By Chris Paine Molecules to metabolism Essential idea: Living organisms control their composition by a complex web of chemical reactions. The background is just a small part of the IUBMB-Sigma-Nicholson Metabolic Pathways Chart aims to show all the metabolic pathways found in eukaryote cells. The chart in it's entirety shows how complex the chemicals reactions needed to support life in a single cell unit.the IUBMB-Sigma-Nicholson Metabolic Pathways Chart

Understandings StatementGuidance 2.1.U1Molecular biology explains living processes in terms of the chemical substances involved. 2.1.U2Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist. 2.1.U3Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids. Sugars include mono-saccharides and disaccharides. Only one saturated fat is expected and its specific name is not necessary. The variable radical of amino acids can be shown as R. The structure of individual R-groups does not need to be memorized. 2.1.U4Metabolism is the web of all the enzyme-catalyzed reactions in a cell or organism. 2.1.U5Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions. 2.1.U6Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

Applications and Skills StatementGuidance 2.1.A1Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized. (SL only) 2.1.S1Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid. (Bio 2 - project, SL test) Only the ring forms of D-ribose, alpha–D- glucose and beta-D-glucose are expected in drawings. 2.1.S2Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (Bio 2 - project, SL test) Students should be able to recognize from molecular diagrams that triglycerides, phospholipids and steroids are lipids. Drawings of steroids are not expected. Proteins or parts of polypeptides should be recognized from molecular diagrams showing amino acids linked by peptide bonds.

2.1.U1 Molecular biology explains living processes in terms of the chemical substances involved. The discovery of the structure of DNA in 1953 was a turning point for modern molecular biology and our understanding of living processes The central idea can be simplified to “DNA makes RNA makes protein”. The information in this flow cannot be reversed and the protein generated cannot change the RNA or DNA

2.1.U1 Molecular biology explains living processes in terms of the chemical substances involved. The approach of a molecular Biologist is a reductionist one – they identify the steps in a metabolic pathway and breakdown each one into it’s component parts. Organic molecules, especially proteins, are very complex and varied in structure and in function. Some scientists think that the reductionist approach alone is ultimately limited, perhaps overlooking the “forest for the trees.”

2.1.U2 Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist. Despite only being the 15 th most abundant element on the planet carbon forms the backbone of every single organic molecule. Covalent bonds are the strongest type of bond between atoms. Stable and sometimes very large molecules can be formed: Titin is the largest known protein and it contains 539,000 atoms (chemical formula C H N O S 912. ). Carbon atoms contain four electrons in their outer shell allowing them to form four covalent bonds with potential four other different atoms, e.g. methane (CH 4 ). The result of these properties is an almost infinite number of different possible molecules involving carbon.

2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids. CARBOHYDRATES – made of C, H & O, with H:O ratio always 2:1 LIPIDS – all insoluble in water but otherwise quite diverse – made of C, H, & O (but not 2:1 ratio like carbohydrates) PROTEINS – made of one or more chains of amino acids – mostly C,H,O & N but two natural amino acids also contain S NUCLEIC ACIDS - DNA & RNA, both are long chains of subunits called nucleotides made of C, H, O, P, S & N MONOMERPOLYMER SIMPLE SUGAR MONOSACCHARIDE eg. glucose, ribose POLYSACCHARIDE eg. starch, cellulose Glycerol backbone & Fatty acids chains Triglycerides such as solids fats, liquid oils; waxes, steroids Amino acids (20 possible) Polypeptides (folded into proteins) Nucleotides, made of a sugar, a phosphate group & a N-containing base DNA, RNA

ArginineAlanineLeucine Here are three of the twenty-one amino acids found in eukaryotes. Identify what parts of their structures are identical. 2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams (Bio 2 – not on test but a model project is due, SL – test)

ArginineAlanineLeucine Yeah, that bit… 2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (Bio 2 – not on test but a model project is due, SL – test)

Drawn slightly differently you can see the bit that is always the same and the R Group. The R group is like x in an algebra equation. It is a variable that stands in for a bunch of different side chains 2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (Bio 2 – not on test but a model project is due, SL – test)

The amine group (NH 2 ) The carboxyl group (COOH) n.b. this is an acidic group A simple H group Central (α) carbon atom Look out for this structure 2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (Bio 2 – not on test but a model project is due, SL – test)

Hmmm… an amine group and an acid group… What shall we call this class of molecule?

The amine and acid groups could be at opposite ends, the R could be on top, bottom or side depending on orientation. 2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (Bio 2 – not on test but a model project is due, SL – test)

Or it could be represented differently: 2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (Bio 2 – not on test but a model project is due, SL – test)

Don’t freak out, you don’t need to know them all, just the general formula

H 3 C (CH 2 ) n C O OH General structural formula for a fatty* acid Carboxylic group Chain (or ring) of carbon and hydrogen atoms S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (Bio 2 – not on test but a model project is due, SL – test)

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. (SL only)

2.1.S1 Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid. (SL only) Try drawing by hand (or on eMolecules) the following molecules: Glucose Ribose A generalised saturated fatty acid A generalised amino acid An example amino acid e.g. Alanine (the simplest) n.b. you also need to test yourself 15 mins, 1 day and one week later to make sure you remember eMolecules online drawing tool

2.1.U4 Metabolism is the web of all the enzyme-catalyzed reactions in a cell or organism. Revisit the essential idea of this topic. Explore the IUBMB-Sigma-Nicholson Metabolic Pathways Chart and realize that most cells use the majority of the pathways and that every path is controlled by a different enzyme. The metabolism as a concept is the sum of all the pathways used in a particular cell.IUBMB-Sigma-Nicholson Metabolic Pathways Chart

2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions. 2.1.U6 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

2.1.A1 Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized. (SL only) Source: Vitalism nowadays has no credit as a theory, but above statement is seen by many from a historical perspective to be untrue. For an outline on vitalism read this article by William Betchel. The application statement above implies that the central tenet Vitalism is ‘only organisms can synthesize organic compounds’. This is not accurate, in essence, vitalism proposes that an unknowable factor is essential in explaining life. Vitalism on this premise is both unscientific and and unfalsifible.this article by William Betchel Nature of Science: Falsification of theories—the artificial synthesis of urea helped to falsify vitalism. (1.9) Wöhler accidentally synthesized urea in 1828, whilst attempting to prepare ammonium cyanate. In a letter to a colleague he says “I can no longer, so to speak, hold my chemical water and must tell you that I can make urea without needing a kidney, whether of man or dog". This is supposed to undermine vitalism as organic chemicals were previously thought to be synthesized only by organisms. Source: