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Chapter 5: The Structure and Function of Macromolecules
Polymer formation – large molecules (macromolecules) make up most things in the cell Types of polymers Carbohydrates – sugars (mono- di- and poly-saccharides) Lipids are macromolecules that do NOT form polymers – fats and phospholipids Proteins – function, structure, conformation, folding. Simple protein changes can cause disease Determination of protein structure Nucleic Acids – DNA and RNA
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Overview: The Molecules of Life
Within cells, small organic molecules are joined together to form larger molecules Macromolecules are large molecules composed of thousands of covalently connected atoms Most macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks called monomers Three of the four classes of life’s organic molecules are polymers: Carbohydrates Proteins Nucleic acids
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The Synthesis and Breakdown of Polymers
Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Monomers form larger molecules by condensation reactions called dehydration reactions (they release free water molecules) Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction (water actually breaks the bonds between individual monomers) Longer polymer Dehydration reaction in the synthesis of a polymer Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer
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The Diversity of Polymers: Many different types!
Each cell has thousands of different kinds of macromolecules 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
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Carbohydrates serve as fuel and building material
Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or single sugars Monosaccharides have molecular formulas that are usually multiples of CH2O Glucose is the most common monosaccharide Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks
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Sugars Monosaccharides serve as a major fuel for cells and as raw material for building molecules Though often drawn as a linear skeleton, in aqueous solutions they form rings Linear and ring forms Abbreviated ring structure
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Disaccharide formation
A disaccharide is formed when a dehydration reaction joins two monosaccharides This covalent bond is called a glycosidic linkage 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
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Polysaccharides Polysaccharides, the polymers of sugars, have storage and structural roles The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages between the individual sugar monomers that build the polymer
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Storage Polysaccharides: Starch
Starch, a storage polysaccharide of plants, consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids Starch Chloroplast 1 µm Amylose Amylopectin Starch: a plant polysaccharide
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Storage Polysaccharides: Glycogen
Mitochondria Glycogen granules Glycogen is a storage polysaccharide in animals Humans and other vertebrates store glycogen mainly in liver and muscle cells 0.5 µm Glycogen Glycogen: an animal polysaccharide
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Structural Polysaccharides: Cellulose
Cellulose is a major component of the tough wall of plant cells Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ The difference is based on two ring forms for glucose: alpha () and beta () Polymers consisting of glucose form starch Polymers consisting of glucose form cellulose a Glucose b Glucose a and b glucose ring structures Starch: 1–4 linkage of a glucose monomers. Cellulose: 1–4 linkage of b glucose monomers.
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Cellulose Polymers with alpha glucose are helical
Cellulose microfibrils in a plant cell wall Cell walls Microfibril Polymers with alpha glucose are helical Polymers with beta glucose are straight In straight structures, H atoms on one strand can bond with OH groups on other strands Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants 0.5 µm Plant cells Cellulose molecules b Glucose monomer
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Breakdown of cellulose
Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta 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
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Chitin Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods Chitin also provides structural support for the cell walls of many fungi Chitin can be used as surgical thread
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Lipids are a diverse group of hydrophobic molecules
Lipids are the one class of large biological molecules that do not form polymers The unifying feature of lipids is having little or no affinity for water Lipids are hydrophobic becausethey consist mostly of hydrocarbons, which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids, and steroids
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Fats Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid consists of a carboxyl group attached to a long carbon skeleton Fatty acid (palmitic acid) Glycerol Dehydration reaction in the synthesis of a fat
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Fats are hydrophobic molecules
Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats The long hydrocarbon chains of fatty acids are unable to form any hydrogen bonds with the water molecules and are thus hydrophobic In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride
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Fat molecule (triacylglycerol)
Ester linkage
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Types of fats Fatty acids vary in length (number of carbons in the hydrocarbon chain) and in the number and locations of double bonds in the chain Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds The major function of fats is energy storage Fats made from saturated fatty acids are called saturated fats Most animal fats are saturated Saturated fats are solid at room temperature A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits
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Saturated fats are not so good for you!!
