Exam 2: Bioenergetics and Enzymes, Membranes, Compartments, and Transport

How does cell concentration influence the favorability of processes?

High to low concentrations (left to right):

High (concentration of reactants) to low (concentrations of products) concentrations drives the reaction forward. This movement follows the net direction of the cell (a.k.a down the concentration gradient which is the path of least resistance), meaning delta G is negative . High to low concentrations are energetically favorable because they decrease the net potential energy of products- resulting in a more stable state and a spontaneous process. No additional energy is needed for the process to occur. This process also releases energy for the cell to use. (Exergonic)

Low to high concentrations (right to left):

Low (concentrations of reactants) to high (concentrations of products) concentrations are reverse reactions. This movement moves against the concentration gradient/ net direction for the cell, meaning delta H is positive. Low to high concentrations are energetically unfavorable because they require energy input (the products have a higher net potential energy. This makes the process less likely to occur spontaneously. (endergonic)

Note: Favorable processes moves system closer to equilibrium, unfavorable processes move system away from equilibrium.

Why do energetically favorable processes release energy?

Because the products are in a lower energy state than the reactants. Energy is released when more stable bonds are formed in the products. (These bonds are lower in energy than the bonds broken in the reactants).

What does delta G describe in Gibb’s free energy?

Delta G describes the amount of energy released by or required for a reaction or process, as well as how far away from equilibrium a system is

Why do cells need a constant energy input? How do do they achieve this?

Cells need a constant energy input to maintain disequilibrium. Disequilibrium conditions provide potential energy for other work. They achieve this through cellular respiration. A process that break down glucose to release energy that is stored in ATP molecules. ATP is the energy currency of the cell.

Note: This means cells are constantly making ATP through cellular respiration.

-Cells use these non-equilbrium conditions as sources of energy

How do cells carry out unfavorable synthesis reactions?

The dephosporylation (removal of a phosphate group) of ATP releases free energy, to form ADP and a free phosphate group. The unfavorable synthesis reaction is coupled with this favorable reaction (ATP hydrolysis).

What is the definition of equilibrium?

The natural tendency for the system to proceed towards its lowest energy state. At equilibrium there’s no net movement- molecule movement into the cell occurs at the same rate as movement out of the cell.

Note: At equilibrium there’s no energy to do work.

What is the definition for a chemical reaction?

A chemical reaction involves the breaking and forming of covalent bonds as reactant are converted to products.

What is the definition of a couple reaction?

Linking reactions that release energy to reactions that require energy.

Explain how coupling an unfavorable reaction to ATP (favorable reaction) help drive the unfavorable reaction?

By using the phosphates from ATP. The first reaction creates an activated phosphorylated intermediate, which has a higher potential energy than the original reactant. The activated phosphorylated intermediate makes the next reaction energetically favorable.

This provides the necessary energy through the transfer of a phosphate group, making the overall process spontaneous.

Note: The energy released by the breaking down of the ATP makes it a highly favorable reaction

What does a reaction being spontaneous mean?

Spontaneous means no net energy input is required for this reaction to occur?

What does activation energy mean?

The energy level of molecules needed for a reaction to occur. This is energy needed from chemical reactions to occur.

How does increasing temperature affect a molecule’s activation energy?

Increasing temperature increases the number of molecules that are above the activation energy, and are able to form products. The temperature increase, increases the reaction rate, as more molecules have sufficient energy to react.

How do enzymes (proteins) affect chemical reactions?

Enzymes (protein) are able to speed chemical reactions by lowering the activation energy of those chemical reactions.

How do enzymes and substrates bind?

They bind by making transient covalent and weak non-covalent IMF’s (H-bonds, ionic, hydrophobic clustering, and LDF’s)

How is enzyme function regulated?

By allosteric inhibitors. They change the shape of the enzyme. This either prevents the enzyme from catalyzing the reaction or it can speed up the reaction depending on how they change the shape of the enzyme.

How does competitive inhibition and non competitive inhibition differ?

-With competitive inhibition, the competitive inhibitior binds to the active site, competing with the substrate-slowing down the reaction rate.

-With non competitive inhibition, the non competitive inhibitior binds to a site other than the active site, changing the shape of the enzyme.

What internal compartment does eukaryotic cells have that prokaryotic cells don’t?

Eukaryotic cells have plasma membranes. These membranes contain amphipathic lipids and proteins.

Note: amphipathic means containing distinct polar and non-polar regions

What are phosoplipids and explain what they form and explain how they affect the membrane.

