Chapter 2: Biochemistry & the Chemical Basis of Life

1. Chapter 2: Biochemistry & the Chemical Basis of Life

2. Introduction • Chemistry: • Branch of science studying the composition of matter and how it changes • Biochemistry: • Branch of science studying how chemistry affects living organisms • Focuses on carbon molecules called macromolecules • Ex: nucleic acids, lipids, proteins, carbohydrates

3. Elements and Atoms • Element: • A chemical substance with only one type of atom • Ex: oxygen, hydrogen, carbon, nitrogen • 110+ known (92 naturally found) • Usually combine to form compounds and molecules • Living organisms require about 20 elements • Ex: O, C, H, N (95% of biomass) • Others: Ca, K, S, Cl, Na

5. Elements and Atoms • Atoms: • Smallest particle of an element which still retains properties of that element • Made of subatomic particles: • 1) Proton: + charge, in nucleus (middle of atom) • 2) Neutron: neutral, in nucleus • 3) Electron: - charge, circles the nucleus in cloud/shells • Atoms vary in weight, chemical properties and physical properties • Form attractions to other atoms (chemical bonds)

7. Chemical bonds • Chemical bond: • Def: an attraction between two or more atoms • Will form between atoms of same element or atoms of differing elements • Same element: Example – Nitrogen gas (N2 – two atoms of nitrogen) • Different elements: Example – Water (H2O – two atoms of hydrogen, one of oxygen)

8. Chemical bonds • Bonding involves the sharing or transfer of electrons • Atoms will bond to fill their electron shells • 1st shell(closest to nucleus): 2 electrons needed to fill • Ex: Hydrogen in water bond • 2nd shell: 8 • Ex: Oxygen in water bond (fills 1st level with 2, then fills the 2nd level with 8) • 3rd shell: 8

9. Chemical bonds • Three types of bonds: • 1) Ionic: • Bond that forms between two charged atoms (ions) • Atoms involved have transferred electrons – giving them opposite charges • Ex: NaCl (Na+ lost electron, attracted to Cl- (gained elec.)) • FORMS BETWEEN atoms of the SAME MOLECULE

10. Chemical bonds • Three types of bonds: • 2) Covalent: • Bond that forms when two atoms SHARE electrons • Polar: unequal sharing of electrons, ex: water • Nonpolar: equal sharing of electrons, ex: N2, H2 • Forms BETWEEN atoms of the SAME MOLECULE

11. Chemical bonds • Three types of bonds: • 3) Hydrogen: • Bond that forms between hydrogen atom and the negative atom of another molecules • Ex: between water molecules, connects two strands of DNA, important in protein folding

12. Chemical reactions • Chemical reactions: • Reactants: Molecules/compounds which start a reaction • Products: Molecules/compounds which are formed during a reaction

13. Chemical reactions • Chemical reactions: • Def: Form or break bonds between atoms, ions, or molecules; generates new chemical combinations • Ex: digestion, macromolecule synthesis, cellular respiration, photosynthesis

14. Chemical reactions • Types of chemical reactions: • 1) Synthesis: • When two or more atoms bond to form a more complex structure; requires energy input • Ex: DNA replication, condensation reaction (formation of macromolecules) • 2) Decomposition: • When bonds within a reactant break to form simpler molecules; energy is released • Ex: Digestion • 3) Exchange reaction/double displacement: • When two types of molecules trade atoms • Ex:Acid/Base reactions form water and salts

15. Synthesis Decomp Double displacement

16. Chemical reactions • Many are reversible • Shown with a double-arrow • Reversible reactions meant that the products of the reaction can change back into the reactants • Chemical equilibrium: • When the concentrations of both reactants and products do not change • Reaction continues!

17. Chemical reactions • Chemical reaction rates: • Dependent upon a variety of environmental variables • Ex: pH, temperature, concentrations of reactants/products, energy availability, salt/salinity • Catalyst: • Def: A molecule that can change the rate (usually increase) of a chemical reaction • Ex: enzymes • Human body relies upon these to sustain life • Ex: Enzymes involves in DNA replication (helicase, DNA polymerase, ligase)

18. Acids and Bases • Electrolyte: • Substances that release ions in water • The solution then can conduct electricity • Acids: • Def: An electrolyte that release hydrogen ions (H+) in water • Ex: Hydrochloric acid (HCl) releases H+ and Cl- ions in water • Base: • Def: An electrolyte that release hydroxide ions (OH-) in water • Ex: Sodium hydroxide (NaOH) releases OH- in water

19. pH scale • Concentrations of H+ and OH- ions in body fluids can greatly affect chemical reactions • Ex: Blood pressure, breathing rate • We measure these ion concentrations using pH scale • pH scale: Measurement of H+ ion concentration • Scale range: 0-14 • Each number represents 10-fold difference in H+ ions • Ex: pH of 6 has 10X H+ ions than pH of 7 • pH of 7 means there is an equal concentration of H+ and OH- ions (neutral)

20. pH scale • Acid: pH = 0-7ish • Ex: hydrochloric acid in stomach, battery acid, vinegar • More H+ ions (than OH-) = lower number • Ex: pH of 2 has MORE H+ than pH of 5 • Neutral: pH = 7ish (optimal for most life) • Ex: Distilled water, cow’s milk (6.6), human blood (7.4) • Base: pH = 7ish-14 • Ex: bleach, egg white, ammonia • More OH- (than H+) = higher number • Ex: pH of 14 has MORE OH-/less H+ than does 11

