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The Structure and Function of Large Biological Molecules Introduction to Macromolecules Biological Molecules • One of the most important understandings in nature is that the same elements are used multiple times in various ways to get the diversity that is seen. • Noticing patterns in molecules can help you to understand form and function of a molecule Functional Groups • At times, a chemical group may replace one or more of the hydrogens bonded to the carbon skeleton. • These groups may participate in reactions and may play a role in the function of the molecule because of shape Functional Groups 1)Hydroxyl – Hydrophilic; increases solubility Functional Groups 2) Carbonyl – Hydrophilic; increases solubility – Know the difference between a ketone and an aldehyde Functional Groups 3) Carboxyl – Hydrophilic; increases solubility Functional Groups 4) Amino – Hydrophilic; increases solubility Functional Groups 5) Sulfhydryl – Hydrophilic; increases solubility Functional Groups 6) Phosphate – Hydrophilic; increases solubility Functional Groups 7) Methyl – Non-Reactive – Acts as a recognizable tag on biological molecules Macromolecules • Macromolecules (or polymers) are long, chain-like molecules – Consists of many similar or identical building blocks (monomers) linked by covalent bonds • Includes carbohydrates, nucleic acids, and proteins – Lipids are not a true macromolecule • Built via condensation or dehydration reaction (or dehydration synthesis) – Take away water molecule – Helped by enzymes to speed reaction • Breakdown via hydrolysis – Add water molecule – Occurs in digestion Carbohydrates • Monomers: monosaccharides or simple sugars – Simplified formula is CH2O – Structure is used to classify sugars • General structure includes a carbonyl group and multiple hydroxyl groups – Location of carbonyl will determine if it is aldose or ketose (aldehyde or ketone sugars) • Sugars are made up of 3-7 carbons in skeleton which may be linear or ringed • Spatial arrangement around asymmetric carbons is important – Examples: glucose, fructose, galactose – Important in cellular respiration and synthesis of materials Carbohydrates • Disaccharides: 2 sugars joined by a covalent bond – The covalent bond is known as a glycosidic linkage when it is between 2 monosaccharides – The bond is formed by dehydration reaction – Examples: Maltose, sucrose, lactose Carbohydrates • Polymers: polysaccharides; these are macromolecules also formed via glycosidic linkages – Storage polysaccharides • Starch – polymer of glucose monomers found in plants; starch allows plants to stockpile glucose – α configuration of glucose – Humans consume these in potatoes and grains • Glycogen – a branched polymer of glucose found in most vertebrates; largely stored in liver and muscle cells and is released when the body needs sugar Carbohydrates – Structural Polysaccharides • Cellulose – major component in cell walls – β configuration of glucose (every other glucose monomer is upside down) – Important in digestion – humans do not have the appropriate enzymes to digest β linkages, but promotes healthy digestion – Most abundant organic compound on Earth • Chitin – used by arthropods in exoskeletons – Similar structure to cellulose, but contains nitrogen Lipids • Lipids do not include true polymers and are not generally considered macromolecules • They are grouped together because they are hydrophobic • Largely composed of hydrocarbons • Includes: fats, phospholipids, steroids, waxes and pigments Lipids • Fats (triacylglycerol or triglyceride) – composed of glycerol attached to 3 fatty acids bonded via an ester linkage – Ester linkage occurs between hydroxyl and carboxyl groups – Glycerol – alcohol with 3 carbons each with its own hydroxyl group – Fatty acid – long carbon skeleton (16-18 common) with one carbon end associated with a carboxyl group. The rest is a long hydrocarbon chain. • Important in energy storage and protection • Fats Lipids – Saturated fat or fatty acid • No double bonds which allows the greatest number of hydrogens to be attached to the carbon skeleton • Includes most animal fats • Solid at room temp – Unsaturated fat or fatty acid • Has 1 or more double bonds and thus fewer hydrogen atoms • A kink in the chain will occur whenever a cis double bond occurs (as opposed to trans double bonds – ie trans fats found in hydrogenated veg. oil) • Includes plant and fish oils • Liquid at room temp Lipids • Phospholipids – essential for cell membrane composition – Similar to fat molecule, but only have 2 fatty acids attached to glycerol • The 3rd hydroxyl group is attached to a phosphate group (these can in turn bond to other molecules) • Hydrocarbon tail is hydrophobic (inside the bilayer), phosphate group is hydrophilic (face outward) Lipids • Steroids – carbon skeleton composed of 4 fused rings with different chemical groups attached – Includes many hormones and cholesterol – Fat can affect cholesterol levels Proteins • Proteins account for ~50% of cell’s dry mass and extremely important in functions Proteins • Monomers are amino acids – 20 different amino acids that are composed of an asymmetric carbon surrounded by an amino group, carboxyl group, hydrogen and an R group or side chain which varies • Polymers are polypeptides – Different combinations of A.A. allows for the variety of proteins – A.A. are attached with a covalent bond between the carboxyl group of one to the amino group of another called a peptide bond Proteins • Protein structure and function are intimately linked • The specific folds of a protein are determined by the ordering of A.A. in the polypeptide chain. This folding in turn determines shape. • Shape will then determine function. Proteins • Primary Structure – the unique sequence of amino acids • Secondary Structure – coils and folds in the polypeptide chain caused by hydrogen bonds between repeating constituents – α helix – a coil held together by hydrogen bonds at every 4th A.A. – β pleated sheet – folding creating pleats at particular intervals Proteins • Tertiary Structure – Overall shape of a polypeptide do to interactions of R groups – Shape may be reinforced by disulfide bridges • Covalent bond between sulfhydryl groups • Quaternary Structure – overall protein structure (potentially several polypeptide chains interacting) Proteins • Changes in primary structure lead to changes in further structures, potentially leads to a misfunctioning or nonfunctioning protein – Example: Sickle Cell • Protein shape and function can also be changed via denaturation – pH, temperature, salt concentration, etc. Proteins • Chaperonins or chaperone structure are specialized proteins that assist in the proper folding of proteins – Are not specific, but keep the protein away from potentially bad influences – Folding is spontaneous Nucleic Acids • Main function is to store and transmit genetic information • 2 kinds: RNA and DNA – These are both polymers/macromolecules – The monomers are nucleotides • Composed of a nitrogenous base, a 5-carbon sugar, and a phosphate group – Nucleosides are this unit minus the phosphate group Nucleic Acids • Two groups of nitrogenous bases – Pyrimidines: single 6-C ring • Cytosine, thymine, uracil – Purines: double fused rings (1 5-C, 1 6-C) • Adenine, guanine • Two kinds of sugars – RNA – ribose – DNA – deoxyribose Nucleic Acids • Nucleotides are linked together by phosphodiester linkages – Covalent bond between a phosphate group and a sugar • This creates the sugarphosphate backbone • One end will have a phosphate attached to a 5’ carbon; the other will have a hydroxyl group on a 3’ carbon (these are the ends of DNA and this plays a role in replication) • The opposing sides of DNA are linked via hydrogen bonds and twist about an imaginary axis creating the double helix ATP • Adenosine Triphosphate – Organic molecule consists of an adenosine molecule attached to a string of 3 phosphate groups – A reaction with water causes the release of one of the phosphate groups also releasing energy. • Molecule becomes ADP – Notice the similarities between ATP and nucleic acids