Phosolipids are the main lipid found in membranes.

Phosolipids form bilayers in aqueous, neutral pH environments. In an aqueous many will form a bilayer with no energy input needed.

Hydrophobic clustering forms the membrane, and the bilayer arrangement minimizes the interactions between the hydrophobic tails. The LDF’s formed between the fatty acid tails affect the fluidity of the membrane.

How does temperature, saturation, and length of the fatty acid tail all respectively help regulate membrane fluidity?

Temperature:

Temperature increasing makes the membrane more fluid, temperature decreasing makes the membrane less fluid.

Saturation:

An increase of saturation decreases membrane fluidity, a decrease of saturation increases membrane fluidity.

Length:

Shorter fatty acid tails increase membrane fluidity, longer fatty acids decrease membrane fluidiity.

Why is cholesterol a key membrane in animal cells?

The amphipathic structure of cholesterol allows it to pack tightly with phospholipids.

Why do small, non polar molecules pass more easily across the membrane than polar charged, and larger molecules?

Because to pass through the membrane, a substance has to travel through the hydrophobic non-polar tails- so usually the substance has molecules that are non-polar and small. Non-polar molecules are able to interact with non-polar tails in the membrane, making them more compatible.

Note: Molecules that aren’t small or non-polar will need membrane proteins for efficient transport.

How do the delta G’s of synthesis reactions and breakdown reactions differ? What do the signs of delta G tell you about the forward and reverse reactions.

Synthesis reactions generally have a positive delta G, while breakdown reactions generally have a negative Delta G.

• If delta G is negative, the forward reaction (forming C+D) occurs more than the reverse reaction.

• If delta G is positive, the reverse reaction (forming A+B) occurs more than the forward reaction

Explain Le Chatelier’s Princicple.

A principle that says when a system in equilibrium is stressed (a change in molecule concentration), the system shifts to relieve the stress and re-establish equilibrium.

• If concentration of reactants increases, more product is produced in response

• If concentration of products increases, more reactant is produced in response

Explain the function of the nucleus.

The nucleus houses the genome and is the site of transcription (produces RNA). It’s surrounded by a double membrane called the nuclear envelope, Small molecules and ions can passively diffuse through the pores, but larger proteins and RNA require active transport)

Explain the function of the endoplasmic reticulum (ER)

The ER is involved in protein and lipid synthesis. The synthesis of protein is destined for secretion of specific organelles in the cell. It also synthesizes fatty acids and phosoplipids (Smooth ER)

Explain the function of the golgi apparatus.

The golgi apparatus modifies and sorts proteins. It adds sugar molecules to proteins (glycosylation), helps fold them correctly, and protects proteins from degradation. It also sorts the proteins for transport to other organelles (lysosome).

Explain the functions of the lysosome.

The lysosome recycles macromolecules via hydrolysis (a reaction where molecules are broken down with water). It breaks down Marco molecules to their monomer components.

The acidic environment is essential for the lysosome to function. Most enzymes only function when the pH is near 7. Changes in pH can alter the tertiary protein structure. Acid hydrolases (the enzyme) can only function in an acidic pH of 5.

To keep acidic environment, a proton pump transport H+ into the lysosome. As the proton concentration increases the pH becomes more acidic (pH decreases) then the environment. The acid hydrolase proteins break down the macromolecules using hydrolysis reactions.

Other transporters move breakdown products into the cytosol, where they can be reuse. As transporter moves, it removes protons (decreasing the pH).

Note: Hydrolysis the opposite of dehydration synthesis (the process that turns nucleotides into nucleus acids and amino acids into proteins). It’s a reaction that joins molecules, resulting in a release of water

-Protons are only there to increase pH and aren’t involved in the reaction to breakdown macromolecules.

Explain the function of the mitochondria (animal) and chloroplasts (plants).

The mitochondria and chloroplasts are involved in cellular energy management. The mitochondria carries out cellular respiration in all types of eukaryotic cells.

In plant cells, the chloroplasts carry out photosynthesis.

Note: Mitochondria and chloroplasts have their own DNA.

Give the definition for both passive transport and active transport.

Passive transport: Occurs by diffusion: the random movement of moleculoes. Passive transport involves diffusion- the net movement is down the concentration gradient, toward equilbrium and requires no additional energy.

Active transport: uses ATP (energy) to move polar solutes away from equilibrium (primary). Concentration gradients across membranes represent disequilibrium conditions (these conditions store potential energy).

