Chapter 3 Molecules of Life Nucleic Acids, Proteins, and Enzymes

Trans Fats Trans fats Partially hydrogenated vegetable oils formed by a chemical hydrogenation process Straightens the double bond the molecule Pack tightly; solid at room temperature Bonds are cis or trans, depending on the way the hydrogens are arranged around them

Cis and Trans Fatty Acids A Oleic acid, a cis fatty acid. Figure 3.1 Trans fats, an unhealthy food. A fat has three fatty acid tails, each a long carbon chain. Hydrogenation changes the arrangement of hydrogen atoms around double bonds in those chains from (A) a cis configuration to (B) a trans configuration. This small difference in structure makes a big difference in our bodies. B Elaidic acid, a trans fatty acid.

Organic Molecules All organic molecules (molecules of life) are built with carbon atoms We can use different models to highlight different aspects of the same molecule

Carbon – The Stuff of Life Organic molecules are complex molecules of life, built on a framework of carbon atoms Carbohydrates Lipids Proteins Nucleic acids

Atomic Structure Is the Basis for Life’s Chemistry Element A pure substance that contains only one kind of atom Living things are mostly composed of 6 elements: Carbon (C) Hydrogen (H) Nitrogen (N) Oxygen (O) Phosphorus (P) Sulfur (S)

Carbon – The Stuff of Life Carbon atoms can be assembled and remodeled into many organic compounds Can bond with one, two, three, or four atoms Can form polar or nonpolar bonds Can form chains or rings

Carbon Rings A Carbon’s versatile bonding Figure 3.2 Carbon rings. Carbon rings form the framework of many sugars, starches, and fats, such as those found in doughnuts. A Carbon’s versatile bonding behavior allows it to form a variety of structures, including rings. B Carbon rings form the framework of many sugars, starches, and fats, such as those found in doughnuts.

Representing Structures of Organic Molecules Structural model of an organic molecule Each line is a covalent bond; two lines are double bonds; three lines are triple bonds glucose

Representing Structures of Organic Molecules Carbon ring structures are represented as polygons; carbon atoms are implied glucose glucose

Representing Structures of Organic Molecules Ball-and-stick models show positions of atoms in three dimensions; elements are coded by color glucose

Representing Structures of Organic Molecules Space-filling models show how atoms sharing electrons overlap glucose

Hemoglobin Molecule: Space-Filling Model Figure 3.4 Visualizing the structure of hemoglobin, the oxygen-transporting molecule in red blood cells. Models that show individual atoms usually depict them color-coded by element. Other models may be shown in various colors, depending on which features are being studied. A space-filling model of hemoglobin. A A space-filling model of hemoglobin.

Hemoglobin Molecule: Surface Model B A surface model of the same molecule reveals crevices and folds that are important for its function. Heme groups, in red, are cradled in pockets of the molecule.

Hemoglobin Molecule: Ribbon Model C A ribbon model of hemoglobin shows all four heme groups, also in red, held in place by the molecule’s coils.

How are all molecules of life alike? The molecules of life (carbohydrates, lipids, proteins, and nucleic acids) are organic, which means they consist mainly of carbon and hydrogen atoms The structure of an organic molecule starts with its carbon backbone, a chain of carbon atoms that may form a ring We use different models to represent different characteristics of a molecule’s structure; considering a molecule’s structural features gives us insight into how it functions

From Structure to Function The function of organic molecules in biological systems begins with their structure The building blocks of carbohydrates, lipids, proteins, and nucleic acids bond together in different arrangements to form different kinds of complex molecules Any process in which a molecule changes is called a reaction

Assembling Complex Molecules Monomers Molecules used as subunits to build larger molecules (polymers) Polymers Larger molecules that are chains of monomers May be split and used for energy

What Cells Do to Organic Compounds Metabolism Activities by which cells acquire and use energy to construct, rearrange, and split organic molecules Allows cells to live, grow, and reproduce Requires enzymes (proteins that increase the speed of reactions)

What Cells Do to Organic Compounds Condensation Covalent bonding of two molecules to form a larger molecule Water forms as a product Hydrolysis The reverse of condensation Cleavage reactions split larger molecules into smaller ones Water is split

Condensation B Condensation. Cells build a large molecule from smaller ones by this reaction. An enzyme removes a hydroxyl group from one molecule and a hydrogen atom from another. A covalent bond forms between the two molecules, and water also forms.

