Chapter #2. Reading requirements: All Problems (p.46): In notebooks: Date due (R) 1-10,13 2/7/06 (E) 1,3,5,6,7,8,12 2/7/06.

Transcription

1 Macromolecules/Chemistry Chapter #2 Reading requirements: All Problems (p.46): In notebooks: Date due (R) 1-10,13 2/7/06 (E) 1,3,5,6,7,8,12 2/7/06 Handout Why study Chemistry in Biology? To understand life processes, one must know the basic principles of chemistry. All living matter is composed of chemical elements. 98% of an organism s mass is composed of only six elements: xygen, Carbon, Hydrogen, Nitrogen, Calcium, and Phosphorus. Why study chem in biology? Element Deficiency Lack of iodine: results in a Goiter an enlarged thyroid. Increased growth which can be reversed with the addition of iodine (trace element) Nitrogen deficient corn Biological Hierarchies Hierarchy = system of organization based on a graded series of organizational levels. Cellular Hierarchies Cell = smallest unit of biological organization. contains all the properties of life. Cell is organized hierarchically. composed of organelles and macromolecules. Composed of molecules. Composed of atoms. rganismal Hierarchies Unicellular organisms: Cellular = organismal Multicellular organisms: cells associate to form tissues. Muscle (animals) or epidermis (plants) Tissues are organized into organs Tissues and organs form organ systems rgan systems form an organism. 1

2 Ecological Hierarchies Species of an organism exist in populations. Members of a species that live in the same area at the same time Populations interact to form communities. Populations that live together and interact Communities interact to form an ecosystem. A community and its environment Ecosystems compose biosphere. All of earth inhabited by organisms What are the parts of an atom? Matter, Atoms, & Subatomic Particles Matter: anything with mass that takes up space. composed of atoms. Atoms made of 3 types of subatomic particles. Protons & Neutrons Both in nucleus of atom. Protons have + charge Neutrons have no charge Both similar-sized. Electrons rbit around nucleus. Negatively charged. 1/1840 the size of protons. Atoms made of 3 types of subatomic particles. Particle Charge Location Protons: + AtomicNucleus Neutrons: o Atomic Nucleus Electrons: - utside Nucleus Using The Periodic Table Atomic Number Element Atomic Mass Atomic Number: the number of protons in the atomic nucleus Atomic Mass: Is the number of protons and neutrons in the atomic nucleus. Where are the electrons Electrons: Are negatively charged particles found in orbitals/shells. What is the attraction that keeps them in the orbitals? Energy levels/orbital: Where the electrons are found 1. K orbital: closest to the nucleus - holds two electrons 2. L orbital: Second level - can accommodate eight electrons 3. M orbital: Third level - can accommodate eight electrons rbitals Number of electrons ctet Rule K; holds two electrons L: holds eight M: holds eight K: 2 electrons L: 8 electrons M: 8 electrons All atoms are trying to maintain a full outer orbital - they want it filled. 2

3 Bonding Ionic and covalent bonding: method used to fill the outer orbital. Valence electrons: the electrons in the outermost orbital, they are responsible for chemical activity. Make Bohr Models Bohr Models show the structure of the atom: Location of proton, neutrons and electrons. Make models for the following atoms:, C USE AP CD Electron rbitals Chemical Reactions Chemical bond: is the attractive force that holds two atoms together (remember the octet rule?). ATMS WANT A FULL UTER RBITAL sharing of electrons between two atoms. Covalent bonding: Covalent bonding Polar covalent bonds: There is an unequal sharing of electrons (Hydrogen bonding). Non-polar covalent bonds: There is equal sharing of electrons. Ionic Bonding: when an electron is transferred from one atom to another. FRMATIN F INS Ions: electrically charged atoms, as result of ionic bonding (two types of ions). 1. Cations: positively charged ions 2. Anions: negatively charged ions The ionic bond is the result of the attraction between the two different ions. 3

4 Ionic Bonding Covalent Bonding Review bonding Polarity/electronegativity Polarity of H2 CVALENT SHARING BNDING 3 TYPES INIC TRANSFERING HYDRGEN H2 The electrons shared by the atoms spend more time around the atom than the H atoms This causes one end of the molecule to become positive and the other end negative Why are water molecules polar? Polarity However an oxygen atom, with 8 protons in its nucleus, has a much stronger attraction for electrons than does the hydrogen atom with a single proton. Thus, there is a greater probability of finding the shared electrons near the oxygen atom than near the hydrogen atom. A water molecule is polar because there is an uneven distribution of electrons between the oxygen and hydrogen atoms. Hydrogen Bonds Because of their partial positive and negative charges, polar molecules can attract each other. 4