Stearic acid Saturated fat and fatty acid.
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Unsaturated fats Fats made from unsaturated fatty acids are called unsaturated fats Plant fats and fish fats are usually unsaturated Plant fats and fish fats are liquid at room temperature and are called oils Oleic acid cis double bond causes bending Unsaturated fat and fatty acid.
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Phospholipids In a phospholipid, two fatty acids and a phosphate group are attached to glycerol The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head Choline Hydrophilic head Phosphate Glycerol Hydrophobic tails Fatty acids Hydrophilic head Hydrophobic tails Structural formula Space-filling model Phospholipid symbol
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Phospholipids behavior in water
When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior They also may assemble into a micelle – a sperical shaped arrangement of phospholipids where the hydrophobic tails all point into the center of the sphere The structure of phospholipids results in a bilayer arrangement found in cell membranes Phospholipids are the major component of all cell membranes
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The structure of a typical phospholipid bilayer:
cell membranes WATER Hydrophilic head Hydrophobic tails WATER
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Steroids Steroids are lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol, an important steroid, is a component in animal cell membranes Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease
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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, and defense against foreign substances Proteins are what does the ‘business’ of the cell – they are responsible for carrying out almost all of the essential biochemical reactions and processes that contribute to life
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What do proteins do? A more appropriate question
may be what don’t proteins do!
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Protein functions: Enzymes
Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life
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Protein functions: Enzymes Substrate (sucrose) Glucose Enzyme
(sucrase) Fructose
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Proteins are built from and sometimes called Polypeptides
Polypeptides are polymers of amino acids A protein consists of one or more polypeptides
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Amino Acid Monomers Amino acids are the ‘building blocks’ of proteins
Amino acids are organic molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains, called R groups Cells use 20 amino acids (of three main classes) to make thousands of proteins a carbon Amino group Carboxyl group
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Amino Acid Polymers Amino acids are linked together by peptide bonds to form the polypeptides that comprise a protein Polypeptides range in length from a few amino acids monomers to more than a thousand Each polypeptide has a unique linear sequence of amino acids The amino acid sequences of polypeptides were first determined by chemical methods Most of the steps involved in sequencing a polypeptide are now automated
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Four Levels of Protein Structure
The primary structure of a protein is simply its unique sequence of amino acids Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure is determined by interactions among various side chains (R groups) to yield a fully folded single polypeptide protein Quaternary structure results when a protein consists of multiple polypeptide chains, or multiple proteins
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Four Levels of Protein Structure
b pleated sheet +H3N Amino end Amino acid subunits helix Primary Secondary Tertiary** **Quaternary if there are more than one polypeptide chain present in the final protein structure
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Primary Structure Amino end Amino acid subunits Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information Carboxyl end
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Secondary Structure The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an alpha helix and a folded structure called a beta pleated sheet b pleated sheet Amino acid subunits helix
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Tertiary Structure Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein’s conformation Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond
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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
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Quaternary Structure Polypeptide chain b Chains Iron Heme a Chains
Hemoglobin Polypeptide chain Collagen
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Protein Conformation and Function
A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape The sequence of amino acids determines a protein’s three-dimensional conformation A protein’s conformation determines its function Ribbon models and space-filling models can depict a protein’s conformation Groove A ribbon model Groove A space-filling model
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What Determines Protein Conformation?
