AP Biology - Chapter 3 Test

activation energy

the minimum amount of energy required to start a chemical reaction

transition state

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

Reactants

elements or compounds that enter into a chemical reaction

Products

elements or compounds produced by a chemical reaction.

catalysis

the acceleration of a chemical reaction by a catalyst

catalyst

substance that speeds up the rate of a chemical reaction

Enzymes

Catalysts for chemical reactions in living things

exergonic reaction

A chemical reaction that releases energy

endergonic reaction

Reaction that absorbs free energy from its surroundings.

enzymes lower the ______ but increase the _____ of the reaction

activation energy of the reaction, rate

Substrate

reactant of an enzyme-catalyzed reaction

active site

a region on an enzyme that binds to a protein or other substance during a reaction.

allosteric site

A specific receptor site on some part of an enzyme molecule remote from the active site.

enzyme-substrate complex

A temporary complex formed when an enzyme binds to its substrate molecule(s).

An enzyme's active site is uniquely suited to bind to a particular _____, with a special _______, _______, and ______.

substrate, shape, size and chemical behaviour.

Denatured

loss of an enzyme's normal shape so that it no longer functions; caused by a less than optimal pH and temperature

lock and key model

The model of the enzyme that shows the substrate fitting perfectly into the active site (not correct)

induced fit

The change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substrate.

T or F: enzymes are reusable.

True

regulatory molecules

Enzyme activity may be turned "up" or "down" by activator and inhibitor molecules that bind specifically to the enzyme.

Cofactors

Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.

Compartmentalization

Storing enzymes in specific compartments can keep them from doing damage or provide the right conditions for activity.

feedback inhibition

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

competitive inhibition

substance that resembles the normal substrate competes with the substrate for the active site

noncompetitive inhibition

inhibitor binds elsewhere on the enzyme; alters active site so that the substrate cannot bind

enzyme kinetics plot

used to visualize how inhibitors affect enzymes

T OR F: The light dependent reactions produce O2

True, l.d. reactions do this.

enzyme saturation

A point of substrate concentration at which all enzymes are engaged, and adding more substrate will not increase reaction rate.

allosteric enzymes

have both an active site for substrate binding and an allosteric site for binding of an allosteric effector (activator, inhibitor)

System

A group of parts that work together as a whole

open system

A system in which matter can enter from or escape to the surroundings.

closed system

A system in which no matter is allowed to enter or leave

isolated system

A system that can exchange neither energy nor matter with its surroundings.

first law of thermodynamics

Energy can be transferred and transformed, but it cannot be created or destroyed.

second law of thermodynamics

Every energy transfer or transformation increases the entropy of the universe.

ATP

(adenosine triphosphate) main energy source that cells use for most of their work

ATP hydrolysis

ATP is converted to ADP & phosphate energized myosin heads (removal of phosphate) need energy

ATP+H2​O⇋ADP+Pi​+energy

ATP hydrolysis

ATP cycle

How a cell regenerates its ATP supply. ADP forms when ATP loses a phosphate group, then ATP forms as ADP gains a phosphate group.

reaction coupling

an endergonic reaction occurs because it is paired with an exergonic reaction

Metabolism

All of the chemical reactions that occur within an organism

Anabolism

Metabolic pathways that construct molecules, requiring energy.

Catabolism

Metabolic pathways that break down molecules, releasing energy.

Photosynthesis

Plants use the sun's energy to convert water and carbon dioxide into sugars

majority of photosynthesis occurs in

leaves

the primary site of photosynthesis in the leaves is

the mesophyll

Stoma (of a plant)

found on leaf surface; used for gas exchange; opening controlled by guard cells (CO2 in O2 out)

Chloroplast

An organelle found in plant and algae cells where photosynthesis occurs

Chlorophyll

A green pigment found in the chloroplasts of plants, algae, and some bacteria

thylakoids

A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy.

Granum

stack of thylakoids

Grana

A stacked portion of the thylakoid membrane in the chloroplast. Grana function in the light reactions of photosynthesis

The light-dependent reactions take place in the

thylakoid membrane

light-dependent reactions

reactions of photosynthesis that use energy from light to produce ATP and NADPH

The Calvin cycle takes place in the

stroma

Calvin Cycle requires what?

CO2, NADPH, ATP

Calvin Cycle

reactions of photosynthesis in which energy from ATP and NADPH is used to build high-energy compounds such as sugars

redox reaction

A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction.

Photosystems

light-collecting units of the chloroplast

P680

Reaction center chlorophyll in the photosystem II.

P700

Reaction center cholophyll in the photosystem I.

non-cyclic photophosphorylation

The light-requiring part of photosynthesis in higher plants, in which an electron donor is required (typicaly H20), and oxygen is produced as a waste product. It consists of two photoreactions, resulting in the synthesis of ATP and NADPH 2.

chemiosmosis (oxidative phosphorylation)

the process of converting ADP to ATP by using the proton gradient to force protons through the turbine-like ATP synthase

light absorption in PSII

When light is absorbed by one of the many pigments in photosystem II, energy is passed inward from pigment to pigment until it reaches the reaction center. There, energy is transferred to P680, boosting an electron to a high energy level. The high-energy electron is passed to an acceptor molecule and replaced with an electron from water. This splitting of water releases the O2 we breathe.

