Exam 1 Study Guide PCB3134 Spring 2013 1 Four Tenets of the Cell Theory a The cell is the basic unit of life b All organisms are composed of one or more cells c New cells arise only from division of pre existing cells d Cells evolved from more primitive common progenitor cells along three branches of an evolutionary tree 2 Principles of modern microscopy methods a The optical path of a conventional light microscope i Conventional Light Microscope bright field microscope light passes through the specimen and forms the image directly b How to determine the resolution of an objective lens c Fluorescence and principles of fluorescence microscopy i Fluorescent molecules absorb light at one wavelength and emit it at another longer wavelength 1 Excitation 2 Excited State Lifetime 3 Fluorescence Emission Jablonski diagram d Applications of fluorescence microscopy FRAP i FRAP Fluorescence recovery after photobleaching e Transmission electron microscopy resolution and sample preparation LM TEM 1 Resolution 2 Sample prep 3 Detection 3 Protein structure and function by peptide bond a 20 AAs and properties of their R groups elongation of a polypeptide i There are 20 different R groups seen in AA thus forming the 20 AA seen throughout the cell ii There are three different classification of AA due to their R groups 1 They are either Hydrophobic Hydrophilic or in the Special AA class iii During Elongation of a poly peptide Petidyl tranferase keeps on adding to the chain thus elongating the polypeptide chain 1 Peptide bonds form between the carboxyl end of the first AA and the amino end of the second AA b Primary structure sequence of AAs secondary structure local folding helix and sheet tertiary structure overall conformation of a polypeptide three dimensional structure quaternary structure number and relative positions of subunits in a multimeric protein complex Types of bonds interactions required for stabilizing these structures i A helices made with hydrogen bonds between the CO double bond of aan and the N H bond in aan 4 the R groups stick out from the Helix ii Beta Pleated Sheets the pleated sheets are formed by hydrogen between the CO double bond of an AA in one stand and the NH bond of an AA in the other strand R groups alternate sticking up and down iii Tertiary structure 1 Overall conformation of polypeptide chain Determined by amino acid sequence stabilized by hydrophobic interactions between aa side chains may be stabilized by Cys disulfide bonds inextracellular proteins For some proteins tertiary structure highest level of organization iv Quaternary Structure 1 Quaternary organization of several polypeptide chains to make single multimeric protein complex a Number and relative positions of polypeptides in multimeric protein b polypeptide subunits held together by hydrogen bonds and or disulfide bonds c From structure to function case studies sickle cell anemia mad cow disease and Alzheimer s disease i Sickle Cell Anemia ii Mad Cow Disease iii Alzheimer s Disease diseases 1 Abnormally folded proteins aggregate to cause human Amyloid Precursor Beta Amyloid 4 Biological membrane a Chemical compositions of the biological membrane hydrophobic core and polar heads three types of lipids phosphoglycerides sphingolipids and steroids amphipathic molecules b How do unsaturated fatty acids contribute to membrane fluidity i Unsaturated double bond forms inflexible kink in tail ii Kinked tails pack more loosely in membrane core c Fluid mosaic model of biomembrane experimental data that support it i The plasma membrane is described to be fluid because of its hydrophobic integral components such aslipids and membrane proteins that move laterally or sideways throughout the membrane That means the membrane is not solid but more like a fluid The membrane is depicted as mosaic because like a mosaic that is made up of many different parts theplasma membrane is composed of different kinds of macromolecules such as integral proteins peripheralproteins glycoproteins phospholipids glycolipids and in some cases cholesterol lipoproteins ii Amphipathic one end hydrophilic differs in solubility from other end hydrophobic d Three types of membrane associated proteins integral lipid anchored and peripheral membrane proteins i Integral membrane proteins transmembrane proteins three domains segments ii Lipid anchored membrane proteins covalently bound to lipid molecules iii Peripheral membrane proteins bound to integral or lipid anchored proteins or interacts with lipid polar head groups e Lipid synthesis 4 steps of phospholipid synthesis key steps of cholesterol synthesis i Step 1 formation of phosphatidic acid ii Step 2 formation of diacyl glycerol iii Step 3 phosphotransferase adds the head group iv Step 4 Flippase catalyzes the movement of phospholipid from the inner to the outer leaflet 5 Membrane transport a Facilitated transport vs simple diffusion permeability of biological membrane Simple Diffusion Net movement of a molecule across a membrane down its concentration gradient at a rate proportional to the gradient and the permeability of the membrane also called passive diffusion o Done by gases such as O2 and CO2 and small uncharged polar molecules such as urea and ethanol o No metabolic energy is expended because movement is from a high to low concentration of the molecule down its chemical concentration gradient Facilitated Transport Protein aided transport of an ion or small molecule across a cell membrane down its concentration gradient at a rate greater than that obtained by simple diffusion Biological membrane Barrier that defines aqueous compartments in which the internal environment has properties different from the external environment Membrane properties depend on properties of component parts o Major structural components are lipids esp phospholipids o Most prevalent membrane lipids have glycerol backbone and fatty acid tails b Protein transporters uniporter symporter and antiporter basic principles Uniport A type of transport in which a membrane protein uniporter mediates movement of a small molecule across a membrane down its concentration gradient via facilitated transport o The glucose transporters GLUT proteins are well studied examples of uniporters o Glut 1 uniporter Glucose binds to site on Glut1 protein 12 TM alpha helices on one side of membrane high conc Glucose o Glucose biding causes protein conformation change that opens access of glucose to other side of membrane glucose forms H