Biochemistry The Chemistry of Life http://farm1.static.flickr.com/127/336030502_d3f28f1a9d_o.jpg 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/nucl ear_energy/fuel/atom.jpg Atomic Structure • Hydrogen (H) • Carbon (C) • Nitrogen (N) • Oxygen (O) Chemistry Video Chemistry http://www.ider.herts.ac.uk/sc hool/courseware/materials/ima ges/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 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 Chemistry • pH scale – measure of H+ ions in a solution 0 7 14 Strong acid H+ Neutral Strong base OH- Chemistry • Buffers – Maintain a stable pH, even when acids or bases are added – Used to maintain homeostasis www.chemcollective.org/buffers/buffers3.php pH Lab Solution Hypothesis pH Actual pH Strong/Weak Acid/Base/ Neutral Water Milk Soda Vinegar Ammonia pH Lab Questions: 1. Which substances appeared to have a pH below 7? Which substances appeared to have a pH above 7? 2. Which solutions were neutral? 3. Which solutions donated H+ ions? 4. What term describes the body’s balancing of acidic and basic conditions? 5. Which part of this lab contained the dependent variable? 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 http://img.tfd.com/wn/75/120881-wet.gif 1 Small + 1 + small = many = larger + water + water 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 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 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 Organic Compounds – Nucleic Acids 1. Nucleic Acids monomer Nucleotide polymer nucleic acid Nucleic Acid Video A nucleotide is a ____ of DNA? A) Monomer B) Polymer Where can nucleic acids be found in the cell? A) In the nucleus B) In the cytoplasm C) In the ribosome D) All the above DNA Extraction 1. 2. 3. 4. 5. 6. 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 7. Draw up DNA with pipette 8. To keep your DNA, add 1 pipette alcohol and DNA into plastic container, close lid DNA Extraction 2 1. 2. 2. 3. 4. 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 5. Gather DNA with glass rod (twirl) 6. To keep your DNA, add 1 pipette alcohol and DNA into plastic container, close lid Organic Compounds 2. Carbohydrates http://www.retrotuckshopsweetsdirect.co.uk/images/sugar%20free%20bears.jpg – sugars, starches, fiber – End in “–OSE” • Glucose, cellulose, sucrose – Quick energy source: • 1 gram = 4 calories of food energy http://whatscookingamerica.net/Cookie/CookiePhotos/PowderedSugar2.jpg http://coppola.rsmart.com/files/u2/potato_2.gif http://www.treehugger.com/cellulose -jj-001.jpg 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 Carbohydrates • Ex. Glucose C6H12O6 - made by plants during photosynthesis Carbohydrates Video Biochemistry Labs Purpose: What macromolecules are necessary for life processes? Hypotheses: (within data tables) • Carbohydrates • Lipids • Proteins o Enzymes Biochemistry Lab - Carbohydrates Carbohydrate (Sugar) Test – use Benedict’s Solution Tests for monosaccharides Sample Water Milk Bread Potato Hypothesis Initial Color Final Color Result (+,-) 1. 2. 3. 4. 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 Juice Biochemistry Lab - Carbohydrates Carbohydrate (Starch) Test – use Iodine Tests for polysaccharides Sample Water Milk Bread Potato Hypothesis Color Result (+,-) 1. Place each food sample in a separate test tube 2. Add pipette of Iodine solution 3. Note results: + = blue/black - = brown/other Juice 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_b utter.jpg/800px-NCI_butter.jpg http://fitness102.blogspot.com/search/label/cholesterol http://nymag.com/daily/intel/20061205donuts.jpg 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 Lipids - Fats Monomer G L Fatty acid chain Y C Fatty acid chain E R O Fatty acid chain L Polymer Lipid Lipids Video Biochemistry Lab - Lipids Lipids Test – use Sudan III and brown paper bag Sample Water Potato chips Gelatin Oil Juice Hypothesis Color w/ Sudan III Paper bag Result (+,-) 1. Place each sample in a separate test tube 2. Add several drops of Sudan III solution 3. 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 Organic Molecules 4. Proteins – Structural foods – Used to build tissues – For transport of materials – Composed of C, H, O, N 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 .. Proteins Monomer • Amino acid (aa) Polymer • Protein • aka = polypeptide – 20 different aas aa aa aa Peptide Bonds – between amino acids aa aa aa Proteins Video Biochemistry Lab - Proteins Protein Test – use Biuret’s Solution Sample Water Milk Gelatin Bread Juice Hypothesis Initial Color Final Color Result (+,-) 1. Place each food sample in a separate test tube 2. Add pipette of Biuret’s solution 3. Note results: + = dark purple/black color change - = no change Biochemistry Labs - Conclusion 1. List the various substances tested and the organic molecules found in each one. 2. Of the substances tested, which one(s) would have the highest calorie count? Give evidence. 3. What was the control in each experiment? Why? Read a food label 1. Calculate total calories: use total fat, total carbohydrates, and total proteins 2. From the total carbohydrates, how many calories come from sugars alone? 3. How many servings are there in a container, and what is the serving size? 4. What other nutrients are available from this food? 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. 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 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 Proteins - Enzymes How do enzymes work? Induced Fit Model – enzyme changes shape to fit Enzyme substrate, then returns to original shape Enzyme Substrate Active Site Substrate Complex chsweb.lr.k12.nj.us/.../enzymesap/image136.gif 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 Enzyme Video http://videos.howstuffworks.com/hsw/10320matter-and-energy-enzymes-video.htm Biochemistry Lab - Enzymes Hydrogen peroxide is broken down by the enzyme peroxidase (found in potatoes) H2O2 + peroxidase H2O + O2 (bubbles) Sample Empty Dish Cooked Potato Raw potato – sliced Raw potato – mashed Potato in NaOH (base) Potato from refrigerator Hypothesis Reaction (0 – 5) (0 – 5) Explanation 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? Enzyme Worksheet Toothpickase Lab Table 1: Toothpickase Activity Time (sec.) Number Broken Total Broken 10 sec. 20 sec. (30 sec. total) 30 sec. (60 sec. total) 60 sec. (120 sec. total) Table 2: Rate of Toothpickase Enzyme Activity Time Initial (0 – 10 sec.) 60 – 120 sec. Rate = Number / sec. Toothpickase Lab - Analysis 1. 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?