Identify the characteristics of carbon that allow it to play such an important role in the chemistry of life.

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1 Module 1D Biochemistry Biochemistry is the chemistry of living organisms. In this module we will focus on the structure, function, and properties of the various organic molecules that make up living organisms. bjective # 18 Distinguish between organic and inorganic molecules. 1 2 bjective 18 Inorganic molecules: Relatively small, simple molecules that usually lack (a few have one atom). Examples: 2, 2, 3, 2, 2 Η Ο bjective 18 rganic molecules: Larger, more complex molecules whose structure is based on a backbone of atoms (always contain as a major part of their structure). Examples: , 2 Living organisms are composed of both inorganic and organic molecules. Η 3 4 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. bjective # 19 Identify the characteristics of carbon that allow it to play such an important role in the chemistry of life. bjective 19 arbon has an atomic # of 6. ow many valence electrons does it have? arbon can form 4 strong covalent bonds with up to 4 other atoms. arbon atoms can form strong covalent bonds with each other to produce unbranched chains, branched chains, and rings. 6 1

2 bjective 19 arbon rings can join with each other to form interlocking rings or chains of rings. arbon can form single, double, or triple covalent bonds with other atoms. bjective # 20 Explain what isomers are. 7 8 bjective 20 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. Isomers of Structural isomer Stereoisomer Fructose Glucose Galactose 9 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 10 bjective # 21 Explain what a a) hydroxyl functional group is, b) carboxyl and be able to identify the c) amine structure and d) methyl characteristics of each of the following functional groups: e) phosphate bjective 21 A functional group is a small group of atoms that is part of a larger molecule and gives it specific properties

3 Functional Group ydroxyl arbonyl arboxyl Structural Formula Example Ethanol Acetaldehyde Found In carbohydrates, proteins, nucleic acids, lipids carbohydrates, nucleic acids proteins, lipids opyright The McGraw-ill ompanies, Inc. ermission reproduction or display. Acetic acid 13 required for reproduction or display. Alanine 14 opyright The McGraw-ill ompanies, Inc. ermission required for Amino Sulfhydryl hosphate Methyl S 3 Alanine 2 S 2 ysteine Glycerol phosphate 2 proteins, nucleic acids proteins nucleic acids proteins bjective # 22 Define the following terms and be able to give or recognize examples of each: a) Monomer, dimer, polymer b) ondensation reaction (or dehydration synthesis) c) ydrolysis reaction bjective 22a 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 bjective 22a 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. bjective 22b Subunits are joined during a type of reaction called condensation or dehydration synthesis. An is removed from one subnunit, an is removed form the other, and 2 is formed:

4 ondensation or Dehydration Synthesis bjective 22c 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: opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display ydrolysis opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. bjective # 23 Describe the structure and functions of each of the following groups of organic compounds. Also be able to identify examples from each group: a) arbohydrates b) Lipids c) roteins d) ucleotide-based compounds bjective 23a arbohydrates 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,, and in an approximate ratio of 1:2:1. 23 bjective 23a Monosaccharides are classified according to the number of atoms they contain: 3 = triose e.g. glyceraldehyde 4 = tetrose = pentose e.g. ribose, deoxyribose 6 = hexose e.g. glucose, fructose, galactose Monosaccharides in living organisms generally have 3,, or 6: 24 4

5 Triose (3-carbon sugar) entoses (-carbon sugars) opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. exoses (6-carbon Sugars) 3-carbon Sugar -carbon Sugars Glyceraldehyde Ribose Deoxyribose Glucose Fructose Galactose opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display bjective 23a When monosaccharides with or more 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: hain and Ring Forms of Glucose opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. α-glucose or β-glucose bjective 23a Two monosaccharides can be joined by condensation to form a disaccharide plus 2. Many organisms transport sugar within their bodies in the form of disaccharides. Fructose and α-glucose can be joined by a condensation reaction to produce the disaccharide sucrose: a. α-glucose Fructose Sucrose opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display

