Chapter 2: Chemistry. Raw materials and fuel for our bodies. Lecture 2 Outline. I. Atoms and Bonds. Everything is made of atoms.

Transcription

1 Announcements hapter 2: hemistry Problem Set #1 will be posted on website tomorrow. Answers will be posted next Friday. No Sections or ffice ours this week. Please attend the section of your choice next week and sign in. Raw materials and fuel for our bodies Lecture 2 utline I. Atoms and Bonds II. Water III. Acids, Bases, and Buffers IV. hemistry of arbon V. arbohydrates VI. Lipids VII. Proteins VIII. Nucleic Acids I. Atoms and Bonds Everything is made of atoms. q An element is a substance that cannot be broken down chemically into any other substances. q An atom is a bit of matter that cannot be subdivided any further without losing its essential properties.

2 Atomic Structure Atomic Numbers Insert new figure Elements Found in Your Body and the Big An atom s electrons determine how (and whether) the atom will bond with other atoms. Electron shells

3 Electron Shells Molecules Insert new fig 2-6 Products of bonding! Ions and Ionic Bonds ovalent Bonds Insert fig 2-10 Insert fig 2-9 to right side of slide

4 ydrogen Bonds Insert fig 2-11 Insert fig 2-12 II. Water Most important molecule for life on Earth. Life began in water and evolved here for 3 Billion years before spreading to land. ur cells are 70-95% water; we can only survive for 1 week without water. 2 0 is a polar molecule attracted to itself. This is the critical factor for all of water s most important properties. Properties of Water: ESIN: Water molecules stay close together due to hydrogen bonding. IG SPEIFI EAT: A great deal of energy is required to break -bonds to release/vaporize individual molecules. EVAPRATIVE LING: 2 0 molecules with highest energy leave water reservoir as vapor, lowering the T of remaining liquid. IE FLATS: Solid 2 0 is ~10% less dense than liquid form. This unusual feature results in a crystal-like matrix of 2 0 molecules in ice. Insulates water underneath. EXELLENT SLVENT: Dissolves polar, nonpolar substances and salts.

5 2.4 ydrogen bonds make water cohesive. Insert fig 2-13 eat apacity ohesion

6 Low Density as a Solid Why do coastal areas have milder, less variable climates than inland areas? A water-soluble protein (a) Lysozyme molecule in a nonaqueous environment (b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva δ+ δ This oxygen is attracted to a slight positive charge on the lysozyme molecule. This hydrogen is attracted to a slight negative charge on the lysozyme molecule. (c) Ionic and polar regions on the protein s Surface attract water molecules. opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

7 III. Acids, Bases, and Buffers ydrogen Ions and ydroxide Ions 2.6 Living systems are highly sensitive to acidic and basic conditions. - 2 Ionized ydroxide Molecule Non-Ionized Water Molecule opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings p Scale q The amount of + in a solution is a measure of its acidity and is called p. q Acids q Bases opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

8 Blood p q Buffers can quickly absorb excess + ions to keep a solution from becoming too acidic can quickly release + ions to counteract any increases in concentration Four Types of Macromolecules q arbohydrates q Lipids q Proteins q Nucleic acids opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings MARMLEULES IV. hemistry of arbon Whereas 2 is the universal medium for life, makes up the majority of the cell s structures. IV. hemistry of arbon,... rganic hemistry: The study of carbon compounds rganic compounds range from simple structures to huge macromolecules: The in our bodies ultimately derives from the action of plants. Plants harness the power of sunlight to convert 2 into arbon-based macromolecules. Methane ell walls ellulose microfibrils in a plant cell wall 0.5 µm Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 4 Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and ellulose molecules A cellulose molecule is an unbranched β glucose polymer. β Glucose monomer

