Biology Test 2

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The presence of amino (basic) and carboxyl (acidic) functional groups inspired the name amino acid.

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At pH 7 (in water)

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amino acids ionize. The concentration of protons at this pH causes the amino group act as a base and it attracts a proton to form -NH3+.

The carboxyl group in contrast acts as an acid. The two highly electronegative oxygen atoms in this group pull the electron away from its hydrogen atom, which means that it is relatively easy ofr this group to lost a proton to form -COO+

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charges

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The charges on these functional groups are important for two reasons: (1) They help amino acids stay in solution, where they can interact with one another and with other solutes, and (2) they affect the amino acids chemical reactivity.

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Side chains

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Several of the side chains found in amino acids contain carboxyl, sulfhydryl, hydroxyl, or amino functional groups. Under the right conditions, these functional groups can participate in chemical reactions.For example amino acids with a sulfhydryl group ( -SH) in their side chains can disulfide (S-S) bonds that help link different parts of large proteins. Such bonds form naturally between proteins in hair; curly hair contains many of these cross links while straight hair has far fewer. In contrast, some amino acids contain side chains that have no functional groups they consist solely of carbon and hydrogen atoms. These R-groups rarely participate in chemical reactions. Thus, the influence of these amino acids on protein function depends primarily on their size and shape rather than reactivity.

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Both polar and electrically charged R-groups interact readily with water are hydrophilic. Hydrophilic R-groups dissolve easily in water.

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Nonpolar R-groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving hydrophobic R-groups tend to coalesce in aqueous solution.

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Three types of amino acids

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charged, which includes acidic and basic;

uncharged polar

nonpolar.

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amino acids polymerize when a bond forms between the carboxyl group of one amino acid and the amino group of another. The C-N covalent bond that results from this condensation reaction is called a peptide bond. When a water molecule is removed in the condensation reaction, the carboxyl group is converted to a carbonyl functional group (C=O) and the amino group becomes simply N-H in the resulting polymer.

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The peptide bond

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Compared to monomer linkages in other types of macromolecules, peptide bonds are unusually stable. This is because the nitrogen can intermittently donate its pair of unshared valence electrons to the carbon in the C-N bond, forming a (C=N) double bond. When this occurs, a pair of electrons are pushed from the carbonyl (C=O) to the oxygen atom, forming and a single bond with an oxygen anion (C-O-). These different bond configurations oscillate, but the degree of electron sharing is great enough that peptide bonds have some of the characteristics of a double bond. For example, the peptide bond is planar, limiting the movement of the atoms participating in the peptide bond

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redisidues

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When amino acids are linked by peptide bonds into a chain, they are referred to as residues to distinguish them from free amino acid monomers.

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three key points to note about the peptide bonded backbone:

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R-group orientation The side chains of each residue extend out from the backbone, making it possible for them to interact with each other and with water.

Directionality There is an amino group (-NH3+) on one end of the backbone and a carboxyl group (-COO-) on the other. The end of the residue sequence that has the free amino group is called the N-terminus, or amino terminus, and the end with the free carboxyl group is called the C-terminus, or carboxy terminus. By convention, biologists always write amino acid residue sequences from the N-terminus to the C-terminus, because the N-terminus is the start of the chain when proteins are synthesized in cells.

Flexibility Although the peptide bond itself cannot rotate because of its double bond nature, the single bonds on either side of the peptide bond can rotate. As a result, the structure as a whole is flexible.

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oligopeptide

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Generally, when fewer than 50 amino acids are linked together in this way, the resulting polymer is called an oligopeptide or simply peptide.

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polypeptides

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Polymers that contain 50 or more amino acids are called polypeptides.

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protein

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The term protein is often used to describe any chain of amino acid residues. But in formal use, “protein” refers to the complete, often functional form of the molecule. Most proteins are large enough to be considered polypeptides, some consist of a single polypeptide, and others are functional only when multiple polypeptide subunits interact with one another.

