Chapter 5: The Structure and Function of Large Biological Molecules PDF

Chapter 5: The Structure and Function of Large Biological Molecules © 2017 Pearson Education, Inc.  Alcohol dehydrogenase Alcohol dehydrogenase, a protein that breaks down alcohol in the body, is shown here as a molecular model. The form of this protein that an i...

Chapter 5: The Structure and Function of Large Biological Molecules © 2017 Pearson Education, Inc.  Alcohol dehydrogenase Alcohol dehydrogenase, a protein that breaks down alcohol in the body, is shown here as a molecular model. The form of this protein that an individual possesses affects how well that person tolerates drinking alcohol. Proteins are one class or large molecules, or macromolecules. Genetic variation: https://www.nature.com/articles/4001497 © 2021 Pearson Education, Inc. Figure 5.1 © 2021 Pearson Education, Inc. Figure 5.1a CONCEPT 5.1: Macromolecules are polymers, built from monomers Large polymers are known as macromolecules for their huge size A polymer is a long molecule consisting of many similar building blocks The repeating units that serve as building blocks are called monomers Carbohydrates, proteins, and nucleic acids are polymers © 2021 Pearson Education, Inc. The Synthesis and Breakdown of Polymers Enzymes are specialized macromolecules that speed up chemical reactions such as those that make or break down polymers A dehydration reaction occurs when two monomers bond together through the loss of a water molecule Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 5.2 The Diversity of Polymers A cell has thousands of different macromolecules Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species A huge variety of polymers can be built from a small set of monomers © 2021 Pearson Education, Inc. CONCEPT 5.2: Carbohydrates serve as fuel and building material Carbohydrates include sugars and polymers of sugars The simplest carbohydrates are monosaccharides, or simple sugars Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks © 2021 Pearson Education, Inc. Sugars Monosaccharides have molecular formulas that are usually multiples of CH2O Glucose (C6H12O6) is the most common monosaccharide Monosaccharides are classified by – The location of the carbonyl group (as aldose or ketose) – The number of carbons in the carbon skeleton © 2021 Pearson Education, Inc.  The structure and classification of some monosaccharides Look closely at the structures- How do you know it’s a carb and not one of the other 3 main molecules? © 2021 Pearson Education, Inc. Figure 5.3  Though often drawn as linear skeletons, in aqueous solutions many sugars form rings Monosaccharides serve as a major fuel for cells and as raw material for building molecules © 2021 Pearson Education, Inc.  Linear and ring forms of glucose © 2021 Pearson Education, Inc. Figure 5.4  A disaccharide is formed when a dehydration reaction joins two monosaccharides This covalent bond between two monosaccharides is called a glycosidic linkage © 2021 Pearson Education, Inc.  Examples of disaccharide synthesis © 2021 Pearson Education, Inc. Figure 5.5 Polysaccharides Polysaccharides, the polymers of sugars, have storage and structural roles The architecture and function of a polysaccharide are determined by its sugar monomers and the positions of its glycosidic linkages © 2021 Pearson Education, Inc. Storage Polysaccharides Starch, a storage polysaccharide of plants, consists of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose © 2021 Pearson Education, Inc.  Glycogen is a storage polysaccharide in animals Glycogen is stored mainly in liver and muscle cells Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases © 2021 Pearson Education, Inc.  Polysaccharides of plants and animals (a) starch, (b) glycogen © 2021 Pearson Education, Inc. Figure 5.6a,b Structural Polysaccharides The polysaccharide 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 (α) and beta (β) © 2021 Pearson Education, Inc.  Cellulose Figure 5.6c © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 5.7  Starch (α configuration) is largely helical Cellulose molecules (β configuration) are straight and unbranched Some hydroxyl groups on the monomers of cellulose can hydrogen-bond with hydroxyls of parallel cellulose molecules © 2021 Pearson Education, Inc.  Enzymes that digest starch by hydrolyzing α linkages can’t hydrolyze β linkages in cellulose The 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 © 2021 Pearson Education, Inc.  Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods Chitin also provides structural support for the cell walls of many fungi © 2021 Pearson Education, Inc.  Figure 5.8 © 2021 Pearson Education, Inc. CONCEPT 5.3: Lipids are a diverse group of hydrophobic molecules Lipids are the one class of large biological molecules that does not include true polymers The unifying feature of lipids is that they mix poorly, if at all, with water Lipids consist mostly of hydrocarbon regions The most biologically important lipids are fats, phospholipids, and steroids © 2021 Pearson Education, Inc. 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 © 2021 Pearson Education, Inc.  Fats separate from water because water molecules hydrogen-bond to each other and exclude the fats In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride The fatty acids in a fat can be all the same or of two or three different kinds © 2021 Pearson Education, Inc.  The synthesis and structure of a fat, or triacylglycerol © 2021 Pearson Education, Inc. Figure 5.9  Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds © 2021 Pearson Education, Inc.  Saturated and unsaturated fats and fatty acids Figure 5.10 © 2021 Pearson Education, Inc.  