Biology 1113 - Exam 2 (Pearson Textbook)

Chapters 8 - 14

System

A defined set of interacting chemical components under observation; the substances you want to focus attention on

Law of conservation of mass

Mass cannot be created or destroyed, but it may be rearranged through chemical reactins

Open system

• Can exchange energy with environment

• Can exchange matter with environment

Closed system

• Can exchange energy with environment

• Cannot exchange matter with environment

Isolated system

• Cannot exchange energy with environment

• Cannot exchange matter with environment

What effect does changing the concentration of reactants or product or changing the temperature do to a chemical equilibrium?

It can disturb the chemical equilibrium

Endothermic

Referring to a chemical reaction that absorbs heat

The transformation of liquid water to water vapor is an example of: ______

An endothermic reaction

Exothermic

Referring to a chemical reaction that releases heat

The transformation of water vapor to liquid water is an example of: ______

An exothermic reaction

Energy

The capacity to do work or to supply heat. May be stored (potential energy) or available in the form of motion (kinetic energy)

Potential energy

Energy stored in matter as a result of its position or the position of electrons that form chemical bonds between atoms

Chemical energy

The potential energy stored in chemical (covalent) bonds between atoms (a molecule’s potential to form stronger bonds)

When are covalent bonds long and weak?

When the shared electrons are far from the nuclei

When are covalent bonds short and strong?

When the shared electrons are shifted closer to one or both of the atoms

Atoms with what kind of bond have higher chemical energy, weak or strong?

Atoms with weak bonds

What factors affect bond strength?

• electronegativity of the atoms

• double/triple bonds

Kinetic energy

The energy of motion

Thermal energy

The total kinetic energy of a system that includes the motion of matter and is measured as temperature; kinetic energy of molecular motion

Temperature

A measurement of thermal energy present in an object or substance, reflecting how much the constituent matter is moving; measure of how much thermal energy the object’s molecules possess

Heat

Thermal energy that is transferred from an object at higher temperature to one at lower temperature

First law of thermodynamics

The principle of physics that energy is conserved in any process. Energy can be transferred and converted into different forms, but it cannot be created or destroyed

Spontaneous chemical reactions

The chemical reaction can proceed on its own, without any continuous external influence such as added energy

What determines if a reaction will proceed spontaneously?

• The products have lower potential energy than the reactants

• The product molecules are less ordered than the reactant molecules

Entropy

The amount of disorder in a system

When does entropy increase in a system?

When the products of a chemical reaction are less ordered than the reactant molecules

Second law of thermodynamics

The principle of physics that the entropy of the universe or any closed system always increases

Physical and chemical changes tend to proceed in what direction?

The direction that results in lower potential energy, increased entropy, or both

What are some forms of kinetic energy?

Sound, thermal energy, electricity, and electromagnetic radiation (e.g., light)

What are some forms of potential energy?

Gravitational, electrical, or chemical gradients, energy in chemical bonds

Enthalpy (H)

A quantitative measure of the amount of potential energy, or heat content, of a system plus the pressure and volume caused by kinetic energy it exerts on its surroundings

Delta H

Based on the difference in potential energy

Positive delta H means the reaction is ______

Endothermic

Negative delta H means the reaction is ______

Exothermic

Gibbs free energy

The energy of a system that can be converted into work. The amount of this energy that is available can be measured only by how it changes in a reaction

Standard free-energy change

The equation used to measure the change in Gibbs free energy (delta G) by calculating the changes in enthalpy (delta H) and entropy (delta S) that occur in a given chemical reaction; T is temperature measured on the Kelvin scale

delta G = delta H - T*delta S

Are spontaneous chemical reactions exergonic or endergonic?

Exergonic

Are nonspontaneous chemical reactions exergonic or endergonic?

Endergonic

What delta G value is when reactions are equal to equilibrium?

delta G = 0

When do more collisions occur between substances in a mixture?

• When the concentration of reactants is high

• When the temperature of reactants is high, because the reactants will move faster and collide more frequently

Energetic coupling

In cellular metabolism, the mechanism by which energy released from an exergonic reaction (commonly, hydrolysis of ATP) is used to make an endergonic reaction spontaneous

How does energetic coupling occur in cells?

