The Molecules of Life: Overview PDF

The Molecules of Life: Overview Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules composed of thousands of covalently...

The Molecules of Life: Overview Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules composed of thousands of covalently connected atoms Molecular structure and function are inseparable © 2011 Pearson Education, Inc. Figure 5.1 Why do scientists study the structures of macromolecules? Concept 5.1: Macromolecules are polymers, built from monomers A polymer is 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 – Lipid is not polymer © 2011 Pearson Education, Inc. The Synthesis and Breakdown of 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 © 2011 Pearson Education, Inc. Figure 5.2a (a) Dehydration reaction: synthesizing a polymer 1 2 3 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond. 1 2 3 4 Longer polymer Figure 5.2b (b) Hydrolysis: breaking down a polymer 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond. 1 2 3 The Diversity of Polymers Each cell has thousands of different macromolecules 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 © 2011 Pearson Education, Inc. Concept 5.2: Carbohydrates serve as fuel and building material Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or single sugars Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks © 2011 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 © 2011 Pearson Education, Inc. Figure 5.3a Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Trioses: 3-carbon sugars (C3H6O3) Glyceraldehyde Dihydroxyacetone Figure 5.3b Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Pentoses: 5-carbon sugars (C5H10O5) Ribose Ribulose Figure 5.3c Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Hexoses: 6-carbon sugars (C 6H12O6) Glucose Galactose Fructose  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 © 2011 Pearson Education, Inc. Figure 5.4 1 6 6 2 5 5 3 4 1 4 1 4 2 2 5 3 3 6 (a) Linear and ring forms 6 5 4 1 3 2 (b) Abbreviated ring structure  A disaccharide is formed when a dehydration reaction joins two monosaccharides This covalent bond is called a glycosidic linkage © 2011 Pearson Education, Inc. Figure 5.5 1–4 glycosidic 1 linkage 4 Glucose Glucose Maltose (a) Dehydration reaction in the synthesis of maltose 1–2 glycosidic 1 linkage 2 Glucose Fructose Sucrose (b) Dehydration reaction in the synthesis of sucrose 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 © 2011 Pearson Education, Inc. Storage Polysaccharides Starch, a storage polysaccharide of plants, consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose © 2011 Pearson Education, Inc. Figure 5.6 Chloroplast Starch granules Amylopectin Amylose (a) Starch: 1 m a plant polysaccharide Mitochondria Glycogen granules Glycogen (b) Glycogen: 0.5 m an animal polysaccharide  Glycogen is a storage polysaccharide in animals Humans and other vertebrates store glycogen mainly in liver and muscle cells © 2011 Pearson Education, Inc. 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 () and beta () © 2011 Pearson Education, Inc. Figure 5.7a 4 1 4 1  Glucose  Glucose (a)  and  glucose ring structures Figure 5.7b 1 4 (b) Starch: 1–4 linkage of  glucose monomers 1 4 (c) Cellulose: 1–4 linkage of  glucose monomers  Polymers with  glucose are helical Polymers with  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 © 2011 Pearson Education, Inc. Figure 5.8 Cell wall Cellulose microfibrils in a plant cell wall Microfibril 10 m 0.5 m Cellulose molecules  Glucose monomer  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 © 2011 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 © 2011 Pearson Education, Inc. Figure 5.9a Chitin forms the exoskeleton of arthropods. Figure 5.9b Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Concept 5.3: 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 becausethey consist mostly of hydrocarbons, which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids, and steroids © 2011 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 © 2011 Pearson Education, Inc. Figure 5.10a Fatty acid (in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat  Fats separate from water because water molecules form hydrogen bonds with 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 © 2011 Pearson Education, Inc. Figure 5.10b Ester linkage (b) Fat molecule (triacylglycerol)  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 © 2011 Pearson Education, Inc. Figure 5.11a (a) Saturated fat Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid Figure 5.11b (b) Unsaturated fat Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Cis double bond causes bending.  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 © 2011 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 © 2011 Pearson Education, Inc.  Certain unsaturated fatty acids are not synthesized in the human body These must be supplied in the diet These essential fatty acids include the omega-3 fatty acids, required for normal growth, and thought to provide protection against cardiovascular disease © 2011 Pearson Education, Inc.  