Proteins, Carbohydrates, and Lipids

Proteins, Carbohydrates, and Lipids

• Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, often used for energy storage and structural functions.
• Monosaccharides are simple sugars such as glucose and fructose, serving as monomers for carbohydrates.
• Disaccharides consist of two monosaccharides linked by a glycosidic bond, examples include sucrose and lactose.
• Oligosaccharides are short chains of monosaccharides, typically 3–20 units long, and are often involved in cell recognition and signaling.
• Polysaccharides are long chains of monosaccharides used for storage, like starch and glycogen, or structure, such as cellulose and chitin.
• Sugars are simple carbohydrates, including monosaccharides and disaccharides.
• Starch is a polysaccharide used by plants for energy storage.
• Cellulose is a polysaccharide providing structural support in plant cell walls.
• Glycogen is a branched polysaccharide used for energy storage in animals.
• Lipids are hydrophobic molecules that include fats, oils, phospholipids, and steroids.
• A fatty acid is a hydrocarbon chain with a carboxyl group and serves as a building block for lipids.
• Triglycerides are lipids composed of three fatty acids linked to a glycerol molecule.
• Glycosidic linkage is a covalent bond between carbohydrate monomers.
• Ester linkage creates the bond between a fatty acid and glycerol in lipids
• Steroids are lipids characterized by a four-ring structure, examples include cholesterol and hormones.
• Carotenoids are pigments found in plants and some animals, important for photosynthesis.
• Waxes are hydrophobic lipid molecules providing protection and waterproofing.
• Phospholipids are lipids with a hydrophilic head and hydrophobic tails, essential for forming cell membranes.
• Acid is a fatty acid with no double bonds between carbon atoms. Usually solid at room temperature.
• Unsaturated fatty acids have one or more double bonds; typically liquid at room temperature.
• Monounsaturated fatty acids have one double bond.
• Polyunsaturated fatty acids have multiple double bonds.
• Amphipathic molecules possess both hydrophobic and hydrophilic properties, e.g., phospholipids.

Bonds

• Glycosidic linkages connect monosaccharides in carbohydrates.
• Alpha and beta glucose structures refer to different orientations of hydroxyl groups in glucose.
• 1-2 vs. 1-4 glycosidic linkages create different bonding patterns in carbohydrates.
• Lipids are not polymers because they are not made of repeating monomers.
• Phospholipid bilayers are cell membrane structures with hydrophilic heads and hydrophobic tails.
• Recognizing structures involves identifying alpha and beta glucose, triglycerides, phospholipids, and cholesterol.
• Classes of carbohydrates include monosaccharides (energy), disaccharides (transport), and polysaccharides (storage, structure).

