The Structure and Function of Large Biological Molecules

Chapter 5 The Structure and Function of Large Biological Molecules PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp

Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: Carbohydrates Lipids Proteins nucleic acids Within cells, small organic molecules are joined together to form larger molecules Macromolecules are large molecules composed of thousands of covalently connected atoms Molecular structure and function are inseparable

Fig. 5-1 Why do scientists study the structures of macromolecules? The architecture of a biological molecule helps explain how that molecule works

Concepts in this Chapter 1. Macromolecules are polymers, built from monomers 2. Carbohydrates serves as fuel and building material 3. Lipids are a diverse group of hydrophobic molecules 4. Proteins have many structures, resulting in a wide range of functions 5. Nucleic acids store and transmit hereditary information

CONCEPT 5.1 MACROMOLECULES ARE POLYMERS, BUILT FROM MONOMERS

Concept 5.1: Macromolecules are polymers, built from monomers Polymer A long molecule consisting of many similar building blocks These small building-block molecules are called monomers Three of the four classes of life s organic molecules are polymers: Carbohydrates Proteins Nucleic acids

The Synthesis and Breakdown of Polymers Monomers are connected together by a condensation reaction or more specifically a dehydration reaction occurs when two monomers bond together through the loss of a water molecule Enzymes are macromolecules that speed up the dehydration process

Dehydration reaction HO 1 2 3 H HO H Short polymer Dehydration removes a water molecule, forming a new bond Unlinked monomer H 2 O HO 1 2 3 4 H (a) Longer polymer Dehydration reaction in the synthesis of a polymer

Hydrolysis Polymers are disassembled to monomers by hydrolysis a reaction that is essentially the reverse of the dehydration reaction

HO 1 2 3 4 H Hydrolysis adds a water molecule, breaking a bond H 2 O HO 1 2 3 H HO H (b) Hydrolysis of a polymer

The Synthesis and Breakdown of Polymers Animation: Polymers

The Diversity of Polymers Each cell has thousands of different kinds of macromolecules 2 3 H HO Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species An immense variety of polymers can be built from a small set of monomers

SUMMARY Macromolecules are polymers, built from monomers Polymer A long molecule consisting of many similar building blocks called Monomer Small building blocks that make polymers Dehydration reaction The process by which two monomers are bonded Why called dehydration? Hydrolysis 2 3 H HO The reaction that disassembles polymers

CONCEPT 5.2 CARBOHYDRATES SERVE AS FUEL AND BUILDING MATERIAL

Concept 5.2: Carbohydrates serve as fuel and building material Carbohydrates include sugars and the polymers of sugars Monosaccharides The simplest carbohydrates simple sugars Disaccharides two monosaccharides joined by a covalent bond Polysaccharides polymers composed of many sugar building blocks macromolecules

Sugars Monosaccharides have molecular formulas that are usually multiples of CH 2 O Glucose (C 6 H 12 O 6 ) is the most common monosaccharide Trademarks of sugars Carbonyl group Multiple OH groups Glucose

Sugars Monosaccharides are classified by: 1. The location of the carbonyl group aldose or ketose 2. The number of carbons in the carbon skeleton 3-7 carbons long Trioses (C 3 H 6 O 3 ) Hexoses (C 6 H 12 O 6 ) Glyceraldehyde Fructose

Fig. 5-3a Trioses (C 3 H 6 O 3 ) Pentoses (C 5 H 10 O 5 ) Hexoses (C 6 H 12 O 6 ) Glyceraldehyde Ribose Glucose Galactose

Fig. 5-3b Trioses (C 3 H 6 O 3 ) Pentoses (C 5 H 10 O 5 ) Hexoses (C 6 H 12 O 6 ) Dihydroxyacetone Ribulose Fructose

Sugars Many sugars form rings in aqueous solutions Monosaccharides serve as a major fuel for cells Carbon skeletons- raw material for building molecules Amino acids and fats Disaccharides or polysaccharides Amino acids and fats

