BI108 Quiz #2

Electrical Energy

Energy related to interactions among charged particles.

Thermal Energy

The energy of motion in ions and molecules, measured as temperature.

Potential Energy

Energy that is related to an object's position.

Chemical Reaction

Conversion of substances (ions or molecules) into other substances via breaking and forming chemical bonds.

Free Energy

The total energy available to do work—a combination of entropy and thermal and potential energy.

Energetic Coupling

A phosphorylation reaction that makes a nonspontaneous reaction spontaneous, because it raises the free energy of the reactants. Uses free energy released from spontaneous reactions to drive nonspontaneous reactions

Endergonic Reaction

One that results in an increase in free energy; another way of referring to a nonspontaneous reaction.

Exergonic Reaction

One that results in a decrease in free energy; another way of referring to a spontaneous reaction.

Activation Energy

The amount of energy required to get a chemical reaction through its transition state.

Transition State

During a chemical reaction, an intermediate state where old bonds are being broken but new bonds have not yet formed.

Enzyme

A protein that catalyzes a chemical reaction.

Active Site

The place on an enzyme (or ribozyme) where a reaction is catalyzed.

Redox (reduction-oxidation) reactions

Chemical reactions involving the gain (reduction) or loss (oxidation) of an electron.

Cellular Respiration

A multi-step process that uses energy captured from carbon oxidation to power ATP production via an electron transport chain and ATP synthase.

Electron Transport Chain (ETC)

A series of machines that uses an electric current to pump protons across a membrane, establishing a proton gradient that is then used to generate ATP.

Inputs: NADH, FADH2, O2, H+

Outputs: NAD+, FAD, H20, Proton Gradient (low concentration in matrix, high in membrane)

-Gives up electrons (oxidation) to make pumps that push protons into inner membrane

- Oxygen allows process to continue. Its the final electron acceptor to create H2O

Oxidative Phosphorylation

ATP synthesized by oxidation of electron carries in the presence of O2. When the ETC uses oxygen as an electron acceptor, ATP production via the combined action of the ETC and ATP synthase.

ATP Synthase

The multi-protein machine that transforms the kinetic energy in a flow of protons to mechanical energy that catalyzes the addition of a phosphate group to ADP to form ATP.

Inputs: 4H+ per ADP, ADP + Pi

Outputs: ATP (around 28 per glucose)

- move protons down the gradient from high to low concentration

Glycolysis

Takes place in cytosol. A sequence of ten enzyme-catalyzed reactions that begins with glucose and ends with 2 pyruvate, producing 2 net ATP and 2 NADH per molecule of glucose.

Steps 1-5 require ATP (energy-investing reactions) gain

input: 1 glucose, 2 ATP, 2 NAD + Pi

Steps 6-10 yield NADH and ATP (energy-harvesting reactions) release

Outputs: 2 Pyruvate, 4 ATP (2 net), 2 NADH

Pyruvate Processing

Pyruvate is transferred to the mitochondrial mix. A series of enzyme-catalyzed reactions that begins with pyruvate as a substrate and produces acetyl-CoA and NADH.

Inputs (per 1 glucose): 2 pyruvate, 2 NAD+, 2 coenzyme A - oxidizes Carbon in glucose and makes Co2

Outputs (per 1 glucose): 2 Acetyl CoA, 2 CO2, 2NADH

Citric Acid Cycle

A sequence of nine enzyme-catalyzed reactions that begins with acetyl-CoA, completes the oxidation of glucose to CO2, and produces ATP, NADH, and FADH2.

Step 1: Acetyl CoA reacts with Oxaloacerate (4 carbons) to create citrate (6 carbons) --- Coenzyme A is released (4 carbons) are supports

Step 3-4: acetyl group is oxidized to CO2, resulting in a 4 carbon molecule in the cycle

Step 8: malate is oxidized to regenerate oxaloacerate

Inputs (per 1 starting glucose): 2 Acetyl CoA, 6 NAD+, 2 FAD+, 2 GDP (like ADP) + Pi

Outputs (per 1 starting glucose): 2 GTP (like ATP they are interchangeable), 4 CO2, 6 NADH, 2 FADH2

NADH, FADH2, Q

Molecules that function as electron carriers during cellular respiration, meaning that they transport electrons to or within the electron transport chain.

Fermentation

A pathway that transfers electrons from NADH to a carbon-based molecule to regenerate NAD+ and keep glycolysis running to produce small amounts of ATP.

Aerobic Respiration

Cellular respiration that uses O2 to accept electrons from the electron transport chain and produces water as a byproduct.

ex: O2 + 4e- + 4H+ --> 2H20 -redox reaction

Anaerobic Respiration

Cellular respiration that uses any ion or molecule other than O2 to accept electrons from the electron transport chain.