9 IV. hemistry of arbon,... With a VALENE (# of covalent bonds an atom can form) of 4, carbon is able to simultaneously bond to 4 other elements. This is key to the formation of complex macromolecules. ydrogen (valence = 1) xygen (valence = 2) Nitrogen (valence = 3) arbon (valence = 4) The bonding versatility of carbon Allows it to form many diverse molecules, including carbon skeletons Name and omments (a) Methane Molecular Formula 4 Structural Formula Ball-and- Stick Model Space- Filling Model N (b) Ethane 2 6 This electron configuration gives it covalent compatibility with many different elements. (c) Ethene (ethylene) 2 4 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings Molecular Diversity Arising from arbon Skeleton Variation arbon chains Form the skeletons of most organic molecules Vary in length and shape opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings (a) Length Ethane Propane (b) Branching Butane 2-methylpropane (commonly called isobutane) (c) Double bonds 1-Butene 2-Butene (d) Rings yclohexane Benzene ydrocarbons Molecules consisting of arbon and ydrogen. Found in many of the cell s organic molecules. Store a great deal of potential energy in their many bonds. (a) A fat molecule opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings Fat droplets (stained red) 100 µm (b) Mammalian adipose cells

10 I. hemistry of arbon,... The diversity of products that can form is due to: 1) Endless geometries possible due to its valency 2) Its ability to bond to a wide variety of functional groups. Functional groups are the parts of molecules involved in chemical reactions. MARMLEULES,... Polymers Four main classes of biological macromolecules: Monomers: 1) ARBYDRATES (Polysaccharides) SUGARS 2) (LIPIDS - Make up membranes) Glycerol / FAs 3) PRTEINS - Enzymes, etc. Amino Acids 4) Nucleic Acids - DNA, RNA Nucleotides MARMLEULES,... V. arbohydrates Polysaccharides = sugar polymers = ( 2 ) n 2 = basic formula for Monosaccharides Simplest Sugars an be used for fuel, converted into other organic molecules or combined into polymers Two major purposes of carbohydrates: 1) Store energy (Glycogen in animals; Starch in plants) 2) Provide structural support (ellulose in plants; hitin in insects, crustaceans) arbohydrates q,, and q Primary fuel for organisms q ell structure opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

11 Glucose q Most carbohydrates ultimately converted into glucose Storage Polysaccharides STAR: omprised entirely of Glucose monomers and is the major form of energy storage in plants hloroplast Starch 1 µm q Blood sugar Amylose Amylopectin Starch: a plant polysaccharide opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings Storage Polysaccharides,... GLYGEN: omprised entirely of Glucose monomers and is the major form of energy storage in animals. Mitochondria Giycogen granules 0.5 µm Glycogen Glycogen: an animal polysaccharide opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

12 ellulose Is a major component of the tough walls that enclose plant cells ell walls ellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. ellulose,... Not digestible by humans. ows and termites possess symbiotic bacteria that break down cellulose into glucose monomers for energy utilization by their hosts. 0.5 µm Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings β Glucose monomer A cellulose molecule is an unbranched β glucose polymer. ellulose molecules opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings Structural Polysaccharides hitin ELLULSE: Also made with Glucose monomers BUT uses Glucose enantiomer. 2 4 α glucose β glucose another important structural polysaccharide Is found in the exoskeleton of arthropods an be used as surgical thread STAR: all monomers right-side up. ELLULSE: every other monomer is upside down. (a) α and β glucose ring structures (b) Starch: 1 4 linkage of α glucose monomers (c) ellulose: 1 4 linkage of β glucose monomers 2 N 3 (a) The structure of the chitin monomer. (b) hitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) hitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

