Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Module 1D – Biochemistry Biochemistry Objective # 18 is the chemistry of living organisms. Distinguish between organic and inorganic molecules. In this module we will focus on the structure, function, and properties of the various organic molecules that make up living organisms. 1 2 Objective 18 Objective 18 Organic molecules: ¾ Larger, more complex molecules whose structure is based on a backbone of C atoms (always contain C as a major part of their structure). ¾ Examples: C6H12O6, C2H5COOH Inorganic molecules: ¾ Relatively small, simple molecules that usually lack C (a few have one C atom). ¾ Examples: H2O, CO2, NH3, O2, H2 Η Living organisms are composed of both inorganic and organic molecules. Ο Η Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3 4 Objective # 19 Objective 19 Carbon has an atomic # of 6. How many valence electrons does it have? Carbon can form 4 strong covalent bonds with up to 4 other atoms. Carbon atoms can form strong covalent bonds with each other to produce unbranched chains, branched chains, and rings. Identify the characteristics of carbon that allow it to play such an important role in the chemistry of life. 5 6 1 Objective 19 Objective # 20 Carbon rings can join with each other to form interlocking rings or chains of rings. Carbon can form single, double, or triple covalent bonds with other atoms. Explain what isomers are. 7 8 Objective 20 Isomers of C6H12O6 Isomers are molecules that have the same molecular formula (same number and type of atoms) but which have different properties because the atoms are arranged differently. H C OH C O HO C H H C H H c) d) e) Stereoisomer C O C OH H C OH C H HO C H OH H C OH HO C H C OH H C OH H C OH C OH H C OH H C OH H Glucose H Galactose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Objective # 21 b) O H 9 a) C Structural isomer HO H Fructose Explain what a functional group is, and be able to identify the structure and characteristics of each of the following functional groups: H H H 10 Objective 21 hydroxyl carboxyl amine methyl phosphate A functional group is a small group of atoms that is part of a larger molecule and gives it specific properties. 11 12 2 Functional Group Structural Formula H Hydroxyl OH Found In Example H H C C H H OH O H H Amino N H carbohydrates, proteins, nucleic acids, lipids H HO C C N CH3 H proteins, nucleic acids Alanine Sulfhydryl COOH S H H C CH2 S H Ethanol proteins NH2 Cysteine H O Carbonyl H C O C H C H carbohydrates, nucleic acids Phosphate O– H Carboxyl C H OH C H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Glycerol phosphate O Methyl HO C C NH2 13 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Objective # 22 proteins H C H H OH Acetic acid O H H C H proteins, lipids C O O P O– H C C C O P O– nucleic acids H H H O– O Acetaldehyde O OHOH H H Alanine 14 Objective 22a Define the following terms and be able to give or recognize examples of each: a) Monomer, dimer, polymer b) Condensation reaction (or dehydration synthesis) c) Hydrolysis reaction Large organic molecules are called macromolecules. Macromolecules are formed by joining smaller organic molecules called subunits, or building bocks, or monomers. When 2 similar or identical monomers are joined we get a dimer. 15 16 Objective 22a Objective 22b Subunits are joined during a type of reaction called condensation or dehydration synthesis. An –OH is removed from one subnunit, an –H is removed form the other, and H2O is formed: When many similar or identical monomers are joined we get a polymer. Joining many similar or identical subunits together to form a polymer is called polymerization. 