Biochemistry

1. Biochemistry Life is all about bags of biochemical reactions • Atoms, Molecules and Chemical Bonds • The Chemistry of Water • The Chemistry of Carbon • Carbohydrates • Lipids • Nucleic Acids • Protein

2. The Chemistry of Life • All living things are made of cells, and all cells are made of a set of molecules known as biochemicals. • There are two very different types of biochemicals • small inorganic molecules such as water and salt ions, • large organic molecules such as sugars, fats, proteins, and DNA • By definition, organic molecules contain atoms of the element carbon. • Organic molecules are composed primarily of carbon, hydrogen, oxygen, and nitrogen.

3. Atoms • All of the matter in the universe is made from atoms. • Atoms are composed of protons, neutrons, and electrons. • Protons have a positive charge and a mass of 1 atomic unit • Neutrons have no charge, but also have a mass of 1 • Electrons carry a negative charge but have very little mass

5. The Atom • The protons and neutrons form the nucleus of the atom, which contains most of the mass and the positive charges. • The electrons orbit very rapidly around the nucleus carrying negative charges. • Protons and electrons have equal and opposite charges. • In its neutral state, an atom has the same number of protons and electrons

6. Elements • All of the atoms in the universe fall into a set of distinct categories called elements based on the number of protons in the nucleus. • All of the atoms of an element have the same number of protons (atomic number) and they share the same chemical properties. • The Periodic Table of Elements groups elements according to their atomic number and shared chemical properties.

8. Chemical Bonds • Atoms interact with each other by either sharing or exchanging electrons. • This interaction can take place between atoms of the same element, or atoms of different elements. • Sharing a pair of electrons creates a covalent bond that holds atoms tightly together in a structure known as a molecule. • Some pairs of atoms may share more than one pair of electron, forming double or even triple covalent bonds, which are proportionately stronger. • Atoms often form covalent bonds with several other atoms, creating larger molecules.

10. Ionic Bonds • Exchanging electrons creates charged atoms (ions), which form weak ionic bonds. • An atom that picks up an extra electron gets a negative charge, an atom that gives up an electron gains a positive charge. • An entire molecule may also exchange an electron with another molecule or with a single atom to form an ion, so a group of covalently linked atoms can be both a molecule and an ion.

12. Chemistry of Water • All life, and all biochemistry, occurs in water. • Water has a number of special properties that make it both an essential matrix and an essential ingredient for biochemistry • The water molecule is composed of one oxygen atom covalently bound to two hydrogen atoms: • H-O-H = H20

13. Water is Polar • In water, the two hydrogen atoms are not located on opposite sides of the oxygen atom, but instead are both on one side, forming an H-O-H angle of 104.45°.

14. Water is Polar (cont.) • The oxygen has a stronger attraction for the shared electrons, • so the oxygen end of the molecule has a slightly negative charge and the hydrogen end has a net positive charge. • This makes water a polar molecule. • In liquid water, groups of H2O molecules stack up in loose head-to-tail formations where the positive end of one water molecule is attracted to the negative end of one or more other water molecules.

16. Water ions = pH • Water also has a tendency to form ions. • One hydrogen splits off, leaving behind its electron, so a positive H+ ion and a negative OH- ion are formed. • These ions are constantly available to participate in any biochemical reaction that might take place in a water solution. • An excess of H+ gives an acid pH, excess OH- give basic pH.

17. Carbon Chemistry • The carbon atom has 6 protons and 6 electrons • 4 of these electrons are held in an outer position where they can easily interact with other atoms: generally forming covalent bonds. • The 4 outer electrons tend to mutually repel each other, making a tetrahedron shape

19. Carbon Bonds • The tendency of carbon to interact with four other atoms at once allows it to form the central linkage point of complex molecules that are assembled like tinkertoys.

20. Carbon Bonds • The simplest carbon molecules are hydrocarbons – combinations of carbon and hydrogen. • The simplest hydrocarbon molecule is methane: one carbon bound to 4 hydrogen atoms. • This is a non-polar molecule with very little attraction between molecules, and as a result, it is a gas at room temperature.

21. Carbon Bonds (cont.) • Hydrocarbon molecules can grow larger by adding carbon-carbon bonds • either in a straight line, such as ethane (2 carbons) or hexane (6 carbons) • in a branching structure such as isohexane • or in a ring such as cyclohexane.

22. Double Bonds • Each carbon atom has 4 bonds - either to hydrogen, or to another carbon. • Carbon atoms can also form double and triple bonds, providing a great deal of flexibility in the linkage possibilities. • Double and triple bonds hold more energy than single bonds.

23. -OH groups • Any of the hydrogen atoms can be substituted for other atoms or larger groups. • In a simple hydrocarbon like ethane, if one hydrogen is replaced by a hydroxyl group (–OH), it forms the alcohol ethanol. • This is a polar molecule that is liquid at room temperatures and is much more biologically active than ethane.

24. Other Carbon Bonds • Organic molecules can also contain carbon-oxygen double bonds, and carbon-nitrogen bonds.

25. Classes of Biochemicals • Biochemistry is primarily concerned with a few types of complex organic molecules • The most common types of bio-molecules are • sugars • fats • proteins • nucleic acids • Other complex organic molecules such as alkaloids do play important roles in biology,but only in certain specific organisms.

