AP Biology Unit 3: Cellular Energetics

Catalysts

Speeds up chemical reactions because many of the chemical reactions needed to support living systems happen too slowly to meet the changing needs of organisms.

Enzymes

Biological catalysts, most are made of proteins, which have a three-dimensional tertiary structure that is specific to their function.

Ribozymes

Biological catalysts that are made of RNA. They have a tertiary structure that enables them to act like a protein enzyme in catalyzing biochemical and metabolic reactions within a cell.

Active Site

This part of an enzyme interacts with the substrate/reactant. The shape of it is specific to the shape of the substrate.

Substrate

Must be able to fit into the active site to interact with the enzyme. If there are any charged R-groups on amino acids within the active site of the enzyme, there must be compatible charges on this.

Environmental Factors that affect Enzyme Function

Enzymes catalyze reactions most efficiently at optimum temps and pHs that are specific to the enzyme. If the temp in the environment is too low, the rate of collisions between the enzyme and its substrate will be reduced, and the reaction will slow down. If the temp is too high, bonds that hold the enzyme together may be disrupted, and the shape of the enzyme can be altered. A pH that is too far from optimum can disrupt bonds in the enzyme and result in a change in its tertiary structure. Changes to the ionic environment of an enzyme can also disrupt bonds in the enzyme.

Denaturation

A change to an enzymes structure, it can limit the enzymes ability to catalyze chemical reactions. Sometimes it can be reversed when the environment returns to more optimum conditions.

Competitive Inhibitors

Similar in shape to substrates and compete with them for the active site of an enzyme. This competition lowers the rate of enzyme-catalyzed reactions. The effect of these can be diluted by adding higher concentrations of substrate so it can outcompete these.

Noncompetitive/Allosteric Inhibitors

Do not bind to the active site but rather the allosteric site. The binding of these to the allosteric site changes the shape of the enzyme, affecting its function. Because they do not bind to the active site, adding higher concentrations of solute does not affect their action. They function in feedback mechanisms, adjusting the rate of chemical reactions in the cell to suit changing environmental conditions.

Cofactors (inorganic molecules) and Coenzymes (organic molecules)

Increases the efficiency of enzyme-catalyzed reactions, usually by binding to the active site or substrate, which enhances the binding of the substrate to the active site.

Free Energy (G)

All molecules have a given amount of this. The chemical reactions necessary for life involve changes in molecules, which can create higher or lower levels of this.

Endergonic Reactions

Has products with a higher free energy level than its reactants and is considered energetically unfavorable.

Exergonic Reactions

Has products with a lower free energy level than its reactants and is considered energetically favorable.

Activation Energy

The difference between the energy level of the reactants and the transition state of the reaction. Higher ones result in slower chemical reactions. The enzymes speed up chemical reactions by lowering this part of reactions. They can do this in several ways:

1\. Bringing substrates together in the proper orientation for a reaction to occur.

2\. Destabilizing chemical bonds in the substrate by bending the substrate.

3\. Forming temporary ionic or covalent bonds with the substrate.

Enzymes cannot change an endergonic reaction into an exergonic reaction.

Coupled Reactions

When processes that release energy are paired/coupled with processes that require energy. They occur in multiple steps to allow for the controlled transfer of energy between molecules, leading to more efficiency. Coupling an exergonic reaction with an endergonic reaction allows the energy released by the exergonic reaction to drive the endergonic reaction.

Photosynthesis

The process by which plants, algae, and photosynthetic bacteria convert light energy to chemical energy in the form of sugar. During it, the carbon atoms from carbon dioxide gain hydrogen atoms (carbon is reduced) and the oxygen atoms in water lose hydrogen atoms (oxygen is oxidized).

Heterotrophs

Organisms that consume other organisms to obtain organic molecules.

Autotrophs

Organisms that can produce their own organic molecules from inorganic molecules.

Photoautotrophs

Autotrophs that use light energy to power the production of organic molecules from inorganic molecules.

Light-Dependent Reactions

These reactions of photosynthesis use energy from sunlight to split water, producing oxygen gas, p+, and high-energy e-. Oxygen gas is released into the atmosphere. The p+ and high-energy e- are used to power the production of ATP and NADPH, which are sent to the light-independent reactions.

Photophosphorylation

The process in the light-independent reactions where light energy is used to drive the production of ATP. Light energy excites the e- in the chloroplast to higher energy levels, causing them to move through the chloroplast releasing energy. At the end of the light-dependent reactions, NADP+ accepts these e-, forming NADPH, which is a source of reducing power for the light-independent reactions.