6 Two α-glucose molecules can be joined by a condensation reaction to produce the disaccharide maltose: Galactose and α-glucose can be joined by a condensation reaction to produce the disaccharide lactose: 2 2 Maltose opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display Galactose opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 2 Glucose Lactose 32 bjective 23a olysaccharides 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. bjective 23a Storage olysaccharides: α-glucose subunits can be joined by α-1,4 linkages to form long unbranched chains α-glucose 2 2 α-1,4 linkages 2 33 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 34 bjective 23a Branches can be added to the chain using α-1,6 linkages: 2 α-1,6 linkage 2 2 bjective 23a lants use α-glucose to make starches, including amylose (coiled and unbranched) and amylopectin (coiled and branched): α-1,4 linkage opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 3 Amylose + Amylopectin opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 36 6

7 bjective 23a Animals use α-glucose to make glycogen which is more extensively branched than amylopectin: bjective 23a Structural olysaccharides: ellulose is a long unbranched chain of β-glucose subunits. It is a major component of plant cell walls β-glucose 2 2 β-1,4 linkages 2 Glycogen opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 37 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 38 bjective 23a hitin 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. bjective 23b Lipids are structurally diverse molecules that are greasy and insoluble in 2. We will examine 4 types of lipids: Fats and oils hospholipids Terpenes Steroids bjective 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: 41 bjective 23b A fatty acid has a long hydrocarbon chain with a carboxyl group at one end. It may be saturated (no double bonds between the atoms of the hydrocarbon chain), monounsaturated (one double bond), or polyunsaturated (more than one double bond). can be added to unsaturated fatty acids using a process called hydrogenation. 42 7

8 Fatty Acids: bjective 23b Glycerol + 1 fatty acid = monoglyceride Glycerol + 2 fatty acids = diglyceride Glycerol + 3 fatty acids = triacylglycerol (also called a triglyceride or fat.) Saturated fat Unsaturated fat opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display bjective 23b Most animal fats contain saturated fatty acids and tend to be solid at room temperature. Most plant fats contain unsaturated fatty acids. They tend to be liquid at room temperature, and are called oils. bjective 23b 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

9 bjective 23b In phospholipids, two of the groups on glycerol are joined to fatty acids. The third 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). 49 olar ydrophilic eads onpolar ydrophobic Tails holine hosphate Glycerol F a t t y a c I d F a t t y a c I d ( 3) 3 hospholipid opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 0 bjective 23b In water, phospholipids will spontaneously orient so that the nonpolar tails are shielded from contact with the polar 2 molecules. hospholipids are major components of cell membranes. Micelle Water hospholipid bilayer Lipid head (hydrophilic) Lipid tail (hydrophobic) Water Water 1 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 2 bjective 23b Terpenes are long-chain lipids that are components of many important biological pigments such as chlorophyll. 2 bjective 23b 3 3 Terpene (citronellol) opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 4 9

10 bjective 23b bjective 23b Steroids are lipids whose principle component is the steroid nucleus, a structure made of 4 interlocking rings of carbon atoms Examples: 3 holesterol is a component of animal cell membranes. Steroid (cholesterol) opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 6 bjective 23b Testosterone and estrogen are steroids that function as sex hormones. ormones 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: 7 8 bjective 23c roteins perform many essential functions in living organisms: Function lass of rotein atalysis enzymes Defense immunoglobulins, toxins ell recognition antigens Transport through globins the body Membrane transport transporters 9 bjective 23c Function lass of rotein Structure/support fibers Motion muscle smotic regulation albumin Gene regulation repressors, activators Messengers hormones Storage Ion binding 60 10

11 bjective 23c ne 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: bjective 23c roteins are composed of monomers called amino acids. An amino acid consists of a central carbon atom joined to 4 other groups: atom Amino group ( 2 ) arboxyl group () R group (varies) 63 Three amino acids with the central carbon in red, the amino group in blue, and the R group shaded in white: henylalanine (he) Tryptophan (Trp) opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display Tyrosine (Tyr) 64 bjective 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 2. The bond between 2 amino acids is called a peptide bond. 6 R R Amino acid Amino acid 2 R R Dipeptide opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display

12 bjective 23c A polypeptide consists of many amino acids joined by peptide bonds to form a long unbranched chain: R R R R R R bjective 23c 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. eptide bond opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display bjective 23c Scientists generally recognize 4 levels of protein structure: 1) rimary structure is the sequence of amino acids in the polypeptide chains that make up a protein e.g. Ala-Gly-Val-Ser-Glu-Val-is- bjective 23c rimary Structure of a protein R R R The primary structure can fold into a pleated sheet, or turn into a helix R 69 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 70 bjective 23c bjective 23c 2) Secondary structure is the regular, repeated pattern of coiling or folding that occurs in certain areas of the polypeptide chain. the two most common patterns are the β-pleated sheet and the α-helix Secondary Structure β-pleated sheet opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. Secondary Structure α-helix

