Chemistry

1. Chemistry Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis P.S. In Biology we talk mainly about Organic Chemistry: The chemistry of molecules containing Carbon.

2. Chemistry Joke of the Day a Poem…. Susan was in chemistry. Susan is no more, for what she thought was H2O was really H2SO4.

3. Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization. a. Molecules and atoms from the environment are necessary to build new molecules . Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids. • Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids, or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms.

4. Living systems depend on properties of water that result from its polarity and hydrogen bonding. • Cohesion • Adhesion • High specific heat capacity • Universal solvent to support reactions • Heat of vaporization • Heat of fusion (exovs.endo) • Water’s thermal conductivity.

5. Review of Chemistry Review of Chem Review of Water

6. Trans fats Essential knowledge 4.a.1: the subcomponents of biological molecules and their sequence determine the properties of that molecule. a. Structure and function of polymers are derived from the way their monomers are assembled. . Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Cellulose vs. Starch. Why does one dissolve? • Lipids are nonpolar; however phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids. Lipids

7. Is this a carbohydrate or a lipid? How can your tell?

8. Is this a carbohydrate or a lipid? How can you tell?

9. What is the difference between Linear vs. branched polysaccharides? slow release starch (plant) energystorage glycogen (animal) What doesbranching do? fast release

10. Cow can digest cellulose well; no need to eat other sugars Gorilla can’t digest cellulose well; must add another sugar source, like fruit to diet

11. How do animals break down cellulose? • How can herbivores digest cellulose so well? • Mutualism • BACTERIA live in their digestive systems & help digest cellulose-rich (grass) meals Tell me aboutthe rabbits,again, George! Coprophage I eatWHAT! Ruminants

12. a. Structure and function of polymers are derived from the way their monomers are assembled. • In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (A,T,C,G,U). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions. • In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (Hydrophobic/philic, ionic), and the interactions of these R groups determine structure and function of that region of the protein.

13. What are the three parts of Nucleotides? • nitrogen base (C-N ring) • pentose sugar (5C) • ribose in RNA • deoxyribose in DNA • phosphate(PO4)group Nitrogen baseI’m the A,T,C,G or Upart! Are nucleic acidscharged molecules?

14. H2O Because everybody needs a Chaperonin! How are Proteins structured? • monomer =amino acids • 20 different amino acids • polymer =polypeptide • protein can be one or more polypeptide chains folded & bonded together • large & complex molecules • complex 3-D shape hemoglobin RuBisCOcan’t do photosynthesis without it!

15. Sickle cell anaemia Just 1out of 146amino acids! I’mhydrophilic! But I’mhydrophobic!

16. Isomers • Molecules with same molecular formula but different structures (shapes) • different chemical properties • different biological functions 6 carbons 6 carbons 6 carbons

17. Form affects function • Structural differences create important functional significance • amino acid alanine • L-alanine used in proteins • but not D-alanine • medicines • L-version active • but not D-version • sometimes withtragic results… stereoisomers

18. Form affects function • Thalidomide • prescribed to pregnant women in 50s & 60s • reduced morning sickness, but… • stereoisomer caused severe birth defects

19. b. Directionality influences structure and function of the polymer. • Nucleic acids have ends, defined by the 3’ and 5’ carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5’ to 3’) • Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate.

20. Learning Objectives: • LO 4.1: The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. • LO 4.2: The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer

21. A Review for You! Chemistry of Carbon Building Blocks of Life

22. Why study Carbon? • All of life is built on carbon • Cells • ~72% H2O • ~25% carbon compounds • carbohydrates • lipids • proteins • nucleic acids • ~3% salts • Na, Cl, K…

23. Chemistry of Life • Organic chemistry is the study of carboncompounds • C atoms are versatile building blocks • bonding properties • 4 stable covalent bonds H C H H H

24. Diversity of molecules • Substitute other atoms or groups around the carbon • ethane vs. ethanol • H replaced by an hydroxyl group (–OH) • nonpolar vs. polar • gas vs. liquid • biological effects! ethanol (C2H5OH) ethane (C2H6)