Hydrolysis C Hydrolysis. Cells split a large molecule into smaller ones by this water-requiring reaction. An enzyme attaches a hydroxyl group and a hydrogen atom (both from water) at the cleavage site.

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Functional Groups Hydrocarbon An organic molecule that consists only of hydrogen and carbon atoms Most biological molecules have at least one functional group functional group - A cluster of atoms that imparts specific chemical properties to a molecule (polarity, acidity)

Table 3-1 p41

Table 3-1 p41

Table 3-1 p41

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Glucose: Conversion of Straight Chain to Ring Form Glucose. This simple sugar converts from a straight-chain into a ring form when the highly reactive aldehyde group (on carbon 1) reacts with a hydroxyl group (on carbon 5). In water, the cyclic structure is the more common one. Figure 3.6 Glucose. This simple sugar converts from a straight-chain into a ring form when the aldehyde group (on carbon 1) reacts with a hydroxyl group (on carbon 5). In water, the cyclic structure is the more common one.

How do organic molecules work in living systems? All life is based on the same organic compounds: complex carbohydrates, lipids, proteins, and nucleic acids By processes of metabolism, cells assemble these molecules of life form monomers. They also break apart polymers into component monomers. Functional groups impart chemical characteristics to organic molecules; such groups contribute to the function of biological molecules An organic molecule’s structure dictates its function in biological systems

Carbohydrates Carbohydrates are the most plentiful biological molecules in the biosphere Cells use some carbohydrates as structural materials; they use others for fuel, or to store or transport energy

Carbohydrates Carbohydrates Organic molecules that consist of carbon, hydrogen, and oxygen in a 1:2:1 ratio Three types of carbohydrates in living systems Monosaccharides (simple sugars) Oligosaccharides (short-chain carbohydrates) Polysaccharides (complex carbohydrates)

Simple Sugars Monosaccharides (one sugar unit) are the simplest carbohydrates Used as an energy source or structural material Backbones of 5 or 6 carbons Very soluble in water Example: glucose

Short-Chain Carbohydrates Oligosaccharides Short chains of monosaccharides Example: sucrose, a disaccharide sucrose glucose + fructose + water The synthesis of sucrose is an example of a condensation reaction. Sucrose us common table sugar. Stepped Art

Complex Carbohydrates Polysaccharides Straight or branched chains of many sugar monomers The most common polysaccharides are cellulose, starch, and glycogen All consist of glucose monomers Each has a different pattern of covalent bonding, and different chemical properties

Cellulose Cellulose Polysaccharide Major structural material in plants Consists of long, straight chains of glucose monomers Does not dissolve in water; not easily broken down Dietary fiber or “roughage” in our vegetable foods Structure of cellulose, starch, and glycogen. All three carbohydrates consist only of glucose units, but the different bonding patterns that link the subunits result in substances with very different properties.

Cellulose Figure 3.8 Structure of (A) cellulose, (B) starch, and (C) glycogen, and their typical locations in a few organisms. All three carbohydrates consist only of glucose units, but the different bonding patterns that link the subunits result in substances with very different properties. A Cellulose, a structural component of plants. Chains of glucose units stretch side by side and hydrogen-bond at many —OH groups. The hydrogen bonds stabilize the chains in tight bundles that form long fibers. Very few types of organisms can digest this tough, insoluble material. Cellulose, a structural component of plants. Chains of glucose units stretch side by side and hydrogen-bond at many —OH groups. The hydrogen bonds stabilize the chains in tight bundles that form long fibers. Very few types of organisms can digest this tough, insoluble material.