Nucleic Acids & Origin of Life

• Nucleic acids are polymers of nucleotides that store and transmit genetic information.
• A nucleoside consists of a pentose sugar and a nitrogenous base, without a phosphate group.
• A nucleotide is the monomer of nucleic acids, composed of a sugar, phosphate, and nitrogenous base.
• Oligonucleotides are short nucleotide chains involved in gene expression.
• Polynucleotides are long nucleotide chains such as DNA and RNA.
• DNA is a double-stranded nucleic acid that stores genetic information.
• RNA is a single-stranded nucleic acid involved in protein synthesis.
• Purines are double-ring nitrogenous bases including adenine and guanine.
• Pyrimidines are single-ring nitrogenous bases including cytosine, thymine, and uracil.
• ATP, or adenosine triphosphate, is the primary energy carrier in cells.
• GTP, guanosine triphosphate, is involved in protein synthesis.
• cAMP, cyclic adenosine monophosphate, acts as a secondary messenger in cell signaling.
• Replication is the process of copying DNA.
• Transcription is the process of converting DNA to RNA.
• Translation is the process of synthesizing proteins from RNA.
• Gene expression is the process by which genes produce proteins.
• A genome is the complete set of genetic material in an organism.
• A gene is a segment of DNA that codes for a protein.
• Phosphodiester linkages are bonds linking nucleotides in DNA/RNA.
• Ribozymes are RNA molecules with enzymatic activity.
• Protocells are primitive cell-like structures that may have led to life.
• Reverse transcriptase is an enzyme that converts RNA into DNA.
• DNA double helix has a specific structure and function.
• Molecular structure of nucleotides includes a sugar, phosphate, and nitrogenous base.
• DNA and RNA differ in structure, function, and types of nitrogenous bases.
• Complementary base-pairing rules are A-T and C-G in DNA and A-U and C-G in RNA.
• The antiparallel nature of DNA means that the two strands run in opposite directions.
• Nucleic acids grow in a 5' to 3' direction.
• The central dogma outlines the flow of genetic information: DNA → RNA → Protein.
• Chimpanzees are the closest living relatives to humans, sharing the most DNA.
• Evidence suggests that life may have originated from outside Earth because some meteorites contain organic molecules.
• The Chemical evolution & Stanley-Urey experiment simulated early Earth conditions to produce organic molecules.
• The experiment simulating early Earth conditions did not include oxygen gas, reflecting the early atmosphere's composition.
• Polymer synthesis occurred under conditions with solid mineral surfaces, hydrothermal vents, and hot pools.
• The RNA World Hypothesis is supported by evidence that RNA can store genetic information and catalyze reactions.
• Cell membranes are essential for the evolution of life, maintaining homeostasis.
• Protocells serve as a model for evolution, representing simple vesicles capable of containing molecules and reactions.
• Ancient rock fossils provide evidence of early microbial life dating back 3.5 billion years.
• Cyanobacteria are considered the first organisms capable of photosynthesis which produced oxygen.

Energy & Enzymes

• Energy is the capacity to do work or cause change.
• Potential energy is stored energy in chemical bonds, concentration gradients, or charge imbalances.
• Kinetic energy is the energy of movement.
• Product is the end result of a chemical reaction.
• Metabolism is the total sum of chemical reactions occurring in an organism.
• Anabolism involves energy-requiring reactions that build complex molecules.
• Catabolism involves energy-releasing reactions that break down molecules.
• The First Law of Thermodynamics states that energy cannot be created or destroyed, only converted.
• The Second Law of Thermodynamics states that energy transformations result in increased disorder (entropy).
• Enthalpy (H) is the total energy of a system.
• Free energy (G) is the usable energy available for work.
• Entropy (S) is a measure of disorder in a system.
• A metabolic pathway is a series of enzyme-catalyzed reactions.
• An endergonic reaction absorbs free energy (+∆G).
• An exergonic reaction releases free energy (-∆G).
• Chemical equilibrium is a state where forward and reverse reactions occur at the same rate.
• ATP, or adenosine triphosphate, is the main energy carrier in cells.
• A catalyst is a substance that speeds up a reaction without being consumed.
• An enzyme is a protein that catalyzes chemical reactions.
• A ribozyme is an RNA molecule that acts as an enzyme.
• Activation energy is the energy required to start a reaction.
• Transition state intermediates are unstable molecules formed during reactions.
• Reactants or substrates are molecules that participate in chemical reactions.
• The active site is the region on an enzyme where a substrate binds.
• The enzyme-substrate complex is the intermediate formed when an enzyme binds a substrate.
• A competitive inhibitor binds to an enzyme's active site, preventing substrate binding.
• A non-competitive inhibitor binds elsewhere on an enzyme, altering its shape.
• An uncompetitive inhibitor binds only to the enzyme-substrate complex, preventing the release of products.
• A reversible inhibitor binds temporarily to an enzyme.
• A non-reversible inhibitor permanently inactivates an enzyme.
• Allosteric regulation is the regulation of an enzyme by binding at a site other than the active site.
• A coenzyme is a non-protein organic molecule that assists enzymes.
• A cofactor is an inorganic ion that aids enzyme activity.
• A prosthetic group is a permanently bound non-protein component of an enzyme.
• Intermediates are molecules that form between the initial reactants and the final products in a metabolic pathway.
• End products are the final molecules produced in a pathway.
• Effector molecules regulate enzyme activity by acting as activators or inhibitors.
• Systems biology is a computational approach to studying biochemical pathways.
• The commitment step is the first irreversible reaction in a metabolic pathway.
• Isozymes are different forms of an enzyme that catalyze the same reaction.
• Protein kinase is an enzyme that adds phosphate groups to proteins.
• Protein phosphatase is an enzyme that removes phosphate groups from proteins.
• Enzyme optimum temperature is the temperature at which an enzyme functions best.
• Enzyme optimum pH is the pH at which an enzyme functions best.
• Denaturation is the loss of enzyme structure and function due to extreme temperature or pH.
• ATP acts as an energy carrier in metabolism.
• ATP synthesis is endergonic.
• ATP breakdown, or hydrolysis, is exergonic.
• ATP is a nucleotide.
• ATP links exergonic and endergonic reactions in energy coupling.
• The energy released from ATP hydrolysis is between -7.3 to -14 kcal/mol.
• Bioluminescence is the production of light by organisms via ATP-driven reactions.
• Enzymes function with specificity, catalysis, and activation energy reduction.
• Mechanisms of enzyme catalysis include acid-base catalysis, covalent catalysis, and metal ion catalysis.
• Enzymes lower activation energy, speeding up reactions.
• Enzymes do not affect equilibrium or ΔG, they only speed up reactions.
• The induced-fit model describes how an enzyme changes shape when binding substrates.
• Enzyme saturation occurs when all enzyme active sites are occupied.
• Control of enzyme activity happens through feedback inhibition and environmental factors.
• Aspirin inhibits cyclooxygenase (COX) to reduce pain and inflammation.
• Methotrexate, a cancer drug, acts as a competitive inhibitor in purine synthesis.
• Allosteric molecules stabilize either the active or inactive enzyme form.
• Most allosteric enzymes have quaternary structures.
• Allosteric enzymes show sigmoidal curves on a graph of enzyme action.
• Reverse phosphorylation deactivates enzymes by removing phosphate groups.
• Isozymes allow organisms to adapt to different conditions.
• Competitive inhibition can be overcome by more substrate.

