The Structure and Function of Macromolecules 1 Macromolecules

The Structure and Function of Macromolecules 1

Macromolecules – Are large molecules composed of smaller molecules – Are complex in their structures Figure 5. 1 2

Macromolecules • Most macromolecules are polymers, built from monomers • Four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids – Lipids 3

The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration synthesis HO 1 2 3 H Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO 1 2 H HO 3 H 2 O 4 H Longer polymer Figure 5. 2 A (a) Dehydration reaction in the synthesis of a polymer 4

The Synthesis and Breakdown of Polymers • Polymers can disassemble by – Hydrolysis (addition of water molecules) HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 H H H 2 O HO H Figure 5. 2 B (b) Hydrolysis of a polymer 5

Carbohydrates • Serve as fuel (like glucose/sugars) and building material (like cellulose) and a carbon source, and storage (starch) 6

Sugars • Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers 7

• Examples of monosaccharides Triose sugars Pentose sugars (C 3 H 6 O 3) (C 5 H 10 O 5) Aldoses H C O H O C H C OH H C OH HO C H C OH H Glyceraldehyde H H C OH H HO C H C OH HO C H H C OH H H Glucose Galactose H C OH C O O C OH HO H H C OH Dihydroxyacetone H C OH H H O H H C OH C Ketoses H C Ribose Figure 5. 3 Hexose sugars (C 6 H 12 O 6) Ribulose C H H Fructose 8

• Monosaccharides – May be linear – Can form rings (more common) H H HO H O 1 C 2 6 CH C OH 3 4 H 5 H 6 C C OH OH 2 OH 5 C H OH O H OH 4 C 3 C H 6 CH H 2 C OH H 1 C H O H 5 C H OH 4 C OH 2 OH 3 C H CH 2 OH O H H 1 2 C OH H C OH 6 5 4 HO H OH 3 H O H 1 2 OH OH H 9

• Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage 10

(a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units H forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the HO number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. H (b) Dehydration reaction in the synthesis of HO sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. CH 2 OH O H OH HO H OH H 2 O CH 2 OH H H OH Glucose CH 2 OH HO H 2 O O H H OHOH H HO O H OH H H OH CH 2 OH H 1– 4 1 glycosidic linkage HO OH H Fructose O H OH OH Maltose H H 4 O CH 2 OH O H OH Glucose O H OH CH 2 OH H HO O H OH H H 1– 2 H glycosidic 1 linkage O CH 2 OH O 2 H HO H CH 2 OH OH Sucrose Figure 5. 5 11

Polysaccharides • Polysaccharides – Are polymers of sugars – Serve many roles in organisms such as storage of glucose and for structure 12

Storage Polysaccharides Chloroplast • Starch – Is a polymer consisting entirely of glucose monomers – Is the major storage form of glucose in plants (like in peas) Starch 1 m Amylose Amylopectin Figure 5. 6(a) Starch: a plant polysaccharide 13

• Glycogen - a storage polysaccharide – Consists of glucose monomers – Is the major storage form of glucose in animals (like in us) Mitochondria Giycogen granules 0. 5 m Glycogen Figure 5. 6 (b) Glycogen: an animal polysaccharide 14

– Cellulose - structural polysaccharide – major component of the tough walls that enclose plant cells Microfibril Cell walls Cellulose microfibrils in a plant cell wall About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0. 5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. Figure 5. 8 OH CH 2 OH O O OH OH O O O CH OH OH CH 2 OH 2 H CH 2 OH OH O O O CH OH OH CH 2 2 OH H CH 2 OH OH OH CH 2 OH O O OH OH OH O O O O CH OH OH CH 2 OH 2 H Glucose monomer Cellulose molecules A cellulose molecule is an unbranched glucose polymer. 15

• Cellulose (also known as dietary fiber) is difficult to digest – Cows have microbes in their stomachs to facilitate this process – Fiber stimulates our digestive tract to make mucus and keep things moving along Figure 5. 9 16

Lipids • Lipids are a diverse group of hydrophobic molecules (water hating) • The nonpolar bond between Carbon and Hydrogen make the molecules nonpolar • These are fats, oils, waxes, phospholipids, and steroids. • Biological functioning: part of membranes, energy storage, cell signaling, vitamins A, D, E, and K are fat soluble and stored in adipose (fatty tissue) 17

Fats – Are constructed of a single glycerol and usually three fatty acids (sometimes called triglycerides) – Vary in the length and number and locations of double bonds they contain 18

• Saturated fats (saturated fatty acids) – Saturated with hydrogens – Have no carbon-carbon double bonds Stearic acid (a) Saturated fat and fatty acid Figure 5. 12 19

