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BIOL 130
Heidi Engelhardt

BIOL120 MIDTERM REVIEW NOTES CHAPTER 1 – A PREVIEW OF A CELL  Latin word cellula meaning “little room”  Cell theory: all organisms consist of one or more cells; the cell is the basic unit of structure for all organisms; all cells arise only from preexisting cells.  Electron microscope designs: transmission electron microscope (TEM) “black and white sketched images” and scanning electron microscope (SEM) “3D images”.  Prokaryote: no nucleus, single celled organism, cell wall. Ex. Bacteria  Eukaryote: true nucleus, multicelled organism, cell wall depends. Ex protists.  Cytoplasm: everything between plasma membrane and nuclear membrane, includes all membrane bound organelles.  Cytosol: fluid only component of cytoplasm.  Rough ER: wrapped around nucleus, studded with ribosomes, takes RNA transcripts, proteins for export.  Smooth ER: synthesize lipids and steroids, metabolize carbohydrates and steroids (but not lipids), and regulate calcium concentration, drug metabolism and attachment of receptors on cell membrane proteins. Lacks ribosomes.  Golgi apparatus: collection, packing, distribution  Lysosomes: cell “stomachs”, enzymes to digest four macromolecules/worn out organelles, material brought into cell by phagocytosis.  Mitochondria and chloroplasts contain DNA for some of their own proteins, both have double layers of membranes.  Nucleus: dense core in centre, consists of protons, neutrons, membrane bound. CHAPTER 2 – WATER & CARBON: THE CHEMICAL BASIS OF LIFE  C, H, N, O make up 96% of all matter found in organisms.  Cohesion: binding between like molecules. Water molecules stay together because of the hydrogen bonds that form between individual molecules.  Adhesion: binding between unlike molecules. Usually analyzed in regard to interactions between a liquid and a solid surface, ie water adheres to surfaces that have any polar or charged components.  Surface tension: makes water surface act as if it had an elastic membrane.  Acids are proton donors (increase [H+] in solution) and bases are proton acceptors (decrease [H+] in solution). A chemical reaction that involves transfer of protons is called an acid-base reaction. This is important because the transfer of protons changes the charge of donor and acceptor, this means the charge changes reactivity with respect to hydrogen bonding. Ex blood acidity.  pH = -log[H+]. [H+] = 10^-pH  Electrons in outer shells have more potential energy than do electrons in inner shells, because negative charges in outer shells are farther from the positive charges in the nucleus. If the opportunity arises, an electron residing in an outer electron shell will fall into a lower electron shell closer to the positive charges of the protons in the nucleus.  Thermodynamics: relations between forms of energy, interconversions of forms of energy. First Law of Thermodynamics: Energy can be transferred and transformed but cannot be created or destroyed. Second Law of Thermodynamics: energy tends to spontaneous disperse from being localized, in order to become spread out or disordered. Entropy = disordered.  Exergonic reaction: results in net release of energy. Thermodynamically favourable, spontaneous, energy used or lost as heat, less complex products.  Endergonic reaction: requires energy input, thermodynamically unfavourable, more complex products.  Reactions tend to be spontaneous if the products have lower potential energy than the reactants, or when the product molecules are less ordered than the reactant molecules.  Reactions occur when reactants collide in a precise orientation and have enough kinetic energy to overcome repulsion between electrons that come into contact as bond forms.  Functional groups: in general, the carbon atoms in an organic molecule furnish a skeleton that gives the molecule its overall shape. All behave consistently. All are hydrophilic/polar.  Amino R-NH2. Acts as a base- tends to attract protons  Aldehyde R-C=O-H. React with compounds of form H-R2 to produce larger molecules.  Ketone R-C=O-R.  Carboxyl R-C=0,-OH. Acts as an acid- tends to lose a proton.  Hydroxyl R-OH. Highly polar, makes compounds more soluble through hydrogen bonding with water, also may act as weak acid and drop a proton.  Phosphate R-P-O-O-O=O. Breaking O-P bonds releases large amount of energy.  Sulfhydryl R-SH. When present in proteins, can form disulfide (S-S) bonds that contribute to protein structure. CHAPTER 3 – PROTEIN STRUCTURE & FUNCTION  Proteins are made of 21 different amino acid building blocks, which all have a common backbone structure: a central carbon bonded to an amino functional group, a carboxyl, a hydrogen, and a R group (side chain).  