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IB104 - Lecture 7 - Molecules of life Reading - Chapter 3 (but not individual amino acid structures) Buckminster Fuller was a famous American architect who designed domes. Soccer balls used to use the same C60 architecture. Fullerenes are now major players in nanotechnology. Life involves organic molecules that are based on carbon. You are familiar with inorganic carbon, like graphite, diamonds, and hopefully Buckminsterfullerenes or buckyballs (handout). Jan 10 1964 graphite diamond Buckminsterfullerene C60 Carbon can make four covalent bonds. Carbon has the atomic number 6, and atomic weight 12. Thus six each of protons, neutrons, and electrons. These electrons occupy the inner orbital completely with two, and then one each in the four second level orbitals. This means there are four electrons available to form four stable covalent bonds by “pairing” with electrons from other atoms. If we simply add hydrogens to carbon we have hydrocarbons, e.g. methane. Keep doing this with multiple carbons and you get propane, etc. Long hydrocarbon chains are the stuff of natural gas and oil. Also rings, e.g. benzene. 1 1. Carbohydrates are the simplest of the four major kinds of biochemicals (a subset of organic molecules) involved in life. Carbohydrates are the basic energy sources and stores for all organisms, and are also commonly structural. The simplest carbohydrates are the monomers called sugars, known technically as monosaccharides (from the same root as the word saccharin for the artificial sweetener). Glucose and fructose are two major ones. These are six carbon sugars, in the form of a ring with hydroxyl (-OH) groups on most of the carbons and a double-bond ketone or aldehyde group somewhere (C=O and H-C=O). Disaccharides consist of two such monomers. Famous examples are: Sucrose (common sugar) formed from glucose and fructose. Maltose (e.g. for beer) is two glucose monomers together. Lactose (e.g. in mammalian milk) is glucose and galactose. While fructose is a normal sugar we consume all the time in foods, it is metabolized somewhat differently from glucose, hence some believe that high-fructose drinks and other foods are part of the obesity problem. Sucrose Linear OR “weird” ring Polysaccharides are many sugar monomers joined together. This joining chemical reaction involves loss of a water molecule from two hydroxyls leaving an ester bond, so is variously called condensation or synthesis or dehydration. The opposite reaction is hydrolysis (splitting or lysis with water). These two reactions mediate every example of monomers to polymers we will consider today. condensation hydrolysis Plus H2O Polysaccharides fill both energy storage and structural roles. Glycogen is the animal storage form and has many branching chains of glucose monomers. This is your first energy source after using free glucose in the blood stream. Exchange between glycogen and glucose is regulated by hormones like insulin and glucagon. Diabetes results from mis-regulation of this exchange. Starch is the plant storage form and has linear stiff chains. It is therefore useful for making collars on shirts stiff. Animals eat starch in plants like corn and potatoes, etc., hydrolyse it to glucose, and then store it as glycogen. 2 Chitin is the animal structural form making the exoskeletons of arthropods and nematodes (and cell walls of fungi). Most animals cannot digest it. Cellulose is the plant structural form and constitutes the outer walls of plant cells. Wood is dried out cellulose - it consists of cross-linked polysaccharides. Again, most animals cannot digest it. 2. Lipids are primarily involved in energy storage and membrane structure, but there are also waxes for protection against desiccation, and unusual lipids that function as hormones. Most lipids are made up of monomers called fatty acids. These are long hydrocarbon chains, e.g. 20 carbons, with a carboxyl or acid group (HOC=O) on the end (acid because they easily release a H+ ion in solution in water). Linoleic acid is one example. These are the monomeric building blocks that are put together in various ways. Triglycerides are the major polymer of fatty acids, consisting of a threecarbon alcohol (glycerol) linked to three fatty acids by condensation reactions and the loss of three water molecules. This is the form in which fatty acids are stored in our bodies as fat to provide energy when needed. The fatty acid chains can be saturated, or unsaturated, meaning that at least one carbon-carbon bond is a double bond - which causes the fatty acid to kink. “bad” “good” Triglycerides with saturated fatty acids can be packed more tightly and typically are solid at room temperature, e.g. animal fats like butter and lard. Those with at least one unsaturated fatty acid are usually liquid at room temperatures, generally plant oils like olive and coconut oil. 3 Phospholipids are triglycerides with one of the fatty acids replaced by a phosphate group, which gives it an ambivalent character, with one side being polar and the other nonpolar, and they make up membranes. Waxes involve various combinations of long fatty acids; they are nonpolar and hydrophobic. They commonly function to protect plants from water loss, form the combs in honey bee nests, protect our outer ear passage, and are employed by us in innumerable ways (e.g. skiing). polar nonpolar Finally, there is a group of lipids that do not have fatty acids. These can be long chains too, or rings, the most famous being the steroids, which are all based on a backbone provided by cholesterol. These are some of the lipid hormones such as testosterone and oestrogen. 