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Primary Structure

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Each protein has a unique sequence of amino acids. That simple conclusion was the culmination of 12 years of study by Frederick Sanger and co-workers during the 1940’s and 1950s. Sangers group worked out the first techniques for determining the amino acid sequence of insulin, a hormone that helps regulate sugar concentrations in the blood of humans and other mammals. When other proteins were analyzed, it rapidly became clear that each protein has a definite and distinct amino acid sequence. Biochemists refer to the unique sequence of amino acids in a protein as its primary structure. With 20 types of amino acids available and chain lengths of up to tens of thousands of amino acid residues, the number of primary structures that are possible is practically limitless. There may, in fact, be 20^n different combinations of amino acid residues for a polymer with a given length of n. For example, a chain of just 10 amino acids has 20^10 possible sequences. This is over 10,000 billion variations.

As an example, consider hemoglobin, an oxygen binding protein in human red blood cells. In some individuals, one of the two different polypeptide sequences that make up hemoglobin has a valine instead of glutamate at the 6th position. Valine and glutamate have radically different side chains. The change in R-group produces hemoglobin molecules that stick to one another and form fibers when oxygen concentrations in the blood are low. Red blood cells that carry these fibers adopt a sickle-like shape. Sickled red blood cells get stuck in small blood vessels called capillaries, thereby starving downstream cells of oxygen. A debilitating illness called sickle cell disease results.

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Compare the primary structure of normal hemoglobin (a) with that of hemoglobin molecules in people with sickle cell disease (b). The single amino acid change at residue 6 causes red blood cells to alter from their normal disc shape (a) to a sickled shape (b) when oxygen concentrations are low.

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Secondary Structure

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Even though variation in the amino acid sequence of a protein is virtually limitless, it is only the tip of the iceberg in terms of generating structural diversity. The next level of organization in proteins, secondary structure, is generated in part by interaction between functional groups in the peptide-bonded backbone. Secondary structures are distinctively shaped section of linear sequence that are stabilized largely by hydrogen bonding that occurs between the oxygen on the carbonyl (C=O) group of one amino acid residue and the hydrogen on the amino (N-H) group of another. The oxygen atom in the (C=O) group has a partial negative charge due to its high electronegativity, while the hydrogen atom in the N-H group has a partial positive charge because it is bonded to nitrogen, which also has high electronegativity.

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Neighboring regions in a polypeptide chain can form hydrogen bonds between N-H and (C=O) groups along the peptide-bonded backbone. (b) These interactions can result in helical coils or folds that form pleated sheet structures in the polypeptide. ( c) Ribbon diagrams represent secondary structures using coils for helices and arrows for pleated sheets.

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Hydrogen bonding between section of the same backbone is possible only when a polypeptide bends in a way that brings (C=O) and N-H groups close together. In most proteins, these polar groups are aligned and form hydrogen bonds with one another when the backbone bends to form on of two possible structures:

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An alpha-helix, in which the polypeptides backbone is coiled or

A Beta-pleated sheet, in which segments of a peptide chain bend 180 degrees and then fold in the same plane.

In both structures, the residues that hydrogen-bond to one another are often close together in the linear sequence of a polypeptides primary structure. In an alpha-helix, H-bonds form between residues that are just four linear positions apart. The linear distance between residues that form a beta-pleated sheet may be larger because 180 degrees bends in the polypeptide chain can bring them close enough together to hydrogen bond. Biologists use illustration called ribbon diagrams to portray the secondary structures within the overall shape of a protein. Ribbon diagrams represent alpha-helices as coils and beta-pleated sheets as groups of arrows side by side in a plane. Unlike space filling models, ribbon diagrams don't show the presence of each atom and its volume, only the underlying contours of the protein backbone. Which secondary structures form, if either, depend on the molecule’s primary structure, specifically, the identities of the amino acids in the sequence. Certain amino acids are more likely to be involved in alpha-helices than in beta-pleated sheets, and vice versa, due to the specific geometry of their side chains. Proline, for example, is rarely found in alpha-helices due to its unusual R-group, which bonds not only to the central carbon of the residue but also to the nitrogen of the residues core amino group. Proline often introduces kinks in the peptide bonded backbone that do not conform to the shape of an alpha-helix. Each of the hydrogen bonds in an alpha-helix or a beta-pleated sheet is weak relative to a covalent bond, but the large number of hydrogen bonds in these secondary structures makes them highly stable. As a result, they increase the stability of the molecule as a whole and help define its shape. For overall shape and stability, though, the tertiary structure of a protein is even more important

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Tertiary Structure

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A proteins distinctive overall three dimensional shape, or tertiary structure, results from interactions between residues that are brought together as the backbone bends and folds in space. The residues that interact with one another are often far apart in the linear sequence. In contrast to secondary structures, which involve only hydrogen bonds between backbone amino and carbonyl groups, tertiary structures form using a variety of bonds and interaction between R-groups or between R-groups and the backbone.

