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Introductions Jessica Torres About MIT • MIT is the Massachusetts Institute of Technology located in Cambridge, Massachusetts • The mission of MIT is to advance knowledge and educate students in science and technology to serve the world in the 21st century About Me • Hometown: Houston, Texas • Major: Chemical Biological Engineering • Concentration: Education • Graduation: 2016 • I am currently a Junior More About Me • XXX = Fun pictures The Basics • I love class participation! • Ask questions • Answer my questions • Tell me if I speak too quickly • Anything! Feedback • I love feedback • At the end of every class, write down thoughts about the class • Things you liked or disliked • Suggestions you have • Things you did not understand or want more information about • Questions were too hard or too easy Question: Which U.S. State is the best? 1. California 2. New York 3. Texas Teach Me Italian! 1. Form a line at the chalkboard 2. Introduce yourself to me 3. Put a word on the board in Italian and write the English translation next to it Ex. Per favore - Please Introduction to Biochemistry Why Biochemistry? • Biochemistry: study of chemical processes for living organisms • It explains things happening inside you right now! • How we get energy • How we grow • How we move • Research in modern science almost always involves biochemistry Building Blocks - Elements • Elements are necessary for life • Only 6 elements make up make up 99% mass of human body • Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), and Calcium (Ca) Macromolecules • Macromolecule: large molecule made by putting together smaller repeating units • polymers = monomer + monomer + monomer + … + monomer • There are 4 main macromolecules in biochemistry Carbohydrates Lipids Nucleic Acids Proteins Lipids Lipids • Main functions: energy storage, signaling, and structure • Types: fats, oils, waxes, steroids Lipids • Properties: hydrophobic or amphipathic • Hydrophobic: nonpolar; water-hating • Hydrophilic: polar; water-loving • Amphipathic: has both hydrophobic and hydrophilic parts Fatty Acids • Fatty acids are parts of lipids • Fatty acid = hydrocarbon chain ending with a carboxylic acid group • Ex. Question: Which end of the fatty acid is hydrophilic? 1 2 Correct Answer: 2 • Hydrophilic: polar; water-loving Saturated v. Unsaturated • Saturated fatty acid characteristics: • Solid at room temperature • Contains no double bonds in hydrocarbon chain • Unsaturated fatty acid characteristics: • Liquid at room temperature • Contains double bonds in hydrocarbon chain • Linear structure • Typically Kinked structure • Examples: animal fats • Examples: plant oils (olive oil, corn oil) Fatty Acid Saturation • Saturated: no double bonds in hydrocarbon chain • Unsaturated: 1 or more double bonds in hydrocarbon chain Cis v. Trans Unsaturated Kinked Linear • Most naturally occurring fatty acids are found as the cis isomer • Trans fats are uncommon in nature, but can be man-made • Dangerous to our health • Raises bad cholesterol levels (LDLs) and lowers good cholesterol levels (HDLs) • Shown to increase risk of coronary heart disease Question: Is the fatty acid shape 1) linear, 2) kinked, or 3) circular? Correct Answer: 2) kinked • Unsaturated fatty acid: 1 or more double bonds in hydrocarbon chain • This is an example of a monounsaturated fatty acid, because it has only 1 double bond in the hydrocarbon chain Correct Answer: 2) kinked → • This fatty acid is considered an omega-3 (ω-3) fatty acid • ω-3 fatty acid: first double bond is on the 3rd carbon (C) • ω -3s in a diet has health benefits • Found in many fish (salmon, mackerel) and fruits and vegetables Triacylglycerols • Triacylglycerols are a types of lipids • Triacylglycerols = glycerol + 3 fatty acids Triacylglycerols • Function: energy storage • Storage fat in animal tissues • How do we get energy from triacylglycerols? • Answer: breaking hydrocarbon bonds to form lower energy products • β-oxidation converts components of triacylglycerols into a form that can be converted to energy like carbohydrates Sterol Lipids • Sterol lipids can act as signaling molecules • Hormone: signaling molecule produced by glands that regulate physiology and behavior • Used to communicate between organs and tissues • Ex. Estrogen and testosterone Sterol Lipids • Sterol lipids also play a role in cell structure • Cholesterol is the principle sterol synthesized by animals Cholesterol • Cholesterol is an essential structural component of animal cells • Helps maintain membrane structural integrity and fluidity • Because of cholesterol, animal cells do not need a cell wall, thus it can: • Change shape • Move around Cholesterol • Dietary sources: cheese, egg yolk, meats • Certain cholesterol is not good for your body • Bad: LDL • Diseases: atheroma Good: HDL Phospholipids • Phospholipid = phosphate + glycerol + 2 fatty acids • Phospholipids are lipids that make up cell membranes • They form a lipid bilayer Discovering the Lipid Bilayer • How do we know the cell membrane is a lipid bilayer? • Scientific discovery! • Here is how • 1925: Gorter and Grendel red blood cell experiment Review • Macromolecules: large molecule made by