Chapters 9-10: Cellular Energetics

ATP

ATP

High energy phosphodiester bonds between phosphate groups ⟶ many close together with highly negative charges

How does NAD⁺ become NADH•H⁺?

• Dehydrogenase enzymes remove a pair of hydrogen atoms (2 protons, 2 electrons) from the substrate

• 2 electrons and 1 proton are transferred to NAD⁺, the coenzyme

• 1 proton is released into the solution

NADH•H⁺ Oxidation/Reduction

• NAD⁺ is reduced when it gains electrons and becomes NADH•H⁺

• Their oxidation number goes down when reduced

• Oxidizing agent is pyruvate

How does redox relate to covalent bonds?

Some redox reactions might not include the complete transfer of electrons, as their degree of electron sharing in covalent bonds changes instead of the amount of electrons

Why is the series of redox reactions important?

It draws out the reactions as they go through multiple enzymes to reduce, meaning energy can be more efficiently harnessed

How does redox work in cellular respiration (C₆H₁₂O₆ + 6O₂ ⟶ 6CO₂ + 6H₂O)?

Redox reactions in cellular respiration involve the transfer of electrons from glucose (C₆H₁₂O₆) to oxygen (O₂), resulting in the oxidation of glucose to carbon dioxide (CO₂) and the reduction of oxygen to water (H₂O). This process releases energy, which is captured in the form of ATP.

What kind of reaction is cellular respiration?

Cellular respiration is an spontaneous, exergonic reaction that converts biochemical energy from nutrients into ATP, releasing waste products. (-ΔG, -ΔH, +ΔS)

Proton-Motive Force

The force generated by the electrochemical gradient of protons across a membrane, driving ATP synthesis during cellular respiration.

Oxidative vs. Substrate-Level Phosphorylation

Oxidative phosphorylation occurs in the mitochondria and involves the electron transport chain and chemiosmosis to produce ATP, while substrate-level phosphorylation directly generates ATP from a reaction in glycolysis or the citric acid cycle without the involvement of the electron transport chain.

Chemiosmosis

• Energy-coupling mechanism in which energy in the form of H⁺ forms a gradient across a membrane and is used to drive cellular work, like ATP synthesis

• Transform redox energy to a proton-motive force

Terminal electron acceptor

O₂

How are proteins broken down?

• Broken into the backbone and R group in a process called deamination 

• Only the liver can turn them into usable energy because they are so toxic (urea—in urine—is a consequence of breaking down ammonia)

• The backbone goes into the Krebs Cycle, but only nets 2 ATP

• The R group may go to where they match into the Krebs Cycle

• Gives less than 10 ATP

• Humans can make about half of the 20 amino acids and have to obtain the rest through consumption 

Obligate Anaerobes

Carry out only fermentation or anaerobic respiration and cannot survive in the presence of oxygen

Facultative Anaerobes

Cells that can only carry out aerobic respiration or both fermentation and respiration

Results of Lactic Acid Fermentation:

• Causes lactic acid buildup along with necessary products

• Can be helpful to muscles and shuttled to the liver or kidneys for glucose formation

• Red muscles prefer to completely break down glucose, while white muscle cells prefer to undergo a variation of fermentation

How do O₂ levels determine the fate of the pyruvate?

There is a protein on the surface of the mitochondria that bonds to O₂, made out of hemoglobin

• When O₂ bonds, it keeps the mitochondria “on”

• Without O₂ the ETC will stop, and mitochondrial transport will be turned “off”

Phosphofruktokinase

Allosteric enzyme that slows down/speeds up glycolysis and the Krebs Cycle by noncompetitively binding ATP (inhibiting) or AMP (stimulating); affected by citrate levels (more causes glycolysis and the supply of pyruvate and acetylCoA to the Krebs Cycle to slow down) and involved in glycogen breakdown.

