Chapter 3 The Molecules of Cells Lecture by Richard L. Myers

Chapter 3 The Molecules of Cells Lecture by Richard L. Myers
The Molecules of Cells General biology students might not have previously taken a chemistry course. The concept of molecular building blocks that cannot be seen can be abstract and difficult to comprehend for such students. Concrete examples from our diets and good images will increase comprehension. Lecture by Richard L. Myers

Introduction: Got Lactose?
Most of the world’s population cannot digest milk-based foods They are lactose intolerant, because they lack the enzyme lactase This illustrates the importance of biological molecules, such as lactase, to functioning living organisms When a lactose-intolerant person ingests milk-based foods, the person will experience nausea, cramps, and bloating. Copyright © 2009 Pearson Education, Inc.

INTRODUCTION TO ORGANIC COMPOUNDS
Organic chemistry is the study of organic compounds. Copyright © 2009 Pearson Education, Inc.

3.1 Life’s molecular diversity is based on the properties of carbon
Diverse molecules found in cells are composed of carbon bonded to other elements Carbon-based molecules are called organic compounds By sharing electrons, carbon can bond to four other atoms By doing so, it can branch in up to four directions The ability to bond in four directions is called tetravalence. This is one facet of carbon’s versatility that makes large, complex molecules possible. One of the great advantages of life based on carbon is its ability to form up to four bonds, permitting the assembly of diverse components and branching configurations. Challenge your students to find another element that might also permit this sort of adaptability. (Like carbon, silicon has four electrons in its outer shell.) Copyright © 2009 Pearson Education, Inc.

Methane (CH4) is one of the simplest organic compounds Four covalent bonds link four hydrogen atoms to the carbon atom Each of the four lines in the formula for methane represents a pair of shared electrons Copyright © 2009 Pearson Education, Inc.

The four single bonds of carbon point to the corners
Structural formula Ball-and-stick model Space-filling model Methane Figure 3.1A Three representations of methane (CH4). The four single bonds of carbon point to the corners of a tetrahedron.

Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons Carbon, with attached hydrogens, can bond together in chains of various lengths Hydrocarbons are the major components of petroleum. Hydrocarbons consist of the partially decomposed remains of organisms that lived millions of years ago. Copyright © 2009 Pearson Education, Inc.

Animation: Carbon Skeletons
3.1 Life’s molecular diversity is based on the properties of carbon A chain of carbon atoms is called a carbon skeleton Carbon skeletons can be branched or unbranched Therefore, different compounds with the same molecular formula can be produced These structures are called isomers Animation: L-Dopa Animation: Carbon Skeletons Animation: Isomers Copyright © 2009 Pearson Education, Inc.

Carbon skeletons vary in length.
Ethane Propane Carbon skeletons vary in length. Figure 3.1B Variations in carbon skeletons.

Skeletons may be unbranched or branched.
Branching. Butane Isobutane Figure 3.1B Variations in carbon skeletons. Skeletons may be unbranched or branched.

Skeletons may have double bonds, which can vary in location.
1-Butene 2-Butene Skeletons may have double bonds, which can vary in location. Figure 3.1B Variations in carbon skeletons.

Skeletons may be arranged in rings.
Cyclohexane Benzene Figure 3.1B Variations in carbon skeletons. Skeletons may be arranged in rings.

3.2 Characteristic chemical groups help determine the properties of organic compounds
An organic compound has unique properties that depend upon The size and shape of the molecule and The groups of atoms (functional groups) attached to it A functional group affects a biological molecule’s function in a characteristic way Functional groups may participate in chemical reactions or may contribute to function indirectly by their effects on molecular shape. Copyright © 2009 Pearson Education, Inc.

Compounds containing functional groups are hydrophilic (water-loving) This means that they are soluble in water, which is a necessary prerequisite for their roles in water-based life Copyright © 2009 Pearson Education, Inc.

The functional groups are Hydroxyl group—consists of a hydrogen bonded to an oxygen Carbonyl group—a carbon linked by a double bond to an oxygen atom Carboxyl group—consists of a carbon double-bonded to both an oxygen and a hydroxyl group Amino group—composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton Phosphate group—consists of a phosphorus atom bonded to four oxygen atoms You may want to add the methyl group as a functional group because of its importance in methylating certain compounds. For example, a methyl group on DNA may affect expression of genes. Another example is the arrangement of methyl groups in male and female sex hormones to affect their shape and function. Copyright © 2009 Pearson Education, Inc.

