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MOLECULAR BIOLOGY Slide 2 Elements present in your body other than water Carbon-30% of all biomass, original source of C is CO2 from photosynthesis Hydrogen Nitrogen Oxygen Phosphorus Sulfur If carbon is present then the compound is considered organic. Carbon is the most versatile element b/c of its ability to bond to itself and other elements. It is tetravalent (4 bonds). If C and H are present it is a hydrocarbon: most are energy sources (fossil fuels) Slide 3 Molecules in living organisms: proteins, carbohydrates, lipids, nucleic acids Most are polymers of smaller, covalently bonded, molecules called monomers. Functional groups: groups of atoms with specific chemical properties and consistent behavior. The consistent behavior of functional groups allows one to recognize the properties of molecules that contain them. i.e. polarity, electronegativity Slide 4 Figure 3.1 Some Functional Groups Important to Living Systems (Part 2) Amines- contain N, act as a base Phosphat es- involved in E transfers Sulfur in sulfhydrls make disulfide bridges in protein Slide 5 Figure 3.1 Some Functional Groups Important to Living Systems (Part 1) Hydroxyls - act as an alcohol or polar Aldehydes, Ketones, have one double bond to O Carboxyls have two Os, one double, one single bond Slide 6 FUNCTIONAL GROUPS SERVE IMPORTANT PURPOSES IN MOLECULES Estradiol Testosterone Male lion Female lion Slide 7 Isomers Structural isomer- same chemical formula, different arrangement of atoms. Structural Isomers Slide 8 Figure 3.2 Optical Isomers Bio Optical Isomers Same chemical formula, arranged differently around an asymmetrical carbon Slide 9 Biochemical Unity Biochemical unity-organisms can acquire needed biochemicals by consuming other organisms. Because all macromolecules have the same chemistry: The four biological molecules are present in the same proportions in all living things. Argument for common ancestor Slide 10 Figure 3.3 Substances Found in Living Tissues 70% water Slide 11 The function of macromolecules is directly related to their 3-D shape and their chemical properties/formula. This will determine molecular interactions such as solubility. Slide 12 Synthesis Question Question: Carbon is an extremely important element to all life forms on the planet. Life on Earth, as we know it, could not exist without this element. In no more than three sentences, A) Identify the ultimate source of all Carbon for living organisms alive today and B)provide two brief explanations of why Carbon is important molecularly speaking. Slide 13 Scoring Rubric: 1pt. The ultimate source is CO2 from the atmosphere. 1pt. Discussion of source of carbon for making Carbohydrates, Lipids, Proteins, and Nucleic Acids. 1pt. Discussion of the tetravalence allowing for a wide range of different molecules. 1pt. Correct use of scientific terms. 1pt. Answer has no more than three sentences. (Following Directions.) Slide 14 Molecular Biology Polymers are formed in condensation reactions AKA dehydration synthesis. Condensation reactions result in monomers joined by covalent bonds. These require E http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html The reverse of a dehydration synthesis is hydrolysis reaction which break apart polymers and turn them into monomers. These make E Slide 15 Figure 3.4 Condensation and Hydrolysis of Polymers (A) Slide 16 Figure 3.4 Condensation and Hydrolysis of Polymers (B) Slide 17 DEHYDRATION AND HYDROLYSIS REACTIONS Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Dehydration reaction in the synthesis of a polymer Longer polymer Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer Slide 18 Carbohydrates See the Carbonyls and Hydroxides? Slide 19 Carbohydrates (C,H,O 1:2:1) Molecules that contain carbons flanked by a H group and an OH group. Four major types of carbs: mono, di, poly, and oligo saccharides. Two major functions: Source of energy that can be released in a usable form to body tissues Serve as carbon skeletons for other 3 macromolecules. Slide 20 Monosaccharides Produced through photosynthesis. All living cells contain glucose. Most monosaccharides are in the D series of optical isomers (proteins are L) Slide 21 Figure 3.13 Glucose: From One Form to the