bio unit 3

ap biology

What is the monomer that makes up an enzyme?

What is the monomer that makes up an enzyme?

Amino acids (proteins)

How does a substrate bind to an enzyme?

Via its active site; When the substrate enters the active site, it forms a weak bond with the enzyme, inducing a shape change on the enzyme. This change allows additional weak bonds to form, causing the active site to enfold the substrate and hold it in place.

What happens after the substrate binds to the enzyme?

There is a slight shape change in the enzyme when the active site of the enzyme interacts with the chemical groups of the substrate. This shape changes allows the enzyme to fit better to the substrate.

What is the function of an enzyme?

Catalyze chemical reactions

How does the enzyme complete its function?

Lower the activation energy so that the reactants can absorb enough energy to reach the transition state

How does an enzyme affect the rate of biological reactions?

Speeds them up; lowers the activation energy so that the reaction is faster

What is an enzyme-catalyzed reaction?

A reaction that uses an enzyme to catalyze the rate of the reaction

How is the activation energy of an enzyme-catalyzed reaction and an uncatalyzed reaction different?

The activation energy is lower in an enzyme-catalyzed reaction and higher in an uncatalyzed reaction

How is the change in free energy of an enzyme-catalyzed reaction and an uncatalyzed reaction different?

Enzymes do not affect the Gibbs free energy of a reaction. That means that they do not increase or decrease how much products are formed and how much reactants are used up nor do they increase or decrease the free energy values of the products and reactants.

How is the reaction rate of an enzyme-catalyzed reaction and an uncatalyzed reaction different?

The reaction rate of an enzyme-catalyzed rxn is much faster.

Identify two conditions that affect the structure of an enzyme. What happens to the structure of the enzyme in these conditions?

Temperature: thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures.

pH: would be denatured in unsuitable pH

How does a change in structure affect the function of an enzyme?

If the structure of the enzyme changes then the function will also change (it won't be functional).

Predict the three different possible outcomes when there is a change in structure of an enzyme.

Active site will be affected and substrate cannot bind; enzyme's function is impaired; enzyme is denatured

What is denaturation?

Alteration of a protein shape through some form of external stress (for example, by applying heat, acid or alkali), in such a way that it will no longer be able to carry out its cellular function.

True or False? Denaturation can be reversible.

True

Identify one example of a protein that is reversible after denaturation.

Insulin

Identify one example of a protein that is nonreversible after denaturation.

Cooking an egg (the egg white) is nonreversible

What happens to the pH when the concentration of hydrogen ions increases?

pH decreases (more acidic)

What happens to the pH when the concentration of hydrogen ions decreases?

pH increases (more alkaline)

What happens to an enzyme when the pH increases?

This depends on the enzyme. Pepsin is an enzyme found in the stomach, which works best in an acidic environment. If it is not in its ideal pH, it will most likely denature.

What happens to an enzyme when the pH decreases?

This depends on the enzyme. Trypsin is an enzyme found in the human intestine works best in an alkaline environment. If it is not in its ideal pH, it will most likely denature.

How does the concentration of reactants affect the reaction rate?

Increasing the concentration of one or more reactants will often increase the rate of reaction. This occurs because a higher concentration of a reactant will lead to more collisions of that reactant in a specific time period.

How does the concentration of products affect the reaction rate?

It does not.

What happens to an enzyme when the temperature increases?

Generally, an increase in temperature increases the reaction rate, but there is a threshold. Too high of a temperature may denature the protein.

What happens to an enzyme when the temperature decreases?

A decrease in temperature slows down the kinetic energy of the molecules, causing less collisions, so it is less likely that an enzyme will come into contact with its substrate causing the reaction rate to decrease.

How does a change in temperature affect the molecules in the reaction?

Temperature makes the molecules move faster, increasing the rate of reaction

What is a competitive inhibitor?

A competitive inhibitor mimics the substrate, competing for the active site.

How can a researcher overcome a competitive inhibitor?

You can increase the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites.

What is a noncompetitive inhibitor?

Noncompetitive inhibitors bind to the enzyme away from the active site, altering the shape of the enzyme so that even if the substrate can bind, the active site functions less effectively, if at all.

How does an inhibitor affect the reaction rate?

Slow down or even stop the catalyst.

What is the first law of thermodynamics?

Energy is neither created nor destroyed, only transferred.

What is the second law of thermodynamics?

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

How is order (entropy) maintained in a system?

Organisms create ordered structures from less organized starting materials. As open systems, organisms can increase their order as long as the order of their surroundings decreases, with an overall increase in entropy in the universe.

How are cellular processes powered?

Free energy

What is an endergonic reaction?

Absorbs free energy from the surroundings

What is an exergonic reaction?

Net release of free energy into the surroundings

What is energy coupling?

The use of an exergonic process to drive an endergonic one. Oxidative phosphorylation works by using energy-releasing chemical reactions to drive energy-requiring reactions. The two sets of reactions are said to be coupled. This means one cannot occur without the other.