ATP synthesis in chloroplasts

The high-energy electron travels down an electron transport chain, losing energy as it goes. Some of the released energy drives pumping of H+ ions from the stroma into the thylakoid interior, building a gradient. (H+ ions from the splitting of water also add to the gradient.) As H+ ions flow down their gradient and into the stroma, they pass through ATP synthase, driving ATP production in a process known as chemiosmosis.

Light absorption in PSI

The electron arrives at photosystem I and joins the P700 special pair of chlorophylls in the reaction center. When light energy is absorbed by pigments and passed inward to the reaction center, the electron in P700 is boosted to a very high energy level and transferred to an acceptor molecule. The special pair's missing electron is replaced by a new electron from PSII (arriving via the electron transport chain).

NADPH formation

The high-energy electron travels down a short second leg of the electron transport chain. At the end of the chain, the electron is passed to NADP+ (along with a second electron from the same pathway) to make NADPH.

cyclic photophosphorylation

involves photosystem 1 in a pattern of electron flow where ATP is generated. no NADPH is generated.

resonance energy transfer

the process by which energy can be transferred to adjacent pigment molecules during photosynthesis

special pair

two chlorophyll a molecules, located in the reaction center of a photosystem, that catalyze the conversion of solar energy into chemical energy

primary electron acceptor

in chloroplasts, an acceptor of electrons lost from chlorophyll a; found in the thylakoid membrane

Pheophytin

primary electron acceptor in PSII

chlorophyll A0

primary electron acceptor of PSI

Once an electron is lost, each photosystem is replenished by electrons from a different source.

True

The PSII reaction center gets electrons from water, while the PSI reaction center is replenished by electrons that flow down an electron transport chain from PSII.

True

electron transport chain

A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.

NADP+ reductase

enzyme that transfers a proton and two electrons from ferredoxin to NADP+, forming NADPH (2 ELECTRONS are required).

plastoquinone, cytochrome complex (Cyt), plastocyanin (Pc)

electron transport chain for PS II

Ferredoxin-NADP+ reductase

electron transport chain for PS I

Why does cyclic photophosphorylation occur?

to make up for an ATP debt or when the ratio of NADPH to NADP+ is too high (when too little NADP+ is available to accept electrons)

Stroma

fluid portion of the chloroplast; outside of the thylakoids

Carbon Fixation (Calvin Cycle)

Three molecules of carbon dioxide are added to three molecules of a five-carbon sugar abbreviated RuBP. These molecules are then rearranged to form six molecules called 3-PGA, which have three carbons each.

Reduction (Calvin Cycle)

In the second stage, ATP and NADPH are used to convert the 3-PGA molecules into molecules of a three-carbon sugar, glyceraldehyde-3-phosphate (G3P). This stage gets its name because NADPH donates electrons to, or reduces, a three-carbon intermediate to make G3P.

Regeneration (Calvin Cycle)

Some G3P molecules go to make glucose, while others must be recycled to regenerate the RuBP acceptor. Regeneration requires ATP and involves a complex network of reactions.

In order for one G3P to exit the Calvin cycle (and go towards glucose synthesis), what must happen?

three CO2 molecules must enter the cycle, providing three new atoms of fixed carbon. When three CO2 molecules enter the cycle, six G3P molecules are made. One exits the cycle and is used to make glucose, while the other five must be recycled to regenerate three molecules of the RuBP acceptor.

How many turns of the Calvin cycle are required to produce one molecule of glucose?

Three turns of the Calvin cycle are needed to make ONE G3P molecule that can exit the cycle and go towards making glucose, so six turns are needed to produce one glucose molecule.

6 CO2, 18 ATP, and 12 NADPH

produce one molecule of glucose from the calvin cycle

Great Oxygenation Event

The time in Earth's history, about 2.4 billion years ago, when the concentration of oxygen in the atmosphere increased dramatically.

substrate-level phosphorylation

The enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism.

electron carriers

proteins arranged in chains on the membrane to allow the transfer of electrons from one carrier to another.

cellular respiration gets its electrons from

glucose

2 examples of electron carriers used in cellular respiration

NAD+ and FAD

oxidize (biology)

undergo or cause to undergo a reaction in which electrons (H+) are lost to another species.

reduce (biology)

undergo or cause to undergo a reaction in which electrons (H+) are gained by one atom from another.

LEO goes GER

Loss of electrons is oxidation, gain of electrons is reduction.

Glycolysis

first step in releasing the energy of glucose, in which a molecule of glucose is broken into two molecules of pyruvic acid

pyruvate oxidation

Each pyruvate from glycolysis goes into the mitochondrial matrix—the innermost compartment of mitochondria. There, it's converted into a two-carbon molecule bound to Coenzyme A, known as acetyl CoA. Carbon dioxide is released and NADH is generated.

citric acid cycle

The acetyl CoA made in the last step combines with a four-carbon molecule and goes through a cycle of reactions, ultimately regenerating the four-carbon starting molecule. ATP, NADH and FADH2 are produced, and carbon dioxide is released.

oxidative phosphorylation

The NADH and FADH2 made in other steps deposit their electrons in the electron transport chain, turning back into their "empty" forms (NAD+ and FAD). As electrons move down the chain, energy is released and used to pump protons out of the matrix, forming a gradient. Protons flow back into the matrix through an enzyme called ATP synthase, making ATP. At the end of the electron transport chain, oxygen accepts electrons and takes up protons to form water.

How many ATP are produced in glycolysis?

4 are formed, but 2 are used during glycolysis reactions, so net gain is 2.