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● Monomers: stable molecule but readily bonds with other monomers ● Polymers: monomers in a chain formation of that group ● Dehydration synthesis: the reaction to build polymers from monomers (polymerization) (water molecule is released: H and OH that bonds) ○ Anabolic: build complex molecules from simpler ones => Endergonic (construction) => Consumption of Energy => +𝚫G => Nonspontaneous ● Hydrolysis: the reaction to break down polymers into monomers (water molecule is a reactant) ○ Catabolic: break down complex molecules to simpler ones => Exergonic (releasing energy from the energy stored in the bonds) => Release of Energy => -𝚫G => Spontaneous ● Directionality influences the Structure and Function of the Polymer ○ Amino Acids: N-terminus and C-terminus determine from which side can more amino acids be added and thus the structure and function of the protein is influenced ○ Nucleic Acids: linear sequence of nucleotides that have ends, defined by the 3’ hydroxyl and 5’ phosphates of the sugar in the nucleotide. During DNA and RNA synthesis, nucleotides are added to the 3’ end of the growing strand, resulting in the formation of a covalent bond between nucleotides. ● Uniqueness of Carbon: ○ Atom is small in size with the valence electrons close to the nucleus, so it creates stable bonds ○ 4 valence electrons allows it to bond up to 4 different elements ○ Multiple types of Carbon Bonds: C-C, C=C, C☰C, C≣C Macromolecul e Class Elemental compositi on Monomer (or subcompon ents) Polymer Shape / structure Biological function/s Key example/s Structure-funct ion relationship example/s Other notes or properties Carbohydrates CHO^ monosacch aride polysaccharid e (carbon) rings Energy storage (long and short), structure Cellulose, starch (lots of glucose), glycogen Cellulose: Alpha Glucose chain is a rigid structure Glycosidic bond Covalent bonds C-C Most end in -ose (classified by # of carbons)
Lipids CHO Subcompon ents: glycerol head and fatty acids N/A Starfish (fatty acids attached to glycerol head) Long term energy storage, insulation/cushio ning, membranes Saturated fats, unsaturated fats, phospholipids , and steroids, triglyceride Phospholipids (amphipathic) = spherical membranes Ester Linkage bond Nonpolar Nucleic acids CHONP Nucleotide: bases, phosphate group, pentose sugar Nucleic Acids (Double) Helix Information storage and transmission (across generations) DNA & RNA ATP, CTP, GTP, and TTP are all nucleotides! Hydrogen bonds in between to easily break them for replication Direction matters Phosphodesiter bond: sugar to phosphate Purines: Adenine & Guanine Pyrimidines: Cytosine, Thymine, Uracil A-T : G-C = stability of DNA molecules Proteins CHONS Amino Acids Polypeptides (a lot of polypeptides create a protein) Literally everything except for information storage, and energy storage The shape determined after all properties are applied: shape determines function Active Transport: goes through Enzyme: has a convex as an active site Peptide Bond End in -ase (enzymes) or -in Amine group, C-R, carboxylic acid Polar backbone
○ Easy to break which helps in the “unzipping” with helicase during replication ● Structural differences between DNA and RNA: ○ DNA contains deoxyribose and RNA contains ribose. ○ RNA contains uracil and DNA contains thymine. ○ DNA is usually double stranded; RNA is usually single stranded. ○ The two DNA strands in double-stranded DNA are antiparallel in directionality. PROTEINS ● Functions ○ Enzymes: control chemical reactions, Structure, Carriers & Transport, Cell Communication, Defense, Movement, Storage ● Varying R-group structures (20 different) ○ Determine and allow for the complex tertiary structure of proteins ■ The properties need to be applied of the R-Groups ● Hydrophobic on the inside, Hydrophilic on the outside, Acids and Bases touching, Cysteine touching ● Primary > Secondary > Tertiary > Quaternary Protein Structure ○ Primary: the ORDER of the amino acids (determined by DNA) ○ Secondary: local folding of the amino acid chain into elements such as alpha-helices and beta-sheets ■ Results from hydrogen bonds in primary structure ○ Tertiary: overall three-dimensional shape of the protein and often minimizes free energy ○ Quaternary: interactions between multiple polypeptide units. ● Protein Denaturation: Unwinding through a change in heat, pH, or salinity
○ Irreversible b/c water or other polar molecules (H+^ or OH-) bind to the polar backbone
ENERGY
● Energy: the capacity to do work - ability to rearrange a collection of matter ● Kinetic energy: Energy of Motion ● Potential Energy: Stored Energy ○ Chemical Energy: form of PE stored in molecules as a result of the arrangement of atoms
■ The energy living things are powered by ● Laws of Thermodynamics:
○ 1 st: Energy is constant, it can neither be created nor destroyed. It can only be transformed and transferred
○ 2 nd: Each energy transfer makes the universe more disordered (increases entropy) = a no go for organisms