13 MARMLEULES,... Polymers Four main classes of biological macromolecules: Monomers: 1) ARBYDRATES (Polysaccharides) SUGARS 2) (LIPIDS - Make up membranes) Glycerol / FAs 3) PRTEINS - Enzymes, etc. Amino Acids 4) Nucleic Acids - DNA, RNA Nucleotides MARMLEULES,... VI. Lipids Three main types of lipids: 1) FATS = Glycerol + 3 Fatty Acids 2) PSPLIPIDS = Spontaneously form membranes 3) STERIDS = Skeleton consists of 4 fused carbon rings Macromolecule but NT a polymer (no covalent bonds) Share the common trait of being YDRPBI VI. Lipids,... 1) FATS = Glycerol + 3 Fatty Acids (b) Fat molecule (triacylglycerol) Glycerol Fatty acid (palmitic acid) (a) Dehydration reaction in the synthesis of a fat Ester linkage opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings Fatty Acids Saturated: ave the maximum number of hydrogen atoms possible ave no double bonds (a) Saturated fat and fatty acid Stearic acid

14 Fatty Acids,... VI. Lipids,... Unsaturated: ave one or more double bonds auses kinks in tail resulting in looser packing 2) PSPLIPIDS ydrophilic head P 2 + N( 3 ) 3 holine Phosphate Glycerol leic acid ydrophobic tails Fatty acids ydrophilic head ydrophobic tails Figure 5.13 (a) Structural formula (b) Space-filling model (c) Phospholipid symbol (b) Unsaturated fat and fatty acid opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings cis double bond causes bending ave only TW Fatty Acids, with a P group replacing third FA onsist of a ydrophilic head and two ydrophobic tails Phospholipids Spontaneously form lipid bilayers due to amphipathic nature of lipid molecules. Found in all cell membranes. ydrophilic head WATER ydrophobic tail WATER opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

15 VI. Lipids,... 3) STERIDS Lipids characterized by a skeleton with 4 fused rings MARMLEULES,... Polymers Four main classes of biological macromolecules: Monomers: 1) ARBYDRATES (Polysaccharides) SUGARS 2) (LIPIDS - Make up membranes) Glycerol / FAs holesterol: A steroid important in cell membranes and acts as a precursor to some sex hormones. 3) PRTEINS - Enzymes, etc. Amino Acids 4) Nucleic Acids - DNA, RNA Nucleotides VII. Proteins Proteins are bodybuilding macromolecules. Amino Acids q Twenty different amino acids q Strung together to make proteins

16 2.16 A protein s function is influenced by its three-dimensional shape. q Peptide bonds q The sequence of amino acids Primary Structure Secondary Structure q ydrogen bonding between amino acids q The two most common patterns: twist in a corkscrew-like shape zig-zag folding

17 Tertiary Structure q Folding and bending of the secondary structure q Due to bonds such as hydrogen bonds or covalent sulfursulfur bonds. Quaternary Structure q When two or more polypeptide chains are held together by bonds between the amino acids on the different chains. q emoglobin Take-home message 2.14 q Unique combinations of 20 amino acids give rise to proteins, the chief building blocks of physical structures that make up all organisms. q Proteins perform myriad functions, from assisting chemical reactions to causing blood clotting to building bones to fighting microorganisms. VIII. Nucleic Acids Nucleic acids are macromolecules that store information.

18 2.20 DNA holds the genetic information to build an organism. Two Types of Nucleic Acids q Deoxyribonucleic acid (DNA) Insert new fig 2-46 q Ribonucleic acid (RNA) q Both play central roles in directing the production of proteins. Insert fig 2-45 to right 2.21 RNA is a universal translator, reading DNA and directing protein production. RNA differs from DNA in three important ways. q The sugar molecule of the sugarphosphate backbone Insert fig 2-47 q Single-stranded q Uracil (U) replaces thymine (T)

19 Take-home message 2.21 q RNA acts as a middleman molecule taking the instructions for protein production from DNA to another part of the cell where, in accordance with the RNA instructions, amino acids are pieced together into proteins. Building Blocks of Life Reading: hapter 2 For Next Week: hapter 3 (Architecture of the ell) Problem set #1 will be posted on the website tomorrow PS#1 will form basis of discussion sections next week PS#1 answers posted next Friday