17 18 3 Objective 22c Condensation or Dehydration Synthesis The reverse reaction is called hydrolysis. It involves breaking a macromolecule into smaller subunits. A molecule of water is added for each subunit that is removed: Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 19 20 Objective # 23 Hydrolysis Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Describe the structure and functions of each of the following groups of organic compounds. Also be able to identify examples from each group: a) Carbohydrates b) Lipids c) Proteins d) Nucleotide-based compounds 21 Objective 23a 22 Objective 23a Carbohydrates are made of monomers called simple sugars or monosaccharides. Monosaccharides are used for short term energy storage, and serve as structural components of larger organic molecules. They contain C, H, and O in an approximate ratio of 1:2:1. 23 Monosaccharides are classified according to the number of C atoms they contain: ¾ 3 C = triose e.g. glyceraldehyde ¾ 4 C = tetrose ¾ 5 C = pentose e.g. ribose, deoxyribose ¾ 6 C = hexose e.g. glucose, fructose, galactose Monosaccharides in living organisms generally have 3C, 5C, or 6C: 24 4 Pentoses Triose (3-carbon sugar) O 5-carbon Sugars 5 CH2OH C 1 C 2 OH H C 3 OH H Glyceraldehyde 4 H H 3 OH 6 CH2OH 5 5 CH2OH O H Hexoses (6-carbon Sugars) (5-carbon sugars) 3-carbon Sugar H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H OH 1 H 2 OH Ribose O 4 H H 3 OH H OH 1 H H 2 H 4 HO 6 CH2OH H 1 5 OH HO 4 OH Glucose Deoxyribose O OH H H 2 OH 3 H 5 OH H 2 4 OH OH CH2OH H 1 3 3 H H O O H H OH 6 CH2OH Fructose H 1 H 2 OH Galactose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 25 26 Objective 23a Chain and Ring Forms of Glucose When monosaccharides with 5 or more C atoms are dissolved in water (as they always are in living systems) most of the molecules assume a ring shape. Glucose can form 2 types of rings, α-glucose and β-glucose: CH2OH 5 C O H H H C C OH H 4 1 OH OH 3 C C2 α-glucose O C 1 H OH H H 2C HO C 3 OH C 4 H C 5 H C 6 H OH H C H 6 H 5C O O C H C OH H 4 1 OH C2 H 3C H H H H OH OH or CH2OH 5 C O OH C C H OH H 4 1 OH H C2 3C OH H OH H β-glucose OH Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 27 28 Objective 23a Fructose and α-glucose can be joined by a condensation reaction to produce the disaccharide sucrose: Two monosaccharides can be joined by condensation to form a disaccharide plus H2O. CH2OH CH2OH H Many organisms transport sugar within their bodies in the form of disaccharides. HO H OH + H OH HO H OH α-glucose CH2OH O O H H H OH H CH2OH OH H Fructose HO H2O H OH H CH2OH O O H H OH O H OH Sucrose H OH CH2OH H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. 29 30 5 Galactose and α-glucose can be joined by a condensation reaction to produce the disaccharide lactose: Two α-glucose molecules can be joined by a condensation reaction to produce the disaccharide maltose: CH2OH H HO CH2OH O H H OH H H OH H O O H OH H H OH H OH OH H Maltose H H OH Glucose H OH Galactose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 31 CH2OH O H OH H CH2OH O H H H OH H O OH Lactose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Objective 23a 32 Objective 23a Storage Polysaccharides consist of many monosaccharides joined by condensation to form long branched or unbranched chains. Some polysaccharides are used to store excess sugars, while others are used as structural materials. Polysaccharides: subunits can be joined by α-1,4 linkages to form long unbranched chains ¾ α-glucose CH2OH H 4 H OH HO O H 1 H OH H H OH α-glucose CH2OH O OH H H OH H O CH2OH O OH H H O H OH α-1,4 linkages CH2OH O OH H H OH H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 33 Objective 23a Objective 23a use α-glucose to make starches, including amylose (coiled and unbranched) and amylopectin (coiled and branched): ¾ Plants ¾ Branches can be added to the chain using α-1,6 linkages: H 34 CH2OH O H H OH H O α-1,6 linkage H OH CH2 CH2OH O H O H H H H H OH H OH H O H OH OH H α-1,4 linkage Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 35 Amylose + Amylopectin Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 36 6 Objective 23a ¾ Animals use α-glucose to make glycogen which is more extensively branched than amylopectin: Objective 23a Structural Polysaccharides: ¾ Cellulose is a long unbranched chain of β-glucose subunits. It is a major component of plant cell walls. CH2OH H 4 H OH HO H CH2OH O OH 1 H H OH β-glucose H O H O O H OH H H OH H H OH H OH H CH2OH H H O O CH2OH β-1,4 linkages O H OH H H OH O H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Glycogen Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 37 38 Objective 23a Objective 23b Lipids are structurally diverse molecules that are greasy and insoluble in H2O. We will examine 4 types of lipids: ¾ Fats and oils ¾ Phospholipids ¾ Terpenes ¾ Steroids ¾ Chitin is similar to cellulose, but a nitrogen group is added to each glucose. It is found in the exoskeleton of arthropods and cell walls of fungi. 