5 The attraction between the hydrogen atoms on one molecule and the oxygen atom on another water molecule is an example of a hydrogen bond. Hydrogen bonds are not as strong as covalent or ionic bonds. A single water molecule may be involved in as many as four hydrogen bonds at a time. Water s ability to form multiple hydrogen bonds is responsible for many of its special properties. Hydrogen bonds form between water molecules. Hydrogen Bonds: occur between charged molecules Cohesion is an attraction between molecules of the same substance. Because of hydrogen bonding, water is extremely cohesive. Water's cohesion causes molecules on the surface of water to be drawn inward, which is why drops of water form beads on a smooth surface. Cohesion also explains why some insects and spiders can walk on a pond's surface. Adhesion is an attraction between molecules of different substances. The surface of water in a graduated cylinder dips in the center because adhesion between water molecules and glass molecules is stronger than cohesion between water molecules. Adhesion between water and glass causes water to rise in a narrow tube against the force of gravity. This effect is called capillary action. Capillary action is one of the forces that draw water out of the roots of a plant and up into its stems and leaves. Cohesion holds the column of water together as it rises. 5

6 Why water dissolves NACL Acids, Bases, and ph H2 Bonding Salt dissolving in H2 What are acidic solutions? What are basic solutions? Acids, Bases, and ph Acids, Bases, and ph A water molecule can react to form hydrogen and hydroxide ions. Water is neutral because the number of positive hydrogen ions (H + ) produced is equal to the number of negative hydroxide ions (H - ) produced. Acids, Bases, and ph The ph scale Chemists devised a measurement system called the ph scale to indicate the concentration of H + ions in solution. The ph scale ranges from 0 to 14. ACIDS and BASES The ph Scale The ph Scale The ph Scale At a ph of 7, the concentration of H + ions and H - ions is equal. Pure water has a ph of 7. Sea water Human blood Pure water Milk Normal rainfall Solutions with a ph below 7 are called acidic because they have more H + ions than H - ions. Solutions with a ph above 7 are called basic because they have more H - ions than H + ions. ven cleaner Bleach Ammonia solution Soap The lower the ph, the greater the acidity. Acid rain Tomato juice Lemon juice Stomach acids The higher the ph, the more basic the solution. 6

7 Acids, Bases, and ph Strong acids tend to have ph values that range from 1 to 3. The hydrochloric acid produced by the stomach to help digest food is a strong acid. Acids, Bases, and ph Strong bases, such as lye, tend to have ph values ranging from 11 to 14. Acids, Bases, and ph Buffers The ph of the fluids within most cells in the human body must generally be kept between 6.5 and 7.5. If the ph is lower or higher, it will affect the chemical reactions that take place within the cells. Acids, Bases, and ph Controlling ph is important for maintaining homeostasis. ne of the ways that the body controls ph is through dissolved compounds called buffers. Buffers are weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in ph. Structural Formula: Shows not only the types and numbers of atoms in a molecule but also shows their arrangement. Example Water: H-H- or H--H Why is molecular shape important? Molecular Mimic Macromolecules: Macro: Large Molecules: A combination of atoms that are bonded together Four distinct groups: Carbohydrates Lipids Proteins Nucleic Acids Use and btain energy Why do we eat? Energy Get nutrients Things needed to build other things 7

8 Terms Monomers: The repeating units (molecules) which make-up macromolecules. Polymer: a molecule made of many repeating units. A macro molecule is a polymer made of many monomers. Macromolecule song Water Makes and Breaks Biomolecules Water plays a key role in synthesis and degradation of organic molecules. Dehydration synthesis: forms a bond; H 2 is released. Energy required! = condensation reaction. Builds polymers. Hydrolysis: break bonds; H 2 is required. Energy released! Degrades polymers. How do monomers come together? Dehydration (condensation) reactions: the process by which two molecules are linked by the removal of water. Dehydration of two sugars How are molecules broken? Hydrolysis reactions: the breaking apart of a molecule by the addition of water. All macromolecules/monomers are linked by dehydration reactions and broken by hydrolysis reactions. Hydrolysis of a Disaccharide Protein Building Protein breaking 8