Other (Part 2) Slide 22 Figure 3.14 Monosaccharides Are Simple Sugars (Part 1) Slide 23 Figure 3.14 Monosaccharides Are Simple Sugars (Part 2) Structural These are structural isomers. Slide 24 Glycosidic Linkages Monosaccharides covalently bind together in condensation reactions to form glycosidic linkages. Glycosidic linkages can be or . Examples of disaccharides sucrose table sugar = glucose + fructose lactose milk sugar = glucose + galactose maltose malt sugar = glucose + glucose Slide 25 Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages (Part 1) Slide 26 Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages (Part 2) ThiThis is cellobiose, a subunit of cellulose, humans dont have the enzymes to break this down, but cows do. To us it is merely roughage. Cellulose is a very stable glucose polymer, and is the principle component of cell walls. Slide 27 Oligosaccharides (3-20) Often covalently bonded to proteins and lipids on cell surfaces and act as recognition signals. ABO blood groups Slide 28 Polysaccharides Formed by glycosidic linkages, animal and plant energy storage form. Three forms: starch, glycogen, cellulose, and chitin. Starch and glycogen easily hydrolyzed for energy. Starch- all contain alpha linkages, stored in plants. Cellulose- plant cell wall structure; most abundant organic molecule on earth Glycogen-energy storage in animals Chitin- found in exoskeletons and fungi cell walls Slide 29 Polysaccharides Glucose must be stored as glycogen because glycogen does not exert as much osmotic pressure on the cell as one glucose molecule Slide 30 Figure 3.16 Representative Polysaccharides (A) Slide 31 Carbohydrate Energy Storage Slide 32 Figure 3.16 Representative Polysaccharides (B) Cellulose, Starch, & Glycogen Slide 33 Chemically Modified CHOs Some CHO can be modified by adding functional groups such as a phosphate or amino group. Phosphate sugars and amino sugars Slide 34 Lipids C,H,O Lipids are hydrocarbons that are insoluble in water because of their nonpolar, covalent bonds. All the extra H= 2x E of CHO Hydrophobic. One lipid molecule consists of a glycerol (alcohol) bonded to 3 fatty acid chains. The fatty acids are held together through van der Waals forces not covalent bonds; therefore they are not true polymers. Slide 35 Lipids The bond that holds each fatty acid molecule to the glycerol is formed through dehydration synthesis, and is called an ester linkage. The ester linkage is a covalent bond. Slide 36 ESTER LINKAGE AND LIPIDS Dehydration reaction in the synthesis of a fat Glycerol Fatty acid (palmitic acid) Slide 37 Math Quiz Tell if each pH or pOH is an acid, base, or neutral by writing ACID, BASE, or NEUTRAL on the line next to the prompt. (1 points each) pH 3 ____________ pOH 7 ______________ pH 14 _______________ pH 7 ____________ pH 4 ______________pOH 0 ______________ pOH 14 ____________ pOH 9 _____________ pOH 2 ____________ pH 10 _____________ Slide 38 Calculate pH differences in H concentration pH 2- pH 5 pH 1- pH 2 pH 3- pH 8 pH 7 pH 10 pH 1- pH 14 pH 1- pH 3 pH 10- pH 14 pH 3- pH 7 pH 5 pH 10 pH 1- pH 11 Slide 39 Figure 3.18 Synthesis of a Triglyceride Slide 40 Lipid Functions Fats and oils store energy Phospholipids in cell membrane for structure Carotenoids Hormones and vitamins Fat = insulation (Camels) Lipids coat neurons for electrical insulation Oil and wax on skin surface repel water Slide 41 Lipids One lipid unit is called a triglyceride/triglycerol. Triglycerides solid at room temp. are fats. Saturated fatty acid- all C-H bonds are single Animal fat, least healthy. Triglycerides liquid at room temp. are oils. Unsaturated fatty acid (mono, poly) some of the C-H bonds are double causing kinking in the hydrocarbon chain. Plant oils, lower melt. pt., healthier Polyunsaturated Fats- many double bonds, usually in plants Hydrogenated or Trans Fat- Unsaturated turned saturated Slide 42 Saturated vs. Unsaturated Slide 43 Figure 3.19 Saturated and Unsaturated Fatty Acids Slide 44 Phospholipids A phosphate molecule bonds to the glycerol replacing one hydrocarbon chain (fatty acid). Since phosphate functional group is (-) it is hydrophilic and attracts polar H20 molecules. In aqueous environment, phospholipids line up with hydrophobic region tails on one end, and hydrophilic heads on the other. Phospholipids form a bilayer. Slide 45 Figure 3.20 Phospholipids (A) Slide 46 Figure 3.20 Phospholipids (B) Phospholipid bilayers form biological membranes. Slide 47 Waxes Slide 48 Steroid Structure Slide 49 LE 4-9 Estradiol Testosterone Male lion Female lion Slide 50 Cell Membranes Slide 51 Lipid storage Slide 52 Energy and Macromolecules Data Set 6 Slide 53 Proteins- suffix lin eg insulin Contain: C, H, O, N, P, and S Protein monomers are known as amino acids, which then fold into the polypeptide form of proteins. 