MCB 450 1st EditionExam # 1 Study Guide Lectures: 1 - 7Lecture 1 (January 20)Summary:I. Living systems require a limited variety of atoms and moleculesII. There are four major classes of biomoleculesIII. The central dogma describes the basic principles of biological information transferIV. Membranes define the cell and carry out cellular functionsStudy Questions:1.What is meant by the Unity of Biochemistry?Organisms are remarkably uniform at the molecular level. 2.Carbon compounds & stereochemistry: configuration vs conformationConfiguration is conferred by either...Double bonds - no freedom of movement around themChiral centers - groups arranged around a C-atom in a specific orientationRotation about C-C bonds is pretty free, allowing substituents on adjacentC-atoms to take up many different positions relative to one another = conformations3. Know your functional groupsMethyl PhenylCarbonyl (aldehyde)Carbonyl (ketone)CarboxylHydroxyl (alcohol)EtherEster AnhydrideAmino AmidoGuanidinoImidazoleSulfhydrylDisulfideThioesterPhosphorylPhosphoanhydrideMixed anhydride (acyl phosphate)4.Know the four types of biological molecules & their general roles in cells Proteins, nucleic acids, lipids, and carbohydratesProteins – serve as signal molecules, receptors for signal molecules, play structural roles, allow mobility, provide defenses against environmental dangers, and act as catalystsNucleic Acids – store and transfer information, contain the instructions for all cellularfunctions and interactionsLipids – dual nature: hydrophobic and hydrophilic parts, which allows them to form barriers (cell membranes); also important storage form of energy and can act assignal moleculesCarbohydrates – important fuel source for most living creatures5.What is meant by the Central Dogma?Developed by Crick; information flows from DNA to RNA and then to protein6.What are the Domains of Life?Bacteria, Eukarya, and Archaea 7.Know the basics of cellular organization and the roles of organellesPlasma membrane – separates the inside of the cell from the outside and one cell from another cell; impermeable to most substancesPlant cell wall – surrounds the plasma membrane; constructed largely from cellulose; protective layerCytoplasm – the background substance of the cell; the material that is surrounded by the plasma membrane; site of a host of biochemical processesNucleus – largest organelle and double-membrane-bounded; location of organism’s genome; has pores that allow transport into and out of the nucleus; Mitochondrion – has two membranes; fuel molecules undergo combustion into carbon dioxide and water with the generation of cellular energy, ATP; 90% of the energy used in a cell is produced hereChloroplast – only found in plant cells and double-membrane-bounded; converts sunlight into chemical energy: photosynthesisEndoplasmic Reticulum – a series of membranous sacs; many biochemical reactions take place here; ribosomes are attached to the rough endoplasmic reticulum that synthesize proteinsGolgi Complex – a series of stacked membranes; sorts proteinsSecretory Granules – formed when a vesicle filled with the proteins destined for secretion buds off the Golgi complex, the contents of the secretory granule is dumped into the extracellular environmentEndosome – used to bring material into the cell by endocytosis; the plasma membrane invaginates and buds offLysosomes – contains a wide variety of digestive enzymes; garbage can of the cellPlant vacuoles – only in plants; can occupy up to 80% of the cell; store water, ions, and different nutrients Lecture 2 (January 22) Summary:I. Thermal motions power biological interactionsII. Biochemical interactions take place in an aqueous solutionIII. Weak interactions are important biochemical propertiesIV. Hydrophobic molecules cluster togetherV. pH is an important parameter of biochemical systemsStudy Questions:1. Know the properties of water: a. it's dipolar, forms H-bonds, has a high dielectric constant (what's that?) Dielectric constant - the ability of water molecules to surround ions and diminish the attraction of opposite charges for each other2. What are polar, non-polar, and amphipathic molecules?Non-polar – cannot dissolve in water; charge distributed evenlyPolar – charge distribution of molecules is unevenAmphipathic - have polar and non-polar regions3. What are the four types of weak, non-covalent interactions?a. What are hydrogen bonds? What types of atoms do they form between?Polar ends on water interact with one anotherb. What are ionic interactions, and how does water affect them?Interactions between distinct electrical charges on atoms; water weakens them, the individual ions bind to water molecules rather than to each otherc. What are van der Waals forces? What's meant by "strength in numbers"?The distribution of electronic charge around an atom changes with time and the charge distribution is not perfectly symmetric which allows the molecules to interact electrostatically. The more van der Waals forces there are the more significant the impact the forces have. d. What are hydrophobic interactions? What is meant by their being entropically driven? How do water molecules play a role?Hydrophobic – cannot interact with water moleculesNonpolar solute molecules are driven together in water not primarily because they have a high affinity for each other but because they release water molecules4. What is meant by Brownian (thermal) motion?Water and gas molecules of the environment are bouncing randomly about at a rate determined only by the temperature; causes dust or pollen to move5. What are Kw and pH? Can you solve problems involving pH and Kw?Kw – ion product of water; Kw = [H+] [OH-]6. What are strong acids, weak acids, and polyprotic acids?Strong acid – completely dissociate in solutionWeak acid – incompletely dissociate in solutionPolyprotic acid – able to donate two H+ in a reaction7. What are the expressions Ka, pKa?Ka – equilibrium constant; [H+] [A-]/ [HA]pKa – log(1/Ka)a. What does it mean when these values are relatively large or small?The lower the pKa the stronger the acid. 8. Know the relationship between pH and pKa (Henderson-Hasselbalch eq.)a. Be able to solve problems using Henderson-HasselbalchpH = pKa + log([A-]/[HA])9. Explain the shape of a titration curve for a weak acidS-shaped, slight changes in pH. a. Where is the buffering region?Where the pH change is gradualb. Explain why