Table 3.2 Functional Groups of Organic Compounds.

An example of similar compounds that differ only in functional groups is sex hormones Male and female sex hormones differ only in functional groups The differences cause varied molecular actions The result is distinguishable features of males and females Copyright © 2009 Pearson Education, Inc.

Estradiol Female lion Testosterone Male lion
Figure 3.2 Differences in the chemical groups of sex hormones. Testosterone Male lion

3.3 Cells make a huge number of large molecules from a small set of small molecules
There are four classes of biological molecules Carbohydrates Proteins Lipids Nucleic acids Copyright © 2009 Pearson Education, Inc.

The four classes of biological molecules contain very large molecules They are often called macromolecules because of their large size They are also called polymers because they are made from identical building blocks strung together The building blocks are called monomers Macromolecules are large and complex. A protein may consist of thousands of atoms that form a molecular colossus with a mass well over 100,000 daltons. Copyright © 2009 Pearson Education, Inc.

A cell makes a large number of polymers from a small group of monomers Proteins are made from only 20 different amino acids, and DNA is built from just four kinds of nucleotides The monomers used to make polymers are universal As an example of the universality of monomers, the amino acids in your student’s proteins are the same ones found in a bacterium’s or plant’s proteins. Copyright © 2009 Pearson Education, Inc.

Monomers are linked together to form polymers through dehydration reactions, which remove water Polymers are broken apart by hydrolysis, the addition of water All biological reactions of this sort are mediated by enzymes, which speed up chemical reactions in cells The bulk of the organic material we ingest is in the form of polymers that are much too large to enter our cells. Within our digestive tract, various enzymes attack the polymers, speeding up hydrolysis. Animation: Polymers Copyright © 2009 Pearson Education, Inc.

Short polymer Unlinked monomer
Figure 3.3A Dehydration reactions build a polymer chain.

Short polymer Unlinked monomer Dehydration reaction Longer polymer
Figure 3.3A Dehydration reactions build a polymer chain. Longer polymer

Figure 3.3B Hydrolysis breaks a polymer chain.

Hydrolysis Figure 3.3B Hydrolysis breaks a polymer chain.

Dehydration Hydrolysis Short polymer Monomer Longer polymer

3.4 Monosaccharides are the simplest carbohydrates
Carbohydrates range from small sugar molecules (monomers) to large polysaccharides Sugar monomers are monosaccharides, such as glucose and fructose These can be hooked together to form the polysaccharides Monosaccharides have molecular formulae that are multiples of CH2O. Copyright © 2009 Pearson Education, Inc.

Figure 3.4A Bees with honey, a mixture of two monosaccharides.

3.4 Monosaccharides are the simplest carbohydrates
The carbon skeletons of monosaccharides vary in length Glucose and fructose are six carbons long Others have three to seven carbon atoms Monosaccharides are the main fuels for cellular work Monosaccharides are also used as raw materials to manufacture other organic molecules Monosaccharides, particularly glucose, are major nutrients for cells. Glucose is the starting compound for an important metabolic pathway called cellular respiration. If your lectures will eventually include details of cellular respiration (glycolysis or aerobic respiration), this is a good point to introduce the basic concepts of glucose as fuel. Copyright © 2009 Pearson Education, Inc.

Glucose (an aldose) Fructose (a ketose)
Figure 3.4B Structures of glucose and fructose. Glucose (an aldose) Fructose (a ketose)

Structural formula Abbreviated structure Simplified structure
Figure 3.4C Three representations of the ring form of glucose. Structural formula Abbreviated structure Simplified structure

3.5 Cells link two single sugars to form disaccharides
Two monosaccharides (monomers) can bond to form a disaccharide in a dehydration reaction An example is a glucose monomer bonding to a fructose monomer to form sucrose, a common disaccharide Sucrose is the sugar (disaccharide) we keep around the kitchen to sweeten coffee or use for dozens of other things. Animation: Disaccharides Copyright © 2009 Pearson Education, Inc.

