Biochemistry

1. Biochemistry The Chemistry of Life http://farm1.static.flickr.com/127/336030502_d3f28f1a9d_o.jpg

2. Chemistry • Atomic structure • Atoms – • smallest unit of matter • everything is made of atoms • atoms contain: protons, neutrons, electrons • Elements important in life • Make up organic molecules • Hydrogen, carbon, nitrogen, oxygen • CHON http://www.eskom.co.za/nuclear_energy/fuel/atom.jpg

3. Atomic Structure • Hydrogen (H) • Carbon (C) • Nitrogen (N) • Oxygen (O)

4. Chemistry Video

5. Chemistry http://www.ider.herts.ac.uk/school/courseware/materials/images/covalent_bonding.gif • Chemical Bonds • Covalent bonds share electrons • Ionic bonds borrow electrons • Hydrogen bonds form between Hydrogen and O, F, or N http://lc.brooklyn.cuny.edu/smarttutor/core3_21/images/nature/9.a.Ionicbond-nacl.gif www.elmhurst.edu/.../images2/160hbondwater.gf

6. Chemistry • pH – scale used to measure “power of Hydrogen” • If a solution is acidic (0 – 6), neutral (7), or basic (8 – 14) ghs.gresham.k12.or.us/.../notes/chpt2/water.gif

7. Chemistry • pH scale – measure of H+ ions in a solution 0 7 14 Strong acidNeutral Strong base H+ OH-

8. Chemistry • Buffers • Maintain a stable pH, even when acids or bases are added • Used to maintain homeostasis www.chemcollective.org/buffers/buffers3.php

9. pH Lab

10. pH Lab Questions: • Which substances appeared to have a pH below 7? Which substances appeared to have a pH above 7? • Which solutions were neutral? • Which solutions donated H+ ions? • What term describes the body’s balancing of acidic and basic conditions? • Which part of this lab contained the dependent variable?

11. Organic molecules are macromolecules • How are they made? • Dehydration Synthesis • Aka: Condensation • to make larger by removing water • Ex. building proteins, sugars, and fats • Monomer + monomer = polymer + H2O 1 + 1 = many + water Small + small = larger + water http://img.tfd.com/wn/75/120881-wet.gif

12. Organic Molecules • How are they broken down? • Hydrolysis – breaking down into smaller pieces with water • Ex. digestion • Polymer + H2O = monomer + monomer • Large + water = smaller + smaller • Many + water = 1 + 1 www.dkimages.com/discover/previews/742/68543.JPG

13. Organic Compounds or Molecules • Must contain carbon and hydrogen (C & H) • Four groups • Nucleic Acids – DNA , RNA • Carbohydrates – Sugar, starch, fiber • Lipids – fats, oils, waxes • Proteins – enzymes, meat, nuts http://newtraditions.chem.wisc.edu/FPTS/fbform/1styrenf.gif

14. Organic Compounds 1. Nucleic Acids • DNA (deoxyribonucleic acid) • carries genetic or hereditary code in nucleus of cell • Controls protein production in cells • RNA (ribonucleic acid) • Actually makes the protein at ribosomes

15. Organic Compounds – Nucleic Acids 1. Nucleic Acids monomer polymer Nucleotide nucleic acid

16. Nucleic Acid Video

17. A nucleotide is a ____ of DNA? • Monomer • Polymer

18. Where can nucleic acids be found in the cell? • In the nucleus • In the cytoplasm • In the ribosome • All the above

19. DNA Extraction 1. Chew your cheeks • Spit cheek cells and saliva into cup • Add 1 pipette full of extraction solution • Swirl cup with liquids • Pour into test tube • Gently layer one pipette of cold alcohol on top of liquid • Draw up DNA with pipette • To keep your DNA, add 1 pipette alcohol and DNA into plastic container, close lid

20. DNA Extraction 2 • Mash fruit in plastic bag • Add 1 pipette full of extraction solution • Mash liquids together for 1 minute • Strain with cheesecloth into test tube • Gently layer one pipette of cold alcohol on top of liquid • Gather DNA with glass rod (twirl) • To keep your DNA, add 1 pipette alcohol and DNA into plastic container, close lid

21. Organic Compounds http://www.retrotuckshopsweetsdirect.co.uk/images/sugar%20free%20bears.jpg 2. Carbohydrates • sugars, starches, fiber • End in “–OSE” • Glucose, cellulose, sucrose • Quick energy source: • 1 gram = 4 calories of food energy http://www.treehugger.com/cellulose-jj-001.jpg http://whatscookingamerica.net/Cookie/CookiePhotos/PowderedSugar2.jpg http://coppola.rsmart.com/files/u2/potato_2.gif

22. Carbohydrates • Monomer • Monosaccharide = glucose mono = 1 saccharide = sugar • Polymer • Disaccharide = sucrose (table sugar) di = 2 sugars • Polysaccharide = cellulose, starch poly = many sugars www.guineapigcages.com/images/BuddywithHay.jpg

23. Carbohydrates • Ex. Glucose C6H12O6 - made by plants during photosynthesis

24. Carbohydrates Video

25. Biochemistry Labs Purpose: What macromolecules are necessary for life processes? Hypotheses: (within data tables) • Carbohydrates • Lipids • Proteins • Enzymes

26. Biochemistry Lab - Carbohydrates • Carbohydrate (Sugar) Test – use Benedict’s Solution • Tests for monosaccharides • Place each food sample in a separate test tube • Add pipette of Benedict’s solution • Immerse in hot water bath for 1 – 3 minutes • Note results: • + = color change - = no change