39 40 Objective 23b Objective 23b Fats and oils are composed of 2 types of subunits: glycerol and fatty acids. Glycerol is an alcohol with 3 carbons, each bearing a hydroxyl group: A 41 fatty acid has a long hydrocarbon chain with a carboxyl group at one end. It may be saturated (no double bonds between the C atoms of the hydrocarbon chain), monounsaturated (one double bond), or polyunsaturated (more than one double bond). H can be added to unsaturated fatty acids using a process called hydrogenation. 42 7 Objective 23b Fatty Acids: Glycerol + 1 fatty acid = monoglyceride Glycerol + 2 fatty acids = diglyceride + 3 fatty acids = triacylglycerol (also called a triglyceride or fat.) Glycerol 43 Saturated fat 44 Unsaturated fat Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 45 46 Objective 23b Objective 23b Most animal fats contain saturated fatty acids and tend to be solid at room temperature. Because fats and oils are such concentrated sources of energy, they are often used for long term energy storage. In animals, fats also act as insulators and cushions. Most plant fats contain unsaturated fatty acids. They tend to be liquid at room temperature, and are called oils. 47 48 8 In Nonpolar Hydrophobic Tails phospholipids, two of the –OH groups on glycerol are joined to fatty acids. The third –OH joins to a phosphate group which joins, in turn, to another polar group of atoms. The phosphate and polar groups are hydrophilic (polar head) while the hydrocarbon chains of the 2 fatty acids are hydrophobic (nonpolar tails). Polar Hydrophilic Heads Objective 23b N+(CH3)3 CH2 CH2 Phospholipid O O Choline O H2C C O O Glycerol F a t t y a c I d a c I d O– H Phosphate F a t t y P CH2 C OC O CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 CH3 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 49 Objective 23b 50 Micelle Lipid head (hydrophilic) In water, phospholipids will spontaneously orient so that the nonpolar tails are shielded from contact with the polar H2O molecules. Phospholipids are major components of cell membranes. Lipid tail (hydrophobic) Water Phospholipid bilayer Water Water Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 51 Objective 23b 52 Objective 23b Terpenes are long-chain lipids that are components of many important biological pigments such as chlorophyll. CH3 CH2 C CH2 CH2 CH2 CH3 OH CH CH2 CH2 Terpene (citronellol) 53 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 54 9 Objective 23b Objective 23b Steroids are lipids whose principle component is the steroid nucleus, a structure made of 4 interlocking rings of carbon atoms. H3C CH2 CH CH3 CH3 CH2 CH2 CH CH3 CH3 Examples: ¾ Cholesterol is a component of animal cell membranes. Steroid (cholesterol) HO 55 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 56 Objective 23b ¾ Testosterone and estrogen are steroids that function as sex hormones. Hormones are chemical messengers. After being secreted by endocrine glands, they are carried by the blood to specific target cells where they trigger a response, such as the production or activation of a protein: 57 Objective 23c Proteins perform many essential functions in living organisms: Function Class of Protein Catalysis enzymes Defense immunoglobulins, toxins Cell recognition antigens Transport through globins the body Objective 23c Membrane transport transporters 58 59 Function Structure/support Class of Protein fibers Motion muscle Osmotic