Starch Starch Polysaccharide Energy reservoir in plants Covalent bonding pattern between monomers makes a chain that coils up into a spiral Does not dissolve easily in water, but less stable than cellulose An important component of human food

Starch Figure 3.8 Structure of (A) cellulose, (B) starch, and (C) glycogen, and their typical locations in a few organisms. All three carbohydrates consist only of glucose units, but the different bonding patterns that link the subunits result in substances with very different properties. In amylose, one type of starch, a series of glucose units form a chain that coils. Starch is the main energy reserve in plants, which store it in their roots, stems, leaves, fruits, and seeds (such as coconuts). In amylose, one type of starch, a series of glucose units form a chain that coils. Starch is the main energy reserve in plants, which store it in their roots, stems, leaves, fruits, and seeds (such as coconuts).

Glycogen Glycogen Polysaccharide Covalent bonding pattern forms highly branched chains of glucose monomers Energy reservoir in animal cells; stored in muscle and liver cells

Glycogen In humans and other animals, this polysaccharide functions as an energy reservoir. It is stored in muscles and in the liver. Figure 3.8 Structure of (A) cellulose, (B) starch, and (C) glycogen, and their typical locations in a few organisms. All three carbohydrates consist only of glucose units, but the different bonding patterns that link the subunits result in substances with very different properties. Glycogen. In humans and other animals, this polysaccharide functions as an energy reservoir. It is stored in muscles and in the liver.

Chitin Chitin A nitrogen-containing polysaccharide that strengthens hard parts of animals such as crabs, and cell walls of fungi Long, unbranching chains are linked by hydrogen bonds

Structure of starch and cellulose

Lipids Lipids Fatty, oily, or waxy organic compounds that are insoluble in water Lipids function as the body’s major energy reservoir, and as the structural foundation of cell membranes Triglycerides, phospholipids, waxes, and steroids are lipids common in biological systems

Fatty Acids Many lipids incorporate fatty acids Simple organic compounds with a carboxyl group joined to a backbone of 4 to 36 carbon atoms Saturated fatty acids (animal fats) Fatty acids with only single covalent bonds Molecules are packed tightly; solid at room temperature Unsaturated fatty acids (vegetable oils) Fatty acids with one or more double bonds Molecules are kinked; liquid at room temperature

Saturated and Unsaturated Fatty Acids Figure 3.10 Fatty acids. (A) The tail of stearic acid is fully saturated with hydrogen atoms. (B) Linoleic acid, with two double bonds, is unsaturated. The first double bond occurs at the sixth carbon from the end of the tail, so linoleic acid is called an omega-6 fatty acid. Omega-6 and (C) omega-3 fatty acids are “essential fatty acids”: Your body does not make them, so they must come from food.

Fatty acids. (A) The tail of stearic acid is fully saturated with hydrogen atoms. (B) Linoleic acid, with two double bonds, is unsaturated. The first double bond occurs at the sixth carbon from the end of the tail, so linoleic acid is called an omega-6 fatty acid. Omega-6 and (C) omega-3 fatty acids are “essential fatty acids”: Your body does not make them, so they must come from food.

Fats Fats Lipids with one, two, or three fatty acids “tails” attached to glycerol Triglycerides Neutral fats with three fatty acids attached to glycerol The most abundant energy source in vertebrates Concentrated in adipose tissues (for insulation and cushioning)

Triglycerides Lipids with fatty acid tails. Fatty acid tails of a triglyceride are attached to a glycerol head. Fatty acid tails of a phospholipid are attached to a glycerol head with a phosphate group. Figure 3.11 Animated Lipids with fatty acid tails. (A) Fatty acid tails of a triglyceride are attached to a glycerol head. (B) Fatty acid tails of a phospholipid are attached to a glycerol head with a phosphate group.