The major function of fats is energy storage Humans and other mammals store their fat in adipose cells Adipose tissue also cushions vital organs and insulates the body © 2011 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 © 2011 Pearson Education, Inc. Figure 5.12 Choline Hydrophilic head Phosphate Glycerol Hydrophobic tails Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol  When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior The structure of phospholipids results in a bilayer arrangement found in cell membranes Phospholipids are the major component of all cell membranes © 2011 Pearson Education, Inc. Figure 5.13 Hydrophilic WATER head Hydrophobic tail WATER 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 © 2011 Pearson Education, Inc. Figure 5.14 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 Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances © 2011 Pearson Education, Inc. Figure 5.15-a Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Function: Protection against disease Example: Digestive enzymes catalyze the hydrolysis Example: Antibodies inactivate and help destroy of bonds in food molecules. viruses and bacteria. Antibodies Enzyme Virus Bacterium Storage proteins Transport proteins Function: Storage of amino acids Function: Transport of substances Examples: Casein, the protein of milk, is the major Examples: Hemoglobin, the iron-containing protein of source of amino acids for baby mammals. Plants have vertebrate blood, transports oxygen from the lungs to storage proteins in their seeds. Ovalbumin is the other parts of the body. Other proteins transport protein of egg white, used as an amino acid source molecules across cell membranes. for the developing embryo. Transport protein Ovalbumin Amino acids for embryo Cell membrane Figure 5.15-b Hormonal proteins Receptor proteins Function: Coordination of an organism’s activities Function: Response of cell to chemical stimuli Example: Insulin, a hormone secreted by the Example: Receptors built into the membrane of a pancreas, causes other tissues to take up glucose, nerve cell detect signaling molecules released by thus regulating blood sugar concentration other nerve cells. Receptor Signaling protein Insulin High secreted Normal molecules blood sugar blood sugar Contractile and motor proteins Structural proteins Function: Movement Function: Support Examples: Motor proteins are responsible for the Examples: Keratin is the protein of hair, horns, undulations of cilia and flagella. Actin and myosin feathers, and other skin appendages. Insects and proteins are responsible for the contraction of spiders use silk fibers to make their cocoons and webs, muscles. respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Actin Myosin Collagen Muscle tissue Connective 100 m tissue 60 m  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 © 2011 Pearson Education, Inc. Polypeptides Polypeptides are unbranched polymers built from the same set of 20 amino acids A protein is a biologically functional molecule that consists of one or more polypeptides © 2011 Pearson Education, Inc. Amino Acid Monomers Amino acids are organic molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains, called R groups © 2011 Pearson Education, Inc. Figure 5.UN01 Side chain (R group)  carbon Amino Carboxyl group group Figure 5.16a Nonpolar side chains; hydrophobic Side chain Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I) Methionine Phenylalanine Tryptophan Proline (Met or M) (Phe or F) (Trp or W) (Pro or P) Figure 5.16b Polar side chains; hydrophilic Serine Threonine Cysteine (Ser or S) (Thr or T) (Cys or C) Tyrosine Asparagine Glutamine (Tyr or Y) (Asn or N) (Gln or Q) Figure 5.16c Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H) Amino Acid Polymers Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than a thousand monomers Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) © 2011 Pearson Education, Inc. Figure 5.17 Peptide bond New peptide bond forming Side chains Back- bone Amino end Peptide Carboxyl end (N-terminus) bond (C-terminus) Protein Structure and Function A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape © 2011 Pearson Education, Inc. Figure 5.18a Groove (a) A ribbon model Figure 5.18b Groove (b) A space-filling model  The sequence of amino acids determines a protein’s three-dimensional structure A protein’s structure determines its function © 2011 Pearson Education, Inc. Figure 5.19 Antibody protein Protein from flu virus 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 © 2011 Pearson Education, Inc. Figure 5.20a Primary structure Amino acids Amino end Primary structure of transthyretin Carboxyl end  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 © 2011 Pearson Education, Inc. Figure 5.20b Secondary Tertiary Quaternary structure structure structure  helix Hydrogen bond  