regulation albumin Gene regulation repressors, activators Messengers hormones Storage Ion binding 60 10 Objective 23c One of the most important groups of proteins are enzymes. Enzymes are proteins that function as catalysts – substances that facilitate or speed up specific chemical reactions without being altered themselves: 61 Objective 23c 62 Three amino acids with the central carbon in red, the amino group in blue, and the R group shaded in white: Proteins are composed of monomers called amino acids. An amino acid consists of a central carbon atom joined to 4 other groups: ¾ H atom ¾ Amino group (NH2) ¾ Carboxyl group (COOH) ¾ R group (varies) OH NH CH2 H3N+ C CH2 CH2 H O Phenylalanine (Phe) 63 C C O– H3N+ C H3N+ C C O– C O– H O H O Tryptophan (Trp) Tyrosine (Tyr) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 64 Objective 23c About 20 different amino acids occur naturally in proteins. They are identical except for the R group. Two amino acids can join by condensation to form a dipeptide plus H2O. The bond between 2 amino acids is called a peptide bond. H H R N C C H O H OH H R N C C H O Amino acid OH Amino acid H 2O H H R N C C H O H R N C C H O OH Dipeptide 65 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 66 11 Objective 23c Objective 23c A polypeptide consists of many amino acids joined by peptide bonds to form a long unbranched chain: R H H O R H H O R A protein consists of one or more polypeptides which are coiled and folded into a specific 3-D shape. The final overall shape of a protein determines its function. H H C C N C C N C C N C C N C C N C H O H H O H H O R R R Peptide bond Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 67 68 Objective 23c Objective 23c Scientists generally recognize 4 levels of protein structure: 1) Primary structure is the sequence of amino acids in the polypeptide chains that make up a protein Primary Structure of a protein R R H H O C C N C C N C C N C H O R e.g. Ala-Gly-Val-Ser-Glu-Val-His- H H O H H R The primary structure can fold into a pleated sheet, or turn into a helix Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 69 70 Objective 23c Objective 23c 2) Secondary structure is the regular, repeated pattern of coiling or folding that occurs in certain areas of the polypeptide chain. ¾ the two most common patterns are the β-pleated sheet and the α-helix Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Secondary Structure β-pleated sheet 71 Secondary Structure α-helix 72 12 Objective 23c Objective 23c 3) Tertiary structure – the final overall shape of a protein. Proteins can be classified into 2 basic shapes: ¾ Globular – compact, round shape; these proteins are soluble in H2O ¾ Fibrous – thin, threadlike shape; these proteins are insoluble in H2O Tertiary Structure 73 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Objective 23c Objective 23c 4) Quaternary structure – the way the different polypeptide chains of a protein fit together. Only present in proteins composed of more than one polypeptide chain. Quaternary Structure 75 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. R C H O H H O N C C R R N C C H H O H H N C R Four Levels of Protein Structure The way a polypeptide coils and folds is determined by a variety of chemical interactions. The stability of these interactions is affected by environmental conditions such temperature and pH. In addition, cells have chaperone proteins, which help the polypeptides fold correctly. The primary structure can fold into a pleated sheet, or turn into a helix Secondary Structure Secondary Structure β-pleated sheet Tertiary Structure α-helix Quaternary Structure Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 76 Objective 23c Primary Structure C 74 77 78 13 Objective 23c Interactions that Contribute to a Protein’s Shape Objective 23c Interactions that Contribute to a Protein’s Shape 79 Objective 23c Interactions that Contribute to a Protein’s Shape 80 Objective 23c Interactions that Contribute to a Protein’s Shape 81 82 Objective 23c Interactions that Contribute to a Protein’s Shape Objective 23c If a protein’s environment is altered, the protein may change its shape or even unfold completely. This process is called denaturation. When proteins are denatured, they are usually rendered biologically inactive. 