9 Reactions Condensation Reactions Condensation/hydrolysis reactions What carries out the reactions? Four Classes of Macromolecules Carbohydrates General formula = CH 2 ; carbon + water; Monomer = sugar (mainly glucose) Functions = energy store (starch & glycogen) or structural (cellulose & chitin). Lipids Monomer= glycerol (3-carbon alcohol) bound to 3 fatty acids. In phospholipids, one fatty acid replaced by phosphate group. Functions = energy store (fats) or membranes (phospholipids) Carbohydrate Lipid Four Classes of Macromolecules Proteins Monomer = amino acids Functions = enzymes and transport or structural support. Nucleic Acids Monomer = nucleotides 5-C sugar, phosphate group and nitrogenous base. Functions = information storage (DNA) or transfer (RNA). Amino acid Nucleotide Carbohydrates Carbohydrates: used by the body as quick energy used by plants as part of the cell wall (cellulose) used by animals to make a protective coat (exoskeleton of arthropods is make of chitin) contained in breads, rice, crackers and noodles polymers of glucose molecules (many glucose units connected together) Types of Carbohydrates Sugars Ring Structure Monosaccharide: simple sugars, single monomer units (glucose & fructose) Disaccharides: two monosaccharide bonded together (maltose) Polysaccharides: More than two mono s linked together (starch, glycogen & cellulose) 9

10 Carbo s Test for Carbohydrates Iodine test: Iodine will turn black when mixed with a polysaccharide. Benedicts test: Tests for monosaccharide Proteins Made of long chains of amino acids, bonded together by peptide bonds. Form the structure of all living things (give our eyes color, shape our body, used in the immune system, are enzymes etc.) There structure is determined by our DNA Found in beef, pork and fish All proteins are made of 20 amino acids (monomers) Many Functions Proteins Enzymatic - hydrolysis Defense - antibodies Transport - pumps Structure/support - fibers Motion - muscle fibers Formed by peptide bonds between amino acids Shape is important and depends upon chemical bonds at several levels. Table 5.1 An overview of protein functions Chain of Amino Acids The figure to the right shows a molecular model of bovine insulin, with the A chain colored blue and the larger B chain green. Insulin is composed of two peptide chains referred to as the A chain and B chain. A and B chains are linked together by two disulfide bonds, and an additional disulfide is formed within the A chain. In most species, the A chain consists of 21 amino acids and the B chain of 30 amino acids. Protein Insulin Protein assembly Protein Life cycle The proteins review What is an enzyme? ph and enzymes Enzyme basics Enzymes Proteins which help perform chemical reactions. They build and break molecules. Two main types of reactions: Condensation reactions: the linking together of monomers to make a polymer. Water is always a byproduct of these reactions. Hydrolysis reactions: the breaking down of a polymer to it s monomer units. Water is always needed for these reactions. 10

11 Enzymes are catalysts Enzymes cont. Catalyst a substance that speeds up the rate of a chemical reaction without being used up. Enzymes are specific Substrate the substance the enzyme reacts with Active site the part of the enzyme where the substrate binds The following things affect the rate of an enzymatic reaction Enzyme reaction time problem If the amount of product a point B equals 100 molecules and the amount of product a point A equals 10. Time at point B is 10 seconds. What is the rate of the reaction? Protein Folding Protein Folding Enzyme Lab 1. Fill a tube ½ full of salivary solution. 2. Add and equal amount of starch solution. 3. Have Mr. Gregor add transfer pipette full of solution. 4. Put in hot water bath for 30 minutes. 5. Add ten drops of iodine. Questions: 1. Starch and iodine will turn? 2. What happened to the starch? 3. If the enzyme broke the starch down what type of reaction is it? 4. Enzymes are polymers of what? Tests for Proteins Biuret Test: When biuret is added to a protein solution the solution will turn purple. Lipids (Fats) Used by the body for long term energy storage, insulation and the production of hormones. Include animal and plant fat, oils, waxes Monomers are: Fatty acid molecules and glycerol Insoluble in water Lipids Glycerol backbone binds fatty acids or phosphate group. Glycerol = 3-carbon Fatty acids = long chains of carbon and hydrogen components bound by dehydration synthesis Ester bond 11