Photosynthesis

A process that transforms light energy into chemical energy — meaning the potential energy found in electrons that participate in covalent bonds, usually in sugars or other carbohydrates.

Pigment

A molecule that absorbs specific wavelengths of light. Pass energy from excited electrons until the excited electron arrives at a specific location where reduction - and thus energy transformation - takes place

Chlorophyll

The primary photosynthetic pigment in land plants and most algae.

Photosystem I (PSI)

A complex of molecular machines that receive low-energy electrons at the end of the electron transport chain, use the energy in sunlight to excite those electrons to a high-energy state, and pass them on to electron carriers that either feed the electron transport chain or an enzyme that catalyzes the reduction of NADP+ to NADPH.

Photosystem II (PSII)

A complex of molecular machines that acquire electrons by oxidizing water, use the energy in sunlight to excite those electrons to a high-energy state, and pass them on to an electron carrier that feeds the electron transport chain, leading to ATP production by ATP synthase.

Calvin Cycle

A series of reactions that results in carbon from CO2 being "fixed," or reduced, and used to synthesize sugars.

Rubisco

The enzyme that catalyzes the reduction of CO2 and its incorporation into sugars. Most abundant and important enzyme. It is slow (only catalyzes 3 reactions per second) and when CO2 levels in the chloroplast are low, O2, instead of CO2 can bind to the active sites and be added to the 5-carbon sugar that acts a substrate. Can be summarized as an insufficient enzyme.

Stomata

Openings in stems and leaves that allow gas exchange via diffusion along their concentration gradients — most importantly, CO2 to enter and O2 to leave.

ATP

Source of energy that makes cells and organisms run

Phosphorylation

Provides the input of energy that makes nonspontaneous chemical reactions increase potential energy.

First Law of Thermodynamics

Energy is neither created nor destroyed but can be converted from one form to another.

Second Law of Thermodynamics

When energy is converted from one form to another, some of that energy becomes unavailable to do work. No energy transformation is 100% efficient - some energy is lost as heat

Energy

Capacity to do work. To produce a change, it must be transformed from one state to another or transferred from one location to another.

Change in free energy (G)

Difference in free energy between the products and the reactants

Anabolic Reactions

Complex molecules are made from simple molecules and energy input is required.

Catabolic Reactions

Complex molecules are broken down into simpler ones and energy is released.

Characteristics of Enzymes

1. lowers the activation energy, which speeds up the rate of reaction

2. they don't change reactions from spontaneous to nonspontaneous and vice versa

3. specific: bind only to their specific reactions

4. recycled: not altered during the reaction, they can be used again.

Enzyme-Substrate Complex (ES)

Held together by hydrogen bonds, electrical attraction, temporary covalent bonds, and van der waals

Substrate Binding

Bind to active sites by noncovalent interactions

Enzymes are controlled by:

1. Regulation of gene expression

2. regulation of enzyme activity

3. enzymes can be positively or negatively regulated

Inhibitors

slow or stop reaction rates

Active Site Inhibition (competitive inhibition)

prevents substrates from entering the active site (wall)

Allosteric Inhibition

Inhibitors bind elsewhere on enzyme and alters shape of active site, preventing substrate holding. Can be permanent or reversible.

Activators

Increase reaction rates

Allosteric Activation

Activator binds elsewhere on enzyme and altars shape of active site to encourage substrate binding.

Allostery

Other molecules can cause a conformational change in an enzyme which then alters its activity.

Cellular respiration involves 2 things:

1. a fundamental category of chemical reactions (reduction-oxidation reactions)

2. a fundamental principle about how the universe works (first law of thermodynamics)

-chemical reactions are about transferring energy, and the first law of thermodynamics is about transforming energy.

Oxidation

loss of electrons, almost always a spontaneous process

Reduction

Gain of electrons and is nonspontaneous. Electron is often accompanied by an H+ ion

Cellular Respiration Cycle

Glycolysis (cytoplasm), ------> (mitochondria) Pyruvate Processing, Citric Acid Cycle, Electron Transport Chain, and ATP Synthase

Fermentation

Occurs right during glycolysis if there is no Oxygen, increases fitness under certain environmental conditions but doesn't actually make ATP, and cellular respiration resumes once O2 is available as pyruvate can now be processed to feed the citric acid cycle and ETC.