3. Proteins bring us to another level of complexity, where the building blocks are rather varied, and the final polymers are essentially infinitely varied. Proteins are both the building blocks of cells and the enzymes that facilitate all cellular activities. They also do almost everything else, from being hormones to energy reserves of last resort, and we will have occasion to learn about several of them during this course. Generic structure of the monomer, an amino acid. Amino group (basic) Carboxyl group (acidic) R group (20 kinds with distinct properties in the 20 amino acids found in proteins) 4 8 of the 20 amino acids showing the range of R groups possible. Note that glycine is the most simple with a single hydrogen R group. tyrosine (tyr) lysine (lys) glutamate (glu) UNCHARGED, POLAR AMINO ACID POSITIVELY CHARGED, POLAR AMINO ACID NEGATIVELY CHARGED, POLAR AMINO ACID valine (val) phenylalanine (phe) methionine (met) glycine (gly) Note the very different sizes of the R groups. I only require memorizing the names of two of these amino acids. Both have sulfur atoms in their R groups. They are cysteine, and methionine (shown below; cysteine is similar to methionine but doesn’t have the methyl or CH3 group attached to the sulfur on the end of the R group). proline (pro) alanine (ala) valine (val) tryptophan (trp) methionine (met) proline (pro) Polypeptide chains are formed by condensation reactions between AAs. All 20 amino acids Take biochemistry if you want to learn them all. newly forming polypeptide chain 5 A. The primary or 1D structure of proteins is the linear arrangement of covalently linked amino acids. Note that there is a polarity to proteins; they always start with an amino group and end with a carboxy group. These are sometimes abbreviated as the N- and C-termini of proteins. B. The secondary or 2D structure of proteins is maintained by hydrogen bonds, between the carboxy group of one amino acid and the amino group of another. disulfide bridges Amino acid sequence of two linked polypeptides that make up the protein hormone insulin. Note that the two are linked via disulfide bonds between cysteines. This is common for extra-cellular proteins and these disulfide bonds help maintain the protein structure. Linus Pauling first proposed the alpha helical structure for proteins. He was the greatest American chemist, responsible for much of theoretical chemistry. He proposed the alpha helical secondary structure for proteins in the early 1950s, and received the Nobel Prize in Chemistry in 1954. Later he became a peace activist opposing the US and Russian atom bomb programs and won the Nobel Peace prize in 1962. He is the only person ever to win two unshared Nobel prizes. He spent the last part of his life promoting the usefulness of megadoses of vitamin C, but nevertheless died 18 years ago in his long-time home of California. Alpha helix Hydrogen bonds within a strand Beta pleated sheet Hydrogen bonds between strands C. The tertiary or 3D structure of proteins is maintained by a combination of hydrogen bonds and weaker Van der Waals forces. This final structure is also known as the conformation of the protein and this shape determines its properties and abilities, e.g. globular enzymes, long rigid structural proteins, ion channels that span membranes, etc. 6 D. Some proteins are only functional when several individual proteins join together in a quaternary structure. The most famous example is hemoglobin with four subunits (2 alpha chains and 2 beta chains), each with its own heme group carrying an oxygen molecule. The alpha and beta chains differ slightly. beta chain beta chain heme group twists and coils in the polypeptide chain of a globin molecule alpha chain 4. The nucleic acids - monomers carry energy and signals, while polymers are the medium of inheritance and protein synthesis. Monomer is a nucleotide, made up of three parts, a 5-carbon ribose sugar ring, a ringed base that includes nitrogens, and 1-3 phosphates. The best known of these monomers is ATP or adenosine adenine triphosphate, the universal carrier of energy in biology, pictured here. alpha chain Dinucleotides: Nucleotides can be connected together by condensation reactions to give dinucleotides, e.g. NAD or nicotinamide adenine dinucleotide that also carries energy in the form of an attached hydrogen as NADH. The nucleic acid polymers are the single-stranded RNA and doublestranded DNA, and we will consider their structure and synthesis in more detail later - as we will protein synthesis. nicotinamide RNA DNA adenine 7