Glucose Glucose Figure 3.5 Disaccharide formation by a dehydration reaction.

Glucose Glucose Maltose
Figure 3.5 Disaccharide formation by a dehydration reaction. Maltose

3.6 CONNECTION: What is high-fructose corn syrup and is it to blame for obesity?
When you drink a soda, you are probably consuming a sweetener called high-fructose corn syrup (HFCS) Because fructose is sweeter than glucose, glucose atoms produced from starch are rearranged to make the glucose isomer, fructose This is used to sweeten sodas So, if you overconsume sweeteners as well as fat and do not exercise, you may experience weight gain The population of the United States eats more sweetener made from corn than from sugarcane or beets, gulping it down in drinks as well as in frozen food and baked goods. Even ketchup is laced with it. Copyright © 2009 Pearson Education, Inc.

Figure 3.6 HFCS, a main ingredient of soft drinks and processed foods.

3.7 Polysaccharides are long chains of sugar units
Polysaccharides are polymers of monosaccharides They can function in the cell as a storage molecule or as a structural compound Animals and plants store sugars for later use. Plants store starch while animals store glycogen. Copyright © 2009 Pearson Education, Inc.

Starch is a storage polysaccharide composed of glucose monomers and found in plants Glycogen is a storage polysaccharide composed of glucose, which is hydrolyzed by animals when glucose is needed Cellulose is a polymer of glucose that forms plant cell walls Chitin is a polysaccharide used by insects and crustaceans to build an exoskeleton Most mammals, including humans, do not have enzymes necessary to digest cellulose. Thus the energy in the glucose monomers is not available. Cows have solved this problem by harboring prokaryotes (bacteria) in their rumen that hydrolyze the cellulose of grass and hay to glucose monomers. The glucose can be used for energy as well as building blocks for other nutrients that nourish the cow. Likewise, termites cannot digest cellulose in wood, but the bacteria in their guts can, and so provide a meal for themselves as well as the termites The text notes that cellulose is the most abundant organic molecule on Earth. Ask your students why this is true. Copyright © 2009 Pearson Education, Inc.

STARCH Glucose monomer GLYCOGEN CELLULOSE Cellulose molecules
Starch granules in potato tuber cells STARCH Glucose monomer Glycogen granules in muscle tissue GLYCOGEN CELLULOSE Cellulose fibrils in a plant cell wall Figure 3.7 Polysaccharides Hydrogen bonds Cellulose molecules

3.8 Fats are lipids that are mostly energy-storage molecules
Lipids are water insoluble (hydrophobic, or water fearing) compounds that are important in energy storage They contain twice as much energy as a polysaccharide Fats are lipids made from glycerol and fatty acids Lipids are generally not big enough to be macromolecules. They are grouped together because they mix poorly, if at all, with water. Copyright © 2009 Pearson Education, Inc.

Figure 3.8A Water beading on the only coating of feathers.

Fatty acids link to glycerol by a dehydration reaction A fat contains one glycerol linked to three fatty acids Fats are often called triglycerides because of their structure Animation: Fats Copyright © 2009 Pearson Education, Inc.

Glycerol Fatty acid Figure 3.8B A dehydration reaction linking a fatty acid to glycerol.

Figure 3.8C A fat molecule made from glycerol and three fatty acids.

Some fatty acids contain double bonds This causes kinks or bends in the carbon chain because the maximum number of hydrogen atoms cannot bond to the carbons at the double bond These compounds are called unsaturated fats because they have fewer than the maximum number of hydrogens Fats with the maximum number of hydrogens are called saturated fats Most animal fat is saturated fat. Saturated fats, such as butter and lard, will pack tightly together and will be solid at room temperature. Plant and fish fats are usually unsaturated fats. They are usually liquid at room temperature. Olive oil and cod liver oil are examples. Peanut butter, margarine, and many other products are hydrogenated to prevent lipids from separating out in liquid (oil) form. Copyright © 2009 Pearson Education, Inc.