Citric Acid

Causes the Krebs Cycle to slow down when too much is present

Layers of a leaf:

• Epidermis — top layer

• Palisade Layer — second layer, structured and tightly packed to increase surface area; has many chloroplasts (contains mesophyll)

• Vascular Bundle — third layer, used in the circulatory system; carries H₂O from roots to the leaves and sugar from the leaves to the roots (contains bundle-sheath)

• Spongy Layer — fourth layer, many holes/gaps in between cells (contains mesophyll)

• Epidermis — bottom/last layer

Why does biology have a hard time absorbing green light?

Colors that aren’t green are absorbed by conjugated double bond (alternating single/double bonds), which Carbon frequently forms

Black vs. White

Absorbtion of color (converts into heat) vs. reflection of color

Theodor Wilhelm Englemann’s Experiment

A wet mount of spirogyra was prepared on a microscope, and light was passed through it using a prism. Aerobic bacteria were added, and they clustered around areas with the highest O₂ production (indicating the most photosynthesis). Bacteria concentrated in the blue, purple, orange, and red regions, while few were found in the green/yellow areas.

Created an action spectrum.

Carotenoids

Carotenoids are pigments that give plants and algae red, orange, and yellow colors. They help with photosynthesis and protect plants from too much light by absorb excess light energy and prevent damage to the plant (photoprotection).

Spectrophotometer

Measures how much light is absorbed by a substance. It shines light through the substance and checks how much light comes out the other side. Helps scientists see what colors the substance absorbs and learn more about it.

Absorption Spectrum

• Graph plotting a pigment’s light absorption versus wavelength

• Each organism’s absorption spectrum is unique because different compounds absorb photons whose energy is exactly equal to the energy difference between the ground state and excited state

• Electrons get excited for a billionth of a second before dropping back down and releasing energy as heat

Action Spectrum

Profiles the relative effectiveness of different wavelengths of radiation in driving the process of photosynthesis

Light-Harvesting Complex, Reaction-Center Complex, the Primary Electron Acceptor, and Photosystems (3 Parts)

1. Absorption of Light: The light-harvesting complex absorbs light and transfers the energy to the reaction center.

2. Excitation of Electrons: The reaction center uses the absorbed energy to excite electrons to a higher energy state.

3. Electron Transport: The primary electron acceptor accepts electrons and initiates the flow of electrons in the light-dependent reactions of photosynthesis. The excited electrons are transferred to the electron transport chain.

P680

• P680 is a pair of chlorophyll molecules in Photosystem II that absorbs light at 680 nm.

• When P680 absorbs light, it excites an electron, which is sent to the primary electron acceptor.

• To replace the lost electron, water is split, releasing oxygen, protons (H⁺), and electrons.

• The excited electron moves through the electron transport chain, helping make ATP and NADPH, which are used in the Calvin cycle to produce sugars.

What happens with glucose in the Calvin Cycle?

It is stored as glucose (starch) or used in the Krebs Cycle to synthesize biomolecules

What do plant cells not want to do? (relates to stomata)

They don’t want water to transpire out of the cell. It is needed for Photosystem II, plasmolysis prevention (can result in wilting), hydrolysis, and maintaining protein shape (not denaturing)

C₄

• C₄ plants have mesophyll cells that initially capture CO₂ and turn it into a 4-carbon compound (PEP + CO₂ using PEP-carboxylase enzyme)

• This 4-carbon compound moves through plasmodesmata into the bundle-sheath cells, where CO₂ is released and enters the Calvin cycle.

• Cyclic electron flow helps produce extra ATP for the Calvin cycle in the bundle-sheath cells, making the process more energy-efficient.

Examples: sugarcane, corn

CAM

• CAM plants capture CO₂ at night in their mesophyll cells and store it as an acid (like malic acid).

• During the day, the CO₂ is released from the acid and used in the Calvin cycle to make sugars, all while keeping the stomata closed to conserve water.

Examples: cacti, pineapples