MCB 450 1st Edition Exam 1 Study Guide Lectures 1 7 Lecture 1 January 20 Summary I Living systems require a limited variety of atoms and molecules II There are four major classes of biomolecules III The central dogma describes the basic principles of biological information transfer IV Membranes define the cell and carry out cellular functions Study Questions 1 What is meant by the Unity of Biochemistry Organisms are remarkably uniform at the molecular level 2 Carbon compounds stereochemistry configuration vs conformation Configuration is conferred by either Double bonds no freedom of movement around them Chiral centers groups arranged around a C atom in a specific orientation Rotation about C C bonds is pretty free allowing substituents on adjacent C atoms to take up many different positions relative to one another conformations 3 Know your functional groups Methyl Amino Phenyl Amido Carbonyl aldehyde Guanidino Carbonyl ketone Imidazole Carboxyl Sulfhydryl Hydroxyl alcohol Disulfide Ether Thioester Ester Phosphoryl Anhydride Phosphoanhydride Mixed anhydride acyl phosphate 4 Know the four types of biological molecules their general roles in cells Proteins nucleic acids lipids and carbohydrates Proteins serve as signal molecules receptors for signal molecules play structural roles allow mobility provide defenses against environmental dangers and act as catalysts Nucleic Acids store and transfer information contain the instructions for all cellular functions and interactions Lipids dual nature hydrophobic and hydrophilic parts which allows them to form barriers cell membranes also important storage form of energy and can act as signal molecules Carbohydrates important fuel source for most living creatures 5 What is meant by the Central Dogma Developed by Crick information flows from DNA to RNA and then to protein 6 What are the Domains of Life Bacteria Eukarya and Archaea 7 Know the basics of cellular organization and the roles of organelles Plasma membrane separates the inside of the cell from the outside and one cell from another cell impermeable to most substances Plant cell wall surrounds the plasma membrane constructed largely from cellulose protective layer Cytoplasm the background substance of the cell the material that is surrounded by the plasma membrane site of a host of biochemical processes Nucleus 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 here Chloroplast only found in plant cells and double membrane bounded converts sunlight into chemical energy photosynthesis Endoplasmic Reticulum a series of membranous sacs many biochemical reactions take place here ribosomes are attached to the rough endoplasmic reticulum that synthesize proteins Golgi Complex a series of stacked membranes sorts proteins Secretory 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 environment Endosome used to bring material into the cell by endocytosis the plasma membrane invaginates and buds off Lysosomes contains a wide variety of digestive enzymes garbage can of the cell Plant 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 interactions II Biochemical interactions take place in an aqueous solution III Weak interactions are important biochemical properties IV Hydrophobic molecules cluster together V pH is an important parameter of biochemical systems Study 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 other 2 What are polar non polar and amphipathic molecules Non polar cannot dissolve in water charge distributed evenly Polar charge distribution of molecules is uneven Amphipathic have polar and non polar regions 3 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 another b 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 other c 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 molecules Nonpolar solute molecules are driven together in water not primarily because they have a high affinity for each other but because they release water molecules 4 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 move 5 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 solution Weak acid incompletely dissociate in solution Polyprotic acid able to donate two H in a reaction 7 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 Hasselbalch pH pKa log A HA 9 Explain the shape of a titration curve for a weak acid S shaped slight changes in pH a Where is the buffering region Where the pH change is gradual b Explain why addition of acid or base has relatively little effect in this region The buffer will react with the added acid or base and thus will have little effect on the pH 10 Use H H equation to calculate how to make or