Chlorophyll

A light-absorbing pigment that captures the energy of photons from the sun. They are the primary light-absorbing pigments in photosynthesis and are found in photosystems I and II (PSI and PSII).

Photo System

It is composed of proteins, chlorophyll, and other light-absorbing pigments. PSI and PSII contain different types of chlorophyll that absorb the most light energy at different wavelengths. They are located in the thylakoid membrane of the chloroplast and are connected by an e- transport chain (ETC). The energy in the photons is used to boost e- in chlorophyll to a higher energy level in PSII. These e- from PSII are passed from one protein carrier to another in a series of redox (reducing-oxidation) reactions. The final e- donor in the ETC passes the e- to PSI. As the e- pass through the carrier molecules of the ETC, the energy that is released is used to make a p+ gradient, and H+ ions are actively transported against their concentration gradient across the thylakoid membrane. The e- from the ETC (that is now on PSI) is boosted by another photon of light energy from the sun where it again passes through a series of carriers, where it is transferred with a p+ to NADP+ by the enzyme NADP+ reductase, producing a molecule of NADPH.

Photolysis

The process driven by the energy from the sun (photons) that occurs to replace the e- on PSII since the e- from PSII fell down the ETC and are now on PSI. The e- in PSII come from the splitting of water molecules, which strips e- from the hydrogen atoms, producing the p+ (the H+ ions), e- for PSII, and oxygen gas. The p+ will be used to form a gradient as e- pass through the ETC.

ATP Synthase

An enzyme that directly generates ATP through the p+ gradient from photolysis and the ETC.

Chemiosmosis

The process of using a p+ gradient and ATP synthase to produce ATP.

Light-Independent Reactions (Calvin Cycle)

These reactions of photosynthesis use the ATP and NADPH, along with carbon dioxide, to produce sugars. They then send ADP, Pi, and NADP+ back to the light-dependent reactions so photosynthesis can occur.

Fixation

Turning a biologically unusable form into a usable form.

Fixation of Carbon

In this, the enzyme Rubisco adds one molecule of carbon dioxide to the five-carbon molecule ribulose-biphosphate (RuBP), producing a six-carbon intermediate that is unstable, which then breaks down further into two three-carbon molecules.

Reduction

Now the ATP and NADPH from the light-dependent reactions are used to reduce the three-carbon molecules. The energy to do this comes from the ATP, and the NADPH provides the hydrogen atoms (reducing power). A three-carbon molecule called G3P is produced at the end of this process, which can be used to make sugars.

Regeneration of RuBP

In order for the Calvin Cycle to continue, the five-carbon RuBP must be regenerated. For every five molecules of G3P (a three-carbon molecule), there are fifteen carbon atoms present. Using ATP from the light-dependent reactions, these five G3P molecules rearrange and form three molecules of RuBP (a five-carbon molecule), which also contains fifteen carbon atoms. This process requires energy, which comes from the light-dependent reactions.

Chloroplasts

Where photosynthesis occurs in plants. They have an outer membrane filled with a liquid called stroma and floating in it are stacks of membranous sacs called grana, and each individual sac is called a thylakoid. Light-independent reactions occur in the stroma and light-dependent reactions occur in the thylakoid.

Photosynthetic Prokaryotes

The light-dependent reactions occur on infoldings of the plasma membrane and the light-independent reactions occur in the cytosol.

Cellular Respiration

The process that cells use to release energy from chemical bonds in food. It includes the cellular processes of glycolysis, the oxidation of pyruvate, the Krebs cycle/citric acid cycle, and oxidative phosphorylation.

Oxygen

The presence or absence of this determines which cellular processes a living organism can use to obtain energy from food.

Anaerobic Organisms

They do not have access to/do not require oxygen and can perform glycolysis and fermentation.

Aerobic Organisms

Those that do not have access to oxygen can perform glycolysis and fermentation, but those in the presence of oxygen can also perform the oxidation of pyruvate, the Krebs cycle, and oxidative phosphorylation. They can perform more metabolic processes than anaerobic organisms can perform, allowing them to extract more energy from organic compounds.

