Thermodynamics and Biomolecules

Thermodynamics

• Matter is neither created nor destroyed.
• Heat flows from hot to cold.
• Energy transforms from one system to another without doing work.

Energy in Biomolecules

• Gibbs free energy is the energy stored in biomolecules.
• Gibb's free energy represents energy available after entropy, which can perform work.
• Entropy measures disorder within a system.
• Enthalpy is the total energy in a system.

Anabolism vs. Catabolism

• Anabolic reactions synthesize complex molecules from simpler ones and require energy; example: amino acids to proteins, nucleic acids to DNA.
• Catabolic reactions break down complex molecules into simpler ones releasing energy; example: fats to ATP.

Endergonic vs Exergonic Reactions

• Endergonic reactions (+G) absorb energy from their surroundings and are not spontaneous under standard conditions; example: photosynthesis.
• Exergonic reactions (-G) release energy and are spontaneous under standard conditions; example: cellular respiration.
• Spontaneous reactions are usually exergonic, occur without external energy input, and have a negative delta G.

Reaction Speed & Activation Energy

• Activation energy is the minimum energy required for a reaction.
• It acts as an energy barrier that reactants must overcome, affecting reaction rates without impacting spontaneity.
• Catalysts lower activation energy, increasing reaction rates.

Enzymes

• Catalysts are substances that help a chemical reaction occur.
• Enzymes catalyze biochemical reactions.
• An enzyme’s active site facilitates each reaction step by lowering the activation energy; it binds to reactants (substrate).
• Induced fit involves interaction between enzyme and substrate, bringing a mild shift for ideal arrangement of enzyme-substrate.

Enzyme Inhibition

• An inhibitor molecule similar to the substrate can bind to the active site to competitively inhibit enzyme activity, which is reversed with increased substrate concentration.
• Allosteric inhibition involves molecules binding to enzymes in a location that induces a conformational change, reducing enzyme affinity.
• Feedback control uses reaction product to regulate its own production by slowing down production during anabolic or catabolic reactions when there is an abundance of specific products.

Cellular Respiration

• Redox reactions consist of oxidation and reduction reactions.
• NAD are common electron carriers used; NAD (oxidized form of molecule) is reduced to NADH after the acceptance of 2 e- and a proton.
• ATP is produced by substrate-level that uses excess energy from chemical reactions and transfers from a phosphate group from a reactant and oxidative phosphorylation which uses chemiosmosis in the presence of oxygen.

Phases of Cellular Respiration & Glycolysis

• Major steps of cellular respiration: glycolysis, pyruvate oxidation, Krebs cycle, and oxidative phosphorylation.
• Glucose from photosynthesis is the starting molecule for glycolysis.
• Glycolysis breaks down into 2 molecules of pyruvate.
• There is a net gain of 2 ATP per molecule of glucose in glycolysis.
• In plant cells, glycolysis occurs in the cytosol and plastids.
• In animal cells, glycolysis occurs in the cytosol.

Citric Acid & Fate of Pyruvate

• The citric acid cycle occurs in the mitochondrial matrix of plant/animal cells and follows pyruvate oxidation.
• As pyruvate enters the citric acid cycle, it undergoes decarboxylation and oxidation releasing Acetyl-CoA.
• In the circle, it is further oxidized and releasing energy in the form of ATP, NADH, and FADH2

Electron Transport Chain & Chemiosmosis

• Electron transport chain components in plant cells are in the mitochondrial membrane that generates ATP.
• In animal cells, they’re in the inner mitochondrial membrane (electrons from donor molecules are passed along proteins, pumping protons to drive ATP synthesis)
• The inner mitochondrial membrane generates a proton gradient through chemiosmosis.
• The highest level of protons, from gradient of ETC, is found in the intermembrane space of the mitochondria through chemiosmosis.
• In chemiosmosis, ETC pumps protons from the matrix to the intermembrane, creating a proton gradient, which stores energy to make ATP.
• ATP synthase produces ATP using the proton gradient in the mitochondria.
• ATP is produced due to chemiosmosis in the inner mitochondrial membrane (eukaryotic cells), chloroplasts (plant cells), and plasma membrane (prokaryotic).