• Unsaturated fats (oils) – Have one or more carbon-carbon double bonds (Omega 3 and Omega 6) Oleic acid cis double bond (b) Unsaturated fat and fatty acid causes bending Figure 5. 12 20

Trans fats are fats that have a double bond on the trans side of the molecule (meaning that the hydrogens are on opposite sides) – Cis Fat Trans fat

Hydrophobic tails Hydrophilic head • Phospholipids – Consists of a hydrophilic “head” and 2 hydrophobic “tails” C H 2 CH 2 O O P O– O C C CH H H 2 O C OC O Figure 5. 13(a) Structural formula +N(CH Choline 3)3 Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol 22

• The structure of phospholipids – Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail Figure 5. 14 23

• Steroids (like cholesterol) are lipids with a four carbon ring – Many hormones are synthesized from cholesterol in our liver H 3 C CH 3 Figure 5. 15 HO 24

Proteins • Proteins have many structures, resulting in a wide range of functions • Proteins do most of the work in cells and act as enzymes • Proteins are made of monomers called amino acids 25

• An overview of protein functions Table 5. 1 26

• Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H 2 O Fructose H O 4 Products are released. Figure 5. 16 3 Substrate is converted to products. 27

Polypeptides • Polypeptides – Are polymers (chains) of amino acids joined by peptide bonds – Amino acid polypeptide protein 28

• Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups 29

Twenty Amino Acids • 20 different amino acids make up proteins CH 3 H H 3 N+ C CH 3 O H 3 N+ C H Glycine (Gly) O– C H 3 N+ C H Alanine (Ala) O– CH CH 3 O C CH 2 O H 3 N+ C H Valine (Val) CH 3 O– C CH 2 O C H Leucine (Leu) H 3 C H 3 N+ O– CH C O C H Isoleucine (Ile) O– Nonpolar CH 3 CH 2 S NH CH 2 H 3 N+ C H H 3 N+ C O– Methionine (Met) Figure 5. 17 CH 2 O C H CH 2 O C O– Phenylalanine (Phe) H 3 N+ C H O C H 2 C CH 2 N C O C H O– Tryptophan (Trp) Proline (Pro) 30 O–

OH OH Polar CH 2 H 3 N+ C CH O C H O– Serine (Ser) H 3 N+ C O– H CH 2 H 3 N+ C H CH 2 O C O– C H 3 N+ O C H O– H 3 N+ Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) Electrically charged H 3 N+ CH 2 O CH 2 C H 3 N+ O– C H O NH 3+ NH 2 C C CH 2 CH 2 C O C H O– CH 2 H 3 N+ C H Aspartic acid (Asp) C O C H O– Glutamine (Gln) Basic O– O CH 2 Asparagine (Asn) Acidic –O C NH 2 O C SH CH 3 OH NH 2 O Glutamic acid (Glu) O– Lysine (Lys) NH 2+ H 3 N+ CH 2 O C NH+ CH 2 H 3 N+ C H NH CH 2 O C C O– H O C O– Arginine (Arg) Histidine (His) 31

Amino Acid Polymers • Amino acids – Are linked by peptide bonds 32

Protein Conformation and Function • A protein’s specific conformation (shape) determines how it functions 33

Four Levels of Protein Structure • Primary structure +H – Is the unique sequence of amino acids in a polypeptide 3 N Amino end Gly Pro. Thr. Gly Thr Amino acid subunits Gly Glu Cys Lys. Seu Leu. Pro Met Val Lys Val Leu Asp Ala. Val Arg. Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Lys Trp. Tyr Leu Ala Gly lle Ser Pro Phe. His Glu His Ala. Thr. Phe. Val Asn Glu Val Thr Asp Tyr Arg Ser Arg Gly Pro lle Ala Leu Ser Pro Ser. Tyr Ser Thr Ala Val Glu Thr. Asn. Pro. Lys Figure 5. 20 o c – o Carboxyl end 34

• Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the helix and the pleated sheet – Folding is due to several things (ex. Affinity for oxygen) pleated sheet Amino acid subunits O H H C C N H R R R O C C R N H C H R O C N H N H O C H C R N H O C O C H C O N H N C C H R R H Figure 5. 20 C O H H R C C N N C C R R C C R O H H OH H O R O C H H N HC N H C N C H H C O R R C H O C H H NH C N C H C O R R H C N H O C H helix 35

• Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups Hyrdogen bond CH 2 O H 3 C CH CH 3 H 3 C CH 3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH 2 S S CH 2 Disulfide bridge O CH 2 NH 3+-O C CH 2 Ionic bond 36

• Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptid e chain Collage n Chains Iron Heme Chains Hemoglobin 37

