Biological Foundations Exam 3

Why do active processes like active transport require us to spend energy?

Convert kinetic energy to move the ball back to the top or moving molecules up a concentration gradient, low concentration to high concentration have to convert kinetic energy to do it

How does breaking down chemical bonds (like ATP) give our cells energy to do work?

The chemical potential energy that is stored in the position of electrons in a covalent bond potential energy in that bond is released as kinetic energy into the environment. In ATP, the sodium and potassium pump breaks down the chemical bonds in ATP, using that energy to move sodium and potassium up their concentration gradients, permanent gradients that the pump creates are a permanent source of chemical potential energy for the cell.

Why does a concentration gradient store energy use entropy?

Molecules are organized on one side of the membrane, low entropy system with lots of chemical potential energy

What is the relationship between entropy and energy?

Increasing entropy reduces the amount of potential energy in a cell’s system because it forces that potential energy to be released as kinetic energy

Second law of thermodynamics

The entropy of a system must always increase overtime, unless we spend energy to oppose it

Why does diffusion occur using the concept of entropy and the second law of thermodynamics?

A low entropy system, like a concentration gradient, the laws of the universe will always drive the atoms or molecules to diffuse and spread out so that the entropy of the system increases

Equilibrium

A state in which the concentrations of the atom/molecules is the same on both sides of the membrane

What is the relationship between energy and the formation/breakdown of covalent bonds?

Chemical potential energy is also stored in the position of electrons in a covalent bond, when covalent bond is broken down by the cell that chemical potential energy is converted into kinetic energy, that released kinetic energy can be used by the cell to do work

Enthalpy

Total amount of potential energy in the chemical bonds of a molecule

Delta H positive

The reaction absorbs kinetic energy from its environment

Delta H is negative

The reaction releases kinetic energy into its environment

Change in enthalpy

Add up the total enthalpy of all the products and subtract the total enthalpy of all the reactants, tells us whether energy is absorbed or released by the reaction

Why is entropy involved in chemical reactions?

Changing the position and order of electrons when performing chemical reactions, also changing the system’s entropy

How does concentrating electrons in chemical bonds change the entropy of a reaction?

Concentrated the electrons into fewer bonds/molecules will decrease the entropy of the system

How does spreading out electrons in chemical bonds change the entropy of a reaction?

Spreading out electrons over more bonds/molecules will increase the entropy of the system

Positive Gibbs free energy

Must absorb energy from the environment to happen, non-spontaneous

Negative Gibbs free energy

Release energy into the environment when they happen, spontaneous

How are reactions with positive Gibbs free energy similar to active transport processes?

They are both non-spontaneous processes. To move a molecule up a concentration gradient, we must use kinetic energy to make active transport happen, and the chemical reaction must absorb kinetic energy to make the chemical reaction happen

How are reactions with negative Gibbs free energy similar to diffusion/passive transport processes?

Molecules diffuse down a concentration gradient spontaneously, releases kinetic energy that the cells use to do work. Chemical reactions will release kinetic energy that the cell can use to do work

Activation energy

Some amount of energy to start the chemical reaction

Why does spontaneous not mean fast when it comes to chemical reactions?

Most spontaneous reactions are very slow because they need some amount of activation energy to get started

How does the amount of activation energy needed for a reaction relate to the speed at which that chemical reaction will happen?

The greater the activation energy, the slower a reaction happens, and the lower the activation energy the faster a reaction happens

Transition state

A temporary molecule where the old bonds are breaking and new bonds are forming at the same time

Why does a transition state require a cell to use energy to make them form?

Very organized, a low entropy state, so the cell must use kinetic energy (activation energy) to make them form

Catalysts

Lowers activation energy which increases the speed of reactions

How are enzymes able to speed up chemical reactions?

Bind the molecules that are part of a chemical reaction, binding to an enzyme lowers activation energy which increases the speed of reactions

Substrates

Reactants of a chemical reaction

Binding

Substrates attach to enzymes in the process

Active site

The place where molecules bind to an enzyme

What are 2 ways that enzymes work?

The binding of the substrates of a reaction to an enzyme puts the substrates in the precise physical orientation needed for the chemical reaction to occur quickly. Old bonds are broken, and new bonds are formed when the side chains of the amino acids in the active site chemically interact with the substrate molecules, both of these ways of working massively reduce

How does the 3D shape of a protein allow enzymes to work?

Allows it to form the precise pattern of non-covalent bonds needed to hold the substrates in the proper physical orientation in the active site

What are the possible consequences of genetic changes that change a protein’s sequence?

Any genetic mutations that change the 3D folding of the protein in the active site will change the effectiveness of the enzyme

Conformational shift

Changes in the shape of a protein

Induced fit model

Shape changes in the protein shifts the amino acid in the active site into the correct position to catalyze the chemical reaction

Metabolic pathway

A series of several chemical reactions

Metabolic chain

The product of the final reaction is different from the initial substrate

Metabolic cycle

The product of the final reaction recreates the initial substrate

How is an enzyme activated?