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Phospholipids Phospholipids Molecules with a polar head containing a phosphate and two nonpolar fatty acid tails Heads are hydrophilic, tails are hydrophobic The most abundant lipid in cell membranes Form lipid bilayers with hydrophobic tails sandwiched between the hydrophilic heads

Phospholipids Animated Lipids with fatty acid tails. Fatty acid tails of a triglyceride are attached to a glycerol head. Fatty acid tails of a phospholipid are attached to a glycerol head with a phosphate group. Figure 3.11 Animated Lipids with fatty acid tails. (A) Fatty acid tails of a triglyceride are attached to a glycerol head. (B) Fatty acid tails of a phospholipid are attached to a glycerol head with a phosphate group.

Phospholipids in a Lipid Bilayer hydrophilic head two hydrophobic tails

Phospholipids in a Lipid Bilayer one layer of lipids one layer of lipids

Waxes Waxes Complex mixtures with long fatty-acid tails bonded to long-chain alcohols or carbon rings Protective, water-repellant covering

Steroids Steroids Lipids with a rigid backbone of four carbon rings and no fatty-acid tails Cholesterol Component of eukaryotic cell membranes Remodeled into bile salts, vitamin D, and steroid hormones such as the female sex hormone estrogen, and the male sex hormone testosterone

Estrogen and Testosterone Figure 3.13 Estrogen and testosterone, steroid hormones that cause different traits to arise in males and females of many species such as wood ducks (Aix sponsa), pictured at right. an estrogen testosterone

Effects of Estrogen and Testosterone female wood duck male wood duck

What are lipids? Lipids are fatty, waxy, or oily organic compounds. Common types include fats, phospholipids, waxes, and steroids Triglycerides are lipids that serve as energy reservoirs in vertebrate animals Phospholipids are the main lipid component of cell membranes Waxes are lipid components of water-repelling and lubricating secretions Steroids are lipids that occur in cell membranes; some are remodeled into other molecules

Proteins – Diversity in Structure and Function All cellular processes involve proteins, the most diverse biological molecule (structural, nutritious, enzyme, transport, communication, and defense proteins) Cells build thousands of different proteins by stringing together amino acids in different orders

From Structure to Function Protein An organic compound composed of one or more chains of amino acids Amino acid A small organic compound with an amine group (—NH3+), a carboxyl group (—COO-, the acid), and one or more variable groups (R group)

Amino Acid Structure Figure 3.14 Generalized structure of amino acids. The complete structures of the twenty most common amino acids found in eukaryotic proteins are shown in Appendix I. Stepped Art

Polypeptides Polypeptide Protein synthesis involves the formation of amino acid chains called polypeptides Polypeptide A chain of amino acids bonded together by peptide bonds in a condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid

Polypeptide Formation methionine serine methionine serine glutamine methionine serine arginine Figure 3.15 Animated Polypeptide formation. Chapter 9 offers a closer look at protein synthesis. Two amino acids (here, methionine and serine) are joined by condensation. A peptide bond forms between the carboxyl group of the methionine and the amine group of the serine. Stepped Art

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Levels of Protein Structure Primary structure The unique amino acid sequence of a protein Secondary structure The polypeptide chain folds and forms hydrogen bonds between amino acids Tertiary structure A secondary structure is compacted into structurally stable units called domains Forms a functional protein

Levels of Protein Structure Quaternary structure Some proteins consist of two or more folded polypeptide chains in close association Example: hemoglobin Some proteins aggregate by thousands into larger structures, with polypeptide chains organized into strands or sheets Example: hair

