Chemi stry Revi ew by shashislk


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									Chemistry Review What are we made of, chemically? Reduce human body to elements Oxygen 65% Carbon 18.5% Hydrogen 9.5% Nitrogen 3.3 Calcium 1.5 Phosphorous 1.0 Potassium 0.4 Sulfur 0.3 Sodium 0.2 Chlorine 0.2 Mg 0.1 Trace of B Cr, Co, F, I, Fe, Mn, Mo, Se, Si, V, Zn "organic molecules" carbon compounds. Each element is a different type of atom Atomic number versus atomic mass Characteristic electron shells, 2 in first shell 8 in second 2 in 1s orbital, 2 in 2s, 6 in 2p Valence? Number of unpaired electrons, 1 for H, 2 for O, 3 for N, 4 for C, 5 for P Compounds, molecules Single double and triple bonds Ionic bonds versus covalent bonds ( Some molecules have intermediate (ionic/covalent) bonds (like water) Molarity versus moles Difference between concentration and amount In biology we frequently use nM, µM and mM In cells, abundant molecules are present in mM concentrations Low levels are µM Scarce molecules are nM Sizes in biology Å, nm, um


Energetics Chemical equilibrium ATP + H2O -> ADP + Pi


Potential energy versus kinetic energy An atom with an excited electron has potential energy An atom has kinetic energy proportional to its degree of motion "heat" is directly related to molecular motion, hotter molecules are bouncing around more vigorously. The probability of a chemical reaction can be predicted by ΔG = ΔH - TΔS ΔG is the change in free energy for a reaction ΔH is the change in the potential energy (usually in the form of heat) in the chemical bonds T is the absolute temperature (higher temps, more kinetic energy) ΔS is the entropy, the amount of disorder in the molecules Endothermic versus exothermic Oxidation versus reduction, gaining or losing an electron Functional groups, know structure, chemical properties Amino Carboxyl Hydroxyl Phosphate Sulfhydryl

Water H2O, properties due to the electronegativity of H and O Oxygen has higher affinity for an electron than hydrogen Polar molecule Readily forms H bonds. 1/20 strength of a covalent bond, important in biology Properties of water Cohesive (because of polarity) 2

Liquid more dense that solid High specific heat High heat of condensation and vaporization Acids and bases Proton donors versus acceptors, (carboxyl versus amine) pH is a measure of H+ concentration, important in biology What is a buffer? Origin of Life Oparin and Haldane hypothesis Stanley Miller experiment 1953, Spark Discharge Apparatus Produced sugars, amino acids, nitrogenous bases, fatty acids etc What are the molecules needed to form a living organism? Bacteria have 2-4,000 genes Thus roughly 10,000 kinds of molecules

Summary Table of Biological Molecules Carbohydrates Monomers Polymers Function simple sugars sugar chains energy, structure structure Proteins amino acids proteins enzymes, structure Nucleic acids nucleotides RNA, DNA Lipids fatty acid complex

information energy, protein synthesis membran

Carbohydrates CO2 plus water - Sugars and their polymers Monosaccharides form polysaccharides Glucose, fructose, ribose, deoxyribose Sucrose, table sugar, is a disaccharide formed of glucose + fructose Many glucoses in a chain form starch or glycogen or cellulose Condensation (dehydration) reactions put sugar together 3

Hydrolysis reactions split apart sugars Chirality Most sugars can form as different sterioisomers Example of your hands - mirror structures - not superimposable D sugars and L amino acids Proteins Made of amino acids Structure, note charge Side chains, give proteins their variation in chemical properties Polar versus Non-polar Acidic versus basic? Sulfhydryl group in cysteine Chiral - use L- amino acids

Peptide bond, draw the structure Polypeptides are proteins Typically 50 - 1000 amino acids in a polypeptide chain Proteins have 4 levels of structure Primary structure is the sequence of amino acids Secondary structure - regions of regular folding Two types alpha helices and beta sheets Caused by H-bonds between certain alignments of residues Tertiary structure The 3-dimensional location of all the atoms Quaternary structure The position of polypeptides in proteins with more than one polypeptide The structure of a protein is determined by several different types of chemical bonds. H-bonds Disulfide bonds between cysteines Ionic bonds between charged side chains Hydrophobic interactions Water plays a key role because many parts of the polypeptide bind water. 4

