exams 1-3 review

Big Ideas in Biology

• Structure-Function relationships: understanding that structure determines function in biology
• Emergent Properties: complex systems exhibit properties not found in individual components
• Energy transformation: energy is converted from one form to another
• Regulation: biological processes are controlled and regulated
• Evolution: changes in populations over time
• Cell Theory: all living organisms are composed of cells, cells are the basic units of life, and cells arise from pre-existing cells

Cell Structure and Function

• All cells have a cell membrane (plasma membrane), cytoplasm (cytosol), ribosomes, DNA (chromosomes), and RNA
• Two types of cells: prokaryotes (small, structurally simple) and eukaryotes (larger, structurally complex)
• Eukaryotic cells have an endomembrane system, including the nuclear envelope, rough and smooth endoplasmic reticulum, Golgi apparatus, and vesicles
• Prokaryotes lack internal membranes, limiting compartmentalization
• Eukaryotic cells have membrane-bound organelles (chloroplasts and mitochondria) for photosynthesis and energy storage, obtained through endosymbiosis
• Plant cells have cell walls, a large central vacuole, and chloroplasts, distinguishing them from animal cells

Chemistry of Life in Water

• Elements: atoms with a specific number of protons and electrons
• Electron configuration: electrons occupy shells and orbitals around the nucleus
• Chemical bonds: formed by sharing unpaired electrons between atoms
• Electronegativity: the ability of an atom to attract electrons in a covalent bond
• Polar and non-polar covalent bonds: differences in electronegativity determine bond type
• Ionic bonds: extreme differences in electronegativity result in ion formation
• Water: a highly polar molecule with emergent properties (cohesion, adhesion, surface tension, high heat capacity)
• Hydrogen bonds: weak intermolecular forces between polar molecules
• Acids and bases: ionic molecules that donate or accept H+ or OH- ions, affecting pH

Carbon Backbones and Functional Side Groups

• Organic molecules: composed of carbon backbones with functional side groups
• Cells can manipulate carbon backbones to create diverse molecules
• Functional side groups: add polarity, shape, or reactivity to molecules
• Examples of functional side groups: hydroxyl (OH), carbonyl (=O), carboxyl (COOH), amino (NH3), sulfhydryl (SH), phosphate (PO4), and methyl (CH3) groups

Biological Macromolecules

• Lipids: hydrophobic molecules, including triglycerides, phospholipids, and steroids
• Triglycerides: composed of three fatty acids attached to a glycerol molecule
• Phospholipids: amphipathic molecules with hydrophobic tails and hydrophilic heads
• Steroids: hydrophobic molecules, including cholesterol
• Proteins: polymers of amino acids connected by peptide bonds
• Primary structure: sequence of amino acids
• Secondary structure: hydrogen bonding between carboxyl and amino groups
• Tertiary structure: interactions between R-groups, folding the polypeptide
• Quaternary structure: interactions between R-groups on different polypeptides

Membrane Structure and Transport

• Phospholipid bilayer: semipermeable barrier to diffusion between two aqueous compartments
• Membrane proteins: transport proteins, receptors, junction proteins, and cell recognition proteins
• Fluid mosaic model: phospholipids and proteins can move within the membrane
• Membrane fluidity: influenced by lipid composition and cholesterol content
• Passive transport: facilitated diffusion of polar molecules and ions across the membrane
• Active transport: energy-dependent transport of molecules against their concentration gradient### Photosynthesis
• In eukaryotes, photosynthesis occurs in chloroplasts, using components in the stroma, thylakoid membranes, and the thylakoid lumen.
• The light reactions use two photosystems to capture light and generate high-energy electrons.
• Photosystem II donates high-energy electrons to an electron transport chain (ETC), which starts with the high-energy electron carrier PQ.
• The ETC generates a H+ gradient across the thylakoid membrane, powering the enzyme complex ATP synthase to form ATP in the stroma (photophosphorylation).
• Electrons leave the light reactions in NADPH, and new electrons are obtained by the splitting of water through photolysis by PSII.
• The Calvin Cycle fixes inorganic carbon from CO2 into organic carbon chains, storing energy in chemical bonds.
• CO2 is covalently bonded to the 5C molecule RuBP by the enzyme Rubisco, generating two 3C organic molecules in the carbon fixation phase.
• The product of the reduction phase is glyceraldehyde-3-phosphate (G3P), which is used to make other organic molecules including fatty acids, amino acids, and nucleic acids.

Cellular Respiration

• Cellular respiration is the process of breaking down glucose to make ATP using substrate level and oxidative phosphorylation.
• The first process in cellular respiration is glycolysis, which uses glucose as its preferred substrate to make 2 ATP (via substrate level phosphorylation), 2 NADH, and 2 pyruvate.
• The two pyruvates from glycolysis are imported into the mitochondria via pyruvate oxidation, getting converted into 2 acetyl-CoA at the same time, and making 2 NADH and 2 CO2.
• The 2 acetyl-CoA enter the citric acid cycle, where they are oxidized to CO2, making 2 ATP (via substrate level phosphorylation), 6 NADH, and 2 FADH2.
• In the mitochondrial matrix, the NADH and FADH2 from glycolysis, pyruvate oxidation, and the citric acid cycle donate high-energy electrons to the mitochondrial ETC, which uses their energy to pump H+ into the intermembrane space, generating proton motive force (PMF) across the inner membrane.
• The flow of hydrogen ions back across the inner membrane powers the production of ATP by the enzyme complex ATP synthase through chemiosmosis.
• When the electron transport chain cannot work, such as when oxygen is limited, ATP can only be produced by glycolysis supported by fermentation.
• Fermentation recycles NADH back to NAD+ which is necessary to keep glycolysis going.

Metabolism, Energy, Enzymes, and Redox

• Metabolism is the sum of all anabolic and catabolic reactions in a cell, connected in a network of reaction pathways.
• Anabolic reactions synthesize or "build" molecules with more bonds, making higher free energy products; they also use or store energy (endergonic), reduce entropy, and are non-spontaneous.
• Catabolic reactions degrade or "break" molecules to make lower free energy products with fewer bonds; they also increase entropy and release energy (exergonic), and are spontaneous.
• The First and Second Laws of Thermodynamics state that energy is transformed in many ways, but always at a cost of energy lost through entropy that is not available to do work.
• Free energy (G) is chemical energy available to do work and is expressed as the difference between enthalpy (total energy) and entropy.
• Enzymes are proteins that reduce the activation energy of a reaction, and their specificity and function are the result of the structure (shape) of the protein.
• Substrates interact with enzymes at the active site, forming an enzyme-substrate complex with a close interaction through induced fit.
• Enzymes can be regulated by allosteric effectors that bind somewhere other than the active site (called the allosteric site) and alter the shape of the protein to either inhibit or activate enzyme function.
• Positive ∆G reactions are accomplished by reaction coupling which combines a positive ∆G reaction with a negative ∆G reaction to give a new net negative ∆G for the combined reactions.
• Redox reactions transfer electrons between molecules, with oxidation being the loss of electrons and reduction being the gain of electrons by molecules.