Inputs and Outputs:

- 2 ATP created per glucose molecule

- 2 NAD+ is reduced to NADH in glycolysis

- NADH is oxidized back to NAD+ so glycolysis can continue bc NADH can't go into ETC

-Ethanol fermentation produces CO2

Main function of Oxygen in Respiration

Main function is to accept electrons released by glucose oxidation, forming H2O

Negative Feedback

High concentration of a metabolic product can INHIBIT action of an enzyme in the pathway

Positive Feedback

High concentration of a metabolic product can ACTIVATE an enzyme in another pathway, diverting raw materials away from synthesis of the first products

Glycolysis Control Points

- inhibited by excess ATP- blocking arrow

- inhibited by excess citrate (from citric acid cycle)

- activated by excess ADP

have a lot of energy= decrease cellular respiration

low energy = increase cellular respiration

Citric Acid Cycle Control Point

Step 1: inhibited by excess NADH and ATP

Step 3: inhibited by excess NADH and ATP; activated by excess NAD+ and ADP

Photosynthesis Reaction

CO2 + H2O + light energy ---> carbohydrate + O2

Visible Spectrum

Set of wavelengths that are visible to humans and ranges from shorter. Shorter wavelengths contain more energy than longer wavelengths.

Replacement Electrons

Essentially fuel the electrical circuit that runs photosynthesis-comes from water

PSII "splits" water

Pigment molecules become so oxidized that they pull electrons out of the O-H bonds in water, releasing protons (H+) and molecular oxygen (O2)

Photosynthesis Summary

1. Electrons are taken from water and excited to a high energy state when a pigment in PSII absorbs photons

2. The excited electrons are used to reduce an electron acceptor, then passed by PQ to ETC and that pumps photons

3. The resulting photon gradient drives productions of ATP by ATP synthase

Plant outer skin cells wax

Layer that blocks movement of water away from the plant and keeps stems and leaves from drying out. Also prevents movement of gases into or out of the plant.

Guard Cells

Open and close the pores in response to changes in environmental conditions. Regulates the size of the openings.

Photon

"Packet" of energy

When a photon hits a molecule:

Bounce off: scattered or reflected

Pass through: transmitted

Be absorbed: adding energy to the molecule (excited state)

Photosystem

A protein complex with a light absorbing pigments that absorb photons

Light Reactions

Convert light to chemical energy (ATP and NADPH). Energy capture and electron transport.

1) light energy is absorbed

2) electrons passed through ETC

-proton gradient; ATP synthase then uses proton gradient to phosphorylate ADP

- electron carrier is the final electron acceptor (NADP+ --> NADPH)

Inputs (ETC):

Photons (from light), H2O, NADP+, ADP + Pi

Outputs:

O2 (and H+), proton gradient, NADPH, ATP

-protons move from high concentration thylakoid space down the gradient through ATP Synthase

-capturing energy to move it to Calvin Cycle

Carbon Fixation

CO2 is reduced to carbohydrates, occurs in stroma, and energy needed is ATP and NADPH.

Chemical energy is converted to energy stored in carbohydrates

Calvin Cycle P1: Fixation

CO2 fixed by rubisco into RuBP to form 3-PGA

- By "fixing" rubisco makes sure carbon stays in the plant

Calvin Cycle P2: Reduction

3-PGA is reduced to GBP, uses ATP and NADPH, (NADPH oxidized to NADP+)

Calvin Cycle P3: Regeneration

Some G3P is used to regenerate RuBP for the next turn of the cycle, uses ATP

Inputs: no light required, CO2, ATP, NADPH

Outputs: G3P (to make glucose and other compounds), ADP, Pi

Carbohydrates

Provide the glucose required to fuel cellular respiration and produce the ATP needed to keep plant cells alive and thriving.

Cellular respiration only

Glycolysis, pyruvate processing, citric acid cycle

- overall is a transfer of chemical energy from glucose to ATP

Photosynthesis only

Calvin Cycle, rubisco, photosystems containing the pigment chlorophyll

- overall is about transforming light energy to chemical energy

Both CR and Photosynthesis

ATP synthase, and an electron transport chain (not the same molecules but pass electrons through redox reactions)

Cellular respiration only

-Carbon atoms are oxidized

-Oxygen atoms are reduced

Photosynthesis only

-Carbon atoms are reduced

-Oxygen atoms are oxidized

Both CR and Photosynthesis

-Electron carriers are reduced

-Electron carriers are oxidized

Cellular respiration only

Chemical energy in the forms of C-C and C-H bonds in carbohydrates is transferred to chemical energy in ATP.

Photosynthesis only

Light energy is transformed into chemical energy on the form of C-C and C-H bonds in carbohydrates

Both CR and Photosynthesis

Mechanical energy in the form of ATP Synthase spinning is transformed to chemical energy by addition of a phosphate group to ADP to form ATP

Both CR and Photosynthesis

Chemical energy in the form of electrons being passed through an ETC is transformed to mechanical energy as proton pumps in the ETC create a proton gradient

Both CR and Photosynthesis

Electrical energy in the form of protons flowing down an electrochemical gradient is transformed to mechanical energy as ATP synthase spins

Gluscose

Main input of cellular respiration

Catabolic interconversions

ATP is synthesized using chemical bond energy from macromolecules

Anabolic interconversions

Macromolecules are synthesized from their monomers using condensation reactions. Energy input: ATP or NADH