Sugars Many sugars form rings in aqueous solutions (a) Linear and ring forms

Fig. 5-4b (b) Abbreviated ring structure

Disaccharides A disaccharide is formed when a dehydration reaction joins two monosaccharides Dehydration reaction? This covalent bond is called a glycosidic linkage Examples Maltose 2 glucose; brewing beer Sucrose glucose+ fructose; table sugar; plants Lactose Glucose+ galactose; milk sugar

Dehydration reaction in the synthesis of maltose 1 4 glycosidic linkage Glucose Glucose Maltose

Dehydration reaction in the synthesis of sucrose 1 2 glycosidic linkage Glucose Fructose Sucrose (b) Dehydration reaction in the synthesis of sucrose

Disaccharides Animation: Disaccharides

Polysaccharides Polysaccharides Macromolecules A few to thousands of monosaccharides joined by glycosidic linkages Have storage and structural roles Polymer structure and function of a polysaccharide determined by its sugar monomers the positions of glycosidic linkages

Storage Polysaccharides Starch plants Glycogen animals

Starch Starch a storage polysaccharide of plants consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids Synthesizing starch enables plants to stockpile surplus glucose Starch represents stored energy Most animals have enzymes that can hydrolyze starch Sources- potatoes, wheat, corn, rice, etc

Fig. 5-6 Chloroplast Starch 1 µm Amylose Amylopectin (a) Starch: a plant polysaccharide

Glycogen Glycogen a storage polysaccharide in animals stored mainly in liver and muscle cells Hydrolysis of glycogen releases glucose when the demand for sugar increases Cannot sustain animals long Depleted within a day in humans Need to consume food to replace

Mitochondria Glycogen granules 0.5 µm Glycogen (b) Glycogen: an animal polysaccharide

Structural Polysaccharides Cellulose Chitin Animation: Polysaccharides

Structural Polysaccharides Cellulose the most abundant organic compound on Earth a major component of the tough wall of plant cells a polymer of glucose, but the glycosidic linkages differ from starch The difference is based on two ring forms for glucose: alpha ( ) and beta ( )

Fig. 5-7a α Glucose β Glucose (a) α and β glucose ring structures

Fig. 5-7bc (b) Starch: 1 4 linkage of α glucose monomers (c) Cellulose: 1 4 linkage of β glucose monomers

Structural Polysaccharides CELLULOSE Polymers with glucose are helical Polymers with glucose are straight H atoms on one strand can bond with OH groups on other strands Cellulose is never branched Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants

Fig. 5-8 Cell walls Cellulose microfibrils in a plant cell wall Microfibril 10 µm 0.5 µm Cellulose molecules b Glucose monomer

Structural Polysaccharides CELLULOSE Enzymes that digest starch by hydrolyzing linkages can t hydrolyze linkages in cellulose Cellulose in human food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose Many herbivores, from cows to termites, have symbiotic relationships with these microbes

Fig. 5-9

Structural Polysaccharides- CHITIN Chitin found in the exoskeleton of arthropods Also provides structural support for the cell walls of many fungi Has a nitrogen-containing appendage

Fig. 5-10 (a) The structure (b) Chitin forms the (c) of the chitin exoskeleton of monomer. arthropods. Chitin is used to make a strong and flexible surgical thread.

Summary- Carbohydrates Starch Polymer of glucose In plants Glycogen Polymer of glucose In animals Extensively branched Cellulose Structural polysaccharide; plant cell walls Can t be digested by humans Some prokaryotes can Straight and unbranched Chitin

Summary- Carbohydrates Carbohydrates Sugars and polymers of sugars Monosaccharides, disaccharides and polysaccahrides What bond joins sugar molecules? Glycosidic linkage Monosaccharides classified by Location of carbonly group Length of carbon skeleton Polysaccharides Storage (starch, glycogen) or structural (cellulose, chitin)

