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Bio 3 Ch 3-Notes.Pdf 1 Almost all of the molecules a cell makes are composed of carbon atoms bonded to one another and to atoms of other elements. ORGANIC COMPOUNDS- Carbon-based molecules. Each carbon atom is a connecting point from which a molecule can branch in up to four directions. HYDROCARBONS- Compounds composed of only carbon and hydrogen atoms. Carbon atoms, with attached hydrogens, can bond together in chains of various lengths to form compounds. CARBON SKELETON- The chain of carbon atoms in an organic molecule. May be branched or unbranched. Compounds with the same formula but different structures are called ISOMERS. 2 The unique properties of an organic compound depend on the size and shape of its carbon skeleton and on the groups of atoms that are attached to that skeleton. FUNCTIONAL GROUPS- Affect a molecule’s function by participating in chemical reactions in characteristic ways. These groups are polar, because their oxygen or nitrogen atoms exert a strong pull on shared electrons. This polarity tends to make the compounds containing these groups HYDROPHILIC (water- loving) and therefore soluble in water. A HYDROXYL GROUP consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to the carbon skeleton. In a CARBONYL GROUP a carbon atom is linked by a double bond to an oxygen atom. If this functional group is found at either end then it is called an ALDEHYDE, but if it is located in the middle than it is known as a KETONE. A CARBOXYL GROUP consists of a carbon double- bonded to an oxygen and also bonded to a hydroxyl group. Mostly used as an acid. An AMINO GROUP is composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton. Normally acting as a base by picking up H+ ions. A PHOSPHATE GROUP consists of a phosphorus atom bonded to four oxygen atoms. A METHYL GROUP consists of a carbon bonded to three hydrogens. This molecule affects the expression of genes. 3 MACROMOLECULES- Gigantic chains covalently connected atoms. Cells make most of their large molecules by joining smaller molecules into chains called POLYMERS; a POLYMER is a long molecule consisting of many identical or similar building blocks strung together. The building blocks of polymers are called MONOMERS. 4 Cells link monomers together to form polymers by a DEHYDRATION REACTION, a reaction that removes a molecule of water. Each monomer has an H+ at one end an OH- at the other end. For each monomer added to a chain, a water molecule is removed. 5 Cells not only have to make polymers but also have to break them down. This process is essentially the reverse of a dehydration reaction, because instead of removing a water molecule, we add a water molecule. Both dehydration reactions and hydrolysis require the help of enzymes to make and break bonds. Enzymes are specialized macromolecules that speed up chemical reactions in a cells. 6 7 The name CARBOHYDRATES refers to a class of molecules ranging from the small sugar molecules dissolved in soft drinks to large polysaccharides, such as the starch molecules we consume in pasta and potatoes. The carbohydrate monomers are MONOSACCHARIDES. Monosaccharide's generally have molecular formulas that are some multiple of CH2O. The two trademarks of sugars; a number of hydroxyl groups and a carbonyl group. It is convenient to draw sugars as if their carbon skeletons were linear, but in aqueous solutions, most monosaccharide's form rings. 8 Cells construct a DISACCHARIDE from two monosaccharide’s by a dehydration reaction. The most common disaccharide is sucrose, which is made of a glucose monomer and a fructose monomer. 9 POLYSACCHRIDES are polymers of monosaccharides linked together by dehydration reactions. Polysaccharides may function as storage molecules or as structural compounds. STARCH, a storage polysaccharide in plants, consists entirely of glucose monomers. Starch molecules coil into a helical shape. Animal store excess sugar in the form of another glucose polysaccharide, called GLYCOGEN. In animals glycogen is mainly stored in our liver and muscle cells. CELLULOSE, the most abundant organic compound on earth, forms cable like fibrils in the tough walls that enclose plant cells. A key feature of this polymer is that the branching alternates at every junction. Because humans don’t have enzymes to digest cellulose, therefore cellulose is not a nutrient for humans Another structural polysaccharide, CHITIN, is used by insects and crustaceans to build their exoskeleton, the hard case enclosing the animal. 