3.9 Phospholipids and steroids are important lipids with a variety of functions
Phospholipids are structurally similar to fats and are an important component of all cells For example, they are a major part of cell membranes, in which they cluster into a bilayer of phospholipids The hydrophilic heads are in contact with the water of the environment and the internal part of the cell The hydrophobic tails band in the center of the bilayer The phospholipid bilayer provides the cell with a structure that separates the outside from the inside of the cell. The integrity of the membrane is necessary for life functions. Because of the nature of the phospholipid, many molecules cannot move across the membrane without help. Copyright © 2009 Pearson Education, Inc.

Water Hydrophilic heads Hydrophobic tails Water
Figure 3.9A Section of a phospholipid membrane. Water

3.9 Phospholipids and steroids are important lipids with a variety of functions
Steroids are lipids composed of fused ring structures Cholesterol is an example of a steroid that plays a significant role in the structure of the cell membrane In addition, cholesterol is the compound from which we synthesize sex hormones Unfortunately, a high level of cholesterol in the blood can lead to atherosclerosis. This is a heart disease that results when deposits form in the arteries that supply the heart muscle with oxygen. The deposits block blood flow, and a heart attack results. Both saturated fats and trans fats promote higher levels of cholesterol. Copyright © 2009 Pearson Education, Inc.

Figure 3.9B Cholesterol, a steroid.

3.10 CONNECTION: Anabolic steroids pose health risks
Anabolic steroids are synthetic variants of testosterone that can cause a buildup of muscle and bone mass They can be sold as prescription drugs and used to treat certain diseases They may also be abused with serious consequences, such as liver damage that can lead to cancer There are several important adverse consequences to steroid use to gain an athletic edge. Sports organizations and the public have come out against their use as a means to enhance performance. Athletic governing bodies prohibit their use. The consequences of steroid abuse will likely be of great interest to your students. However, the reasons for the damaging consequences might not be immediately clear. As time permits, consider noting the diverse homeostatic mechanisms that normally regulate the traits affected by steroid abuse. Copyright © 2009 Pearson Education, Inc.

Figure 3.10UN Flexed biceps.

3.11 Proteins are essential to the structures and functions of life
A protein is a polymer built from various combinations of 20 amino acid monomers Proteins have unique structures that are directly related to their functions Enzymes, proteins that serve as metabolic catalysts, regulate the chemical reactions within cells Proteins account for more than 50% of the dry mass of cells. Copyright © 2009 Pearson Education, Inc.

3.11 Proteins are essential to the structures and functions of life
Structural proteins provide associations between body parts and contractile proteins are found within muscle Defensive proteins include antibodies of the immune system, and signal proteins are best exemplified by the hormones Receptor proteins serve as antenna for outside signals, and transport proteins carry oxygen Copyright © 2009 Pearson Education, Inc.

Figure 3.11 Structural proteins of hair, tendons, and ligaments; and contractile proteins of muscles.

3.12 Proteins are made from amino acids linked by peptide bonds
Amino acids, the building blocks of proteins, have an amino group and a carboxyl group Both of these are covalently bonded to a central carbon atom Also bonded to the central carbon is a hydrogen atom and some other chemical group symbolized by R Copyright © 2009 Pearson Education, Inc.

Amino group Carboxyl group
Figure 3.12A General structure of an amino acid.

Amino acids are classified as hydrophobic or hydrophilic Some amino acids have a nonpolar R group and are hydrophobic Others have a polar R group and are hydrophilic, which means they easily dissolve in aqueous solutions Teaching Tips 1. Many analogies help students appreciate the diversity of proteins that can be made from just 20 amino acids. The authors note that our language uses combinations of 26 letters to form words. Proteins are much longer “words,” creating even more diversity. Another analogy is to trains. This builds upon the earlier analogy when polymers were introduced. Imagine making different trains about 100 cars long, using any combination of 20 types of railroad cars. Mathematically, the number of possible trains is 20100, a number beyond imagination. 2. The authors note that the difference between a polypeptide and a protein is analogous to the relationship between a long strand of yarn and a sweater knitted from yarn. Proteins are clearly more complex! Copyright © 2009 Pearson Education, Inc.