pleated sheet  strand Transthyretin Hydrogen Transthyretin protein bond polypeptide  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  helix and a folded structure called a  pleated sheet © 2011 Pearson Education, Inc. Figure 5.20c Secondary structure  helix Hydrogen bond  pleated sheet  strand, shown as a flat arrow pointing toward the carboxyl end Hydrogen bond Figure 5.20d Silk fibers of spider → made of β-pleated sheets  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 structure © 2011 Pearson Education, Inc. Figure 5.20e Tertiary structure Transthyretin polypeptide Figure 5.20f Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Polypeptide backbone Figure 5.20g Quaternary structure Transthyretin protein (four identical polypeptides) Figure 5.20h Collagen Figure 5.20i Heme Iron  subunit  subunit  subunit  subunit Hemoglobin Figure 5.20j  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 © 2011 Pearson Education, Inc. 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 © 2011 Pearson Education, Inc. Figure 5.21 Primary Secondary Quaternary Red Blood and Tertiary Function Structure Structure Cell Shape Structures 1 Normal Molecules do not hemoglobin associate with one 2 Normal hemoglobin another; each carries 3 oxygen. 4 5   subunit  10 m 6 7   1 Exposed Sickle-cell Molecules crystallize hydrophobic hemoglobin into a fiber; capacity Sickle-cell hemoglobin 2 region to carry oxygen is 3 reduced. 4 5  6  10 m 7  subunit   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 A denatured protein is biologically inactive © 2011 Pearson Education, Inc. Figure 5.22 enaturat ion D Normal protein Re Denatured protein na turation 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 Chaperonins are protein molecules that assist the proper folding of other proteins Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins © 2011 Pearson Education, Inc. Figure 5.23 Correctly folded protein Polypeptide Cap Hollow cylinder Chaperonin Steps of Chaperonin 2 The cap attaches, causing 3 The cap comes (fully assembled) Action: the cylinder to change off, and the 1 An unfolded poly- shape in such a way that properly folded peptide enters the it creates a hydrophilic protein is cylinder from environment for the released. one end. folding of the polypeptide.  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 © 2011 Pearson Education, Inc. Figure 5.24a EXPERIMENT Diffracted X-rays X-ray source X-ray beam Digital detector X-ray diffraction Crystal pattern Figure 5.24b RESULTS RNA DNA RNA polymerase II 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 are made of DNA, a nucleic acid made of monomers called nucleotides © 2011 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 Protein synthesis occurs in ribosomes © 2011 Pearson Education, Inc. Figure 5.25-1 DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM Figure 5.25-2 DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm Figure 5.25-3 DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into Ribosome cytoplasm 3 Synthesis of protein Amino Polypeptide acids 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 © 2011 Pearson Education, Inc. Figure 5.26ab Sugar-phosphate backbone 5 end 5C 3C Nucleoside Nitrogenous base 5C 1C Phosphate 3C 5C group Sugar (pentose) 3C (b) Nucleotide 3 end (a) Polynucleotide, or nucleic acid Figure 5.26c Nitrogenous bases Pyrimidines Cytosine Thymine Uracil (C) (T, in DNA) (U, in RNA) Sugars Purines Deoxyribose Ribose Adenine (A) Guanine (G) (in DNA) (in RNA) (c) Nucleoside components  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 © 2011 Pearson Education, Inc. Nucleotide Polymers Nucleotide polymers are linked together to build 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 (phosphodiester bond) 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 © 2011 Pearson Education, Inc. The Structures of DNA and RNA Molecules RNA molecules usually exist as single polypeptide chains DNA molecules have two polynucleotides spiraling around an imaginary axis, forming 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 © 2011 Pearson Education, Inc.  The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) Called complementary base pairing 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 © 2011 Pearson Education, Inc. Figure 5.27 5 3 Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 5 Base pair joined by hydrogen bonding (a) DNA (b) Transfer RNA Concept 5.6 Genomics and Proteomics Analyzing large sets of genes or even comparing whole genome of different species- the approach is called as genomics. Similar analyis of large sets of proteins, including their sequences– is called proteomics. These approaches permeates all fields of biology, including Evolution Paleontology Medical Sciences Conservation Biology Ecology etc 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 © 2011 Pearson Education, Inc. 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 © 2011 Pearson Education, Inc. END of Chapter 2