● A living thing is an open rather than a closed system: exchange energy and materials with the environment ● Cells maintain their orderliness by taking in orderly things (light, polymers) and discharging disorderly things (heat) ○ Life makes its environment more disorderly to be more orderly ● Free Energy (G) : the portion of a system’s energy that is available to perform work with (temperature is uniform throughout the system) = POTENTIAL ● G = H - TS or 𝚫G = 𝚫H = T𝚫S ○ H = total energy of the system ○ S= entropy ○ If H and T are to remain constant, 𝚫G has to be maximized so 𝚫S can be minimized ○ Difference between products and reactants energy levels on a graph ● Endergonic Graphs: Reactants have a lower amount of energy than the products ● Exergonic Graphs: Reactants have a higher amount of energy that the products ● REGARDLESS IF THE REACTION IS ENDERGONIC OR EXERGONIC ○ Breaking bonds requires an input of energy ○ Activation Energy/Energy of Activation (EA): initial investment of energy starting a reaction (energy required to break bonds) ■ Hump maximum to reactant energy level ■ Higher EA, less likely for reaction to occur/the slower the reaction will be ENZYMES ● Metabolism: the chemical processes that occur within a living organism in order to maintain life. ● Catalyst: chemical agent that changes the rate (speeds up) of a reaction without being converted or consumed by the reaction (not a reactant) ● Enzymes: biological catalysts, most often made of protein ○ Few are ribozymes made of RNA
● Control which enzymes are active when and where ○ Don’t need to be conducting all reactions all the time: wasting materials and energy (and toxic concentrations of products) ● Cofactors: non-protein helpers to enzymes for catalytic activity ○ When the active site is NOT made to match the substrate ○ Can be permanent or bind reversibly with the substrate ○ INORGANIC (iron, zinc, copper) ● Coenzymes: organic cofactors (often vitamins) ● Allosteric vs Active Sites ○ Other molecules enable (or diable!) enzymes by binding to the allosteric site ■ Changes the enzyme shape (control enzyme activity) ● Inhibitors: inhibit (reduce or turn off) the action of an enzyme by covalently bonding to the enzyme (usually irreversibly) ○ Competitive inhibitor molecules can bind reversibly or irreversibly to the active site of the enzyme. ■ Block access to active site ● Can be overcome by increasing substrate concentration ○ Noncompetitive inhibitors can bind allosteric sites, changing the conformation of the enzyme: impeding substrate binding (close active site) ● Allosteric Activators/Effectors which bind to allosteric site, change enzyme conformation, to expose or properly shape the active site Active Site Allosteric Site Enables Enzyme Cofactor (Coenzymes) Allosteric Activator Disables Enzyme Competitive Inhibitor Noncompetitive Inhibitor ● Feedback Inhibition: the product of the entire reaction series fits in the allosteric site of the first enzyme and turns into a noncompetitive inhibitor (turning off reaction series when we have a lot of product) ● Localization of Enzymes ○ Organisms are more efficient because the can keep all the enzymes required for a pathway in one place (organ or organelle) ■ Metabolic pathways can be assembled together into a multienzyme complex to keep everything organzied
WATER
● The hydrogen bonds between water molecules result in cohesion, adhesion, and surface tension ○ Water molecules can bond up to 4 hydrogen bonds ● Cohesion: positive ends of polar water molecules attracted to negative ends of neighboring molecules, causing more water molecules to stick together, resulting in water tending to remain together with other water ○ Transpiration: water that evaporates from a leaf draws water in plant vessels upwards towards the leaf ● Adhesion: polar ends of water molecules attract to the polar ends of the molecules of their container, causing water to tend to adhere to the surfaces of its container ○ Plant Xylem: adhesion counters the forces of gravity, preventing all wayter from sinking to the bottom of the organism ● Surface Tension: how strong molecules hold on to each other against gravity or other forces ● Specific Heat: amount of heat that must be absorbed or lost for a substance to change temperature (molecular motion to increase ○ High Specific Heat: Substances requires more energy input before it will change temperature (resistant to temp change) ○ In water: hydrogen bonds absorb much of the heat energy before they will break ○ Water reservoirs (lakes, rivers, oceans) resist sudden strong temperature changes, presenting a more stable living environment for aquatic organisms ○ Cells and bodies, resist sudden changes in temperature ● Versatility as a Solvent: ○ Ionic compounds dissolve easily in water because positive ends of water molecules attract negative ions, and negative ends of water molecules attract positve ions. This attraction seperates ions/pulls them apart from each other and situates water molecules between them ○ Polar covalent compounds dissolve easily in water because charged regions of water molecules have an affinity for opposite-charged regions of solute molecules, causing water molecules to surround solute molecules ○ Biological fluids can contain many different kinds of dissolves solutes, such as salt and other ionic compounds, and polar monmers like sugars and amino acids ○ Aqueous Environments can contan many different kinds of solutes which are in turn available to aquatic organism