Leucine (Leu) Serine (Ser) Aspartic acid (Asp) Hydrophobic Hydrophilic
Figure 3.12B Examples of amino acids with hydrophobic and hydrophilic R groups. Leucine (Leu) Serine (Ser) Aspartic acid (Asp) Hydrophobic Hydrophilic

Amino acid monomers are linked together to form polymeric proteins This is accomplished by an enzyme-mediated dehydration reaction This links the carboxyl group of one amino acid to the amino group of the next amino acid The covalent linkage resulting is called a peptide bond Copyright © 2009 Pearson Education, Inc.

Carboxyl group Amino group Amino acid Amino acid
Figure 3.12C Peptide bond formation. As more and more amino acids are added, a chain of amino acids called a polypeptide results. The combination of amino acids is determined by expression of genes on DNA. Although there seems to be an unlimited number of combinations of 20 amino acids, the combinations are limited in an individual because of inheritance.

Peptide bond Carboxyl group Amino group Dehydration reaction
Amino acid Amino acid Dipeptide Figure 3.12C Peptide bond formation. As more and more amino acids are added, a chain of amino acids called a polypeptide results. The combination of amino acids is determined by expression of genes on DNA. Although there seems to be an unlimited number of combinations of 20 amino acids, the combinations are limited in an individual because of inheritance.

3.13 A protein’s specific shape determines its function
A polypeptide chain contains hundreds or thousands of amino acids linked by peptide bonds The amino acid sequence causes the polypeptide to assume a particular shape The shape of a protein determines its specific function Because of the molecular structure of specific proteins on brain cells, endorphins bind to them. This gives us a feeling of euphoria and pain relief. Morphine, heroin, and other opiate drugs are able to mimic endorphins and bind to the endorphin receptors in the brain. Because of the euphoria that results, we become addicted. Copyright © 2009 Pearson Education, Inc.

Groove Figure 3.13A Ribbon model of the protein lysozyme.

Groove Figure 3.13B Space-filling model of lysozyme.

3.13 A protein’s specific shape determines its function
If for some reason a protein’s shape is altered, it can no longer function Denaturation will cause polypeptide chains to unravel and lose their shape and, thus, their function Proteins can be denatured by changes in salt concentration and pH Excessive heat can also denature a protein. A good example is frying or boiling an egg. The proteins in the egg “white” become solid, white, and opaque upon denaturation. Copyright © 2009 Pearson Education, Inc.

3.14 A protein’s shape depends on four levels of structure
A protein can have four levels of structure Primary structure Secondary structure Tertiary structure Quaternary structure For the BLAST Animation Alpha Helix, go to Animation and Video Files. Copyright © 2009 Pearson Education, Inc.

The primary structure of a protein is its unique amino acid sequence The correct amino acid sequence is determined by the cell’s genetic information The slightest change in this sequence affects the protein’s ability to function Sickle cell disease is manifested by an inability of hemoglobin in red blood cells to carry oxygen, the primary function of hemoglobin. This blood disorder is the result of change in a single amino acid. Copyright © 2009 Pearson Education, Inc.

Protein secondary structure results from coiling or folding of the polypeptide Coiling results in a helical structure called an alpha helix Folding may lead to a structure called a pleated sheet Coiling and folding result from hydrogen bonding between certain areas of the polypeptide chain Hydrogen bonding is an important component of the silk protein of a spider’s web. The many hydrogen bonds makes the web as strong as steel. Copyright © 2009 Pearson Education, Inc.

Figure 3.14UN01 Spider in web.

Polypeptide chain Figure 3.14UN02 Collagen. Collagen

The overall three-dimensional shape of a protein is called its tertiary structure Tertiary structure generally results from interactions between the R groups of the various amino acids Disulfide bridges are covalent bonds that further strengthen the protein’s shape Copyright © 2009 Pearson Education, Inc.

