Chemistry and Biochemistry

1. Chemistry and Biochemistry Water as a solvent Acids, bases and pH Organic compounds Hydrocarbons Functional groups Dehydration synthesis/ hydrolysis

2. Water and life 4. The universal solvent • Water can form hydrogen bonds with any polar or ionic compound. • Therefore, many things can be dissolved in water • The dissolving agent is called the solvent • The dissolved substance is called the solute • A liquid of two or more evenly mixed substances is a solution

3. Acids & Bases • Acids: • Donate H+ ions to a solution. • Bases • Accept H+ ions & remove them from solution.

4. So what is pH?? • pH= A measure of hydrogen ion concentration, but on a logarithmic scale (potential of Hydrogen) • Solutions with high hydrogen ion concentrations • have low pH • are acidic • Solutions with low hydrogen ion concentrations • have a high pH • are basic • There is a 10-fold difference in hydrogen ion concentration between solutions that differ by one pH unit.

5. Acids & Bases • Acids: • Donate H+ ions to a solution. • Bases • Accept H+ ions & remove them from solution.

6. Acids & Bases • Acids: • Donate H+ ions to a solution. • Bases • Accept H+ ions & remove them from solution.

7. Implications of extreme pH in the environment…

8. Acid deposition affects land and aquatic environments

9. What US regions are affected by acid deposition? EPA Air Quality Website

10. Some common acids, bases and salts

11. Salts • Neither acids or bases • Can form when acids and bases react • The dissociated hydrogen ions and hydroxide ions join to form water. • The remaining ions form ionic bonds creating a salt. • This is an example of neutralization. H+Cl-+ Na+OH-→ Na+Cl- + H+OH- Hydrocloric + Sodium Sodium+ Water acid hydroxide chloride

12. Organic compounds • Molecules containing carbon and hydrogen • Long chains or rings of carbon form backbone of diverse biological compounds. C9H8O4

13. The carbon skeleton • All organic molecules have a carbon skeleton. • This determines the overall shape of the molecule. • Organic molecules differ in these ways: 1. The length and arrangement of the carbon skeleton. 2. Which atoms are attached to the skeleton

14. Length: How long is the carbon based skeleton? • Dehydration synthesis: • Single units/ monomers are linked to form large units/ polymers; water removed • Hydrolysis: • Polymers are broken into monomers during metabolism; water is added.

15. Arrangement of the skeleton: Isomers • Organic molecules can have the same number and composition of atoms, but can have different arrangements. • These are called isomers.

16. Isomers

17. Atoms attached to C-H skeleton Polar functional groups= hydrophilic Non-polar functional groups= hydrophobic

18. Macromolecules of life • Macromolecules are very large organic molecules. • The most important organic compounds found in living things are: 1. Carbohydrates 2. Proteins 3. Lipids 4. Nucleic acids

19. Carbohydrates • Compounds with a 1:2:1 ratio of C:H:O • Monomers= monosaccharides • Polymers= polysaccharides • Hydrophobic or hydrophilic? • Function?

20. Simple sugars • Simple sugars are described by the number of carbons in the molecule. • Triose-3 carbons • Pentose-5 carbons • Hexose-6 carbons

21. Making disaccharides • When two simple sugars are combined they form disaccharides • Formed via dehydration synthesis • Examples: Maltose, lactose and sucrose

22. So how is high fructose corn syrup different from sugar? HFCS “Sugar”

23. Making the polymer: Polysaccharides • Contain many simple sugars connected by _________________ • Examples of polysaccharides:

24. Proteins • Primarily C, H and O but not a fixed ratio • Monomer = amino acid • Polymers= proteins or polypeptides • Hydophobic or hydrophilic? • Function?

25. Monomer- the amino acid • An amino acid contains: 1. Amino group 2. Carboxyl group 3. Side chain/ “R group” • There are 20 different amino acids

26. Amino acids

27. Asparagine gets its name from asparagus

28. Making the polymer- polypeptides • Amino acids are joined via dehydration synthesis. • The bond formed between amino acids is called a peptide bond. • Several amino acids joined together form polypeptide chains or proteins.