Oxygen & Fermentation

• Oxygen acts as the final e- acceptor in ETC, to allow oxidation of glucose producing large ATP.
• Fermentation is an anaerobic process releasing energy from glucose absence.
• It begins with glycolysis and regenerates NAD by reducing pyruvate into lactic acid or ethanol.
• Lactic acid fermentation converts pyruvate to lactic acid.
• Alcoholic/ethanol fermentation converts pyruvate to ethanol and CO2 and is carried out by yeasts.
• Both only produce 2 ATP

Photosynthesis

• Photoautotrophs use sunlight for energy and photosynthesis- convert energy to chemical energy and store it in carbohydrates.
• Chemoautotrophs oxidize inorganic chemicals and use the energy to fix CO2 into organic compounds.
• Heterotrophs consume organic compounds.
• The photosynthesis reaction is anabolic.
• 6CO2 + 6H2O yields C6H12O6 + 6O2.

Reactions in Photosynthesis

• Light-dependent reactions occur in the thylakoid membranes and convert light energy into ATP and NADH.
• Light-independent (Calvin cycle) in the stroma uses ATP and NADH produced to fix CO2 into C6H12O6.

Chloroplast Components

• Thylakoids are pigment and protein complexes, are involved in photosynthesis
• Photosystems I & II light-harvesting capture and transfer light energy
• ATP Synthase generates a proton gradient to produce ATP
• Stroma fluid surrounds the thylakoid (Calvin cycle)

Energy Production through Photosynthesis

• ATP is produced in chemiosmosis as protons flow down via synthase
• NADPH forms at the end of the ETC.
• The products of the light reaction are ATP (used in the Calvin cycle), NADPH (provides reducing power), and O2 (byproduct of water splitting).
• ATP is produced during the light reaction on the thylakoid membrane.
• Antenna proteins are light-harvesting complexes embedded in the thylakoid membrane.
• The reaction center is a specialized complex within the photosystems where the primary energy conversion of photosynthesis takes place.
• Specific chlorophyll molecules are excited after receiving energy from antenna to initiate the ETC.

Chlorophyll & Production of ATP

• Photosystem I contains P680 chlorophyll.
• Photosystem II contains P700 chlorophyll.
• ETC product of light reaction is a proton gradient that accumulates in the thylakoid lumen. The gradient creates a concentration between lumen and stroma.
• ATP Synthase utilizes the proton gradient of light released reactions to synthesize ATP.
• Photosysnthesis: the photolysis (water splitting) produces oxygen during light-dependent (LD) reactions in photosystem II.

Calvin Cycle & Carbon Fixation

• The Calvin Cycle occurs in the stroma.
• Carbon Fixation: CO2 attaches to RuBP by RuBisCO
• Reduction: ATP and NADH convert 3-PGA into G3P.
• Regeneration: RuBP is regenerated using ATP.
• In the Calvin cycle, the energy-rich products produces glucose and other energy compounds (G3P)
• Carbon Fixation: photosynthetic organisms convert inorganic carbon into organic compounds.

Fate of Sugars & Chapter Summary

• Glucose is for cellular production, stored in plant parts, serve as precursor for synthesis, or be transported.

Cell Communication

• Paracrine: nearby cells signal to one another.
• Autocrine: signal sent/received by similar cells.
• Endocrine: hormones affect distant target cells through bloodstream.
• Synaptic: neurotransmitters travel between nerve cells.

Cell Signaling Function & Steps

• Gap junctions in animal cells and plasmodesmata in plant cells allow coordinated responses to developmental cues and physiological changes.
• Reception: Ligand binds to a receptor protein on/in the cell surface.
• Transduction: steps where each relay molecule changes the next molecule.
• Response: Signal triggers a cellular response involved in changes in gene, enzyme activation, or alterations in cell metabolism.