CONCEPT 5.3 LIPIDS ARE A DIVERSE GROUP OF HYDROPHOBIC MOLECULES

Concept 5.3: Lipids are a diverse group of hydrophobic molecules Lipids Large biological molecules do not form polymers unifying feature of lipids - hydrophobic Consist mostly of hydrocarbons which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids steroids

Fats Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid a carboxyl group attached to a long carbon skeleton

Fig. 5-11a Glycerol- a three-carbon alcohol with a hydroxyl group attached to each carbon

Fig. 5-11a Fatty acid- a carboxyl group attached to a long carbon skeleton Fatty acid (palmitic acid)

Fig. 5-11a Fatty acid (palmitic acid) Glycerol (a) Dehydration reaction in the synthesis of a fat

Ester linkage (b) Fat molecule (triacylglycerol) In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride

Fats Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats Fatty acids vary in length (number of carbons) the number and locations of double bonds Saturated fatty acids the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids one or more double bonds Animation: Fats

Fig. 5-12a Structural formula of a saturated fat molecule Stearic acid, a saturated fatty acid (a) Saturated fat

Fig. 5-12b Structural formula of an unsaturated fat molecule Oleic acid, an unsaturated fatty acid (b) Unsaturated fat cis double bond causes bending

Fats Fats made from saturated fatty acids are called saturated fats solid at room temperature Most animal fats are saturated Fats made from unsaturated fatty acids are called unsaturated fats or oils liquid at room temperature Plant fats and fish fats are usually unsaturated

Fats A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen Hydrogenating vegetable oils creates unsaturated fats with trans double bonds These trans fats may contribute more than saturated fats to cardiovascular disease

Function of Fats Major function- energy storage Hydrocarbon chains 1g of fat= 2X energy of 1g of polysaccahride Humans and other mammals store their fat in adipose cells Compact reservoir Swell and shrink as fat is deposited and withdrawn Adipose tissue also cushions vital organs insulates the body Thick in whales and other marine mammals

Phospholipids Phospholipids Make up cell membranes Similar to fat molecule BUT two fatty acids- hydrophobic a phosphate group- negative charge, polar, hydrophilic attached to glycerol In water, self assemble in double-layered aggregates that shield hydrophobic tails from water Boundary between cell and external environment Cells could not exist without phospholipids

Fig. 5-13 Hydrophobic tails Hydrophilic head Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol

Fig. 5-14 Hydrophilic head WATER Hydrophobic tail WATER

Steroids Steroids characterized by a carbon skeleton consisting of four fused rings Cholesterol an important steroid component in animal cell membranes Precursor from which other steroids synthesized Liver in verterbrates Many hormones- produced from cholesterol Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease

Fig. 5-15

Video

Summary- LIPIDS Lipids Large molecules, do not form polymers Three kinds Fats, phospholipids and steroids Fats Composed of three fatty acids attached to glycerol via ester linkage Glycerol- a 3-carbon alcohol with -OH groups attached to a carbon Fatty acids- carboxyl group attached to a long carbon skeleton Saturated vs unsaturated fats Saturated- no double bonds, solid Unsaturated- double bonds, liquids

Summary- LIPIDS Functions of fats Energy storage Protect organs Insulate body Phospholipids 2 fatty acids, phosphate group, glycerol Component of cell membranes Polarity? Steroids Carbon skeleton with four fused rings Cholesterol- precursor for hormones

CONCEPT 5.4 PROTEINS HAVE MANY STRUCTURES, RESULTING IN A WIDE RANGE OF FUNCTIONS

Concept 5.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include structural support, storage transport cellular communications movement defense against foreign substances

Table 5-1

Animation: Structural Proteins Animation: Storage Proteins Animation: Transport Proteins Animation: Receptor Proteins Animation: Contractile Proteins Animation: Defensive Proteins Animation: Hormonal Proteins Animation: Sensory Proteins Animation: Gene Regulatory Proteins