27. Biochemistry Lab - Carbohydrates • Carbohydrate (Starch) Test – use Iodine • Tests for polysaccharides • Place each food sample in a separate test tube • Add pipette of Iodine solution • Note results: • + = blue/black - = brown/other

28. Organic Polymers 3. Lipids • Fats, oils, waxes, cholesterol • Stored energy: 1 gram = 9 calories of food energy • Make up cell membranes http://upload.wikimedia.org/wikipedia/commons/thumb/4/45/NCI_butter.jpg/800px-NCI_butter.jpg http://fitness102.blogspot.com/search/label/cholesterol http://nymag.com/daily/intel/20061205donuts.jpg

29. Lipids - Fats • Insoluble in water – doesn’t mix in water • Hydrophobic • hydro = water phobic = fearing • Soluble in alcohol – will mix with alcohol http://www.huntsman.com/advanced_materials/Images/8171/INMR.jpg http://i153.photobucket.com/albums/s222/thepeacemaker_2007/__Hydrophobia___by_Shukaku_chan.jpg

30. Lipids - Fats Monomer Fatty acid chain Fatty acid chain Fatty acid chain Polymer Lipid GLYCEROL

31. Lipids Video

32. Biochemistry Lab - Lipids Lipids Test – use Sudan III and brown paper bag • Place each sample in a separate test tube • Add several drops of Sudan III solution • Note results: • + = deep dark red - = diluted red or pink • 4. Place small amount of each sample on paper bag • + = oily spots on paper bag - = wet spot dries up

33. Organic Molecules 4. Proteins • Structural foods • Used to build tissues • For transport of materials • Composed of C, H, O, N

34. pro.corbis.com/images/CB108198.jpg?size=572... Proteins • 1 gram = 4 calories of food energy • Ex. meats, nuts, eggs www.vegparadise.com/images/protein2.jpg http://www.theroadhousegrill.net/assets/images/steak.jpg

35. Proteins Monomer • Amino acid (aa) • 20 different aas • Polymer • Protein • aka = polypeptide aa aa aa aa aa aa Peptide Bonds – between amino acids

36. Proteins Video

37. Biochemistry Lab - Proteins Protein Test – use Biuret’s Solution • Place each food sample in a separate test tube • Add pipette of Biuret’s solution • Note results: • + = dark purple/black color change - = no change

38. Biochemistry Labs - Conclusion • List the various substances tested and the organic molecules found in each one. • Of the substances tested, which one(s) would have the highest calorie count? Give evidence. • What was the control in each experiment? Why?

39. Read a food label • Calculate total calories: • use total fat, total carbohydrates, and total proteins • From the total carbohydrates, how many calories come from sugars alone? • How many servings are there in a container, and what is the serving size? • What other nutrients are available from this food?

40. Biochemistry Labs Liquid Lunch - YUM! Purpose: Are there all of the necessary macromolecules in your lunch? Your Lunch: Pizza and soda Hypothesis: ??? Procedure: 1. Blend a pizza and soda in a blender 2. Strain through a coffee filter 3. Test for presence of macromolecules using indicators for each substance Analysis: List the organic substances found: Note which indicator was used for each organic substance.

41. Organic Polymers 4. Proteins • Enzymes – specific type of protein • Used to speed up reactions • End in –ASE: lactase, sucrase • Work on specific substrates • Are reusable, not used up in reaction • Can be destroyed (denatured) by heat, pH

42. Proteins - Enzymes Act as a catalyst to speed up reactions by lowering activation (starting) energy • Activation energy – energy (temperature) needed to start a reaction, lowered by enzymes • Optimal energy – energy (temperature) needed for reaction to work best www.columbia.edu/.../purves6/figure06-14.jpg

43. Proteins - Enzymes How do enzymes work? Induced Fit Model – enzyme changes shape to fit substrate, then returns to original shape Enzyme Substrate Complex Enzyme Substrate Active Site chsweb.lr.k12.nj.us/.../enzymesap/image136.gif

44. Proteins - Enzymes Lock and Key Model – enzyme fits with substrate like a key fits a lock, no change in enzyme shape chsweb.lr.k12.nj.us/.../enzymesap/image136.gif

45. Enzyme Video http://videos.howstuffworks.com/hsw/10320-matter-and-energy-enzymes-video.htm

46. Biochemistry Lab - Enzymes Hydrogen peroxide is broken down by the enzyme peroxidase (found in potatoes) H2O2 + peroxidase  H2O + O2 (bubbles)

47. ENZYMES • Define enzyme: • Define catalyst: • Define substrate: • Enzyme names usually end in -_________. • What is the function of the active site in an enzyme? • Explain lock and key model of enzyme activity. • How is the lock and key model different from the induced fit explanation? • How does temperature affect enzyme activity? • Why are only small amounts of enzymes needed in substrate reactions? • What is denaturation? Why is a high fever dangerous? • What is meant by enzyme specificity? • List four factors that affect the rate of an enzyme-substrate reaction. • After an enzyme-substrate reaction takes place, what happens to the structure of the enzyme?

48. Enzyme Worksheet

49. Toothpickase Lab Table 1: Toothpickase Activity Table 2: Rate of Toothpickase Enzyme Activity

50. Toothpickase Lab - Analysis • Calculate initial rate of enzyme activity by dividing the number of toothpicks broken by the change in time (10 sec.). Record the initial rate (no naked numbers!). formula: ∆Y = change in amount ∆X change in time 2. Calculate the rate of enzyme activity between 60 – 120 seconds. 3. What happens to the reaction rate as the supply of unbroken toothpicks runs out? 4. How does the “active site” of toothpickase fit the concept of induced fit?