Fats made from saturated fatty acids are called saturated fats and are solid at room temperature Most animal fats are saturated Fats made from unsaturated fatty acids are called unsaturated fats or oils and are liquid at room temperature Plant fats and fish fats are usually unsaturated © 2021 Pearson Education, Inc.  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 also creates unsaturated fats with trans double bonds These trans fats may contribute more than saturated fats to cardiovascular disease © 2021 Pearson Education, Inc.  The major function of fats is energy storage Humans and other mammals store their long-term food reserves in adipose cells Adipose tissue also cushions vital organs and insulates the body © 2021 Pearson Education, Inc. 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 © 2021 Pearson Education, Inc.  The structure of a phospholipid Figure 5.11 © 2021 Pearson Education, Inc.  When phospholipids are added to water, they self-assemble into double-layered sheets called bilayers At the surface of a cell, phospholipids are also arranged in a bilayer, with the hydrophobic tails pointing toward the interior The phospholipid bilayer forms a boundary between the cell and its external environment © 2021 Pearson Education, Inc. Steroids Steroids are lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol, a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized A high level of cholesterol in the blood may contribute to cardiovascular disease © 2021 Pearson Education, Inc.  Cholesterol, a steroid Figure 5.12 © 2021 Pearson Education, Inc. CONCEPT 5.4: Proteins include a diversity of structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Some proteins speed up chemical reactions Other protein functions include defense, storage, transport, cellular communication, movement, and structural support © 2021 Pearson Education, Inc.  An overview of protein functions (part 1 upper four panels) Figure 5.13a © 2021 Pearson Education, Inc.  An overview of protein functions (part 2 lower four panels) © 2021 Pearson Education, Inc. Figure 5.13b  Enzymes are proteins that act as catalysts to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life © 2021 Pearson Education, Inc.  Proteins are all constructed from the same set of 20 amino acids Polypeptides are unbranched polymers built from these amino acids The bond between amino acids is a peptide bond A protein is a biologically functional molecule that consists of one or more polypeptides © 2021 Pearson Education, Inc. Amino Acids (Monomers) Amino acids are organic molecules with amino and carboxyl groups Amino acids differ in their properties due to differing side chains, called R groups © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 5.14 Polypeptides (Amino Acid Polymers) Amino acids are linked by covalent bonds called peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than 1,000 monomers Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) © 2021 Pearson Education, Inc. Making a polypeptide chain © 2021 Pearson Education, Inc. Figure 5.15 Protein Structure and Function The specific activities of proteins result from their intricate three-dimensional architecture A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 5.16  The sequence of amino acids determines a protein’s three-dimensional structure A protein’s structure determines how it works The function of a protein usually depends on its ability to recognize and bind to some other molecule © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 5.17 Four Levels of Protein Structure The primary structure of a protein is 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) Quaternary structure results when a protein consists of multiple polypeptide chains © 2021 Pearson Education, Inc.  The primary structure of a protein is its sequence of amino acids Primary structure is like the order of letters in a long word Primary structure is determined by inherited genetic information © 2021 Pearson Education, Inc.  Exploring levels of protein structure (part 1: primary structure) © 2021 Pearson Education, Inc. Figure 5.18a  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 α helix and a folded structure called a β pleated sheet © 2021 Pearson Education, Inc.  Exploring levels of protein structure (part 2: secondary through quaternary structure) © 2021 Pearson Education, Inc. Figure 5.18b  Exploring levels of protein structure (part 3: spider silk, photo) © 2021 Pearson Education, Inc. Figure 5.18c  Tertiary structure, the overall shape of a polypeptide, results from interactions between R groups, rather than interactions between backbone constituents These interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein’s structure © 2021 Pearson Education, Inc.  Exploring levels of protein structure (part 4: tertiary stabilization) Figure 5.18d © 2021 Pearson Education, Inc.  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 α and two β subunits © 2021 Pearson Education, Inc.  Exploring levels of protein structure (part 5: collagen) Figure 5.18e © 2021 Pearson Education, Inc.  Exploring levels of protein structure (part 6: hemoglobin) © 2021 Pearson Education, Inc. Figure 5.18f 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 The abnormal hemoglobin molecules cause the red blood cells to aggregate into chains and to deform into a sickle shape © 2021 Pearson Education, Inc.  A single amino acid substitution in a protein causes sickle-cell disease Figure 5.19 © 2021 Pearson Education, Inc. What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can 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 © 2021 Pearson Education, Inc.  