A protein’s primary structure consists of a linear sequence of amino acids (a polypeptide chain). Each type of protein has a unique primary structure. 1 glycine lysine arginine 2 Secondary structure arises as a polypeptide chain twists into a coil (helix) or sheet held in place by hydrogen bonds between different parts of the molecule. The same patterns of secondary structure occur in many different proteins. 3 Tertiary structure occurs when a chain’s coils and sheets fold up into a functional domain such as a barrel or pocket. In this example, the coils of a globin chain form a pocket. 4 Some proteins have quaternary structure, in which two or more polypeptide chains associate as one molecule. Hemoglobin, shown here, consists of four globin chains (green and blue). Each globin pocket now holds a heme group (red). 5 Many proteins aggregate by the thousands into much larger structures, such as the keratin filaments that make up hair. Figure 3.16 Animated Protein structure. Stepped Art Figure 3-16 p47

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Some Functional Proteins Some fibrous proteins contribute to the structure and organization of cells and tissues; others help cells, cell parts, and bodies move Sugars bond to proteins to make glycoproteins that allow a tissue or a body to recognize its own cells Lipids bond to proteins to make lipoproteins such as HDL and LDL, which transport cholesterol to and from the liver

HDL: A Lipoprotein protein lipid Other lipoproteins are aggregated structures that consist of variable amounts and types of proteins and lipids. LDL – transport cholesterol out of liver to cells. HDL – carries cholesterol released from dead cells back to liver. an HDL particle

What are proteins? Proteins are chains of amino acids. The order of amino acids in a polypeptide chain dictates the type of protein. Polypeptide chains twist and fold into coils, sheets, and loops, which fold and pack further into functional domains A protein’s shape is the source of its function

Why Is Protein Structure So Important? Proteins function only as long as they maintain their correct three-dimensional shape Changes in a protein’s shape may have drastic health consequences

Denaturation Heat, changes in pH, salts, and detergents can disrupt the hydrogen bonds that maintain a protein’s shape When a protein loses its shape and no longer functions, it is denatured Once a protein’s shape unravels, so does its function

Prions Prion An infectious agent that is composed primarily of protein. The mis-folded form of the prion protein has been implicated in a number of diseases in a variety of mammals, including Mad cow disease (bovine spongiform encephalitis) Creutzfeldt–Jakob disease in humans Scrapie in sheep All known prion diseases affect the structure of the brain or other neural tissue, and all are currently untreatable. All are infectious diseases characterized by deterioration of mental and physical abilities that eventually causes death.

Nucleic Acids Nucleotides are subunits of nucleic acids such as DNA and RNA Some nucleotides have roles in metabolism

Nucleotides Nucleotide ATP A small organic molecule consisting of a sugar with a five-carbon ring, a nitrogen-containing base, and one or more phosphate groups ATP A nucleotide with three phosphate groups Important in phosphate-group (energy) transfer

base: adenine (A) 3 phosphate groups Figure 3.18 Animated Nucleic acid structure. A ATP, a nucleotide monomer of RNA, and also an essential participant in many metabolic reactions. sugar: ribose A ATP, a nucleotide monomer of RNA, and also an essential participant in many metabolic reactions. Figure 3-18a p49

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A Chain of Nucleotides B A chain of nucleotides is a nucleic acid. The sugar of one nucleotide is covalently bonded to the phosphate group of the next, forming a sugar–phosphate backbone.

Nucleic Acids Nucleic acids Polymers of nucleotides in which the sugar of one nucleotide is attached to the phosphate group of the next RNA and DNA are nucleic acids

RNA RNA (ribonucleic acid) Contains four kinds of nucleotide monomers, including ATP Important in protein synthesis

DNA DNA (deoxyribonucleic acid) Two chains of nucleotides twisted together into a double helix and held by hydrogen bonds Contains all inherited information necessary to build an organism, coded in the order of nucleotide bases

The DNA Molecule The cell uses the order of nucleotide bases in DNA (the DNA sequence) guide production of RNA and proteins

What are nucleotides and nucleic acids? Nucleotides are monomers of the nucleic acids DNA and RNA; some have additional roles DNA’s nucleotide sequence encodes heritable information RNA plays several important roles in the process by which a cell uses the instructions written in its DNA to build proteins