What happens if an organism has a loss of energy or energy flow?

Energy is lost as heat, which organisms cannot use to form usable energy

Why does the cell undergo the step-wise function to control energy release through cellular respiration?

If energy is released from a fuel all at once, it cannot be harvested efficiently.

In a metabolic pathway, how does the product of one reaction relate to the reactants of the subsequent reaction?

Each step in the reaction creates a product or free energy that will be used in a subsequent reaction.

Where does the energy that fuels photosynthesis come from?

Sun

What organism first evolved photosynthesis?

Oxygenic photosynthesis originated in an ancestor of Cyanobacteria when an anoxygenic photosystem gave rise to a water-splitting photosystem

Identify one piece of evidence that supports oxygenation of atmosphere from cyanobacteria.

As the oceans became more oxygenated, the oxygen started entering the atmosphere, which formed rust on iron ore.

What are the light-dependent reactions?

The light-dependent reactions use light energy to make two molecules needed for the next stage of photosynthesis: the energy storage molecule ATP and the reduced electron carrier NADPH.

Where do the light-dependent reactions take place?

Thylakoid membrane

How is ATP synthesized in the light-dependent reactions?

ATP synthase via a proton-motive gradient

How is NADPH synthesized in the light-dependent reactions?

NADP+ picks up 2 electrons and a H+ to form NADPH

What is chlorophyll?

Main light capturing pigment

How does chlorophyll aid in energy capture?

Captures red-violet light and excites electrons

Where is chlorophyll located?

Chloroplasts; specifically in photosystems in thylakoid membrane

What happens to the electrons after energy from light?

They become excited and jump to first Electron Transport Protein (ETC)

How is the photosystem organized to aid in energy capture?

Photosystems, large complexes of proteins and pigments that play a key role in the light reactions. There are two types of photosystems: photosystem I (PSI) and photosystem II (PSII). Both photosystems contain many pigments that help collect light energy, as well as a special pair of chlorophyll molecules found at the core (reaction center) of the photosystem.

As the electrons are passed to each photosystem, they will be excited from energy that chlorophyll has captured.

How is the thylakoid membrane organized to aid in energy capture?

It provides a membrane for the ETC, and a space for H+ to collect to form a gradient. The H+ will flow through the ATP synthase to create ATP.

What is the relationship between the photosystem and the electron transport chain?

Photosystems have chlorophyll molecules inside, which energize the electrons that move through the ETC.

What direction are the protons pumped during the light dependent reactions to generate the proton gradient?

From the stroma into the thylakoid interior

How does the proton gradient result in ATP synthesis?

The H+ will flow down the gradient from an area of high H+ concentration (thylakoid space) to an area of lower H+ concentration (stroma) through the ATP synthase providing energy to synthesize ATP

What is the relationship between the light reactions and the Calvin cycle?

The ATP and NADPH produced from the light reactions will provide energy for the Calvin cycle.

Identify the products of fermentation.

Fermentation is a way to oxidize fuel and generate ATP without oxygen. Fermentation breaks down glucose to pyruvate (glycolysis) and releases 2 ATP and NADH. The NADH is used to break down pyruvate into the byproduct.

Products of fermentation depend on the type:Alcoholic fermentation: pyruvate is converted to ethanolLactic acid fermentation: pyruvate is converted to lactic acid

Identify the products of cellular respiration.

Cellular respiration has 3 steps:1. Glycolysis (glucose to pyruvate; 2 NADH)2. Pyruvate oxidation and citric acid cycle (Acetyl coA, 6 NADH, 2 FADH23. Oxidative phosphorylation (ATP)

What is the electron transport chain?

Collection of molecules embedded in the inner membrane of the mitochondrion in eukaryotic cells

Identify the three locations of the electron transport chains in cells.

Thylakoid membrane (photosynthesis), inner mitochondrial membrane (respiration), prokaryotic plasma membrane (respiration)

What is the pathway of electrons through the process of cellular respiration? (where do the electrons start, what carries the electrons, where do the electrons end)

Electrons come from fuel being oxidized (oxidation is the loss of electrons).

NADH and FADH2 carry electrons to the chain, which give the protein complexes energy to pump H+ into the intermembrane space. O2 is the final acceptor of electrons. Each protein complex is more and more electronegative, so the electrons are pulled to each successive complex.

Identify the final electron acceptor in the electron transport chain of Photosynthesis

NADPH

Identify the final electron acceptor in the electron transport chain of Cellular respiration

O2

How do electrons move through the electron transport chain?

Electrons move from a less electronegative electron carrier to a more electronegative electron carrier down the chain, releasing free energy.

Moved through to the chain via NADH and FADH2 to give each protein pump energy.

What process generates the proton gradient?

The ETC is an energy converter that uses the exergonic flow (release of free energy) of electrons from NADH and FADH2 to pump H+ across the membrane creating a gradient

What direction do the protons get pumped to generate the proton gradient in cellular respiration?

