AP Biology Chapter 6

Entropy

a measure of disorder or randomness

In biology, equilibrium\=

Death

What are enzymes always?

Proteins

What do enzymes do?

Catalyze chemical reactions by lowering activation energy

Are enzymes parts of the reaction? In other words, do they change with the chemical reaction?

No, they do not change

Metabolism

the totality of an organism's chemical reactions

What is metabolism? (Hint: something to do with a chemical property)

An emergent property of life that arises from orderly interactions between molecules.

Metabolic Pathway

how a specific molecule travels through a cell’s metabolism

What happens to a molecule in a metabolic pathway?

A specific molecule is altered in a series of defined steps, resulting in a product

How is each step made successful in a metabolic pathway?

Each step is catalyzed by a specific enzyme

Catabolic pathways

a metabolic pathway that releases energy by breaking down complex molecules into simpler ones

What is an example of a way the cell releases energy?

Breaking down ATP to ADP

Anabolic Pathway

metabolic pathways that consume energy to build complicated molecules from simpler ones

What are anabolic pathways sometimes called?

A biosynthetic pathway

What is an example of an anabolic pathway?

Synthesis of a protein

Bioenergetics

study of how energy flows through living organisms

Energy

the capacity to cause change, the ability to arrange a collection of matter

What does the work of life depend on?

The ability of cells to transform energy from one form to another

Kinetic energy

the relative motion of objects

Thermal energy

kinetic energy associated with the random movement of atoms or molecules

Heat

transfer of thermal energy from one object to another

Potential energy

an object’s not moving energy

Chemical energy

used to refer to the potential energy available for release in a chemical reaction

Thermodynamics

the study of the energy transformations that occur in a collection of matter

System

matter under study

Surroundings

everything outside the system

Isolated System

unable to exchange either energy or matter with its surroundings

What is an isolated system also known as?

A closed system

Open System

energy and matter can be transferred between the system and its surroundings

Are organisms open or closed systems?

Open systems

First Law of Thermodynamics

energy can be transferred and transformed but cannot be created or destroyed

What is the First Law of Thermodynamics also known as?

The Law of Conservation of Energy

Second Law of Thermodynamics

every energy transfer or transformation increases the entropy of the universe

When does an organism have a high entropy?

When an organism has more randomly arranged collection of matter in it

Spontaneous Process

when a process occurs without energy required

Are all spontaneous reactions instantaneous?

No, some are much slower like rust

Nonspontanously

a process that cannot occur on its own

What is another way to state the Second Law of Thermodynamics?

For a process to occur spontaneously, it must increase the entropy of the universe

How are cell structures created? (Hint: don’t over think, has to do with Entropy)

cells create ordered structures from less organized starting material

Can the entropy of a particular system decrease?

Yes as long as the total entropy of the universe increases

Define the Universe in terms of Entropy

system and its surroundings

Equilibrium

the forward and reverse reactions occur at the same rate and there is no further net change in the relative concentrations of products and reactants

When is a process spontaneous and can perform work?

Only when it is moving toward equilibrium

Exergonic Reaction

proceeds with a net release of free energy

What does the greater decrease in free energy mean?

The greater amount of work can be done, change in G is negative

Spontaneous change

free energy of the system decreases, system becomes more stable, released free energy can be harnessed to do work

What does the breaking of bonds do?

Not release energy but requires energy and releases energy when it makes new bonds

Endergonic Reaction

absorbs free energy from its surroundings, essentially stores free energy, change in G is positive

What do reactions in an isolated system eventually do?

Reach equilibrium

Is metabolism as a whole ever at equilibrium?

No

What prevents metabolism from ever being at equilibrium?

The constant flow of materials in and out

Are organisms open or closed systems?