13 bjective 23c 3) Tertiary structure the final overall shape of a protein. roteins can be classified into 2 basic shapes: Globular compact, round shape; these proteins are soluble in 2 Fibrous thin, threadlike shape; these proteins are insoluble in 2 Tertiary Structure bjective 23c 73 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 74 bjective 23c 4) Quaternary structure the way the different polypeptide chains of a protein fit together. nly present in proteins composed of more than one polypeptide chain. Quaternary Structure bjective 23c 7 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 76 rimary Structure R R R The primary structure can fold into a pleated sheet, or turn into a helix Secondary Structure Tertiary Structure R β-pleated sheet Four Levels of rotein Structure Secondary Structure Quaternary Structure α-helix bjective 23c 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 p. In addition, cells have chaperone proteins, which help the polypeptides fold correctly opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 13

14 bjective 23c Interactions that ontribute to a rotein s Shape bjective 23c Interactions that ontribute to a rotein s Shape bjective 23c Interactions that ontribute to a rotein s Shape bjective 23c Interactions that ontribute to a rotein s Shape bjective 23c Interactions that ontribute to a rotein s Shape bjective 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

15 bjective 23d ucleotide- based compounds are composed of subunits called nucleotides. A nucleotide consists of 3 parts: entose ( ) sugar ribose/deoxyribose itrogenous base attached to 1 hosphate group (- 4 ) attached to 8 86 Structure of a ucleotide hosphate group R Sugar itrogenous base opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. in RA in DA 87 bjective 23d There are 2 types of nitrogenous bases: urines have a double ring structure and include adenine (A) and guanine (G). yrimidines have a single ring structure and include cytosine (), thymine (T), and uracil (U). 88 urines yrimidines 2 Adenine 2 ytosine (both DA and RA) itrogenous Bases opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 2 Guanine 3 Thymine (DA only) Uracil (RA only) 89 bjective 23d We will examine 3 groups of nucleotide-based compounds: Adenosine phosphates ucleotide coenzymes ucleic acids 90 1

16 bjective 23d Adenosine phosphates: Ribose + Adenine = Adenosine Adenosine + 1 phosphate = AM (adenosine monophosphate) Adenosine + 2 phosphates = AD (adenosine diphosphate) Adenosine + 3 phosphates = AT (adenosine triphosphate) 91 AT Triphosphate group 2 opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display Ribose itrogenous base (adenine) bjective 23d cam plays an important role as a second messenger. AT 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. bjective 23d ucleotide coenzymes: consist of 2 nucleotides joined by condensation e.g. AD +, FAD, AD + function as electron carriers. They transport e - and + within the cell for use in chemical reactions icotinamide Adenine Dinucleotide Reduction xidation ; Adenine Adenine AD + : xidized form of nicotinamide AD: Reduced form of nicotinamide opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 9 bjective 23d ucleic acids (RA and DA) are polynucleotides. The nucleotides in RA contain the sugar ribose and the bases A, G,, U. The nucleotides in DA contain the sugar deoxyribose and the bases A, G,, T

17 RA: bjective 23d consists of a single, unbranched chain of RA nucleotides. plays several important roles during the process of protein synthesis. 97 end opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. 3 end hosphate group hosphodiester bonds -carbon sugar (ribose) RA itrogenous base (A,,G or U) 98 DA: bjective 23d consists of 2 unbranched chains of DA nucleotides twisted into a double helix. the 2 chains are held together by bonds between the nitogenous bases. A always pairs with T, and G with. functions as the heredity information in all living organisms. 99 DA hosphodiester bond G G T A Sugar-phosphate "backbone" ydrogen bonds between nitrogenous bases opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display. G A T end 3 end

18 DA T G T T A G A Bases ydrogen bonding occurs between base-pairs Deoxyribose-phosphate backbone A T A G DA vs. RA RA Ribose-phosphate A G backbone U A Bases U G opyright The McGraw-ill ompanies, Inc. ermission required for reproduction or display