1. Four classes of macromolecules

1. 1. Four classes of macromolecules • All key components of every living cell are made of macromolecules. Theycan be classified into four main classes: Carbohydrates (sugars, starch and cellulose) Lipids (fats, oils, steroids) Proteins (polypeptide chains and their assemblages) Nucleic acids (DNA and RNA) • These macromolecules are made the same way in all living things, and they are present in all organisms in roughly the same proportions; they make up what we visually recognize as life • Macromolecules are giant polymers (poly means many; mer means units) constructed of many organic molecules called monomers. Some polymers are made of the same monomers, e.g. cellulose, while others, e.g. proteins or nucleic acids, are made of a set of different monomers. Polymer chains can be linear, branching or even circular.

2. 2. Functions of macromolecules • Some of the roles of macromolecules are: • Energy storage • Structural support • Catalysis • Transport • Protection and defense • Regulation of metabolic activities • Maintenance of homeostasis • Means for movement, growth, and development • Heredity • The functions of macromolecules are related to their shape and to the chemical properties of their monomers

3. 3. Chemical composition of biomolecules Here is one way to think of the differences among macromolecule classes: • All carbohydrates such as wood or starch in every plant are made of just three chemical elements: C, H and O. (Some might also have small amounts of S and N.) • All proteins of all organisms on earth are made of five chemical elements: C, H, O, N, S. • All nucleic acids of all organisms on earth are made of C, H, O, N, P. Here we see a uniformity of living organisms at the most elemental level. There is far less diversity in carbohydrates, which are made from just a few monomers. That is why all starches tend close-up to look alike (carrot or baobab), while proteins look startlingly different. Elements such as C, H, O, N, P and S (also called macro elements) make up biomolecules and are therefore the largest dry weight of all living organisms. Other elements are present in small numbers but can still play important roles (e.g. the iron in hemoglobin, which carries oxygen, or the sodium and potassium ions that are responsible for nerve impulses.)

4. 4. Monomers Macromolecule Monomers Carbohydrates monosaccharides Lipids glycerol, fatty acids Proteins amino acids Nucleic acid nucleotides • In living cells, a small set of monomers is used to create a variety of polymers. Each polymer is unique in the number and type of monomers used to build it.

5. 5. Monomers to polymers • To qualify as a building block for polymers, each monomer must be capable of linking with others. When a monomer's functional group, a specific arrangement of atoms, reacts with a functional group of another monomer, the two molecules link together with a stable covalent bond, one that will not break under normal conditions and will not dissolve in water.

6. 6. Sucrose, glucose, fructose • Example: • Sucrose (table sugar) is composed of glucose and fructose.

7. 7. Functional groups defined • A functional group is a group of atoms of a particular arrangement that gives the entire molecule certain characteristics. Functional groups are named according to the composition of the group. For example, COOH is a carboxyl group. • Organic chemists use the letter "R" to indicate an organic molecule. For example, the diagram below can represent a carboxylic acid. The "R" can be any organic molecule.

8. 8. The seven fundamental functional groups present in biological monomers

9. 9. Twenty aminoacids and five nucleotides • The total number of biologically important monomersis surprisingly small, about 40-50, from which the thousands of biologically important macromolecules are constructed. • In particular, the set of amino acids common to all living things includes 20 total different molecules, and the set of nucleotides that compose DNA and RNA include 5 total different molecules

10. 10. Introducing metabolism • Where do the building blocks (monomers) of the macromolecules in living cells come from? METABOLISM • All living things must have an unceasing supply of energy and matter. The transformation of this energy and matter within the body is called metabolism Anabolism • Anabolism is constructive metabolism. Typically, in anabolism, small precursor molecules, or metabolites, are assembled into larger organic molecules. This always requires the input of energy Catabolism • Catabolism is destructive metabolism. Typically, in catabolism, larger organic molecules are broken down into smaller constituents. This usually occurs with the release of energy

11. 11. Polymers, monomers, metabolites Anabolism Photosynthesis CO2 Catabolism Respiration Digestion

12. 12. Chemical reactions in cells • Thousands of biochemical reactions,in which metabolites are converted into each other and macromolecules are build up, proceed at any given instant within living cells. However, the greatest majority of these reactions would occour spontaneously at extremely low rates. • For example, the oxidation of a fatty acid to carbon dioxide and water in a test tube requires extremes of pH, high temperatures and corrosive chemicals. Yet in the cell, such a reaction takes place smoothly and rapidly within a narrow range of pH and temperature. As another example, the average protein must be boiled for about 24 hours in a 20% HCl solution to achieve a complete breakdown. In the body, the breakdown takes place in four hours or less under conditions of mild physiological temperature and pH. • How can living things perform the magic of speeding up chemical reactions many orders of magnitude, specifically those reactions they most need at any given moment?