Open systems

Chemical work

the pushing of endergonic reactions that would not occur spontaneously

Transport work

the pumping of substances across membranes against the direction of the concentration gradient

Mechanical work

the beating of cilia, contraction of muscle cells and the movement of chromosomes during cellular respiration

Energy Coupling

use of an exergonic process to drive an endergonic one

What is responsible for mediating most energy coupling in cells and most cases acts as the immediate source of energy that powers cellular work?

ATP

ATP (adenosine triphosphate)

contains the sugar ribose with the nitrogenous base adenine and a chain of three phosphate groups

What splits ATP to ADP?

Hydrolysis

Phosphorylated Intermediate

the recipient with the phosphate group covalently bonded to ti

What is the key to coupling exergonic and endergonic reactions?

The formation of phosphorylated intermediate which is more reactive than the original unphosphorylated molecule

What functions of cells are nearly always powered by the hydrolysis of ATP?

Transport and mechanical work

Enzyme

a macromolecule that acts as a catalyst

Catalyst

a chemical agent that speeds up a reaction without being consumed by the reaction

What does charming one molecule into another general involve?

Controlling the starting molecule into a highly unstable state before the reaction can proceed

What happens when the new bonds of the product molecules form?

Energy is released as heat and the molecules return to stable shapes with lower energy that the contracted state

Activation Energy

the energy required to contrast the reactant molecules so the bonds can break

How is activation energy often supplied?

By heat in the form of thermal energy that the reactant molecules absorb from the surroundings

What does the absorption of thermal energy do?

Accelerates the reactant molecules so they collide more often and more forcefully

Transition State

when the molecules have absorbed enough energy for the bonds to break

What state are the reactants in?

The transition state

What does activation energy provide?

A barrier that determines the rate of the reaction

In most cases, what is true about the activation energy?

It is so high and the transition state is reached so rarely that the reaction will hardly proceed at all

How does heat speed a reaction?

By allowing the reactants to attain the transition state more often

Why does heating not work for life?

High temperatures denatures proteins and kills cells and would speed up all reactions, not just those that are needed

What does an enzyme catalyze?

A specific reaction by lower the EA barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures

Can an enzyme make a reaction endergonic to exergonic?

No

Can an enzyme change the change in G for a reaction?

No

Substrate

the reactant an enzyme acts on

Enzyme-Substrate Complex

created when an enzyme binds to a substrate

What do most enzyme names end in?

-ase

What does the specificity of an enzyme result from?

Its shape, consequence of its amino acid sequence

Active site

the restricted region of the enzyme molecule that actually binds to a substrate

What usually forms the active site of an enzyme?

A few of the enzymes amino acids

Is the active site a rigid receptacle?

No, it changes shape slightly due to interactions between the substrate’s chemical groups on the side chains of the amino acids that form the active site

Induced Fit

brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical creation

Are most metabolic reactions reversible?

Yes

What is the activation energy proportional to?

The difficulty of breaking the bonds

Optimal Conditions

conditions that the enzyme works better under, favor the most active shape for the enzyme molecule

Denaturation

a process where a protein loses its native shape overtime due to the disruption of weak chemical bonds and interactions thereby becoming inactive

Cofactors

non protein helpers for catalytic activity that many enzymes require

Where are cofactors found on an enzyme-substrate complex?

Tightly bound to the enzyme as permanent residents or bound loosely and reversibly along the substrate

Coenzyme

when a cofactor is an organic molecule

What can most vitamins act as?

Coenzymes or the raw materials to make a coenzyme

How do cofactors and coenzymes function?

In various ways bit in all cases they perform a crucial chemical function in catalysis

How does an inhibitor usually attach itself to the enzyme?

By covalent bonds

Are inhibitors reversible?

Usually irreversible

Competitive Inhibitors

some reversible inhibitor who resembles the normal substrate molecules and competes for admission into the active site

How can competitive inhibitors be overcome?

By increasing the concentration of substrate so that the active sites become available

Noncompetitive inhibitors

do not directly compete with substrate to bind to the enzyme at the active site but instead impede enzymatic reactions by binding to another part of the enzyme