In addition to primary structure, physical and chemical conditions can affect conformation of the folded protein Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel (unfold) This loss of a protein’s native conformation is called denaturation A denatured protein is biologically inactive
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The Protein-Folding Problem
It is hard to predict a protein’s conformation based solely on its primary structure Most proteins probably go through several states on their way to a stable conformation Chaperonins are protein molecules that assist the proper folding of other proteins Denaturation Normal protein Denatured protein Renaturation
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Sickle-Cell Anemia Disease: A Simple Change in Primary Structure affects the proteins function
A slight change in primary structure (the amino acid sequence of the protein) can affect a protein’s conformation and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin 10 µm 10 µm Red blood cell shape Normal cells are full of individual hemoglobin molecules, each carrying oxygen. Red blood cell shape Fibers of abnormal hemoglobin deform cell into sickle shape.
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Sickle-Cell Anemia Disease: A Simple Change in Primary Structure affects the proteins function
Normal hemoglobin Sickle-cell hemoglobin Primary structure Val His Leu Thr Pro Glu Glu Primary structure Val His Leu Thr Pro Val Glu 1 2 3 4 5 6 7 1 2 3 4 5 6 7 Exposed hydrophobic region Secondary and tertiary structures Secondary and tertiary structures b subunit b subunit a a Quaternary structure Normal hemoglobin (top view) Quaternary structure Sickle-cell hemoglobin a a Function Molecules do not associate with one another; each carries oxygen. Function Molecules interact with one another to crystallize into a fiber; capacity to carry oxygen is greatly reduced.
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How can you determine a protein’s tertiary or
quaternary structure? Scientists use X-ray crystallography to determine a protein’s conformation Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization X-ray diffraction pattern Photographic film Diffracted X-rays X-ray source X-ray beam Crystal
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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 There are two types of nucleic acids: Deoxyribonucleic acid (DNA), which we already discussed Ribonucleic acid (RNA) DNA provides directions for its own replication – it serves as a template so it is replicated with each cell division Messenger RNA (mRNA) is synthesized (transcribed) from DNA Protein synthesis (translation) occurs in ribosomes from the mRNA
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The central dogma of molecular biology Genetic information is
stored in DNA. This genetic information is maintained by replication This information is transcribed into RNA. The information is then finally ‘read’ and translated into proteins These proteins are responsible for most of the biochemical reactions in the cell. DNA Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA Movement of mRNA into cytoplasm via nuclear pore Ribosome Synthesis of protein Amino acids Polypeptide
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The Structure of Nucleic Acids
5¢ end Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group The portion of a nucleotide without the phosphate group is called a nucleoside Nucleoside Nitrogenous base Phosphate group Pentose sugar Nucleotide 3¢ end Polynucleotide, or nucleic acid
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Nucleotide Monomers Nitrogenous bases Pyrimidines Nucleotide monomers are made up of nucleosides and phosphate groups Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases: Pyrimidines have a single six-membered ring Purines have a six membered ring fused to a five-membered ring In DNA, the sugar is deoxyribose In RNA, the sugar is ribose Cytosine C Thymine (in DNA) T Uracil (in RNA) U Purines Adenine A Guanine G Pentose sugars Deoxyribose (in DNA) Ribose (in RNA) Nucleoside components
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Nucleotide Polymers Nucleotide polymers are linked together, building a polynucleotide Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next These links 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
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The DNA Double Helix – a review
A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C
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DNA replication occurs in a Semi-conservative fashion
5¢ end 3¢ end DNA replication occurs in a Semi-conservative fashion Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 5¢ end New strands 3¢ end 5¢ end 5¢ end 3¢ end
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Similarities between DNA and RNA
They are both polymers They are both built from four nucleotide monomers, three of which are the same in each (A, C and G) The are both synthesized and joined in a 5’ to 3’ fashion Phosphodiester bonds connect the sugars in their backbones in the 5’ to 3’ linkage
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Differences between DNA and RNA
The sugar in the DNA backbone is deoxyribose, while it is ribose in RNA DNA is double stranded, while RNA is usually single stranded DNA contains A, T, C, and G as its bases while RNA has A, U, C, and G (it has uracil in place of tymine) The 2’ OH group in ribose makes RNA MUCH more unstable and reactive than DNA
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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
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