The Structure and Function of Macromolecules Chapter 5 The Structure and Function of Macromolecules

The Molecules of Life Overview: Another level in the hierarchy of biological organization is reached when small organic molecules are joined together Atom ---> molecule --- compound

Macromolecules Are large molecules composed of smaller molecules Are complex in their structures Figure 5.1

Macromolecules Most macromolecules are polymers, built from monomers Monomer- small compound, subunit that serves as building block for polymer Polymer- long molecule made up of more than one monomer bonded together

The Synthesis and Breakdown of Polymers Monomers form larger molecules by condensation reactions called dehydration synthesis (a) Dehydration reaction in the synthesis of a polymer HO H 1 2 3 4 H2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond Figure 5.2A

Condensation Reaction C6H12O6 + C6H12O6 + C6H12O6 Remember that each time monomers link a water is released.

The Synthesis and Breakdown of Polymers Polymers can disassemble by Hydrolysis (addition of water molecules) (b) Hydrolysis of a polymer HO 1 2 3 H 4 H2O Hydrolysis adds a water molecule, breaking a bond Figure 5.2B

Hydrolysis Reaction C18H32O16 + __ H2O Remember that in a hydrolysis reaction, water is used to break down a polymer.

Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers An immense variety of polymers can be built from a small set of monomers

Macromolecules Carbohydrates Proteins Nucleic acids Lipids Four classes of large biological molecules are: Carbohydrates Proteins Nucleic acids Lipids

Carbohydrates Serve as fuel and building material Include both sugars and their polymers (starch, cellulose, etc.)

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

Examples of monosaccharides Triose sugars (C3H6O3) Pentose sugars (C5H10O5) Hexose sugars (C6H12O6) H C OH H C OH HO C H H C OH C O HO C H H C O Aldoses Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Ketoses Fructose Figure 5.3

Monosaccharides May be linear Can form rings 4C 3 2 OH Figure 5.4 H C OH HO C H H C O C 1 2 3 4 5 6 OH 4C 6CH2OH 5C H OH 2 C 1C 3 C 2C 1 C CH2OH HO 3 2 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. Figure 5.4

Disaccharides Consist of two monosaccharides Are joined by a glycosidic linkage

Figure 5.5 CH2OH O H H OH HO OH H2O Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. (a) (b) H HO H OH OH O CH2OH H2O 1 2 4 1– 4 glycosidic linkage 1–2 glycosidic linkage Glucose Fructose Maltose Sucrose Figure 5.5

Polysaccharides Polysaccharides Are polymers of sugars Serve many roles in organisms

Storage Polysaccharides Chloroplast Starch Amylose Amylopectin 1 m (a) Starch: a plant polysaccharide Figure 5.6 Starch Is a polymer consisting entirely of glucose monomers Is the major storage form of glucose in plants

(b) Glycogen: an animal polysaccharide Consists of glucose monomers Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m (b) Glycogen: an animal polysaccharide Glycogen Figure 5.6

Structural Polysaccharides Cellulose Is a polymer of glucose

Has different glycosidic linkages than starch (c) Cellulose: 1– 4 linkage of  glucose monomers H O CH2OH OH HO 4 C 1 (a)  and  glucose ring structures (b) Starch: 1– 4 linkage of  glucose monomers  glucose  glucose Figure 5.7 A–C

Is a major component of the tough walls that enclose plant cells Cell walls Cellulose microfibrils in a plant cell wall  Microfibril CH2OH OH O Glucose monomer Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. A cellulose molecule is an unbranched  glucose polymer. Cellulose molecules Figure 5.8

Cellulose is difficult to digest Cows have microbes in their stomachs to facilitate this process Figure 5.9

Chitin, another important structural polysaccharide Is found in the exoskeleton of arthropods Can be used as surgical thread (a) The structure of the chitin monomer. O CH2OH OH H NH C CH3 (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Figure 5.10 A–C

Lipids Lipids are a diverse group of hydrophobic molecules Lipids Are the one class of large biological molecules that do not consist of polymers Share the common trait of being hydrophobic

Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Vary in the length and number and locations of double bonds they contain

Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Vary in the length and number and locations of double bonds they contain

Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids

Fats Vary in the length and number and locations of double bonds they contain

(a) Saturated fat and fatty acid Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds (a) Saturated fat and fatty acid Stearic acid Figure 5.12