83 84 14 Objective 23d Nucleotide- based compounds are composed of subunits called nucleotides. A nucleotide consists of 3 parts: ¾ Pentose (5 C) sugar – ribose/deoxyribose ¾ Nitrogenous base attached to 1′ C ¾ Phosphate group (-PO4) attached to 5′ C 85 Phosphate group O –O P O– Objective 23d Nitrogenous base NH2 6 7N 5 N1 8 2 9 N 4 N3 Structure of a Nucleotide There have a double ring structure and include adenine (A) and guanine (G). O ¾ Pyrimidines have a single ring structure and include cytosine (C), thymine (T), and uracil (U). 1’ 3’ 2’ OH OH in RNA R Sugar H in DNA 87 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 88 Objective 23d Nitrogenous Bases We will examine 3 groups of nucleotide-based compounds: ¾Adenosine phosphates ¾Nucleotide coenzymes ¾Nucleic acids Pyrimidines Purines Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H C NH2 N C C N N C N C H H Adenine H C H C NH2 C N N C O H Cytosine (both DNA and RNA) H C O N C C N H N C N C NH2 H Guanine O H3C C H C C N O N H H C C O H C H Thymine (DNA only) are 2 types of nitrogenous bases: ¾ Purines O CH2 5’ 4’ 86 C N N H C O H Uracil (RNA only) 89 90 15 Objective 23d Nitrogenous base (adenine) ATP Adenosine phosphates: ¾ Ribose + Adenine = Adenosine ¾ Adenosine + 1 phosphate = AMP (adenosine monophosphate) ¾ Adenosine + 2 phosphates = ADP (adenosine diphosphate) ¾ Adenosine + 3 phosphates = ATP (adenosine triphosphate) 7N 5 Triphosphate group O –O P O O O O– P O P O– NH2 6 N1 8 5’ O CH2 9N 4 N 2 3 O– O 1’ 4’ 3’ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2’ OH OH Ribose 91 92 Objective 23d Objective 23d Nucleotide coenzymes: ¾ consist of 2 nucleotides joined by condensation e.g. NAD+, FAD, NADP+ ¾ function as electron carriers. They transport e- and H+ within the cell for use in chemical reactions. cAMP plays an important role as a second messenger. ATP is called the “energy currency” of the cell. The energy stored in the bond that connects the third phosphate to the rest of the molecule supplies the energy needed for most cell activities. 93 94 Objective 23d Nicotinamide Adenine Dinucleotide H Nucleic O C O O P NH2 + 2H O O OH P O O– CH2 N O O H H H OH The P O O– NH2 OH NAD+: Oxidized form of nicotinamide N H N CH2 O N Adenine H The H H OH OH nucleotides in RNA contain the sugar ribose and the bases A, G, C, U. H H N N N Adenine O OH H CH2 NH2 + 2H acids (RNA and DNA) are polynucleotides. N O– O NH2 OH N O P H H O O C O O– H Oxidation ; N CH2 H Reduction OH NADH: Reduced form of nicotinamide Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 95 nucleotides in DNA contain the sugar deoxyribose and the bases A, G, C, T. 96 16 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Objective 23d 5’ end RNA: RNA P of a single, unbranched chain of RNA nucleotides. ¾ plays several important roles during the process of protein synthesis. Phosphate group O ¾ consists Phosphodiester bonds P O P 5-carbon sugar (ribose) P O OH 3’ end 97 Objective 23d O Nitrogenous base (A,C,G or U) 98 DNA DNA: of 2 unbranched chains of DNA nucleotides twisted into a double helix. ¾ the 2 chains are held together by H bonds between the nitogenous bases. ¾ A always pairs with T, and G with C. ¾ functions as the heredity information in all living organisms. Sugar-phosphate "backbone" ¾ consists 99 101 P C Hydrogen bonds between nitrogenous bases P G C P P G P A P T P G C P T Phosphodiester bond A P P OH 3’ end 5’ end Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 100 102 17 DNA P P T T A P G C G A P P Deoxyribose-phosphate backbone P P T Bases P P Hydrogen bonding occurs between base-pairs RNA P AP G C T P P P P Ribose-phosphate backbone P P P P P A C C A G U A Bases DNA vs. RNA U P P G Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 103 18