Nucleic Acids Monomers are nucleotides Nitrogenous bases Purines A adenine G guanine Pyrimidines C cytosine T thymine U uracil Polymers made by condensation reactions Phosphate (on 5' C) bonds to ribose (at 3'C) Forms the phosphodiester bond Sugar-phosphate backbone Bases stick out to side RNA ribose sugar use A G C and U DNA deoxyribose (2' C) Use A G C and T DNA is usually in the form of a double helix Structure discovered in part from "Chargaff's Rules" 1. Amount of purines = amount of pyrimidines 2. Amount of A = T, G = C Watson and Crick models, C and G form 3 H bonds A and T form 2 Rosalind Franklin and Maurice Wilkens contributed crystallography data suggesting DNA was probably helical Published in April 1953, 50th anniversary. 5 nitrogenous base + sugar + phosphate

RNA secondary and tertiary structure Single strands of RNA can fold back on themselves, make stem and loop  secondary structure of RNA Some RNAs make a precise folded structure, e.g. ribosomal RNA Lipids Lipids as a class defined by chemical properties, not by structure. Common feature, have a hydrocarbon chain Electrons shared equally between C and H, thus no partial charge, Nonpolar, don't readily bind water Three of the most common lipids Phospholipids Fats Sterols Structure 2 Fatty acids + glycerol + phosphate and a small polar molecules (ser) combine to form a phospholipid 3 fatty acids + glycerol  a fat

fatty acids can be saturated or unsaturated No double bonds in tail versus one or more difference between plants oils and Animal fats differences in solubility, fluidity versus temp What are transfatty acids What is "partially hydrogenated" soybean oil Sterols - four fused rings + hydrocarbon tail  a sterol (e.g. cholesterol) Do these molecules bind water ? Fats do not, form fat droplets, Sterols almost as insoluble part of the reason they may be related to Cardiovascular problems. Phospholipids and sterols have a polar functional group These are amphipathic relative size of nonpolar part of sterol and P-lipid, about same. Phospholipids form micelles or bilayers 6

P-lipids will spontaneously form a closed compartment with lipid bilayers Called vesicles Lipid permeability Charged molecules, or polar molecules, cannot easily cross lipid bilayers Na+ K+ Cl- glucose, ATP, most proteins Bilayers seal the compartment, Keep most water-soluble molecules either in or out. hydrophobic versus hydrophilic H2O is the exception, crosses bilayer readily Diffusion and osmosis. Diffusion --molecules are in constant motion Net flow, from high concentration to low concentration Like a chemical reaction, driven by entropy Diffusion underlies almost all reactions in cells Osmosis is the diffusion of water Water moves from high concentrations to low conc. Solutions can be hypertonic, hypotonic or isotonic Osmosis can be a powerful reaction, can generate a lot of pressure Biological Membranes Barely visible with an electron microscope, look like railroad tracks Isolation of membranes Break open cells by osmotic lysis Put cell homogenate in a tube, spin in a centrifuge For animal cells (no walls etc) 20,000 x g, 30 min Membranes move to bottom pellet, soluble proteins etc stay in solution (if fat present, will float to top) membranes composition typically 40% phospholipids and sterols 7

55% proteins 5% carbohydrates Fluid mosaic model explains how proteins and lipids are put together Lipids form a bilayer Proteins float like boats -- hydrophobic side chains bind to hydrophobic parts of lipids polypeptide with region containing 20 or more hydrophobic amino acids can fold to cross the lipid bilayer.Freeze-fracture and electron microscopy- see bumps ands pits formed by the proteins Major function of membranes is to keep all the molecules dissolved in the fluid within cells from leaking out, and prevent harmful molecules from getting in. The lipid part of the membrane does this. Transport Proteins in Membranes Three types Pumps, carriers, channels Pumps, example V-ATPase, Na+-ATPase Move molecules one (or a few) at a time Use ATP, can transport against a gradient Carriers, example, GLUT-1 glucose transporter Move molecules one (or a few) at a time No direct energy imput, driven by diffusion Channels, examples, Na+ and K+ channels Like a gated pore, 1000's of molecules can move with one opening No direct energy imput, driven by diffusion. An electrochemical gradient is generated and used by membrane proteins Electro - electrical, ion build up one each side Chemical - many chemicals are concentrated inside, Na+ high outside in animals Used for nutrient uptake, sensing, nerve function It is really the way to tell a live cell from a dead cell. 8

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