• Primary: uses ATP (energy) to move polar solutes away from equilibrium (against concentration gradient)

• Secondary: Utilizes an established electrochemical gradient (created by primary active transport) to power the movement of molecules against their gradient.

What is the difference between simple diffusion and facilitated diffusion.

Simple diffusion is the movement of molecules directly across a cell membrane without the help of any transport proteins, while facilitated diffusion involves the movement of molecules across a membrane with the assistance of specific carrier or channel proteins embedded within the membrane.

Explain how ATP moves solutes against their concentration gradients in their

What is the definition for metabolism and metabolic pathways?

Metabolism: The sum of all reactions occuring the cell.

Metabolic Pathways: Series of reactions. The product of one step is a reactant for the next step in the pathway.

Name and explain the two types of anabolic pathways.

Anabolic Pathways: Are synthesis pathways and are a series of chemical reactions to create more complex molecules from simpler molecules. Requires energy input and is energetically unfavorable if not coupled.

Catabolic Pathways: Are breakdown pathways and are a series of chemical reactions to convert more complex molecules into simpler molecules. Releases energy and is energetically favorable

Name the common energy management molecules and explain how they interact with the two types of metabolic pathways.

Common energy management molecules are ATP and NADH/NADPH

Catabolic: The energy released by catabolic pathway reactions is used to produce ATP and NADH/NADPH.

Anabolic: ATP and NADH/NADPH provide energy to anabolic pathways reactions that require energy.

Note: You can use the energy management molecules reactions to predict whether a reaction is a part of catabolic or anabolic pathways.

Explain how energy management molecules perform in their own chemical reactions.

• ATP to ADP reactions by transferring phosphates.

  -releases energy

• NAD+ to NADH and NADP+ to NADPH reactions transfers electrons.

  -A proton (1) and electrons ( 2e-) are added to NADH, leaving behind a proton that’s donated to surrounding environment.

Give a definition of redox reactions.

Redox reactions involve the transfer of electrons from one molecule to another. Redox in biologic reactions often involves gain or loss of bonds between carbon and hydrogen.

What are the differences between reduction and oxidation?

Oxidation: Oxidation is a loss of electrons A loss of bonds between C and H, but a gain of bonds between C and O.

Reduction: Reduction is a gain of electrons. A gain if bonds between C and H, but a loss of bonds between C and O.

How can can cells keep a reaction favorable as it moves towards equilibrium (delta G become less negative)

Since Delta G is the sum of all the individual reactions in the pathway, (even if some reactions are unfavorable), as long as the net some is favorable the process will still happen.

Explain how substrate concentrations influence the favorability of reactions.

• Increased substrate concentrations make a reaction more favorable. Delta G of the forward reaction becomes more negative as the system moves away from equilibrium.

• Decreased substrate concentrations make a reaction less favorable. Delta G of the forward reaction becomes more positive as the system moves toward equilibrium.

Explain how product concentrations influence the favorability of reactions.

If the product concentration is high, the reaction is unfavorable.

• Decreased product concentrations make the reaction more favorable. The delta G of the forward reaction becomes more negative as the system moves away from equilibrium.

• Increase product concentrations make the reaction less favorable. The delta G of the forward reaction becomes more positive as the system moves toward equilibrium.

What must cells do to maintain the metabolic pathways, cellular respiration and photosynthesis?

• Couple favorable and and unfavorable processes

• Maintain high substrate concentrations

• Maintain low product concentrations

Explain osmosis and how aquaporins effects solute concentrations.

Osmosis is the movement of water across a selectively permeable membrane. Solute concentrations are not at equilibrium, but solutes can’t cross membranes, but water movement is towards equilbrium. Water always follows solutes, meaning water moves across the membrane from areas of low concentrations to areas of high concentrations.

Aquaporins are proteins that function as water channels across cell membranes. They’re needed to facilitate to movement of water in the cell.

• Hypertonic: Contains a high solute concentration. Water flows out of the cell and the cell shrinks.

• Isotonic: Similar or the same solute concentration. Water flows in and out of the cell at the same time. Cell is kept stable.

• Hypotonic: Contains a low solute concentration. Water flows into the cell and the cell swells or burst.

Note: Osmosis is facilitated diffusion

Explain where energy to produce ATP comes from?

It comes from cellular respiration. Which takes glucose in the presence of oxygen and breaks it down into CO2 and water. This releases energy that can be used to produce ATP.