Cellular Respiration & Fermentation

• Glycolysis is the anaerobic breakdown of glucose into pyruvate, producing ATP and NADH.
• Cellular respiration is a metabolic process that extracts energy from organic molecules using oxygen.
• Fermentation is a metabolic process that allows ATP production without oxygen by regenerating NAD+.
• Aerobic processes requires oxygen.
• Anaerobic processes occurs without oxygen.
• A redox reaction is a chemical reaction involving the transfer of electrons.
• Oxidation is the loss of electrons from a molecule.
• Reduction is the gain of electrons by a molecule.
• An oxidizing agent is a molecule that accepts electrons.
• A reducing agent is a molecule that donates electrons.
• ATP, or adenosine triphosphate, is the primary energy carrier in cells.
• ADP, or adenosine diphosphate, is a lower-energy molecule that can be converted into ATP.
• NAD+ is an electron carrier that is reduced to NADH during glycolysis and the Krebs cycle.
• NADH carries electrons to the electron transport chain.
• FADH2 stores energy for the electron transport chain.
• Mitochondria are the organelles where cellular respiration occurs.
• Glycolysis happens in the cytoplasm of the cell.
• Aerobic respiration uses oxygen as the final electron acceptor.
• Anaerobic respiration uses molecules other than oxygen as electron acceptors.
• The Krebs Cycle, or Citric Acid Cycle, oxidizes acetyl-CoA to produce NADH, FADH2, ATP, and CO2.
• Substrate-level phosphorylation is ATP production through enzyme-mediated transfer of a phosphate group.
• Oxidative phosphorylation is ATP synthesis powered by redox reactions in the electron transport chain.
• The Electron Transport Chain (ETC) is a series of proteins that transfer electrons, creating a proton gradient for ATP synthesis.
• Chemiosmosis is the process by which ATP is produced using a proton gradient.
• Cytochromes are proteins in the ETC that transfer electrons.
• Ubiquinone (Q) is a lipid-soluble electron carrier in the ETC.
• ATP synthase synthesizes ATP using a proton gradient.
• Gluconeogenesis is the process of forming glucose from non-carbohydrate sources.
• UCP1 dissipates the proton gradient to generate heat instead of ATP.
• Superoxide is a reactive oxygen species formed during cellular respiration.
• Hydroxyl radicals are highly reactive oxygen species that can damage biomolecules.
• Metabolic pathways are governed by principles of energy flow, enzyme regulation, and feedback mechanisms.
• The cellular respiration equation is C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + ATP.
• Cellular respiration is exergonic, releasing free energy.
• Energy from glucose is harvested through breakdown into ATP, NADH, and FADH2.
• Redox reactions release energy because electrons move towards more electronegative acceptors.
• Gycolysis occurs in the cytoplasm, while the Krebs cycle and ETC happen in mitochondria.
• Aerobic respiration and fermentation differ in oxygen use and ATP yield.
• Catabolic and anabolic pathways are interconverted.
• Cells regulate catabolic vs. anabolic pathways through feedback inhibition and enzyme regulation.
• UCP1 in mitochondria generates heat instead of ATP production.
• Metabolic pathways are regulated by negative and positive feedback mechanisms.