When a cell “turns up” or “turns on” an enzyme so that it performs its chemical reaction more quickly

How is an enzyme inhibited?

When a cell “turns down” or “turns off” an enzyme so that it performs its chemical reaction more slowly

What is the main way that the cell alters the ability of its enzymes to perform chemical reactions?

Temporarily altering the 3D shape of the enzyme, changes the speed at which an enzyme performs a chemical reaction

Allosteric site

Enzymes that use this regulation have a second binding site

Regulatory molecule

Allosteric site can bind a molecule

How are enzymes regulated using allosteric regulation?

Systems that can inhibit or activate a protein when a regulatory molecule binds to an allosteric site on an enzyme

How does allosteric activation occur?

When activating an enzyme, a binding site by default binds poorly when the regulatory molecule binds to the enzyme it changes shape so that the substrates now bind easily, and the reaction happens faster

How does allosteric inhibition occur?

By default the active site binds the substrate very easily and when the regulatory molecule binds to the allosteric site and changes the shape of the active site the substrate binds poorly

How does inhibition phosphorylation occur?

By default binds substrates very easily and when a phosphate is added goes through a shape change so the active site binds the substrate very poorly

How does activation phosphorylation occur?

By default binds substrates very poorly and when a phosphate is added it goes through a shape change so that the active site binds the substrate very easily

Competitive inhibition

Regulatory molecule binds to the active site and blocks the substrates from binding

Why do cells have to break down glucose slowly in a metabolic chain rather than burning it?

For cells to harvest this kinetic energy, they have to break down glucose slowly, a few chemical bonds at a time

How does the ATP-ADP cycle work?

When ATP is broken down by hydrolysis, one of its phosphates is removed, converting the potential energy in the phosphate bond to be released as kinetic energy, creating two products, an unattached phosphate and ADP

What are the two ways of capturing energy from glucose?

Substrate-level phosphorylation and electron transfer

Electron carrier

Electrons are transferred to another molecule

ADP

A substrate of an enzyme, 2 phosphate

What happens in substrate-level phosphorylation from ADP to form ATP?

A phosphate is taken from another molecule and added to ADP through a chemical reaction on an enzyme forming ATP, 3 phosphates

What are the 2 phases of glycolysis?

Energy investment phase and energy payoff phase

What molecules are spent or produced in the energy investment phase of glycolysis?

Split glucose into two identical molecules, reactions have a positive Gibbs free energy so spend energy to make them happen, this energy comes from the breakdown of 2 molecules of ATP

What molecules are spent or produced in the energy payoff phase of glycolysis?

4 ATP molecules and 2 NADH molecules is created and 2 pyruvate molecules

What is the net effect of glycolysis?

2 ATP molecules, 2 NADH molecules, 2 pyruvate molecules

Feedback inhibition

To regulate glycolysis, a regulatory molecule is produced by the enzymes in the metabolic chain, an enzyme is inhibited with the exact same mechanism as allosteric inhibition

Why is feedback inhibition a special type of allosteric inhibition?

Regulatory molecule produced by the enzymes of the metabolic pathway bind to allosteric site

PFK (Phosphofructokinase)

An enzyme that phosphorylates the molecule fructose-6-phosphate

How does the cell use ATP levels to regulate PFK?

When ATP in the cell gets close to its maximum levels, then ATP will bind to PFK, slowing down the metabolic chain of glycolysis. When ATP in the cell starts being used up again and its levels go down, ATP will unbind from PFK, returning to its default shape

Why must the cell regulate the speed of glycolysis?

The cell does not need to make more ATP by breaking down glucose when at maximum levels, so ATP binds to PFK and inhibits the enzyme, slowing down glycolysis. ATP used up by the cell again the cell will need to start making more ATP again, so ATP unbinds from PFK and activates glycolysis

In electron transfer what is one of the ways of capturing energy from glucose?

NAD+ and FAD are electron carrier, energy is removed from glucose carried by NADH and FADH2 to the electron transport chain

What is the mitochondria structure?

Nucleus has a double membrane structure, the outer membrane faces the cytoplasm, the inner membrane faces the inside of the organelle, and between the two membranes is a fluid filled intermembrane space. Inner membrane is folded into sacs, cristae, and the innermost space of the organelle is the matrix

Where does glycolysis of cellular respiration happen in the cell?

In the cytoplasm of every type of living cell, in both eukaryotes and prokaryotes

Where does pyruvate processing of cellular respiration happen in the cell?

Matrix of mitochondria in eukaryotic cells and in the cytoplasm of prokaryotic cells

Pyruvate processing

One reaction converts pyruvate into acetyl-CoA, the first place we make CO2 in oxidation of glucose

Where does the citric acid cycle of cellular respiration happen in the cell?

In the mitochondrial matrix

Where does electron transport of cellular respiration happen in the cell?

Inner membrane of mitochondria or plasma membrane of prokaryotes

What goes in and what comes out in pyruvate processing?