Review of Protein Structure +H 3 N Amino end Amino acid subunits helix 38

Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease – Results from a single amino acid substitution in the protein hemoglobin 39

Primary structure Normal hemoglobin Val His Leu Thr Pro Glul Glu 1 2 3 4 5 6 7 Secondary and tertiary structures Red blood cell shape Figure 5. 21 Val His Leu Thr Pro Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Val Glu structure 1 2 3 4 5 6 7 Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Function Sickle-cell hemoglobin . . . Primary Quaternary structure Function 10 m . . . Exposed hydrophobic region subunit 10 m Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Red blood cell shape Fibers of abnormal hemoglobin deform cell into sickle shape. 40

What Determines Protein Conformation? • Protein conformation Depends on the physical and chemical conditions of the protein’s environment • Temperature, p. H, etc. affect protein structure 41

• Denaturation is when a protein unravels and loses its native conformation (shape) Denaturation Normal protein Figure 5. 22 Denatured protein Renaturation 42

The Protein-Folding Problem • Most proteins – Probably go through several intermediate states on their way to a stable conformation – Denaturated proteins no longer work in their unfolded condition – Proteins may be denaturated by extreme changes in p. H or temperature 43

• Chaperonins – Are protein molecules that assist in the proper folding of other proteins Cap Polypeptide Correctly folded protein Hollow cylinder Steps of Chaperonin (fully assembled) Action: An unfolded poly 1 peptide enters the cylinder from one Figure 5. 23 end. The cap comes off, and the cylinder to change shape in properly such a way that it creates a folded protein is hydrophilic environment for released. the folding of the polypeptide. 2 The cap attaches, causing 3 44

• X-ray crystallography – Is used to determine a protein’s threedimensional structure X-ray diffraction pattern Photographic film Diffracted Xrays X-ray beam source Crystal Nucleic acid Protein Figure 5. 24 (b) 3 D computer model (a) X-ray diffraction pattern 45

Nucleic Acids • Nucleic acids store and transmit hereditary information • Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleotide sequences on DNA 46

The Roles of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) 47

Deoxyribonucleic Acid • DNA – Stores information for the synthesis of specific proteins – Found in the nucleus of cells 48

DNA Functions – Directs RNA synthesis (transcription) – Directs protein synthesis through RNA DNA (translation) 1 Synthesis of m. RNA in the nucleus NUCLEUS 2 Movement of m. RNA into cytoplasm via nuclear pore m. RNA CYTOPLASM m. RNA Ribosome 3 Synthesis of protein Figure 5. 25 Polypeptide Amino acids 49

The Structure of Nucleic Acids 5’ end • Nucleic acids – Exist as polymers called polynucleotides 5’C O 3’C O O 5’C O 3’C (a) Polynucleotide, or nucleic acid Figure 5. 26 OH 3’ end 50

• Each polynucleotide – Consists of monomers called nucleotides – Sugar + phosphate + nitrogen base Nucleoside Nitrogenous base O O P 5’C O CH 2 O O Phosphate group Figure 5. 26 3’C Pentose sugar (b) Nucleotide 51

Nucleotide Monomers • Nucleotide monomers Nitrogenous bases Pyrimidines NH 2 O O C C CH C 3 N CH C CH HN HN CH CH C CH N N O O H H H Cytosine Thymine (in DNA)Uracil (in. RNA) Uracil (in U C U T – Are made up of nucleosides (sugar + base) and phosphate groups Purines O NH 2 N C C NH N HC HC C CH N C N NH 2 N N H H Adenine Guanine A G 5” Pentose sugars HOCH 2 O 4’ OH H H 1’ 5” HOCH 2 O OH 4’ H H 1’ H H H 3’ 2’ OH H OH OH Deoxyribose (in DNA) Ribose (in RNA) Figure 5. 26 (c) Nucleoside components 52

Nucleotide Polymers • Nucleotide polymers – Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next 53

Gene • The sequence of bases along a nucleotide polymer – Is unique for each gene 54

The DNA Double Helix • Cellular DNA molecules – Have two polynucleotides that spiral around an imaginary axis – Form a double helix 55

• The DNA double helix – Consists of two antiparallel nucleotide strands 5’ end 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands A 3’ end Nucleotide about to be added to a new strand 5’ end 3’ end Figure 5. 27 5’ end New strands 3’ end 56

A, T, C, G • The nitrogenous bases in DNA – Form hydrogen bonds in a complementary fashion (A with T only, and C with G only) 57

DNA and Proteins as Tape Measures of Evolution • Molecular comparisons – Help biologists sort out the evolutionary connections among species 58

The Theme of Emergent Properties in the Chemistry of Life: A Review • Higher levels of organization – Result in the emergence of new properties • Organization – Is the key to the chemistry of life 59