Cellular Respiration Details

• Main control points in respiration include phosphofructokinase, isocitrate dehydrogenase, and acetyl-CoA regulation.
• During Glycolysis, 2 ATP are used and 4 ATP are produced, resulting in a net of 2 ATP.
• During Glycolysis, 2 NADH are produced and 2 pyruvate molecules are produced.
• Glycolysis uses substrate-level phosphorylation.
• Neither CO2 nor FADH2 are produced in glycolysis.
• In Pyruvate Oxidation, 2 acetyl-CoA, 2 CO2, and 2 NADH are produced per glucose molecule.
• No ATP is directly produced in pyruvate oxidation.
• Pyruvate dehydrogenase converts pyruvate into acetyl-CoA.
• In the Citric Acid Cycle, 4 CO2, 2 ATP (GTP), 6 NADH, and 2 FADH2 are produced per glucose molecule.
• ATP production in the Citric Acid Cycle happens through substrate-level phosphorylation.
• Oxidative Phosphorylation involves the electron transport chain and chemiosmosis.
• Oxidative phosphorylation yields ~28-34 ATP per glucose.
• Many steps are involved to controlled energy release and efficient ATP production.
• Electron carriers include NADH, FADH2, cytochromes, and ubiquinone.
• Concentration gradients are formed by proton pumping into the intermembrane space.
• ATP synthase uses proton flow to synthesize ATP and can also hydrolyze ATP when needed.
• ATP synthesis is favored due to the proton gradient and chemiosmosis.
• Chemiosmosis was demonstrated with experiments showing proton gradients power ATP synthesis.
• NAD+ is regenerated in oxidative phosphorylation through electron donation to the ETC.
• Superoxide and hydroxyl radicals are by-products of oxidative phosphorylation.
• Reactive oxygen species can cause DNA, protein, and membrane damage.
• The body removes radicals using antioxidants like Vitamin E and enzymes.
• Lactic acid fermentation happens in muscle cells and some bacteria.
• Pyruvate is reduced and NADH is oxidized in lactic acid fermentation.
• Lactic acid fermentation produces 2 lactic acid molecules per glucose.
• In lactic acid fermentation, NAD+ regeneration occurs through the reduction of pyruvate.
• Alcohol fermentation happens in yeast and some bacteria.
• The products of alcohol fermentation are ethanol and CO2.
• Alcohol fermentation produces 2 CO2 and 2 ethanol molecules per glucose.
• Acetaldehyde is reduced.
• NAD+ is regenerated in alcohol fermentation through acetaldehyde reduction.