25. Functional groups • Parts of organic molecules that are involved in chemical reactions • give organic molecules distinctive properties hydroxylamino carbonylsulfhydryl carboxylphosphate • Affect reactivity • makes hydrocarbonshydrophilic • increase solubility in water

26. Viva la difference! • Basic structure of male & female hormones is identical • identical carbon skeleton • attachment of different functional groups • interact with different targets in the body • different effects

27. Hydroxyl • –OH • organic compounds with OH = alcohols • names typically end in -ol • ethanol

28. Carbonyl • C=O • O double bonded to C • if C=O at end molecule = aldehyde • if C=O in middle of molecule = ketone

29. Carboxyl • –COOH • C double bonded to O & single bonded to OH group • compounds with COOH = acids • fatty acids • amino acids

30. Amino • -NH2 • N attached to 2 H • compounds with NH2 = amines • amino acids • NH2 acts as base • ammonia picks up H+ from solution

31. Sulfhydryl • –SH • S bonded to H • compounds with SH = thiols • SH groups stabilize the structure of proteins

32. Phosphate • –PO4 • P bound to 4 O • connects to C through an O • lots of O = lots of negative charge • highly reactive • transfers energy between organic molecules • ATP, GTP, etc.

33. Macromolecules Building Blocksof Life

34. Macromolecules • Smaller organic molecules join together to form larger molecules • macromolecules • 4 major classes of macromolecules: • carbohydrates • lipids • proteins • nucleic acids • And a minor one: ATP

35. H2O HO H HO H HO H Polymers • Long molecules built by linking repeating building blocks in a chain • monomers • building blocks • repeated small units • covalent bonds Dehydration Synthesis http://sciencestage.com/v/621/chemistry-experiment-science-dehydration-sugar.html

36. H2O HO H HO H enzyme HO H How to build a polymer You gotta be open to“bonding! • Synthesis • joins monomers by “taking” H2O out • one monomer donates OH– • other monomer donates H+ • together these form H2O • requires energy & enzymes Dehydration synthesis Condensationreaction

37. H2O HO H enzyme H HO H HO How to break down a polymer Breaking upis hard to do! • Digestion • use H2O to breakdown polymers • reverse of dehydration synthesis • cleave off one monomer at a time • H2O is split into H+ and OH– • H+ & OH– attach to ends • requires enzymes • releases energy Hydrolysis Digestion

38. Any Questions?? And now on to Acids and Bases

39. Ph Scale Fig 2.9, pg. 43potential hydrogen • Measured on grams of Hydrogen (H+) • pH of 1= .1g of H+, pH of 2= .01g of H+ • Acid: form hydronium ions (H+) • pH of less than 7 ( 1 to 6.9) • Base: form hydroxide ions (OH-) • pH of more than 7 (7.1 to 14) • Acid + Base: salt & water, the solution is neutral with a pH of 7. • NaOH + HCl = H2O + NaCl with a pH of 7

40. pH Scale

41. What is a Buffer? • Chemical substances that neutralizes small amounts of an acid or base added to a solution. • Why are these important to your body? • Think Blood pH 7.45

42. What is a Buffer? • three main buffers in the body: • bicarbonate buffer system: in the blood and stomach to neutralize acids • protein buffer system: inter and extra cellular buffering used with hemoglobin and blood • phosphate buffer system: used in the urinary system to remove H+ ions and make urine acidic

43. Enzymes (most are Proteins) pg. 21 Barron’s • Catalysts: Lower activation energy needed to start a chemical reaction. See fig 2.22, pg.54 • Nonspecific Inhibitors: Temperature, pH, radiation, electricity: • Terms: substrate, active site, product • Can be denatured • Induced fit

44. Enzymes continued… • Characteristics: • Globular proteins (tertiary structure) • Substrate specific • Not destroyed /reused • Named after substrate with “ase” ending • Catalyze in both directions • Catalyze with help • Cofactor: inorganic • Coenzyme: vitamin • Control of Enzyme Activity • Competitive Inhibition: competes for the space with the substrate • Noncompetitive Inhibition/ Allosteric: secondary site stops enzyme from functioning • PFK too much ATP • Cooperativity: amplifies the response of an enzyme to its substrate. Hemoglobin, more oxygen it has….