13. 13. Introducing enzymes • The ENZYMES are the driving force behind all biochemical reactions happening in cells. • Enzymes lower the energybarrier between reactants and products, thus increasing the rate of the reaction. • Enzymes are biological catalysts. A catalyst is a species that accelerates the rate of a chemical reaction whilst remaining unchanged at the end of the reaction. Catalysis is achieved by reducing the activation energy for the reaction. • Enzymes can catalyse reactions at rates typically 106to 1014 times faster than the uncatalysed reaction. • Enzymes are very selective about substrates they act upon and also where the chemistry takes place on a substrate. • Both the forward and reverse reactions are catalysed. A catalyst cannot change the position of thermodynamic equilibrium, only the rate at which it is attained.

14. 14. The active site • Enzymes are typically large proteins, which are structured specifically for the reaction they catalyze. Their size provide sites for action and stability of the overall structure. • Two important sites within enzymes are: • The catalytic site, which is a region within the enzyme involved with catalysis, and • The substrate binding site which is the specific area on the enzyme to which reactants called substrates bind to. • The catalytic site and substrate binding site are often close or overlapping and collectively they are called the active site. • If the catalytic site is not near the substrate binding site it can move into position once the enzyme is bound to a substrate.

15. 15. The “Lock-and-key” metaphor Schematic representation of the action of a hypothetical enzyme in putting two substrate molecules together. (a) In the "lock-and-key" mechanism the substrates have a complementary fit to the enzyme's active site. (b) In the induced-fit model, binding of substrates induces a conformational change in the enzyme.

16. 16. Aditional components of enzymes • Often enzymes require additional components to become active. These may be: • co-factors: simple cations, or small organic or inorganic molecules that bind loosely to the enzyme, • prosthetic groups: similar to co-factors but more tightly bound to the enzyme, or • co-enzymes – which are more complex than co-factors and prosthetic groups, they often act as a second substrate or bind covalently with the enzyme to affect the active site.

17. The active site of the digestive enzyme carboxypeptidase. (a) The enzyme without substrate. (b) The enzyme with its substrate (gold) in position. Three crucial amino acids (red) have changed positions to move closer to the substrate. Carboxypeptidase carves up proteins in the diet. 17. Structure of carboxypeptidase

18. 18. Metabolic pathways • There are thousands of enzyme-catalyzed reactions in a cell. If the biochemical reactions involved in this process were reversible, we would convert our macromolecules back to metabolites if we stop eating even for a short period of time. • To prevent this from happening, our metabolism is organized in metabolic pathways. These pathways are a series of biochemical reactions which are, as a whole, irreversible. • These reactions are organized in consecutive steps or pathways where the products of one reaction can become the reactants in another. Every biochemical molecule is synthesized in a biochemical pathway with specific enzymes.

19. 19. Metabolic pathways of phenylalanine in human One small part of the human metabolic map, showing the consequences of various specific enzyme failures. (Disease phenotypes are shown in colored boxes.)

20. 20. Enzymes build everything • Thus, enzymes may be considered the quintessence of life. They allow nutrients to be digested; they convert food into energy and new raw materials; they build body structures; they govern all cellular processes. • But, who builds the enzymes?

21. 21. Enzymes are proteins • Enzymes arecomposed of proteins, and proteins arelong polymers of amino acids. Amino acids all have this general formula: • Amino acids have two functional groups (aminic and carbossilyc), which can react together forming covalent bonds called peptide bonds, so that they are linked head-to-tail. • The side chain, or R group, can be anything from a hydrogen atom (as in the amino acid glycine) to a complex ring (as in the amino acid tryptophan). • Each of the 20 amino acids known to occur in proteins has a different R group that gives it its unique properties. • The linear sequence of the amino acids in a polypeptide chain constitutes the primary structure of the protein

22. 22. The sequence of aminoacids The peptide bond. (a) A polypeptide is formed by the removal of water between amino acids to form peptide bonds. Each aa indicates an amino acid. R1, R2, and R3 represent R groups (side chains) that differentiate the amino acids. R can be anything from a hydrogen atom (as in glycine) to a complex ring (as in tryptophan). (b) The peptide group is a rigid planar unit with the R groups projecting out from the CN backbone. Standard bond distances (in angstroms) are shown.

23. 23. Triplets of nucleotides • How is amino acid sequence determined? Quite simply, by the nucleotide sequence present on a macromolecule of DNA. • The specific amino acid sequence of a polypeptide is determined by the nucleotide sequences of the gene that encodes it. • The sequence of nucleotides in the DNA is read three nucleotides at a time. Each group of three, called a triplet codon, stands for a specific amino acid. Since there are four different nucleotides in DNA, there are 4 × 4 × 4 = 64 different possible codons. This means that there are more condons than aminoacids.

24. 24. The genetic code • The table of correspondence between triplets and aminoacids is called the genetic code. • The same genetic code is used by virtually all organisms on the planet. There are some exceptions in which a few of the codons have different meanings. • Thus, the information to arrange aminoacids in a specific sequence with a particular function is coded in a sequence of nucleotides in DNA. • The process and the machinery that generates a protein from a DNA sequence is called the protein synthesis apparatus

25. 25. Codons and aminoacids

26. 26. Information flux in a living cell Structural proteins Carbohydrates Lipids Sugars Fatty acids Metabolic pathways Enzymes Nucleotides Amino acids DNA