The R groups vary – may be H, ring structure, contain carboxyl, sulfhydryl, hydroxyl, or amino acid functional groups (more reactive). Affect solubility, chemical reactivity.  Non polar side chains: no charged or electronegative atoms to form hydrogen bonds, not soluble, bury themselves in peptide chains to “hide” from water.  Charged polar side chains: partial charges form hydrogen bonds, soluble.  Uncharged polar side chains: contain acids or bases, soluble.  Polymerization: the process of linking monomers. Amino acids polymerize to form proteins.  Condensation/dehydration reactions: newly formed bond results in loss of water molecule.  Hydrolysis: opposite of condensation/dehydration. Breaks polymers apart by adding a water molecule. Dominates because it increases entropy and is energetically favourable (lowers potential energy). This is why polymerization reactions are expected to proceed slowly.  Peptide bond: Between a carboxyl group of one amino acid and the amino group of another. Side chains are present, has directionality, flexible. End of the sequence that has the free amino group is on the left and is called N- terminus, and the end with the free carboxyl group appears on the right hand side and is called the C-terminus.  Primary structure: polypeptide chain. Changes in primary structure affect protein function: one single amino acid mutation causes a change. Ex sickle cell anemia (abnormally shaped red blood cells). Caused by a single amino acid mutation in hemoglobin.  Secondary structure: created in part by hydrogen bonding. Distinctively shaped sections of proteins are stabilized largely by hydrogen bonding that occurs between the carboxyl oxygen of one amino acid residue and the hydrogen on the amino group of another. Created by interactions between atoms that are part of the protein’s peptide bonded backbone. Alpha helix or beta pleated sheet shape.  Tertiary structure: A result of interactions between R groups or between R groups of the peptide backbone. Each contact between R groups causes the peptide -bonded backbone to bend and fold in a precise way. Twisted, folded and coiled polypeptides. Include interactions between alpha helices and beta-pleated sheets. Four types of interactions: hydrogen bonds between hydrogen atoms and carboxyl group/hydrogen and atoms with partial negative charges in side chains. Van der Waals interactions, water molecules interact with hydrophilic side chains and force hydrophobic side chains to coalesce. Once hydrophobic side chains are close to each other, they are stabilized by the electrical forces (van der Waals)- weak attracts occur because the constant motion of electrons gives molecules a tiny asymmetry in charge that changes with time. Covalent bonds form between sulfur atoms when a reaction occurs between sulfur containing R groups (disulfide bonds “bridges”). Ionic bonds form between groups that have full and opposing charges. Tertiary structure depends on primary and secondary structure.  Quaternary structure: The combination of polypeptide subunits gives proteins a quaternary structure. Based on tertiary structure, primary structure. Produced by combinations of tertiary structures.  Folding may release enough free energy to be exergonic and occur spontaneously. Proteins can unwind, or become denatured, by treating with compounds (pH, salt concentration, temperature) that break hydrogen bonds and disulfide bonds.  Enzymes catalyze reactions. Catalysts lower activation energy of a reaction and increases rate of reaction.  Enzymes bring reactant molecules called substrates together in precise orientation so the electrons involved can interact.  A collision between reactants creates a combination of old and new bonds called transition state.  Amount of free energy required to reach the transition state is called the activation energy of the reaction. Reactions happen when reactants have enough kinetic energy to reach the transition state. The Ek is a function of the temperature; this is why reactions tend to proceed faster at higher temperatures.  The location where substrates bind and react are the enzyme’s active site. This is where the catalysis occurs.  Interactions with R groups at the active site stabilize the transition state and thus lower the activation energy required for the reaction to proceed.  Enzyme cofactors, which can be metal ions or small organized molecules
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