Either through the transfer of electrons or the transfer of a phosphate group

Redox reactions (reduction-oxidation reactions)

Any chemical reaction that involves either the complete transfer of one or more electrons from one reactant to another, or a reciprocal shift in the position of shared electrons within one or more of the covalent bonds of two reactants

Oxidation

The loss of electrons from an atom or molecule during a redox reaction, either by donation of an electron to another atom or molecule or by the shared electrons in covalent bonds moving farther from the atomic nucleus

Reduction

The gain of electrons by an atom or molecule during a redox reaction, either by acceptance of an electron from another atom or molecule, or by the shared electrons in covalent bonds moving closer to the atomic nucleus

How does oxidation affect potential energy and which half-reaction is it?

It is the spontaneous, exergonic half-reaction and lowers the potential energy of a reactant

How does reduction affect potential energy and which half-reaction is it?

It is the nonspontaneous, endergonic half-reaction and increases the potential energy of a reactant

Electron donor

A reactant that loses an electron and is oxidized in a reduction-oxidation reaction

Electron acceptor

A reactant that gains an electron and is reduced in a reduction-oxidation reaction

Do electron acceptors (reduced reactants) gain or lose potential energy?

Gain potential energy

Do electron donors (oxidized reactants) gain or lose potential energy?

Lose potential energy

FAD/FADH₂ (flavin adenine dinucleotide)

Oxidized and reduced forms, respectively. A nonprotein electron carrier that functions in the citric acid cycle and electron transport chain; an electron carrier

Electron carrier

Any molecule that readily accepts electrons from and donates electrons to other molecules. Protons may be transferred with the electrons in the form of hydrogen atoms

NAD+/NADH (nicotinamide adenine dinucleotide)

Oxidized and reduced forms, respectively. A nonprotein electron carrier that functions in many of the redox reactions of metabolisms

Why is the potential energy of ATP so high?

There is the presence of four negative charges confined to a small area in its three phosphate groups; the negative charges repel each other, so the covalent bonds between the phosphate groups are very weak, leading to high potential energy

What happens in ATP hydrolysis?

ATP reacts with water and the bond between ATP’s outermost phosphate group and its neighbor is broken, resulting in the formation of ADP and an inorganic phosphate P_i; a highly exergonic reaction

Phosphorylation

The addition of a phosphate group to a molecule

Activation energy

The amount of kinetic energy required to initiate a chemical reaction; specifically, the energy required to reach the transition state

Transition state

A high-energy intermediate state of the reactants during a chemical reaction that must be achieved for the reaction to proceed

Why is the free energy of the transition state high?

The bonds that existed in the original reactants must be destabilized

The more unstable the transition state, the _____(higher/lower) the activation energy and the _____(more/less) likely a reaction is to proceed quickly

higher, less

Before any chemical reactions can take place, what two requirements must be fulfilled?

Reactants need to 

1. Collide in a precise orientation

2. Have enough kinetic energy to overcome the activation energy barrier and achieve the transition state

Substrates

A reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction

Enzymes

Catalysts that bring substrates together in a precise orientation that makes reactions more likely to occur

Active site

The location in an enzyme molecule where substrates bind and react

How does active-site binding help speed up a reaction?

It helps the substrates collide in a precise orientation so that particular bonds can break and new bonds can form to generate products

Ribozymes

Enzymes that are made of RNA instead of being proteins

Induced fit

Change in the shape of the active site of an enzyme, as the result of initial weak binding of a substrate, so that it binds substrate more tightly

When is the transition state formed with enzymes?

When the degree of interaction between the substrate and enzyme increases and reaches a maximum strength, at which point bonds in the substrates are destabilized which forms the transition state

Cofactors

An inorganic ion, such as a metal ion, that is required for an enzyme to function normally. May be bound tightly to an enzyme or associate with it transiently during catalysis

Coenzymes

A small organic molecule that is required for an enzyme-catalyzed reaction. Often donates or receives electrons or functional groups during the reaction

Prosthetic groups

A non-amino acid atom or molecule that is permanently attached to an enzyme or other protein and is required for its function

How does temperature affect enzymes?