10 LIPIDS are diverse compounds that are grouped together because they share one trait; they mix poorly with water, if at all. Lipids consist mainly of carbon and hydrogen atoms linked by non-polar covalent bonds. Lipids are HYDROPHOBIC (water-fearing). A FAT is a large lipid made from two kinds of smaller molecules: glycerol and fatty acids. Glycerol is an alcohol with three carbons, each bearing a hydroxyl group. A fatty acid consists of carboxyl group and a hydrocarbon chain. The main function of fats is for storage. In addition to storing energy, fatty tissue cushions vital organs and insulates the body. Some fatty acids contain double bonds, which cause kinks (bends) in the carbon chain. Double bonds prevent the maximum number of hydrogen atoms from bonding to a carbon skeleton. Fatty acids and fats with double bonds in the carbon chain are said to be UNSATURATED- having less than the maximum number of hydrogens. Fats with the maximum number of hydrogens are said to be SATURATED. The kinks in unsaturated fats prevent the molecules from packing tightly together and solidifying at room temperature. Hydrogenation is when we add hydrogen to unsaturated fats, making them saturated. 11 Phospholipids are the major components of cell membranes. Phospholipids are structurally similar to fats, but they contain only two fatty acids attached to glycerol instead of three. The hydrophilic and hydrophobic ends of multiple molecules assemble in a bilayer of phospholipids to form membranes. The hydrophobic tails cluster in the center, and the hydrophilic phosphate heads face the watery environment on both sides of the membrane. 12 Steroids are lipids whose carbon skeleton contains four fused rings. Cholesterol is a common component in animal cell membranes, and animal cells also use it as a starting material for making other steroids, including sex hormones. 13 ANABOLIC STEROIDS are synthetic variants of the male hormone testosterone. Testosterone causes a general build up of muscle and bone mass in males during puberty and maintains muscle traits throughout life. They can be used as a prescription to treat anemia and diseases that destroy body muscle. However, some abuse these drugs, with serious consequences. Overdosing may cause violent mood swings and deep depression. The liver may be damaged, leading to cancer. 14 The most important roles of proteins is as enzymes, the chemical catalyst that speed and regulate virtually all chemical reactions in a cell. A protein is a polymer constructed from amino monomers Each of our many thousands of different proteins has a unique 3D structure that corresponds to a specific function 15 16 Protein diversity is based on differing arrangements of a common set of just 20 amino acids. AMINO ACIDS all have an amino group and a carboxyl group. The central carbon is known as the alpha Carbon. Notice the amino group, carboxyl group, and the Hydrogen atom attached to the alpha carbon which are common to amino acids. The R group (side chain) consists of one or more carbon atoms with various chemical groups attached. The structure of the R group determines the specific properties of each of the 20 amino acids that are found in proteins. 17 Cells join amino acids together in a dehydration reaction that links the carboxyl group of one amino acid to the amino group of the next amino acid as a water molecule is removed. The resulting covalent linkage is called a PEPTIDE BOND. A chain of amino acids, POLYPEPTIDE 18 The 3D shape is what determines its specific function. Their shapes enable them to recognize and attach to its molecular target. The dependence of protein function on a protein’s specific shape becomes clear when proteins are altered. In a process called, DENATURATION, polypeptide chains unravel, losing their specific shape, and as a result their function. Changes in salt concentrations and pH can denature many proteins, as can excessive heat. 19 The PRIMARY STRUCTURE- Is its unique sequence of amino acids. The three letter abbreviations represent amino acids. The SECONDARY STRUCTURE- In the second level of protein structure, parts of the polypeptide coil or fold into local pattern. Coiling of a polypeptide chain results in a secondary structure called an ALPHA HELIX; a certain kind of folding leads to PLEATED SHEETS. The double helix and the pleated sheets are held together by hydrogen bonds. The TERTIARY STRCUTURE- refers to the overall three-dimensional shape of a polypeptide. The indentations and bulges arising from its particular arrangement of coils and folds give the polypeptide the specific shape that fits to its function. Many proteins consist of two or more polypeptide chains, or subunits. Such proteins have a QUATERNARY STRUCTURE, resulting from the association of the subunits. 20 Pauling was studying biological molecules, in 1953 he and a colleague discovered how oxygen molecules attach to iron atoms of hemoglobin. He also discovered how an abnormal hemoglobin molecule causes sickle-cell disease. And it was also Pauling who first described the two fundamental secondary structures of proteins, the alpha helix and the pleated sheets. 21 The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a GENE. GENES consist of DNA one of the two types of polymers known as NUCLEIC ACIDS.
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