50% of organisms biomass Slide 54 Essential Amino Acids Over 20 amino acids 11 non-essential 9 essential These 9 are essential because they cannot be synthesized by the body and must be supplemented. Phenyalanine Valine Threonine Tryptophan Isoleucine Methionine Leucine Lysine Histidine Slide 55 Protein Structure Can be made of more than one polypeptide chain The sequence of amino acids in each polypeptide chain is the source of diversity in protein structure and function. Slide 56 What Are the Chemical Structures and Functions of Proteins? Amino acids have carboxyl and amino groupsthey function as both acid and base. Rgroup= property Slide 57 These hydrophylic amino acids attract ions of opposite charges. Table 3.2 (Part 1) Slide 58 Hydrophylic amino acids with polar but uncharged side chains form hydrogen bonds Table 3.2 (Part 2) Slide 59 Table 3.2 (Part 3) Hydrophobic amino acids Slide 60 Table 3.2 (Part 4) Slide 61 Proteins Amino acids bond together covalently by peptide bonds to form the polypeptide chain. The beginning of all polypeptides begin with the amino group of an amino acid: the N terminus and the end of the chain is the carboxyl group: the C terminus N C orientation Slide 62 Figure 3.6 Formation of Peptide Bonds The peptide bond is inflexibleno rotation is possible. Slide 63 Protein Structure Primary Structure-sequence of amino acids in the polypeptide chain. Peptide backbone N-C-C. Secondary Structure- determined by hydrogen bonds, alpha helix and beta pleated. Bonds between amino (H) and carboxyl (C and O) Tertiary Structure- additional folding between the R groups (side chains). Folded by disulfide bridges, cysteine has the sulfur. Quarternary Structure- result from subunits (separate tertiary structures) folding together. Multiple polypeptides together. Slide 64 Figure 3.7 The Four Levels of Protein Structure (A) Slide 65 Figure 3.7 The Four Levels of Protein Structure (B, C) Slide 66 Figure 3.7 The Four Levels of Protein Structure (D, E) Slide 67 Primary (1) sequence Slide 68 Primary Structure is IMPORTANT Slide 69 SICKLE CELL AND OXYGEN TRANSPORT Primary structure Secondary and tertiary structures 1 2 3 Normal hemoglobin Val His Leu 4 Thr 5 Pro 6 Glu 7 Primary structure Secondary and tertiary structures 1 2 3 Sickle-cell hemoglobin Val His Leu 4 Thr 5 Pro 6 ValGlu 7 Quaternary structure Normal hemoglobin (top view) Function Molecules do not associate with one another; each carries oxygen. Quaternary structure Sickle-cell hemoglobin Function Molecules interact with one another to crystallize into a fiber; capacity to carry oxygen is greatly reduced. Exposed hydrophobic region subunit Slide 70 2 structure Slide 71 3 Structure Slide 72 4 Structure Slide 73 Proteins Natural Form Slide 74 Protein Function Structural support Protection Transport Catalysis- speeding up a chemical reaction Defense Regulation Movement Slide 75 Protein denaturation Denaturation= loss of 3-D shape and function (unfold due to environmental stressors) Proteins are sensitive to their environment due to weaker bonds in the 2 nd and 3 rd structure. 