Comprehensive Biology and Biochemistry: Thermodynamics, Cell Transport, Photosynthesis, and Cellular Respiration

Laws of Thermodynamics

Energy cannot be created nor destroyed, but it can be converted to other forms.

Energy Transformations

All energy transformations are inefficient as they lose some energy to surroundings as heat.

Kinetic Energy

Energy in motion, examples include random molecular movement, sound, light, heat, muscle contraction, and a loose/extended spring.

Potential Energy

Stored energy includes examples such as chemical bonds and concentration gradients.

Endergonic Reactions

require energy to form bonds and build molecules.

Exergonic Reactions

release energy by breaking bonds.

Oxidation

involves the loss of electrons (electron donor becomes ——).

Reduction

involves the gain of electrons (electron acceptor becomes reduced).

Redox Reactions

Oxidation and reduction processes occur simultaneously in redox reactions.

Electron Transport Chain

An electron transport chain is a series of membrane proteins that participate in sequential, linked oxidation-reduction reactions.

ATP

ATP is the energy currency of the cell, releasing stored energy when the endmost phosphate group is removed by hydrolysis.

ATP Formation

ATP is produced from ADP during a series of chemical reactions that release energy from sugar (glucose) in cellular respiration.

Coupled Reactions

Coupled reactions pair an exergonic reaction with an endergonic reaction to drive processes that require energy.

Enzymes

Enzymes are proteins that act as catalysts, speeding up chemical reactions without being consumed.

Activation Energy

Enzymes lower activation energy by binding to their substrate, facilitating the reaction.

Factors Affecting Enzyme Activity

Enzymes have optimal temperatures, salt concentrations, and pH levels at which they function best.

Cofactors

Cofactors are partners that help catalyze reactions, participating in the reaction to increase enzyme activity, such as metal ions or vitamins.

Enzyme Inhibitors

Enzyme inhibitors shut down unneeded reactions, often through negative feedback mechanisms.

Negative Feedback

Negative feedback occurs when the product of a reaction halts or slows the reaction, maintaining homeostasis.

Cell Membrane Crossing Methods

Crossing a cell membrane can occur through passive transport (simple diffusion, osmosis, facilitated diffusion), active transport (against a concentration gradient), or in vesicles (endocytosis or exocytosis).

Passive Transport

Passive transport is the movement of substances down a concentration gradient without the use of energy.

Active Transport

Active transport moves substances against a concentration gradient, requiring energy, unlike passive transport which moves substances down a gradient.

Endocytosis

Endocytosis is the process of taking substances into the cell via vesicles.

Exocytosis

Exocytosis is the process of expelling substances from the cell.

Cell Membrane Permeability

Only certain substances can pass through a cell membrane, which is determined by the membrane's structure and the properties of the substances.

Solute Transport

Solutes enter and exit cells by different methods depending on concentration gradients and the chemical nature of the substance, such as its polarity, charge, and size.

Simple diffusion

A type of passive transport where small, nonpolar molecules, such as CO2 and O2, cross biological membranes down their concentration gradient.

Osmosis

The simple diffusion of water across a selectively permeable membrane, where water moves towards a higher concentration of solute, while solutes cannot pass.

Isotonic solution

A solution with equal concentrations of solutes inside and outside of a cell, resulting in no net water movement.

Hypotonic solution

A solution with a lower concentration of solute outside the cell, leading to net water movement into the cell.

Hypertonic solution

A solution with a higher concentration of solute outside the cell, resulting in net water movement out of the cell.

Facilitated diffusion

A type of passive transport where membrane proteins help transport substances across a cell membrane down their concentration gradient.

Ions and polar molecules crossing cell membrane

Ions and polar molecules must pass through protein channels in the cell membrane because the hydrophobic tails of phospholipids repel them.

Sodium-potassium pump

An example of active transport that moves 2 potassium ions into the cell and 3 sodium ions out, maintaining high K+ and low Na+ concentrations in muscle and nerve cells.

Photosynthesis

The process by which plants, algae, and some bacteria convert solar energy into chemical energy, using CO2, H2O, and light energy to produce O2 and glucose (C6H12O6).

Autotrophs

Organisms that produce their own food, acting as primary producers in ecosystems.

Carbon fixation

The process of incorporating inorganic carbon into an organic carbon molecule during photosynthesis.

Sun energy emission

The sun emits energy in waves, and photosynthesizers capture this light as photons of visible light.

Wavelength and energy relationship

Shorter wavelengths of sunlight have higher energy than longer wavelengths.

Role of pigments in plants

Molecules that capture energy from light, allowing plants to perform photosynthesis.

Leaves appear green

Leaves appear green because plant pigments do not absorb green light; instead, green light is reflected.

Major pigment in photosynthesis

Chlorophyll a.

Accessory pigments

Less abundant pigments, such as Chlorophyll b and Carotenoids, that extend the range of wavelengths that plants can absorb.

Light photons effect on molecules

Light photons move molecules to an excited state, raising electrons to a higher energy orbital.

Photosynthesis location in plants

Photosynthesis occurs in the leaves of plants.

Function of stomata

Leaf pores that facilitate gas exchange, allowing the intake of CO2 and the release of O2.

Stomata

Leaf pores that facilitate gas exchange, allowing the intake of CO2 and the release of O2.

Main reactants of photosynthesis

Light, water, and carbon dioxide.

Main products of photosynthesis

Oxygen and sugar.

Thylakoid membranes

Contain pigment molecules that capture sunlight for photosynthesis.

Photosystems

Consist of antenna pigments and reaction centers that capture photon energy and funnel it to the reaction center.