Enzymes Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Animation: Enzymes

Fig. 5-16 Substrate (sucrose) Glucose OH Fructose H O Enzyme (sucrase) H 2 O

Polypeptides Polypeptides polymers built from the same set of 20 amino acids A protein consists of one or more polypeptides

Amino Acid Monomers Amino acids organic molecules with carboxyl and amino groups Differing side chains (R groups) confer different properties Three main groups Nonpolar Polar charged

Fig. 5-UN1 α carbon Amino group Carboxyl group

Fig. 5-17a Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or ) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P)

Fig. 5-17b Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q)

Fig. 5-17c Electrically charged Acidic Basic Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

Amino Acid Polymers Amino acids are linked by peptide bonds to make polypeptide chains Formed by dehydration reactions Link the carboxyl group of one amino acid to the amino group of the next Polypeptide a polymer of amino acids range in length from a few to more than a thousand monomers each has a unique linear sequence of amino acids

Fig. 5-18 Peptide bond (a) Peptide bond Side chains Backbone (b) Amino end (N-terminus) Carboxyl end (C-terminus)

Protein Structure and Function Functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Groove Groove (a) A ribbon model of lysozyme (b) A space-filling model of lysozyme

Protein Structure The sequence of amino acids determines a protein s three-dimensional structure A protein s structure determines its function

Fig. 5-20 Antibody protein Protein from flu virus

Four Levels of Protein Structure Primary structure The unique sequence of amino acids of a protein Like the order of letters in a long word Determined by inherited genetic information Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure determined by interactions among various side chains (R groups) Quaternary structure results when a protein consists of multiple polypeptide chains Animation: Protein Structure Introduction

Primary Structure The sequence of amino acids in a protein, Like the order of letters in a long word Determined by inherited genetic information Animation: Primary Protein Structure

Fig. 5-21a Primary Structure 1 + H 3 N Amino end 5 10 15 Amino acid subunits 20 25

15 1 + H 3 N Amino end 20 10 5 Amino acid subunits 25 Transthyretin found in blood transports vitamin A and one of the thyroid hormones throughout the body Composed of 127 aa 75 80 85 90 95 100 105 110 115 120 125 Carboxyl end

Secondary Structure The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures a coil called an helix a folded structure called a pleated sheet Animation: Secondary Protein Structure

Fig. 5-21c Secondary Structure β pleated sheet Examples of amino acid subunits α helix

Fig. 5-21d Abdominal glands of the spider secrete silk fibers made of a structural protein containing pleated sheets. The radiating strands, made of dry silk fibers, maintain the shape of the web. The spiral strands (capture strands) are elastic, stretching in response to wind, rain, and the touch of insects.

Tertiary Structure Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions include hydrogen bonds, ionic bonds, hydrophobic interactions van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein s structure Animation: Tertiary Protein Structure

Quaternary Structure Quaternary structure results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Animation: Quaternary Protein Structure

Fig. 5-21e Tertiary Structure Quaternary Structure

Sickle-Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a protein s structure and ability to function Sickle-cell disease, an inherited blood disorder results from a single amino acid substitution in the protein hemoglobin

Fig. 5-22a Primary structure Normal hemoglobin Val His Leu Thr Pro Glu Glu 1 2 3 4 5 6 7 Secondary and tertiary structures subunit Quaternary structure Normal hemoglobin (top view) Function Molecules do not associate with one another; each carries oxygen.

Fig. 5-22b Primary structure Sickle-cell hemoglobin Val His Leu Thr Pro Val Glu 1 2 3 4 5 6 7 Secondary and tertiary structures Exposed hydrophobic region subunit Quaternary structure Sickle-cell hemoglobin Function Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.

Fig. 5-22c 10 µm 10 µm Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen. Fibers of abnormal hemoglobin deform red blood cell into sickle shape.