(b) Unsaturated fat and fatty acid Unsaturated fatty acids Have one or more double bonds (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12

Phospholipids Have only two fatty acids Have a phosphate group instead of a third fatty acid

(a) Structural formula (b) Space-filling model Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails” CH2 O P CH C Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails – Hydrophilic head Choline + Figure 5.13 N(CH3)3

The structure of phospholipids Results in a bilayer arrangement found in cell membranes Hydrophilic head WATER Hydrophobic tail Figure 5.14

Steroids Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings

One steroid, cholesterol Is found in cell membranes Is a precursor for some hormones HO CH3 H3C Figure 5.15

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

An overview of protein functions Table 5.1

Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 2 4 Products are released. Figure 5.16

Polypeptides Polypeptides A protein Are polymers (chains) of amino acids A protein Consists of one or more polypeptides

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

Twenty Amino Acids 20 different amino acids make up proteins H H3N+ C CH3 CH CH2 NH H2C H2N Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) H3C Figure 5.17 S 20 different amino acids make up proteins

Polar Electrically charged OH CH2 C H H3N+ O CH3 CH SH NH2 Polar Electrically charged –O NH3+ NH2+ NH+ NH Serine (Ser) Threonine (Thr) Cysteine (Cys) Tyrosine (Tyr) Asparagine (Asn) Glutamine (Gln) Acidic Basic Aspartic acid (Asp) Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acid Polymers Amino acids Are linked by peptide bonds

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

Four Levels of Protein Structure Primary structure Is the unique sequence of amino acids in a polypeptide Figure 5.20 – Amino acid subunits +H3N Amino end o Carboxyl end c Gly Pro Thr Glu Seu Lys Cys Leu Met Val Asp Ala Arg Ser lle Phe His Asn Tyr Trp Lle

Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the  helix and the  pleated sheet O C  helix  pleated sheet Amino acid subunits N H R H Figure 5.20

Is the overall three-dimensional shape of a polypeptide Tertiary structure Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups CH2 CH O H O C HO NH3+ -O S CH3 H3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond Disulfide bridge

Quaternary structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

Review of Protein Structure +H3N Amino end Amino acid subunits helix

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

Sickle-cell hemoglobin Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin A Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen   10 m Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.  subunit 1 2 3 4 5 6 7 Normal hemoglobin Sickle-cell hemoglobin . . . Figure 5.21 Exposed hydrophobic region Val Thr His Leu Pro Glul Glu Fibers of abnormal hemoglobin deform cell into sickle shape.

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

Denaturation is when a protein unravels and loses its native conformation (shape) Renaturation Denatured protein Normal protein Figure 5.22

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 pH or temperature

Chaperonins Are protein molecules that assist in the proper folding of other proteins Hollow cylinder Cap Chaperonin (fully assembled) Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein Polypeptide 2 1 3 Figure 5.23

X-ray crystallography Is used to determine a protein’s three-dimensional structure X-ray diffraction pattern Photographic film Diffracted X-rays X-ray source X-ray beam Crystal Nucleic acid Protein (a) X-ray diffraction pattern (b) 3D computer model Figure 5.24

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

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

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

Synthesis of mRNA in the nucleus DNA Functions Directs RNA synthesis (transcription) Directs protein synthesis through RNA (translation) 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide Figure 5.25

The Structure of Nucleic Acids 5’ end 5’C 3’ end OH Figure 5.26 O Nucleic acids Exist as polymers called polynucleotides (a) Polynucleotide, or nucleic acid

Each polynucleotide Consists of monomers called nucleotides Sugar + phosphate + nitrogen base Nitrogenous base Nucleoside O O O P CH2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide Figure 5.26

(c) Nucleoside components Nucleotide Monomers Nucleotide monomers Are made up of nucleosides (sugar + base) and phosphate groups CH Uracil (in RNA) U Ribose (in RNA) Nitrogenous bases Pyrimidines C N O H NH2 HN CH3 Cytosine Thymine (in DNA) T HC NH Adenine A Guanine G Purines HOCH2 OH Pentose sugars Deoxyribose (in DNA) 4’ 5” 3’ 2’ 1’ Figure 5.26 (c) Nucleoside components

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

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

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

The DNA double helix Consists of two antiparallel nucleotide strands 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand A 5’ end New strands Figure 5.27

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)

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

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