The Chemical Building Blocks of Life Chapter 3

Carbon Framework of biological molecules consists primarily of carbon bonded to ◦ Carbon ◦ O, N, S, P or H Can form up to 4 covalent bonds Hydrocarbons – molecule consisting only of carbon and hydrogen ◦ Nonpolar ◦ Functional groups add chemical properties 2

3

Isomers Molecules with the same molecular or empirical formula ◦ Structural isomers ◦ Stereoisomers – differ in how groups attached  Enantiomers  mirror image molecules  chiral  D-sugars and L-amino acids 4

Macromolecules Polymer – built by linking monomers Monomer – small, similar chemical subunits 5

Dehydration synthesis ◦ Formation of large molecules by the removal of water ◦ Monomers are joined to form polymers Hydrolysis ◦ Breakdown of large molecules by the addition of water ◦ Polymers are broken down to monomers 6 Making and Breaking Polymers

Carbohydrates Molecules with a 1:2:1 ratio of carbon, hydrogen, oxygen Empirical formula (CH 2 O) n C—H covalent bonds hold much energy ◦ Carbohydrates are good energy storage molecules ◦ Examples: sugars, starch, glucose 7

Monosaccharides Simplest carbohydrate 6 carbon sugars play important roles Glucose C 6 H 12 O 6 Fructose is a structural isomer of glucose Galactose is a stereoisomer of glucose Enzymes that act on different sugars can distinguish structural and stereoisomers of this basic six-carbon skeleton 8

Disaccharides 2 monosaccharides linked together by dehydration synthesis Used for sugar transport or energy storage Examples: sucrose, lactose, maltose 9

Polysaccharides Long chains of monosaccharides ◦ Linked through dehydration synthesis Energy storage ◦ Plants use starch ◦ Animals use glycogen Structural support ◦ Plants use cellulose ◦ Arthropods and fungi use chitin 10

Proteins are polymers ◦ Composed of 1 or more long, unbranched chains ◦ Each chain is a polypeptide Amino acids are monomers Amino acid structure ◦ Central carbon atom ◦ Amino group ◦ Carboxyl group ◦ Single hydrogen ◦ Variable R group 11

Amino acids joined by dehydration synthesis ◦ Peptide bond 12

13 Alanine (Ala) Leucine (Leu) Isoleucine (Ile) Phenylalanine (Phe) Tryptophan (Trp) Tyrosine (Tyr) Glutamine (Gln) Asparagine (Asn) Threonine (Thr) Serine (Ser) Glycine (Gly) Glutamic acid (Glu) Aspartic acid (Asp Histidine (His) Lysine (Lys) Arginine (Arg) Charged Polar uncharged Nonpolar NONAROMATICAROMATIC Valine (Val) CH 3 CC HO CH CC HO CC HO CC HO H C CCCC HO NH C CC HO OH H C CC HO CC HO C NH 2 O CH 2 CCO–O– HO OH C CC HO O H CC HO CC HO C O CC HO NH C CC HO CC HO C N HC NH + CH H CC HO C O CH 3 CH 2 NH 2 CH 3 CH 2 NH 2 H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ O–O– O–O– O–O– O–O– O–O– H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ O–O– O–O– O–O– O–O– O–O– O–O– O–O– CH 2 NH 2 + NH 3 + O–O– HO H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ H3N+H3N+ O–O– O–O– O–O– O–O– O–O– Proline (Pro) CH C NH 2 + O Methionine (Met) CH 2 CCO–O– HO S CH 3 Cysteine (Cys) H3N+H3N+ CCO–O– HO SH SPECIAL FUNCTION CH 2 H3N+H3N+ O–O–

Proteins Protein functions include: 1. Enzyme catalysis 2. Defense 3. Transport 4. Support 5. Motion 6. Regulation 7. Storage 14

4 Levels of structure The shape of a protein determines its function 1. Primary structure – sequence of amino acids 2. Secondary structure – interaction of groups in the peptide backbone ◦ helix ◦ sheet 15

4 Levels of structure 3. Tertiary structure – final folded shape of a globular protein ◦ Stabilized by a number of forces ◦ Final level of structure for proteins consisting of only a single polypeptide chain 4. Quaternary structure – arrangement of individual chains (subunits) in a protein with 2 or more polypeptide chains 16

17

Additional structural characteristics Motifs ◦ Common elements of secondary structure seen in many polypeptides ◦ Useful in determining the function of unknown proteins Domains ◦ Functional units within a larger structure ◦ Most proteins made of multiple domains that perform different parts of the protein’s function 18

19

Chaperones Once thought newly made proteins folded spontaneously Chaperone proteins help protein fold correctly Deficiencies in chaperone proteins implicated in certain diseases ◦ Cystic fibrosis is a hereditary disorder  In some individuals, protein appears to have correct amino acid sequence but fails to fold 20

Denaturation Protein loses structure and function Due to environmental conditions ◦ pH ◦ Temperature ◦ Ionic concentration of solution 21

22 Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the “Normal” or “Slide Sorter” views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at

Nucleic acids Polymer – nucleic acids Monomers – nucleotides ◦ sugar + phosphate + nitrogenous base ◦ sugar is deoxyribose in DNA or ribose in RNA ◦ Nitrogenous bases include  Purines: adenine and guanine  Pyrimidines: thymine, cytosine, uracil ◦ Nucleotides connected by phosphodiester bonds 23

24

Deoxyribonucleic acid (DNA) Encodes information for amino acid sequence of proteins ◦ Sequence of bases Double helix – 2 polynucleotide strands connected by hydrogen bonds ◦ Base-pairing rules  A with T (or U in RNA)  C with G 25

Ribonucleic acid (RNA) RNA similar to DNA except ◦ Contains ribose instead of deoxyribose ◦ Contains uracil instead of thymine Single polynucleotide strand RNA uses information in DNA to specify sequence of amino acids in proteins 26

Other nucleotides ATP adenosine triphosphate ◦ Primary energy currency of the cell NAD + and FAD + ◦ Electron carriers for many cellular reactions 27

Lipids Loosely defined group of molecules with one main chemical characteristic ◦ They are insoluble in water High proportion of nonpolar C—H bonds causes the molecule to be hydrophobic Fats, oils, waxes, and even some vitamins 28

Fats Triglycerides ◦ Composed of 1 glycerol and 3 fatty acids Fatty acids ◦ Need not be identical ◦ Chain length varies ◦ Saturated – no double bonds between carbon atoms  Higher melting point, animal origin ◦ Unsaturated – 1 or more double bonds  Low melting point, plant origin ◦ Trans fats produced industrially 29

30

Phospholipids Composed of ◦ Glycerol ◦ 2 fatty acids – nonpolar “tails” ◦ A phosphate group – polar “head” Form all biological membranes 31

32

Micelles – lipid molecules orient with polar (hydrophilic) head toward water and nonpolar (hydrophobic) tails away from water 33

Phospholipid bilayer – more complicated structure where 2 layers form ◦ Hydrophilic heads point outward ◦ Hydrophobic tails point inward toward each other 34