It affects the folding and movement of an enzyme as well as the kinetic energy of its substrates

How does pH affect enzymes?

It affects the charge on acidic and basic groups in residue side chains, and also the active site’s ability to participate in reactions that involve the transfer of protons or electrons

Competitive inhibition

Inhibition of an enzyme’s ability to catalyze a chemical reaction via a non-reactant molecule that competes with the substrate(s) for access to the active site

Allosteric regulation

Regulation of an enzyme’s (or other protein’s) activity by binding of a regulatory molecule at a site distinct from the active site. Binding often results in a change in the protein’s shape that affects the function of the active site

Metabolic pathways

A linked series of biochemical reactions that sequentially changes an initial substrate to form a final product; the product of one reaction is the substrate of the next reaction

Feedback inhibition

A type of control in which high concentrations of the final product of a metabolic pathway inhibit one of the enzymes early in the pathway. A form of negative feedback

Catabolic pathways

Any set of chemical reactions that breaks down large, complex molecules into smaller ones, releasing energy in the process

Anabolic pathways

Any set of chemical reactions that synthesizes large molecules from smaller ones. Generally requires an input of energy

What is the difference between cellular respiration and fermentation?

• Cellular respiration results in the complete oxidation of the carbons in glucose to CO₂ (harvests more energy)

• Fermentation doesn’t fully oxidize glucose, and instead, small, reduced organic molecules are produced as waste (harvests less energy)

What are the four interconnected processes of cellular respiration?

1. Glycolysis

2. Pyruvate processing

3. Citric acid cycle

4. Electron transport and oxidative phosphorylation

Glycolysis

One six-carbon molecule of glucose is broken into two molecules of the three-carbon compound pyruvate. During this process, ATP is produced from ADP and P_i, and NAD+ is reduced to form NADH

Pyruvate processing

Each pyruvate produced by glycolysis is processed to release one molecule of CO₂, and the remaining two carbons are used to form the compound acetyl CoA. The oxidation of pyruvate results in more NAD+ being reduced to NADH

Citric acid cycle

The two carbons from each acetyl CoA produced by pyruvate processing are oxidized to two molecules of CO₂. During this sequence of reactions, more ATP and NADH are produced, and FAD is reduced to form FADH₂

Electron transport

Electrons from the NADH and FADH₂ produced by pyruvate processing and the citric acid cycle move through a series of electron carriers that together are called an electron transport chain (ETC)

Oxidative phosphorylation

The energy obtained from the ETC is used to create a proton gradient across a membrane; the ensuing flow of protons back across the membrane is used to make ATP. Because this mode of ATP production links oxidation of NADH and FADH₂ with phosphorylation of ADP; production of ATP molecules by ATP synthase using the proton gradient established via redox reactions of an electron transport chain

Cellular respiration

A common metabolic pathway for production of ATP, involving transfer of electrons from compounds with high potential energy through an electron transport chain and ultimately to a final electron acceptor (often oxygen)

How are fats catabolized?

Enzymes break down fats to release the glycerol and convert the fatty acids into acetyl CoA molecules. Glycerol can be furthered processed and enter glycolysis as an intermediate. Acetyl CoA enters the citric acid cycle.

How are proteins catabolized?

Once they are hydrolyzed to their constituent amino acids, enzyme-catalyzed reactions remove the amino (-NH₂) groups. The amino groups are excreted in urine as waste, and the remaining carbon compounds are converted to pyruvate, acetyl CoA, or other intermediates in glycolysis and the citric acid cycle

When carbohydrates, fats, and proteins are all available, which is used first to generate ATP?

Carbohydrates

Homeostasis

The array of relatively stable chemical and physical conditions in an organism’s cells, tissues, and organs. May be achieved by passively matching the conditions of a stable external environment (conformational homeostasis) or by active physiological processes (regulatory homeostasis) triggered by variations in the external or internal environment