From the matrix to the intermembrane space

How does the proton concentration the pH of the area?

More H+ ions, more acidic pH

Identify two differences between the electron transport chain in prokaryotes and eukaryotes.

Prokaryotes- ETC in plasma membrane Creates gradient by pumping H+ ions out of cell. Eukaryotes- ETC in cristae membrane Creates gradient by pumping H+ ions into intermembrane space

What is chemiosmosis?

The H+ gradient that results is referred to as the proton-motive force, meaning it can do work. The force drives H+ channels provided by ATP synthases. Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to do work. ATP synthesis is the work performed.

What is oxidative phosphorylation?

Oxidative phosphorylation is the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH 2 to O 2 by a series of electron carriers

What is photophosphorylation?

Photophosphorylation is the process of utilizing light energy from photosynthesis to convert ADP to ATP. It is the process of synthesizing energy-rich ATP molecules by transferring the phosphate group to ADP molecules in the presence of light.

What is an endotherm?

Organism that maintains a constant body temperature independent of the environment "warm blooded".

How do endotherms maintain their body temperature?

Organisms that maintain their internal temperature independent of the outside environment. The temperature is metabolically favorable. To generate heat endotherms convert the food that they eat into energy through metabolism. Most of the food that an endotherm eats is turned into fuel to maintain a constant body temperature.

What is decoupling oxidative phosphorylation? How does it generate heat?

Oxidative phosphorylation works by using energy-releasing chemical reactions to drive energy-requiring reactions. The two sets of reactions are said to be coupled. This means one cannot occur without the other.

Remember coupling is using an exergonic rxn to drive an endergonic rxn.

What would happen to the energy stored in the proton gradient if it weren't used to synthesize ATP or do other cellular work? It would be released as heat, and some types of cells deliberately use the proton gradient for heat generation rather than ATP synthesis. It's an important strategy for animals that need to keep warm. For instance, hibernating mammals have specialized cells known as brown fat cells. In the brown fat cells, uncoupling proteins are produced and inserted into the inner mitochondrial membrane. These proteins are simply channels that allow protons to pass from the intermembrane space to the matrix without traveling through ATP synthase. By providing an alternate route for protons to flow back into the matrix, the uncoupling proteins allow the energy of the gradient to be dissipated as heat.

What is glycolysis?

Glycolysis is the oxidation (loss of electrons) of glucose to pyruvate.

What are the starting materials of glycolysis?

Glucose Requires 2 ATP to get reaction started

What are the products of glycolysis?

Products: 2 Pyruvate, 2 NADH, 4 ATP (net 2; used 2 to start)

Where does it take place in the cell?

Location: cytosol

Based on the location of glycolysis, what statement can be made about evolutionary history?

All organisms carry out glycolysis in cytoplasm. The first prokaryotes did not have access to a large supply of oxygen in the early Earth atmosphere, so they likely had to use glycolysis to create ATP. Eukaryotes did not always have a mitochondria.

What is the Krebs cycle? What are the starting materials?

Pyruvate enters the mitochondria via active transport and is converted to acetyl coA.

What are the products of krebs cycle?

Acetyl CoA is further oxidized during the citric acid cycle, producing 2 ATP, 6 CO2, 8 NADH, and 2 FADH2

Where does krebs cycle take place in the cell?

This happens in the matrix.

How are electrons transported to the electron transport chain in cellular respiration?

FADH2 and NADH carry electrons to the ETC

Where is the electron transport chain located?

Intermitochondrial membrane

What occurs as electrons are transferred from one cytochrome to the next in the electron transport chain?

More free energy is released, H+ are pumped through the membrane forming the proton-motive gradient, electrons are passed to the next protein complex.

What is the function of fermentation?

Fermentation is the metabolic process following glycolysis where pyruvate is converted into alcohol or lactic acid in the absence of oxygen or any electron transport chain. Fermentation pathways regenerate NAD+ which is used in glycolysis to release energy in the form of ATP.

What are the products of fermentation?

Alcoholic fermentation: Pyruvate + NADH → ethanol + CO2 + NAD+Lactic acid fermentation:: Pyruvate + NADH → lactic acid + NAD+

What is the function of ATP hydrolysis?

Energy! Removal of phosphates releases energy.

How does variation at the molecular level affect the organism's ability to respond to environmental stimuli?

Variation at the molecular level provides organisms with the ability to respond to a variety of environmental stimuli

How does this variation in number of molecules lead to a selective advantage?

Variation in the number and types of molecules within cells provides organisms a greater ability to survive and/or reproduce in different environments.

How does this variation in types of molecules lead to a selective advantage?

Variation in the number and types of molecules within cells provides organisms a greater ability to survive and/or reproduce in different environments.

Hopefully you can make the connections yourself—think about the decoupling proteins and heat production in endotherms, or compartmentalization of cells, or how much more chemical energy is produced in eukaryotes that have a mitochondria vs prokaryotes that ferment.