A denatured protein is biologically inactive Extremely high fevers can be fatal: proteins in the blood tend to denature at very high body temperatures Denaturation can sometimes be reversed when the denaturing agent is removed This is not always possible, however © 2021 Pearson Education, Inc.  Denaturation and renaturation of a protein Figure 5.20 © 2021 Pearson Education, Inc. Protein Folding in the Cell It is hard to predict a protein’s structure from its primary structure Most proteins probably go through several stages on their way to a stable structure Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins © 2021 Pearson Education, Inc.  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 is another approach to prediction of protein structure from amino acid sequences © 2021 Pearson Education, Inc.  Research method: X-ray crystallography © 2021 Pearson Education, Inc. Figure 5.21 CONCEPT 5.5: Nucleic acids store, transmit, and help express hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes consist of DNA, a nucleic acid made of monomers called nucleotides © 2021 Pearson Education, Inc. 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 This process is called gene expression © 2021 Pearson Education, Inc.  Gene expression: DNA → RNA → protein © 2021 Pearson Education, Inc. Figure 5.22  Each gene along a DNA molecule directs synthesis of a messenger RNA (mRNA) The mRNA molecule interacts with the cell’s protein-synthesizing machinery to direct production of a polypeptide The flow of genetic information can be summarized as DNA → RNA → protein © 2021 Pearson Education, Inc. The Components of Nucleic Acids 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 one or more phosphate groups The portion of a nucleotide without the phosphate group is called a nucleoside © 2021 Pearson Education, Inc.  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 © 2021 Pearson Education, Inc.  Components of nucleic acids Figure 5.23 © 2021 Pearson Education, Inc. Nucleotide Polymers Nucleotides are linked together by a phosphodiester linkage to build a polynucleotide A phosphodiester linkage consists of a phosphate group that links the sugars of two nucleotides 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 © 2021 Pearson Education, Inc. The Structures of DNA and RNA Molecules DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix The backbones run in opposite 5′ → 3′ directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes © 2021 Pearson Education, Inc.  Only certain bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) This is called complementary base pairing This feature of DNA structure makes it possible to generate two identical copies of each DNA molecule in a cell preparing to divide © 2021 Pearson Education, Inc.  RNA, in contrast to DNA, is single-stranded Complementary pairing can also occur between two RNA molecules or between parts of the same molecule In RNA, thymine is replaced by uracil (U), so A and U pair While DNA always exists as a double helix, RNA molecules are more variable in form © 2021 Pearson Education, Inc.  The structures of DNA and tRNA molecules Figure 5.24 © 2021 Pearson Education, Inc. CONCEPT 5.6: Genomics and proteomics have transformed biological inquiry and applications Once the structure of DNA and its relationship to amino acid sequence was understood, biologists sought to “decode” genes by learning their base sequences The first chemical techniques for DNA sequencing were developed in the 1970s and refined over the next 20 years © 2021 Pearson Education, Inc.  It is enlightening to sequence the full complement of DNA in an organism’s genome The rapid development of faster and less expensive methods of sequencing was a side effect of the Human Genome Project Many genomes have been sequenced, generating large sets of data © 2021 Pearson Education, Inc.  Automatic DNA sequencing machines and abundant computing power enable rapid sequencing of genes and genomes. © 2021 Pearson Education, Inc. Figure 5.25  Bioinformatics uses computer software and other computational tools to deal with the data resulting from sequencing many genomes Analyzing large sets of genes or even comparing whole genomes of different species is called genomics A similar analysis of large sets of proteins including their sequences is called proteomics © 2021 Pearson Education, Inc.  Figure 5.26 © 2021 Pearson Education, Inc. DNA and Proteins as Tape Measures of Evolution Sequences of genes and their protein products document the hereditary background of an organism Linear sequences of DNA molecules are passed from parents to offspring We can extend the concept of “molecular genealogy” to relationships between species Molecular biology has added a new measure to the toolkit of evolutionary biology © 2021 Pearson Education, Inc.  Scientific skills exercise: Analyzing polypeptide sequence data (part 1) Figure 5.UN02a © 2021 Pearson Education, Inc.  Scientific skills exercise: Analyzing polypeptide sequence data (part 2) Figure 5.UN02b © 2021 Pearson Education, Inc.  Problem-solving exercise: Are you a victim of fish fraud? (part 1) Figure 5.UN03a © 2021 Pearson Education, Inc.  Problem-solving exercise: Are you a victim of fish fraud? (part 2) © 2021 Pearson Education, Inc. Figure 5.UN03b © 2021 Pearson Education, Inc. UNF05-cr  Summary of Key Concepts: Carbohydrates Figure 5.UN04 © 2021 Pearson Education, Inc.  Summary of Key Concepts: Lipids Figure 5.UN05 © 2021 Pearson Education, Inc.  Summary of Key Concepts: Proteins Figure 5.UN06 © 2021 Pearson Education, Inc.  Summary of Key Concepts: Nucleic Acids © 2021 Pearson Education, Inc. Figure 5.UN07