3 Denaturing factors: Increased temperature Alterations in pH Salt concentration changes Denaturation is usually irreversible Slide 76 Figure 3.11 Denaturation Is the Loss of Tertiary Protein Structure and Function Slide 77 Protein Shape Sometimes proteins will bind to the wrong ligand (molecule) while completing their folding process. E.g. alzheimers Chaperonins- type of protein that prevents misfolding. Slide 78 Enzymes Enzymes are proteins that are catalysts that speed up chemical reactions in cells. Words that end in ase are enzymes Enzymes form an enzyme-substrate complex Animation: How Enzymes Work Animation: How Enzymes Work Slide 79 Nucleic Acids- C,H,O,P,N Nucleic acids are polymers designed for storage, transmission, and use of genetic information. DNA & RNA DNA encodes our heredity info. DNA contains the info, uses RNA to create an amino acid sequence (proteins) which carry out lifes functions. Pyrimidines: cytosine, thymine, uracil Purines: adenosine, guanine Slide 80 Nucleotide Nucleotides are the monomers for nucleic acids. Each nucleotide consists of a pentose sugar, phosphate group, and nitrogenous base. Nitrogenous bases can be pyrimidines (single ring) or purines (2 fused rings) Pyrimidines-C,T,U Purines-G, A Slide 81 3.5 What Are the Chemical Structures and Functions of Nucleic Acids? DNAdeoxyribose RNAribose Slide 82 DNA & RNA Backbone Alternate pentose sugar and phosphate groups (S- P-S-P-S-P) The nitrogen bases project off the backbone. Nucleotides bonded by phosphodiester linkages. Phosphodiester linkages form between the sugars linked by the phosphate. Slide 83 Figure 3.24 Distinguishing Characteristics of DNA and RNA (Part 1) Slide 84 DNA Hydrogen bonds link nitrogenous bases together. Base pairing rule-purine and pyrimidine always pair up. A-T and C-G in DNA A-U and C-G in RNA Know why base pairing is complimentary p.59 Slide 85 Figure 3.24 Distinguishing Characteristics of DNA and RNA (Part 1) Slide 86 DNA Relationships DNA in all organisms, chimps and humans share 98% base sequence with humans. Scientists use DNA to determine evolutionary relationships. Nucleotides also are used in energy reactions. (ATP and GTP). Nucleotides are used in hormones and the nervous system (cAMP). Slide 87 HW: Due Friday 8-30-13 Macromolecule Type Name of Molecule SourceRole in Organisms (What does it do?) 5 CarbohydratesglucoseplantsImmediate energy 5 Lipids 5 Proteins 4 Nucleotides Slide 88 How did life begin? Could life have come from outside earth? Allan Hills region of Antartica, meteorite from Mars Miller and Urey experiment 1953- chemical evolution. Took inorganic substances and made them organic Miller and Urey Experiment Miller and Urey Experiment RNA world before DNA- RNA less stable than DNA RNA ribozymes could replicate itself Ribozymes are responsible for peptide bonds Slide 89 Figure 3.27 Was Life Once Here? Slide 90 Energy Source- Stanley Miller Slide 91 Figure 3.28 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 1) Slide 92 4 Steps for Life to Emerge on Earth 1. Abiotic synthesis of amino acids and nucleic acids. 2. Monomers must join to make polymers 3. RNA/DNA form and gain ability to reproduce and stabilize using bonds and complimentary bonding. 4. Evolution of the protobiont first life form Slide 93 Evidence for #1: Abiotic synthesis Miller and Urey- hypothesized about early earths organic composition H2, CH4, NH3 and H2O vapor These things formed amino acids and oils The compounds came from volcanic eruptions and the energy from lightning These compounds collected in the oceans and wala life Slide 94 Evidence for #2: Polymerization Researchers have taken fools gold, sand, and clay, and exposed to it to intense heat In the presence of water (tides) amino acids and oils become polymers Slide 95 Evidence for #3: RNA/DNA Some RNA can act as ribozymes that act as great info storage bins Over time it is believed RNA evolved into a more stable DNA Slide 96 Evidence for #4: Protobiont Formation Experiments show that lipids and other molecules can form membranes (cell) Over millions of years they become prokaryotic cells Slide 97 Representation of a Protobionts Slide 98 Data Set Question (U1,D3) Question: In no more than three sentences, explain why the abiotic synthesis of the nucleic acids RNA and DNA was overall so essential to helping generate life on Earth? (5 Points) Slide 99 Synthesis Question (U1, D3) Question: In no more than three sentences, explain why the abiotic synthesis of the nucleic acids RNA and DNA was overall so essential to helping generate life on Earth? (5 Points) 1pt. Discussion of the ability to store molecular information on the construction of molecule 1pt. Discussion of inheritance of information from one generation to the next 1pt. Discussion of the long term stability of DNA 1pt. Correct use of scientific terms. 1pt. Answer has no more than three sentences. (Following Directions.)