29. Primary (1°) structure • The sequence of amino acids in a polypeptide constitutes the primary structure of the protein

30. Secondary (2°) structure • Polypeptides twist and fold into their secondary structure • Form a-helix or b-pleated sheet

31. Tertiary (3°) structure • The 2° structure folds in a random manner to form a globular 3° structure.

32. Quaternary (4°) structure • Multiple polypeptides interact to form a functional protein

33. Protein shape determines function!

34. Changing the shape of proteins-denaturation • Denaturation: • When heat or other environmental conditions break the bonds that stabilize tertiary structure.

35. Changing the shape of proteins-genetic mutation • The protein’s overall shape determines function • Example: Sickle cell anemia • A mutation in one gene causes the protein to have a different shape- changes RBC shape. • Different shape altered function

36. Lipids or “fats” • Composed of C, H and a little O, but no fixed ratio • There are three types of lipids: • True fats(e.g. pork chop fat and oils) • Phospholipids (membrane components) • Steroids (most hormones) • Hydrophobic/ hydrophilic? • Function?

37. True fats • True fat= triglyceride • Used to provide energy • The building blocks of fats= fatty acid • A glycerol molecule • Three fatty acid tails

38. Saturated vs. unsaturated fats • If the carbon skeleton of a fatty acid has as much hydrogen as possible, the fat is called a saturated fat. • If the carbons of a fatty acid have double bonded carbon molecules in them, the fat is called unsaturated fat.

39. Saturated vs. unsaturated lipids

40. What is a trans fat? ^ Alonso L, Fontecha J, Lozada L, Fraga MJ, Juárez M (1999). "Fatty acid composition of caprine milk: major, branched-chain, and trans fatty acids". Journal of Dairy Science82 (5): 878–84. doi:10.3168/jds.S0022-0302(99)75306-3. PMID10342226.  ^ Alfred Thomas (2002). "Fats and Fatty Oils". Ullmann's Encyclopedia of Industrial Chemistry. Weinheim: Wiley-VCH. doi:10.1002/14356007.a10_173.

41. Phospholipids • Phospholipids: • Are complex organic molecules that resemble fats but contain phosphate groups. • Phospholipids are the major components of cell membranes. • Some are known as lecithins.

42. Steroids • Nonpolar molecules that are arranged in rings of carbon • Steroids are important components of cell membranes. • Cholesterol • Steroids often serve as hormones and serve in regulation of body processes. • Testosterone, estrogen

43. Cholesterol: LDL vs HDLCholesterol does not travel freely in the bloodstream. Carried by lipoproteins (L) LDL LOW Density Lipoproteins Deposit excess cholesterol on arterial walls. “bad” cholesterol HDL HIGH Density Lipoproteins Remove cholesterol from the blood. “good” cholesterol

44. Nucleic acids • Contains C, H as well as lots of N, P and O • Monomer = nucleotide • Polymer= nucleic acids DNA (deoxyribonucleic acid) RNA (ribonucleic acid) • Hydophobic or hydrophilic? • Function?

45. The functions of DNA 1. Replicate itself 2. Store information and pass to offspring 3. Make proteins

46. The nucleotide monomer • Each nucleotide contains • 1. A 5-carbon sugar • DNA: deoxyribose • RNA: ribose • 2. A phosphate group • 3. A nitrogenous group

47. The 4 nucleotides of DNA

48. The DNA polymer • Nucleotides are linked by ______________ • Each DNA molecule is made of two strands. • Strands are held together by hydrogen bonds between the nitrogenous bases. • The bases pair according to base pair rules • Adenine - Thymine • Cytosine – Guanine

49. a-helix structure of DNA

50. DNA, genes, and chromosomes • Each DNA strand is divided into segments called genes • Genes are the recipes for proteins • The sequence of nucleotides in a gene dictate the order of amino acids in a polypeptide. • Each DNA strand is called a chromosome • Human cells have 46 chromosomes in each cell.