12 Lipid Structure Lipids/Fats Types of Lipids Unsaturated fats: produced by plants ils (better for you). Saturated fats: produced by animals usually solid Example: butter (can be bad). Good and bad fats. Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds Unsaturated fatty acids Have one or more double bonds leic acid Stearic acid Figure 5.12 (a) Saturated fat and fatty acid Figure 5.12 (b) Unsaturated fat and fatty acid cis double bond causes bending Phospholipids Phospholipids Have only two fatty acids Have a phosphate group instead of a third fatty acid Phospholipid structure Consists of a hydrophilic head and hydrophobic tails Hydrophilic head CH 2 CH C C CH 2 CH 2 P CH 2 + N(CH 3 ) 3 Choline Phosphate Glycerol Lipid condensation Lipid Review Hydrophobic tails Fatty acids Hydrophilic head Hydrophobic tails Figure 5.13 (a) Structural formula (b) Space-filling model (c) Phospholipid symbol 12

13 Test for Lipids Brown Paper test: When lipids are added to brown paper they will leave a translucent spot. Nucleic Acids long polymers of nucleotides Monomers: Nucleotides (A,T,C,G, & U) RNA: uses ribose sugar. Usually single-stranded. Involved in making protein. DNA: uses deoxyribose sugar. double-stranded. H-bonds link strands Involved in making RNA. Nucleic Acids DNA & RNA: The instructions for making proteins. Monomers are Nucleotides. Information molecules of the cell. DNA The Structure of Nucleic Acids Directs RNA synthesis Directs protein synthesis through RNA 1 Synthesis of mrna in the nucleus NUCLEUS 2 Movement of mrna into cytoplasm via nuclear pore 3 Synthesis of protein mrna CYTPLASM mrna Ribosome Nucleic acids Exist as polymers called polynucleotides 5 C 3 C 5 C 5 end Each polynucleotide Consists of monomers called nucleotides Nucleoside Nitrogenous base 5 C P CH 2 Phosphate 3 C group Pentose sugar Figure 5.25 Polypeptide Amino acids 3 C H 3 end Figure 5.26 (b) Nucleotide Figure 5.26 (a) Polynucleotide, or nucleic acid Nucleotide Monomers Nucleic Acids Nucleotide monomers Are made up of nucleosides and phosphate groups Nitrogenous bases Pyrimidines NH 2 C N CH HN C C CH 3 HN C CH C CH C CH C CH N N N H H H CytosineThymine (in DNA) Uracil (in RNA) C T U NH 2 N C C N HC N C CH H N Adenine A Purines N C C NH HC C N N NH2 H Guanine G The DNA double helix Consists of two strands 5 end 3 end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) ld strands Nucleotide about to be added to a 3 new strand A end 5 end HCH 2 Pentose sugars H HCH 2 H H H H H H H H H H H H H Deoxyribose (in DNA) Ribose (in RNA) Figure end 5 end New strands 3 end Figure 5.26 (c) Nucleoside components 13

14 DNA Activity Journey into DNA DNA Anatomy Structure of nucleic acids Make a graphic organizer using the following terms: Iodine test, Benedicts test, Biuret test, Brown paper test, Macromolecules, Carbohydrates, Proteins, Lipids, Long term energy, Quick energy, Noodles, Wax, Structure, Enzymes, Glucose, Fatty Acids, Peptide bonds, Amino acids, Nucleic acids, DNA, genetic information. Lipids/Fats ph scale Water Makes and Breaks Biomolecules Water plays a key role in synthesis and degradation of organic molecules. Dehydration synthesis: the removal of H group from one molecule and H from another to form a bond; H 2 is released. Energy required! = condensation reaction. Builds polymers. Hydrolysis: addition of H group to one molecule and H to another to break bond; H 2 is required. Energy released! Breaks polymers. Condensation Reactions Condensation of two sugars Hydrolysis of a Disaccharide 14

15 The Synthesis and Breakdown of Polymers Monomers form larger molecules by condensation reactions called dehydration reactions Figure 5.2A H H H Short polymer Dehydration removes a water molecule, forming a new bond H H 2 Longer polymer (a) Dehydration reaction in the synthesis of a polym H H Unlinked monomer Polymers can disassemble by Hydrolysis H H Hydrolysis adds a water H molecule, breaking a bond 2 H H H H Figure 5.2B (b) Hydrolysis of a polymer Review For Quiz: ph: Know the scale 0-14 Neutralization Carbos: - Monosaccharide - Disaccharides - Polysaccharides Proteins: Lipids: Lab Tests: - Iodine - Biuret - Benedicts Reactions - Condensation - Hydrolysis Enzymes Review For Quiz: 15