Two or more polypeptide chains (subunits) associate providing quaternary structure Collagen is an example of a protein with quaternary structure Its triple helix gives great strength to connective tissue, bone, tendons, and ligaments Animation: Protein Structure Introduction Misfolding of proteins cause diseases, such as Alzheimer’s and Parkinson’s. Both are manifested by accumulations of misfolded proteins. Consider an assignment to review the organic molecules in our diets. Have students, working individually or in small groups, analyze a food label listing the components of a McDonald’s Big Mac or other fast food sandwich. Note the most abundant organic molecule class (perhaps by weight) found in each component. For the BLAST Animation Protein Primary Structure, go to Animation and Video Files. For the BLAST Animation Protein Secondary Structure, go to Animation and Video Files. For the BLAST Animation Protein Tertiary Structure, go to Animation and Video Files. For the BLAST Animation Protein Quaternary Structure, go to Animation and Video Files. Teaching Tips 1. Consider this assignment to review the organic molecules in our diets. Have students, working individually or in small groups, analyze a food label listing the components of a McDonalds’ Big Mac or other fast-food sandwich. Note the most abundant organic molecule class (perhaps by weight) found in each component. Animation: Primary Protein Structure Animation: Secondary Protein Structure Animation: Tertiary Protein Structure Animation: Quaternary Protein Structure Copyright © 2009 Pearson Education, Inc.

Four Levels of Protein Structure
Primary structure Amino acids Figure 3.14A Primary structure.

Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Pleated sheet Figure 3.14A Primary structure. Figure 3.14B Secondary structure.

Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Pleated sheet Tertiary structure Figure 3.14A Primary structure. Figure 3.14B Secondary structure. Figure 3.14C Tertiary structure. Polypeptide (single subunit of transthyretin)

Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Pleated sheet Tertiary structure Figure 3.14A Primary structure. Figure 3.14B Secondary structure. Figure 3.14C Tertiary structure. Figure 3.14D Quaternary structure. Polypeptide (single subunit of transthyretin) Transthyretin, with four identical polypeptide subunits Quaternary structure

3.15 TALKING ABOUT SCIENCE: Linus Pauling contributed to our understanding of the chemistry of life
After winning a Nobel Prize in Chemistry, Pauling spent considerable time studying biological molecules He discovered an oxygen attachment to hemoglobin as well as the cause of sickle-cell disease Pauling also discovered the alpha helix and pleated sheet of proteins Pauling was also an advocate for halting nuclear weapons testing and won the Nobel Peace Prize for his work. He was very close to reporting the structure of DNA when Watson and Crick scooped him and correctly described its structure. Copyright © 2009 Pearson Education, Inc.

Figure 3.15 Linus Pauling with a model of the alpha helix in 1948.

3.16 Nucleic acids are information-rich polymers of nucleotides
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are composed of monomers called nucleotides Nucleotides have three parts A five-carbon sugar called ribose in RNA and deoxyribose in DNA A phosphate group A nitrogenous base Copyright © 2009 Pearson Education, Inc.

Nitrogenous base (adenine) Phosphate group Sugar
Figure 3.16A A nucleotide, consisting of a phosphate group, sugar, and a nitrogenous base. Phosphate group Sugar

A nucleic acid polymer, a polynucleotide, forms from the nucleotide monomers when the phosphate of one nucleotide bonds to the sugar of the next nucleotide The result is a repeating sugar-phosphate backbone with protruding nitrogenous bases Copyright © 2009 Pearson Education, Inc.

Nucleotide Figure 3.16B Part of a nucleotide. Sugar-phosphate backbone

Two polynucleotide strands wrap around each other to form a DNA double helix The two strands are associated because particular bases always hydrogen bond to one another A pairs with T, and C pairs with G, producing base pairs RNA is usually a single polynucleotide strand Copyright © 2009 Pearson Education, Inc.

Base pair Figure 3.16C DNA double helix.

A particular nucleotide sequence that can instruct the formation of a polypeptide is called a gene Most DNA molecules consist of millions of base pairs and, consequently, many genes These genes, many of which are unique to the species, determine the structure of proteins and, thus, life’s structures and functions Copyright © 2009 Pearson Education, Inc.

3.17 EVOLUTION CONNECTION: Lactose tolerance is a recent event in human evolution
Mutations are alterations in bases or the sequence of bases in DNA Lactose tolerance is the result of mutations In many people, the gene that dictates lactose utilization is turned off in adulthood Apparently, mutations occurred over time that prevented the gene from turning off This is an excellent example of human evolution Mutations that lead to lactose tolerance are relativity recent events. The mutation was useful because it allowed people to drink milk when other foods were unavailable. In other words, it provided a survival advantage. Copyright © 2009 Pearson Education, Inc.

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