putting together smaller repeating units • Main function of lipids: 1. Energy storage 2. Signaling 3. Structure Review • Fatty acids are amphipathic • Triacylglycerol: glycerol + 3 fatty acids • Energy storage • Sterol lipids are important for signaling and structure • Hormones and cholesterol • Phospholipids are important for structure Proteins Protein • Functions: • Catalyzing metabolic reactions • Replicating DNA • Molecule transport • Structure • Skin, nails, muscles Protein • Protein: macromolecules made up of amino acids • Polymer: polypeptide • Monomer: amino acid • Our polypeptide is our puzzle and our amino acid is our puzzle piece • Proteins differ mainly in their amino acid sequence Standard Amino Acids • Sequence of amino acids in a protein is specified by a gene • Gene says which puzzle pieces to put together • Our genetic code specifies 20 amino acids • We have 20 different types of puzzle pieces to choose from • We can put any combination of amino acids together • Our puzzle can be as big or as small as we want Peptide Bonds • Peptide bond: covalent chemical bond formed between 2 amino acid molecules • Carboxyl group of 1st amino acid bonds with amine group of 2nd amino acid • Condensation reaction – water is released Primary (1º) Structure • Primary structure: amino acid sequence • A chain of puzzle pieces put together • Ex. Serine-Threonine-Valine-Leucine-Valine Secondary (2º) Structure • Secondary structure: repeating structures stabilized by hydrogen bonds α helix β sheet Question: What is the main secondary structure in the protein myoglobin? 1. α helices 2. β sheets Answer: 1. α helices • Myoglobin was the first protein to have its structure solved by X-ray crystallography Tertiary (3º) Structure • Tertiary structure: 3-dimensional structure of a protein • Protein folding • Controls basic function of a protein Question: Which amino acid is most likely to interact with leucine? Quaternary (4º) Structure • Quaternary structure: multiple protein subunits Question: How many quaternary subunits does the following protein have? • Video is here 1. 2. 3. 4. 5. 1 2 5 10 20 Answer: 10 subunits Enzymes • Enzyme: catalyzes chemical reactions • Responsible for thousands of biological processes that sustain life • Enzymes are HIGHLY specific E + S ↔ ES → E + P Question: Which interaction is not favorable? Answer: Interaction 4 Design Challenge • Work in groups of 2 or 3 • Think of a function of the body and design an enzyme that can accomplish this function • Think about primary, tertiary, and quaternary structures • Remember: structure determines function! Example Project • Function: transporting Na+ outside the cell and K+ inside the cell Quaternary structure: 2 subunits Hydrophobic/Nonpolar Amino Acids Hydrophilic/Polar Amino Acids Protein Functions • • • • Catalyzing metabolic reactions Replicating DNA Responding to stimuli Transporting molecules from one location to another Present! 1. 2. 3. 4. Introduce your group Say which function you chose Draw your protein Explain its structure 1. Primary, secondary, tertiary, and quaternary Studying Protein • We study proteins for many reasons • Medicines • Diseases • Methods to studying proteins: • Protein purification • Cellular localization • Proteomics • Bioinformatics Protein Purification • Protein purification: isolation of proteins from cells or organisms • Why? Here. Steps: 1. Isolate all proteins from mixture 2. Separate protein of interest from other proteins Protein Purification 1. 2. 3. 4. 5. Cell lysis Ultracentrifugation Precipitation Chromatography Gel electrophoresis, spectroscopy, or enzyme assays Review • Protein: macromolecules made up of amino acids • Peptide bond: covalent chemical bond formed between 2 amino acid molecules Review • • • • Primary structure: amino acid sequence Secondary structure: repeating structures stabilized by hydrogen bonds Tertiary structure: 3-dimensional structure of a protein Quaternary structure: multiple protein subunits Review • Enzyme: catalyzes chemical reactions • Protein purification: isolation of proteins from cells or organisms Carbohydrates Carbohydrates • Carbohydrates: macromolecules consisting of C, H, and O atoms • Monomer – monosaccharide • Polymer – polysaccharide • Glucose – the main monosaccharide Monosaccharides Glucose (C6H12O6) Fructose (C6H12O6) Galactose (C6H12O6) Function • Energy release • Starch and glycogen • Structure • Cellulose in plants Energy Release • Glycolysis + TCA/Citric Acid/Krebs Cycle +Electron Transport Chain • Generate energy in the form of ATP ATP Glycolysis TCA Cycle Electron Transport Chain Nucleic Acids Nucleic Acids • Nucleic acids: macromolecules essential for all forms of life • Monomer – nucleotide • Polymer – nucleic acid • Examples: DNA and RNA DNA • Deoxyribonucleic acid (DNA): encodes genetic instructions for development and functioning of all living organisms • DNA is only recently understood • 1953: Discovery of the double helix – Watson and Crick • 1984-2003: Human Genome Project • World’s largest collaborative biological project • Really cool video here Fun Stuff Want to See Cool Chemical Reactions? Here is a few. Here is another. How about this one? I think this is pretty neat. But wait, watch this!