off, leaving ADP behind.
ADP and Pi contain WAY less free energy (are more stable / less reactive)
This energy is released, which can be used to do cell work

Question 18

How is ATP made?

General - *not specifically asking what mechanisms are used to make ATP!

Answer 18

ADP + Pi → ATP
Energy must be supplied to build ATP, which has more free energy than ADP and phosphate do separately

Question 19

What processes can provide the energy necessary for regenerating ATP?

Answer 19

Cellular respiration and photosynthesis

Question 20

Define

Reaction Rate

Answer 20

The speed at which reactants are converted to products

Question 21

Define

Catalyst

Answer 21

A chemical that:
1. Speeds up the rate of a chemical reaction
2. Is not used up during the reaction

Question 22

Can catalysts alone make endergonic reactions happen?

Answer 22

NO!
Catalysts speed up reactions that would otherwise happen more slowly
BUT they don’t make reactions happen that otherwise wouldn’t be able to

Question 23

Define

Enzyme

Answer 23

Biological molecules that act as catalysts
- Usually (but not always) proteins
- Encoded by our cells’ DNA

Question 24

Define

Activation Energy

Answer 24

The energy that is required to break reactants / make them enter an unstable state so that they are able to react / form products

Question 25

# Define Transition state

Answer 25

Molecular structure that is highly unstable (and thus can react)

Question 26

How does activation energy limit the rate of reactions?

Answer 26

High activation energy: Requires system to absorb a LOT of energy, making the reaction less likely to occur -> SLOWER

Question 27

What do enzymes do to the rate of reactions?

Answer 27

-Increase rate (more product / faster) by -Lowering activation energy

Question 28

# Define Substrate

Answer 28

A molecule that binds to the enzyme's active site The reactant of an enzyme-catalyzed reaction

Question 29

# Describe Enzyme Structure

Answer 29

Protein (usually) Folded polypeptide, which has an ACTIVE SITE (area where substrate bind), and potentially other sites (ALLOSTERIC SITES) for other molecules to bind

Question 30

How do enzymes increase activation energy?

Answer 30

They don't. They lower them. | haha. i tricked you. or not.

Question 31

How do enzymes lower activation energy?

Answer 31

Possible ways: * **Stress bonds**, making them more likely to reach transition state * **Act as a template** to place substrates together and in correct orientation * Produce a small **microenvironment** where the reaction is more suitable to react

Question 32

How do enzymes affect ΔG of a reaction?

Answer 32

They don't.

Question 33

What type of reaction?

Answer 33

Exergonic -ΔG

Question 34

Identify letters a through e

Answer 34

a: energy in the reactants b: activation energy without enzyme c: activation energy with an enzyme d: ΔG e: energy in the products

Question 35

Identify letters a through e

Answer 35

a: energy in the reactants b: activation energy without enzyme c: activation energy with an enzyme d: ΔG e: energy in the products

Question 36

What kind of reaction is this?

Answer 36

Endergonic (+ΔG)

Question 37

# Define Denaturation

Answer 37

The permanent loss of 3D shape of a molecule In proteins/enzymes: Loss of tertiary and quaternary structure

Question 38

How does denaturation affect an enzyme's ability to catalyze reactions?

Answer 38

Small changes to shape: slight lessening of catalytic ability Complete denaturation: enzyme does not function

Question 39

What conditions may cause an enzyme to denature?

Answer 39

Very high temperatures (above optimal) Acidic conditions (below optimal pH) Basic conditions (above optimal pH)

Question 40

T/F: All enzymes have the same optimal conditions

Answer 40

FALSE!!! Each enzyme has a specific optimal temp, pH, etc and range at which it will work Each enzyme is best suited for the environment in which it evolved

Question 41

Describe the effect of cold temperatures on enzyme-catalyzed reactions, and why.

Answer 41

Low temp = low molecular motion = fewer collisions Reactions slow in cold reactions

Question 42

Describe the effect of high temperatures on enzyme-catalyzed reactions, and why.

Answer 42

High temp = high molecular motion = more collisions BUT high temperatures and excess thermal energy can cause hydrogen bonds (in tertiary and quaternary structure of protein) to break If the enzyme denatures, then the enzyme-catalyzed reaction rate plummets/stops

Question 43

Describe the effect of pH variations on enzyme-catalyzed reactions, and why.

Answer 43

Proteins are stabilized by hydrogen and ionic bonds (among others) These bonds are influenced by proton (H+) concentration Very low pH = high concentration of H+ Very low pH = low concentration of H+ If pH strays from optimal, the enzyme can denature and stop functioning

Question 44

# Define Cofactors

Answer 44

Nonprotein structures (atoms, ions, or molecules) that bind to enzymes and are necessary for proper catalytic function

Question 45

Two types of cofactors

Answer 45

Vitamins (organic molecules) and minerals (inorganic, usually ions)

Question 46

# Define Active Site

Answer 46

**Part of enzyme where substrate binds** * Lock and key model describes active site as perfectly complementary to substrate * Induced fit model describes active site and substrate as somewhat complementary, but binding leads to a better fit

Question 47

# Define Enzyme inhibition

Answer 47

Methods of irreversibly or reversibly stopping or slowing an enzyme's activity

Question 48

What is the importance of enzyme inhibition?

Answer 48

It ensures only necessary enzymes are functioning Ex: If one enzyme is involved in polymerizing amino acids into proteins, while another was involved in hydrolyzing proteins into amino acids, it'd be kind of stupid to have them both functioning simultaneously!

Question 49

# Describe Competitive Inhibition

Answer 49

A molecule (not the substrate) binds to active site of enzyme, blocking correct substrate from binding Increasing concentration of substrate can reduce effect of competitive inhibitor

Question 50

# Describe Noncompetitive inhibition

Answer 50

A molecule (not the substrate) binds to an area other than the substrate, causing a change to the enzyme that prevents binding to the substrate Increasing the substrate concentration does NOT reduce the effect of the noncompetitive inhibitor A type of allosteric regulation

Question 51

# Define Allosteric regulation

Answer 51

Controlling an enzyme's function by having a molecule attached to a part of the enzyme other than the active site

Question 52

# Define Allosteric site

Answer 52

A part of an enzyme (other than the active site) where a molecule can bind, which changes the shape of the active site