26. Sugars • Sugars are relatively simple molecules composed of just carbon, hydrogen, and oxygen (carbohydrates). • Glyceraldehyde is a simple 3-carbon sugar • each carbon has one of its hydrogens replaced with an –OH group • the last carbon has a double bond to its oxygen

27. Glucose • Glucose, a 6-carbon sugar, is the most common sugar molecule in living tissue. • The –CH=O group at the end is somewhat unstable, so the molecule tends to form a ring where the oxygen in the CH=O group reacts with the #2 carbon, replacing one of its hydrogens to form a C–O–C bond

28. Ribose • There are also a number of common 5-carbon sugars, which also tend to form rings. The most important of these is ribose, which is a component of all nucleic acids.

29. Starch • It is very easy to link up sugar molecules into simple chains. • The reaction, called glycosylation, takes two C-OH groups and combines them into a single C–O–C, releasing H2O. . • This reaction costs little energy and is easily reversible.

30. Polymers • Large molecules that are built by linking up many smaller units are called polymers. • Biochemistry is full of polymers. • Starch is a polymer of sugar units • Fats are hydrocarbon polymers • Proteins are amino acid polymers • DNA and RNA are polymers of nucleotides • Plastics are synthetic polymers made from hydrocarbons.

31. Fats & Lipids • Lipids are long chain hydrocarbons with a carbonyl group (COH=O) at one end • lipids are hydrophobic (insoluble in water) and energy rich. • Lipids are the primary component of cell walls. • Individual lipid molecules can be joined up with glycerol to form fats, • It takes cells substantially longer to synthesize and break down fats compared to starch, so they are used for long-term energy storage.

35. Nucleic Acids • DNA and RNA are two types of nucleic acids. • These are one of the primary subjects of bioinformatics • They are both large polymer molecules that are formed from subunits called nucleotides. • Nucleotides play many essential roles in biochemistry, so they are worth quite a bit of attention.

36. Nucleotides • Nucleotides are complex molecules that are composed of three parts: • a ribose sugar (5 carbons) • a phosphate (PO4) group substituted for the OH on the #5 carbon of the ribose • a cyclic nitrogen base substituted for the OH on the #1 carbon.

37. There are 4 different types of nitrogen bases: • the 2 purine bases (adenine and guanine) that have a double nitrogen ring and • the 2 pyrimidine bases (cytosine and thymidine) that have a single nitrogen ring. pyrimidine purine

38. ATP • The phosphate group on a nucleotide is able to form additional chemical bonds. • It can bond to one or two more phosphates, creating nucleotide di-phosphate and tri-phosphates. • These phosphate-phosphate bonds contain a large amount of energy. • Adenosine tri-phosphate (ATP) is the primary form of short-term energy storage for almost all biochemical reactions. • Energy is produced when one or two phosphates are removed, energy is stored by putting them back on.

39. Nucleotide Chains • The phosphate group on a nucleotide can form a bond with the #3 carbon of the ribose sugar in another nucleotide • (phosphodiester bonds: 5C–O–P–O–3C) • links up the nucleotides in a chain. • This nucleotide polymer is a nucleic acid. • The nucleotides in a DNA chain are generally abbreviated as A, C, G, and T • but remember that these letters stand for large, complex molecular sub-units.

41. Poly-nucleotides are Polar • Note that the ends of the nucleotide polymer are not symmetrical. • the 5’ end has a free phosphate group on the #5 carbon • the 3’ end has a free –OH on the #3 carbon. • Also, note that the nitrogen bases do not participate in the phosphodiester bonds between nucleotides in the chain. • The chain is formed by links between the phosphate group and the ribose carbon rings • The nitrogen bases are free to form other chemical bonds.

42. DNA has Two Chians • In the DNA chain, each nucleotide base can form hydrogen bonds with one other nucleotide in another DNA chain. • The geometry of this linkage is very precise and specific: • Adenine can only pair with thymine and guanine only pairs with cytosine. • Note that the G–C linkage involves 3 hydrogen bonds while the A–T linkage involves only 2. • Thus A–T base pairs form a weaker bond than do G–C pairs.

44. The Double Helix • The two chains of a DNA molecule run in opposite directions: • one strand goes 5’ to 3’ and the opposite strand runs 3’ to 5’. • Also, the two chains do not lie flat, but rather twist around each other to form a double helix.

46. RNA • RNA molecules are very similar to DNA, except that the ribose sugar has an extra -OH group on the #2 sugar. • Instead of tyhmine, RNA uses the base uracil • Interestingly, single stranded RNA molecules do not form a double helix with other RNA strands, but only with complementary strands of DNA. • RNA molecules are much less chemically stable than DNA.

48. Proteins Proteins are the most structurally and functionally diverse group of biomolecules. They also make up the majority of the dry weight of all living cells. Proteins are used as motors, structural elements, enzymes, receptors, channels through membranes, intra-cellular transporters, regulatory switches, and much more.

49. Amino Acid Polymers • Proteins are a polymer of amino acids. • There are 20 different types of amino acids, but they all have the same basic structure. • A central carbon atom is linked to an amino group (NH2), a carboxyl group (COOH), and a variable side chain – shown as “R” below.