Receptors

• Ion-Channel Gates open/close to allow ion flow upon ligand binding.
• G-protein coupled receptors (GPCRs) activate G proteins to trigger signaling cascades.
• Enzyme-linked receptors activate enzymatic domains for protein phosphorylation.
• Intracellular receptors bind lipophilic ligands inside the cell.

Signaling Cascades

• Kinase is used for biochemical reactions to propagate signaling cascades.
• Kinases are enzymes that transfer phosphate groups from ATP to specific target proteins which actively modify proteins for cellular stimuli as part of signal transduction.
• Phosphatases are enzymes that remove P-groups from proteins to inactivate signaling proteins, to regulating duration and intensity of signaling cascades.

Messengers & Unicellular Signaling

• Second messengers- intracellular signaling molecule released that binds to cell surface receptors to diffuse w cell to relay and amplify signals; cAMP, cGMP, IP3, DAG, Ca2+, NO
• Second messenger's primary role is to rapidly propagate signals within a cell.
• Unicellular signaling: mating in yeast, biolfilm formation, quorum sensing in bacteria

Cell Reproduction

• Prokaryotic cell division is through binary fission.
• Binary Fission: DNA replication, chromosome segregation, septum formation, and cytokinesis are involved.
• FtsZ protein forms a ring to initiate septum formation helping cell division into 2 daughter cells.
• The nucleosome is the fundamental DNA packaging unit in eukaryotic cells.
• It consists of a segment of DNA wrapped around a histone protein octamer (beads on a string).

Chromatin

• The core particle component of a nucleosome contains 146 base pairs of DNA wrapped around the octamer.
• Linker DNA connects nucleosomes ranging from 10-80 base pairs.
• Linker Histone (HI) helps stabilize structure and compact chromatin further.
• Two phases of the eukaryotic cell cycle: interphase [GI (cell growth), S (DNA replication), and G2 (prep for mitosis)] and mitotic (mitosis and cytokinesis).

Interphase

• GI (cell growth), S (DNA replication), G2 (prep for mitosis)
• G1 Phase - cell grows, synthesizes proteins, and accumulates energy reserves
• S Phase – DNA replication of sister chromatids and duplictating centrosomes
• G2 Phase: replenish energy and synthesize for mitosis to prepare for division
• Mitosis: prophase, prometaphase, metaphase, anaphase, and telophase.
• In prophase, chromosomes condense and the nuclear envelope breaks down.
• In prometaphase, spindle fibers attach to kinetochores.
• In metaphase, chromosomes align at the metaphase plate.
• In anaphase, sister chromatids are pulled apart to opposite poles.
• In telophase, nuclear envelopes reform around separated chromosomes, which then condense.

Cell Cycle & Kinetochore

• 3 checkpoints regulate the cell cycle;
• G1 ensures adequate cell size, energy reserves, and DNA integrity.
• G2 verifies complete and undamaged DNA replication.
• M is the spindle confirms proper attachment to the spindle fibers for anaphase.
• Kinetochore: a protein structure that forms on the centromere of chromosomes to attach to spindle microtubules, ensuring proper chromosome segregation, regulating chromosome movement.

Centrosome/ Centromere

• A centrosome is an organelle serving as the microtubule organizing center organizing motility, adhesion etc.
• A centromere is the constricted region of chromosome.
• It links sister chromatids, separates short arms of chromosome and assembles a site for kinetochore.

Cytokinesis

• Cytokinesis is the final cell division stage, where the cytoplasm divides into two daughter cells, through different mechanisms.
• A cleavage furrow a indentation forms on the surface of animal cells that result from an actin-myosin ring pinching the cell in two.
• A cell plate is a structure formed during cytokinesis creating a boundary in the daughter cells

Positive & Negative Regulators

• Positive Regulators: cyclins bind to cyclin-dependent kinases, and enzymes that become active when bound to cyclins allowing cell progression.
• Negative Regulators: retinoblastoma protein, p53, p21, proto-oncogene, and tumor-suppressor.
• Protein p53 arrests the cell cycle in DNA-damaged cells, prevents progression until damage is repaired or triggers apoptosis.