Glycolysis

It occurs in the cytosol of the cell and since all living organisms have cytosol, all living organisms can perform it. The six-carbon molecule glucose enters it, along with two molecules of the e- carrier NAD+. During it, the glucose molecule is oxidized (loses hydrogen atoms and their e-), and each NAD+ is reduced (gains a hydrogen atom and its e-) to NADH. During cellular respiration, the molecules that contain carbon are oxidized and the e- carriers NAD+ and FAD+ are reduced. Two molecules of ATP are required in the early steps of it, but four molecules of ATP are produced by it, so there is a net gain of two ATP molecules. At the end of it, the six-carbon glucose molecule is cleaved into two three-carbon molecules of pyruvate.

Oxidation of Pyruvate

It occurs in the mitochondria. The three-carbon pyruvate molecule must be modified in order to enter the mitochondria. Pyruvate is oxidized and the e- carrier NAD+ is reduced and becomes NADH. As this happens, one of the carbons in the pyruvate molecule is released as carbon dioxide, leaving behind a two-carbon acetyl group. Coenzyme A attaches to this two-carbon acetyl group and will deliver it to the Krebs cycle. Each molecule of glucose that enters glycolysis will generate two molecules of pyruvate, so this step will occur twice for each molecule of glucose that entered glycolysis.

Krebs Cycle/Citric Acid Cycle

It occurs in the matrix of the mitochondria. Coenzyme A brings the two-carbon acetyl group to this, where it is initially attached to a four-carbon intermediate, forming a six-carbon molecule, which goes through a series of enzyme-catalyzed reactions, during which two more carbon dioxide molecules are released and the four-carbon intermediate is regenerated. At the completion of the cycle, all of the carbon that was originally in the glucose molecule at the start of glycolysis has been released as carbon dioxide. During one turn of this cycle, four e- carriers are reduced. Three molecules of NAD+ are reduced to NADH, and one molecule of FAD+ is reduced to FADH2 (2 is lower than the letters). In addition, one molecule of ATP is produced through substrate-level phosphorylation.

Substrate-Level Phosphorylation

The direct addition of a phosphate group to ADP without the use of an ETC or chemiosmosis.

Oxidative Phosphorylation

The e- carriers (NADH and FADH2) that were generated during glycolysis, the oxidation of pyruvate, and the Krebs cycle bring their e- to the ETC on the inner mitochondrial membrane. As these e- carriers deliver their hydrogen atoms and e- to the ETC, NADH and FADH2 are oxidized to NAD+ and FAD+, which can then be reused in the earlier processes of cellular respiration. As the e- travel through the ETC, their potential energy decreases and energy is released, which is used to pump p+ (H+) out of the matrix and into the intermembrane space of the mitochondria, creating a p+ gradient. At the end of the ETC, molecular oxygen (O2) combines with four p+ (H+) and four e- to form two water molecules, making oxygen the final e- acceptor during cellular respiration. Ideally, each NADH that enters the ETC can generate as many as three ATPs and each FADH2 that enters the ETC can generate as many as two ATPs because it has less potential energy than NADH and enters the ETC at a later point. Therefore, this generates 34 ATPs.

Proton Gradient

Drives ATP synthase.

Chemiosmosis

Using a p+ gradient to drive the production of ATP.

ATP Synthase

This enzyme catalyzes chemiosmosis. It is located on the inner membrane of the mitochondria. P+ flow from an area of higher concentration in the intermembrane space to an area of lower concentration in the matrix through a channel in this enzyme. This flow of p+ down their concentration gradient through this causes a shape change in the enzyme, allowing this to catalyze the production of ATP.

Fermentation

During oxidative phosphorylation, NADH is oxidized to NAD+, but if oxygen is not present, oxidative phosphorylation cannot occur. Without oxygen present, the ETC cannot release its low-energy e- from the final carrier, blocking the chain and shutting the entire system down. In anaerobic conditions, cells carry this out to regenerate the NAD+ needed to keep the process of glycolysis going. If a cell ran out of NAD+, it could no longer perform glycolysis, all generation of ATP would stop, resulting in the death of the cell. It occurs in the cytosol.

Alcohol Fermentation

In this, pyruvate is reduced to an alcohol (typically the two-carbon alcohol ethanol) and carbon dioxide, and NADH is oxidized to NAD+.

Lactic Acid Fermentation

In this, pyruvate is reduced to lactic acid (a three-carbon molecule), and NADH is oxidized to NAD+. No carbon dioxide is produced. It can occur in muscle cells if they do not have enough oxygen to carry out oxidative phosphorylation.