22. Cellular compounds • Two groups of chemicals produced and used in chemical reactions: • 1) Organic: • Def: those that contain both carbon and hydrogen atoms • Ex: macromolecules, methane • Nonelectrolytes (usually do NOT release ions in water) • 2) Inorganic: • Def: the remaining molecules • Usually dissolve in water or react with water to form ions • Electrolytes (Ex: acids, bases)

23. Inorganic substances • Water (H2O): • Most abundant compound in living organisms • 2/3 of the biomass of an adult human • Major component of blood and other body fluids • Important solvent (many substances dissolve easily within it) • Plays important role in moving chemicals (ex: oxygen, salts, sugars, vitamins) • Can absorb and transport heat • Oxygen (O2): • Enter body through respiratory organs and transported via blood • Organelles use oxygen to release energy from food

24. Inorganic substances • Carbon dioxide (CO2): • Produced as waste product during cellular respiration (breakdown of food molecules to produce energy) • Exhaled via lungs • Salts: • Compound composed mainly of oppositely-charged ions • Ex: Na+ and Cl- = NaCl (table salt) • Abundant in cells and tissues • Provide necessary ions important to chemical/metabolic processes • Ex: nervous system action potential, muscle contraction

25. Organic substances • Made of monomers which combine to form polymers • 4 macromolecule groups: • 1) Carbohydrates • Ex: sugar, starch, cellulose • 2) Proteins • Ex: enzymes, antibodies, cell surface receptors • 3) Lipids • Ex: fats, steroids, phospholipids (cell membrane component) • 4) Nucleic acids • Ex: DNAand RNA

26. Carbohydrates • Made of C, H, and O (twice as many hydrogen as oxygen) • Ex: C6H12O6 • Often involves chains or rings of carbon atoms joined with atoms of hydrogen and oxygen • Functions: • Provide much of energy that cells require, • Supply materials to build cell structures, • Stored as energy reserves

27. Carbohydrates • Monomers (ONE sugar) • Monosaccharide • Examples: glucose, fructose, galactose • Dimers (TWO sugars) • Disaccharides • Examples: sucrose and lactose • Polymers (MANT sugars) • Polysaccharides • Examples: starch, glycogen, chitin, and cellulose • Dimers/Polymers are considered complex carbohydrates

28. Carbohydrates

29. Cellulose Chitin Carbohydrates

30. Lipids • Made of C, H, and O (phospholipids have P) • Smaller proportion of Oxygen atoms than do carbs • Ex: Fat tristearin (C57H110O6) • Do not dissolve in water • Will dissolve in ether or chloroform • Functions: • Primary energy storage molecules (fats) • Insulation (fats) • Primary component of cell membrane (phospholipids) • Used to synthesize other fats (steroids) • Important to development of gametes (steroids – sex hormones)

31. Lipids • Parts of Fat molecule: • 1) Glycerol molecule • 2) Fatty acid chains • Fatty acid chains are what make fats diverse • Differ in: • # of chains • Types of chains

32. Lipids • Triglyceride fats • 1 Glycerol, 3 Fatty Acid Chains • Examples: Fats found in adipose tissue • Phospholipid • 1 Glycerol, 2 Fatty Acid Chains • Example: Molecules found in cell membrane • Steroid • 4 Carbon ring structure • Example: cholesterol, testosterone, estrogen, and other hormones

33. Lipids (cont)

34. Lipids (cont) Phospholipid

35. Lipids (cont) Steroids Cholesterol Progesterone Testosterone

36. Protein • Made of C, H, O, N, S (not all) • Functions: • Structural materials • Energy sources • Hormones • Can combine with carbs to function as cell surface receptors • Detect foreign substances in body • Catalysts to speed up chemical reactions

37. Protein • Monomer • Amino Acid (20 found in body) • Polymer • Polypeptide chain • Amino acids are held together by peptide bond (covalent bond) • Polypeptide chain folds to become a functional protein • Primary (simple chain of amino acids) • Secondary (forms alpha/beta chains) • Tertiary (alpha/beta chains fold up-on themselves) • Quaternary (more than one chain) • Conformation (folding of protein) determines its function

38. Amino Acid Structure

39. H H H H H3N+ H3N+ H3N+ H3N+ C C C C COOH COOH COOH COOH R R R R Polypeptide Peptide bonds b/t Amino acids

40. Protein Folding

41. Protein Folding (cont)

42. Protein Folding (cont)

43. Protein Folding (cont)

44. Phosphate Sugar Nitrogen Base Nucleic Acid • Made of C, H, O, N, and P • Functions: • Energy source (molecule is broken apart to release energy) • Genetic source • Monomer- Nucleotide • Parts of a nucleotide: • 1) 5-carbon sugar • 2) phosphate group • 3) nitrogenous base

45. Nucleic Acid • DNA • Sugar- Deoxyribose • Nitrogen Bases- A, T, G, C • RNA • Sugar- Ribose • Nitrogen Bases- A, U, G, C • ATP • Sugar- Ribose • Nitrogen Base- A • Contains three phosphate groups

46. G Nucleic Acid - DNA A = T G = C A T C

47. Nucleic Acid - RNA • Single-stranded

48. Adenine High Energy Bonds Adenosine Ribose Phosphates Nucleic Acid - ATP