What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can also affect structure Alterations in ph, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein s native structure is called denaturation A denatured protein is biologically inactive

Fig. 5-23 Denaturation Normal protein Renaturation Denatured protein

Protein Folding in the Cell It is hard to predict a protein s structure from its primary structure Most proteins probably go through several states on their way to a stable structure Chaperonins are protein molecules that assist the proper folding of other proteins

Fig. 5-24 Cap Polypeptide Correctly folded protein Hollow cylinder Chaperonin (fully assembled) Steps of Chaperonin Action: 1 An unfolded polypeptide enters the cylinder from one end. 2 The cap attaches, causing the 3 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.

Scientists use X-ray crystallography to determine a protein s structure Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization Bioinformatics uses computer programs to predict protein structure from amino acid sequences

Fig. 5-25 EXPERIMENT X-ray source X-ray beam Diffracted X-rays Crystal Digital detector X-ray diffraction pattern RESULTS RNA polymerase DNA RNA

CONCEPT 5.5 NUCLEIC ACIDS STORE AND TRANSMIT HEREDITARY INFORMATION

Concept 5.5: Nucleic acids store and transmit hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid

The Roles of Nucleic Acids There are two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mrna) and, through mrna, controls protein synthesis Protein synthesis occurs in ribosomes

Fig. 5-26-1 DNA 1 Synthesis of mrna in the nucleus mrna NUCLEUS CYTOPLASM

Fig. 5-26-2 DNA 1 Synthesis of mrna in the nucleus mrna NUCLEUS CYTOPLASM 2 Movement of mrna into cytoplasm via nuclear pore mrna

Fig. 5-26-3 DNA 1 Synthesis of mrna in the nucleus mrna NUCLEUS CYTOPLASM 2 Movement of mrna into cytoplasm via nuclear pore mrna Ribosome 3 Synthesis of protein Polypeptide Amino acids

The Structure of Nucleic Acids Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of nitrogenous base a pentose sugar a phosphate group Nucleoside The portion of a nucleotide without the phosphate group

Fig. 5-27ab 5' end 5'C 3'C Nucleoside Nitrogenous base 5'C 5'C 3'C Phosphate group (b) Nucleotide 3'C Sugar (pentose) 3' end (a) Polynucleotide, or nucleic acid

Fig. 5-27c-1 Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) Guanine (G) (c) Nucleoside components: nitrogenous bases

Fig. 5-27c-2 Sugars Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components: sugars

Nucleotide Monomers Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases: Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose Nucleotide = nucleoside + phosphate group

Nucleotide Polymers Nucleotide polymers linked together to build a polynucleotide Adjacent nucleotides joined by covalent bonds form between the OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next create a backbone of sugar-phosphate units with nitrogenous bases as appendages The sequence of bases along a DNA or mrna polymer is unique for each gene

The DNA Double Helix DNA molecule has two polynucleotides spiraling around an imaginary axis, Forms a double helix In the DNA double helix, the two backbones run in opposite 5 3 directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)

Fig. 5-28 5' end 3' end Sugar-phosphate backbones Base pair (joined by hydrogen bonding) 3' end Old strands Nucleotide about to be added to a new strand 5' end New strands 3' end 5' end 5' end 3' end

DNA and Proteins as Tape Measures of Evolution The linear sequences of nucleotides in DNA molecules are passed from parents to offspring Two closely related species are more similar in DNA than are more distantly related species Molecular biology can be used to assess evolutionary kinship

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

Fig. 5-UN2

Fig. 5-UN2a

Fig. 5-UN2b

Fig. 5-UN9

You should now be able to: 1. List and describe the four major classes of molecules 2. Describe the formation of a glycosidic linkage and distinguish between monosaccharides, disaccharides, and polysaccharides 3. Distinguish between saturated and unsaturated fats and between cis and trans fat molecules 4. Describe the four levels of protein structure

You should now be able to: 5. Distinguish between the following pairs: pyrimidine and purine, nucleotide and nucleoside, ribose and deoxyribose, the 5 end and 3 end of a nucleotide