Granum

Stacks of thylakoid membranes within chloroplasts.

Antenna pigments

Capture photon energy and funnel it to the reaction center for photosynthesis.

Reaction center

Contains chlorophyll molecules, such as P680 and P700, which play a crucial role in converting light energy.

Stages of photosynthesis

Photosynthesis occurs in two stages: light reactions and carbon reactions.

Light reactions

Capture and convert light energy to chemical energy.

Byproducts of light reactions

Oxygen gas is released, while ATP and NADPH are produced.

Initial electron donor in light reactions

Water (H2O), which is oxidized.

Electron transport in photosynthesis

Electrons move from photosystem II to an electron transport chain, releasing energy that pumps hydrogen protons into the thylakoid space.

Proton gradient significance

Causes ATP synthase to produce ATP through chemiosmotic phosphorylation.

Carbon reactions

Use ATP and NADPH to fix carbon dioxide and build sugar molecules.

Role of ATP and NADPH in carbon reactions

Carry stored chemical energy that is used to convert CO2 into sugar.

Location of carbon reactions

Occur in the stroma, not in the thylakoid membrane.

Rubisco

An enzyme that catalyzes the first reaction in the carbon cycle, making carbon fixation possible.

First step of carbon reactions

Carbon fixation, where Rubisco adds CO2 to RuBP, producing an unstable six-carbon organic molecule.

Production of PGAL

PGAL is produced when ATP and NADPH from light reactions are used to convert PGA into PGAL.

Fate of PGAL in Calvin Cycle

Some PGAL exits the Calvin Cycle to combine and form glucose or other carbohydrates.

Regeneration of RuBP

Some of the PGAL produced is used to re-form RuBP, allowing the cycle to start anew.

Chemiosmotic phosphorylation

Involves the movement of protons across a membrane, leading to the addition of a phosphate group.

Final product of Calvin Cycle

PGAL, which can be used to create larger carbohydrate molecules.

Photorespiration

Occurs when O2 builds up and Rubisco adds O2 to RuBP instead of CO2, decreasing photosynthesis.

Types of carbon fixation pathways

C3 plants, C4 plants, and CAM plants.

C3 plants

C3 plants do well in cool, moist environments and comprise 95% of plant species.

C4 plants

C4 plants perform photosynthesis in two separate cells: mesophyll cells and bundle sheath cells, which is advantageous in hot, dry climates.

CAM plants

CAM plants only open their stomata at night to minimize water loss.

Cellular respiration

Cellular respiration is the breakdown of glucose in an exergonic reaction that produces ATP.

ATP production pathways

The three pathways are aerobic cellular respiration, anaerobic cellular respiration, and fermentation.

Oxygen in aerobic cellular respiration

Oxygen is inhaled for aerobic cellular respiration and is essential for the process to occur.

Stages of cellular respiration

Cellular respiration occurs in three stages: Glycolysis, Transition step (creation of Acetyl CoA), and Krebs Cycle.

Glycolysis

Glycolysis is the anaerobic splitting of glucose into two pyruvate molecules, occurring in the cytoplasm.

Net energy harvest from glycolysis

The net energy harvest from glycolysis is 2 ATP and 2 NADH.

Transition step

In the transition step, 2 pyruvate molecules are oxidized to form 2 Acetyl CoA and CO2, requiring oxygen.

Krebs Cycle

During the Krebs Cycle, 2 Acetyl CoA molecules are oxidized, producing 4 CO2, 2 ATP, 6 NADH, and 2 FADH2.

Substrate-level phosphorylation

ATP is produced by the direct addition of a high energy phosphate group to ADP during glycolysis and the Krebs cycle.

Electron transport chain (ETC)

The ETC uses electrons from NADH and FADH2 to create a proton gradient, which drives ATP production through ATP Synthase.

ATP Synthase function

ATP Synthase utilizes facilitated diffusion to move protons across the membrane, leading to the synthesis of ATP.

Total theoretical ATP yield

The theoretical yield is 36 ATP, accounting for ATP produced in glycolysis, Krebs cycle, and the electron transport chain.

Actual ATP yield

The actual yield is about 30 ATP due to factors like proton leak and the cost of transporting NADH into the mitochondria.

Role of oxygen in aerobic respiration

Oxygen acts as the final electron acceptor in the electron transport chain, allowing for efficient ATP production.

Utilization of proteins and fats

Proteins and fats can be converted into intermediates like pyruvate or acetyl CoA, entering the Krebs cycle for ATP production.

Anaerobic respiration vs fermentation

Anaerobic respiration includes the Krebs cycle and ETC using electron acceptors other than O2, while fermentation relies solely on glycolysis.

Types of fermentation

Alcoholic fermentation produces ethanol, while lactic acid fermentation produces lactic acid or lactate.

Prokaryotes and anaerobic respiration

Many prokaryotes use anaerobic respiration with alternative electron acceptors, resulting in less ATP production compared to aerobic respiration.

Connection between photosynthesis and respiration

Photosynthesis and respiration are interconnected through the exchange of water, oxygen, carbon dioxide, and sugars.

ATP produced during glycolysis and Krebs cycle

Glycolysis produces 2 ATP, and the Krebs cycle also produces 2 ATP.

Alternative electron acceptors

Alternative electron acceptors include nitrate (NO3-), sulfate (SO4-2), and carbon dioxide (CO2), leading to different end products.

Transporting NADH into mitochondrion

Transporting NADH into the mitochondrion requires 2 ATP, which affects the overall ATP yield from glucose.