In: 2 molecules of pyruvate and 2 molecules of NAD+

Out: 2 molecules of acetyl-CoA, 2 molecules of NADH, 2 molecules of carbon dioxide (CO2)

Isocitrate dehydrogenase

As NADH levels go up it binds to the active site of the enzyme, prevents the substrate from binding

Pyruvate dehydrogenase (PDH)

Processing of pyruvate performed by an enzyme

Pyruvate dehydrogenase kinase

Inhibit pyruvate processing by phosphorylating PDH, pyruvate dehydrogenase

How does kinase regulate the activity of pyruvate dehydrogenase (PDH)?

It’s responsible for turning off the PDH enzyme by adding a phosphate group to it, stopping the pyruvate process when ATP, NADH, or acetyl-CoA levels start to rise above their maximum. When the cell needs to restart pyruvate processing, it will remove the phosphate, which activates the PDH enzyme

What happens in the citric acid cycle?

Break down the remainder of the original glucose molecules into carbon dioxide

What goes into the reactions and what comes out in the citric acid cycle?

In: 2 molecules of acetyl-CoA, 6 molecules of NAD+, 2 molecules of FAD, 2 molecules of ADP

Out: 4 molecules of CO2, 6 molecules of NADH, 2 molecules of FADH2, and 2 molecules of ATP

How does NADH regulate the citric acid cycle?

It regulates isocitrate dehydrogenase by competitive inhibition, when the levels of NADH are high it will bind to the active site and block the enzyme from performing its chemical reaction, slowing down the citric acid cycle

Why does NADH regulate the citric acid cycle?

If NADH levels are extremely high then NAD+ levels are extremely low, running out of NAD+ will stop the reactions that break down glucose immediately because glucose breakdown requires us to use NAD+ to from NADH

What is the net effect of glucose breakdown?

In: 1 molecule of glucose, 10 molecules of NAD+, 2 molecules FAD, 4 molecules of ADP

Out: 6 molecules of CO2, 10 molecules of NADH, 2 molecules of FADH2, and 4 molecules of ATP

What are the 2 ways that NADH is cycled back to NAD+?

Electron transport chain and fermentation

What happens in the electron transport chain?

Receives electrons NADH and FADH2 as the electrons flow through the transport chain, the protons of the chain pump hydrogen ions from the mitochondrial matrix to the intermembrane space, creating the proton gradient

How does fermentation occur in human cells?

Recycle NADH to NAD by reacting the electrons it carries with pyruvate to form lactic acid

Proton gradient

Transport of hydrogen ions across the inner mitochondrial membrane from the matrix into the intermembrane space

How is a proton gradient generated?

Converts the chemical potential in the electrons into a concentration gradient, releasing that energy by diffusing down their concentration gradient

Where is the proton gradient generated?

In the mitochondria

How is the proton gradient used to make ATP?

The energy released by diffusion of protons

Oxidative phosphorylation

ATP is made by the energy released from electron transport

ATP synthase

An enzyme that produces ATP by allowing proton gradient to diffuse and release energy

What is the major limitation of oxidative phosphorylation?

Dependence upon oxygen as the terminal electron acceptor

How do cells deal with not having enough oxygen?

It must cycle some of its electron carriers using fermentation

Why is fermentation sometimes necessary?

If there is not enough oxygen to process all of the NADH the cell is making then NADH levels will rise and the cell will run out of NAD+, this process allows to recycle NAD+ while still making a little bit of ATP using glycolysis

What are the two separate reactions happening simultaneously for both cellular respiration and photosynthesis?

Glucose breakdown and electron transport chain in cellular respiration and in photosynthesis light capture and carbon dioxide capture

What are the two photosystems of photosynthesis?

Photosystem 1 and photosystem 2

Where are the photosystems located in the chloroplast?

In the thylakoid membrane

What kind of pigment do photosystems use?

Chlorophyll pigments

What do the chlorophyll pigments do?

Electrons that can be energized when struck by photons of light

How does photosystem 2 work?

1) Energy in light is captured by photosystem 2 when it strikes a part of the photosystem, light light-harvesting complex 

2) The light-harvesting complex then transfers that energy to a chlorophyll-containing region, the reaction center

3) Electrons in the reaction center are energized by the transferred light energy

4. A molecule called pheophytin will remove energized electrons from the reaction center

5) Pheophytin passes the electrons into the photosynthetic electron transport chain (ETC)

6. The photosynthetic ETC pumps hydrogen ions from the chloroplast stroma to the thylakoid lumen, creates proton gradient (hydrogen ions are in high concentration in the lumen and low concentration in the stroma)

7) An ATP synthase enzyme allows hydrogen ions to diffuse down their concentration gradient (high to low), use transport coupling to use the energy released by diffusion of hydrogen ions to make ATP, get the energized electrons in the form of light, photophosphorylation

Photolysis

Water-splitting reaction that replaces the electrons we took from photosystem 2

Why photolysis is necessary?

The hydrogen ions will be added to NADP to become NADH and the electrons are used to replace the ones we took from photosystem 2