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Five types of interaction involving R-groups are particularly important.

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Hydrogen bonding Hydrogen bonds form between polar side chains and opposite partial charges either on the peptide backbone or other R-groups.

Hydrophobic interactions In an aqueous solution, water molecules interact with the hydrophilic polar side chains of a polypeptide, forcing the hydrophobic nonpolar side chains to coalesce in the interior of the resulting globular mass. Water molecules surrounding the mass form more hydrogen bonds with each other and the polar residues on the surface of the protein, increasing the stability of their own interactions and the disorder of the rest of the aqueous solution.

Van der Waals interactions Once nonpolar side chains are forced close to one another by hydrophobic interactions, their association is further stabilized by van der Waals interactions. A large number of these weak electrical attractions can significantly increase the stability of the protein.

Covalent bonding Covalent bonds can form between the side chains of two cysteines through a reaction between the sulfhydryl groups. These disulfide (“two sulfur”) bonds are frequently referred to as bridges, because they create strong links between distinct regions of the same polypeptide or two separte polypeptides.

Ionic bonding Ionic bonds may form between groups that have full and opposing charges, such as the ionized acidic and basic side chains highlighted.

Ionic bonding is rare in proteins unless ionized R-groups are located in the interior where there is little water. Ionized groups on the exterior are normally exposed to the aqueous environment and enveloped by a shell of water, which prevents them form interacting with one another.

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tertirary structures of proteins

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Quaternary Structure

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The first three levels of protein structure involve single polypeptides. But some proteins contain multiple polypeptides that interact to form a single functional structure. The combination of polypeptides, referred to as subunits, gives some proteins quaternary structure. The individual polypeptides are held together by many of the same types of bonds and interactions found in the tertiary level of structure. In the simplest case, a protein with quaternary structure can consist of just two subunits that are identical. The Cro protein found in a virus called bacteriophage Lambda is an example. Proteins with two polypeptide subunits are called dimers (“two parts”), when the two polypeptide subunits are identical, they are called homodimers; heterodimers when they are non-identical. The quaternary structure of a protein may also include polypeptides that are distinct in primary, secondary, and tertiary structures. For example, hemoglobin consists of four polypeptides: two identical copies of an alpha subunit and two identical copies of a Beta subunit. Hemoglobin is an example of tetramer (“four parts”).

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The Cro protein is a homodimer, it consists of two identical polypeptide subunits, colored light and dark green in this figure. (b) Hemoglobin is a tetramer, it consists of four polypeptide subunits:two identical alpha subunits (light and dark green) and two identical Beta subunits (light and dark blue).

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macromolecular machines:

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In addition, cells contain macromolecular machines: complexes of multiple proteins that assemble to carry out a particular function. Some protein complexes also include other types of macromolecules. The ribosome is an example, it consists of several nucleic acid molecules as well as over 50 different proteins. Table 3.1 summarizes the four levels of protein structure, using hemoglobin as an example. The key thing to note is that protein structure is hierarchical. The order and type of amino acids in the primary structure is responsible for the secondary structures, which then fold up to form tertiary structure. Quaternary structure (if present) is based on interaction between the tertiary structures of the polypeptide subunits.

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Folding and Function

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If you could synthesize one of the polypeptides in hemoglobin from individual amino acids, and you then placed the resulting chain in an aqueous solution, it would spontaneously fold into the shape of the tertiary structure shown in Table 3.1. In terms of entropy, this result may seem to conflict with the second law of thermodynamics. Because an unfolded protein has many more ways to move about, it has much higher entropy than the folded version. But folding does tend to be spontaneous because the chemical bonds and interactions that occur release enough energy to overcome this decrease in entropy and will also increase entropy in the surrounding environment. As a result, the folded molecule has less surrounding environment. As a result, the folded molecule has less potential energy and is thus more stable than the unfolded molecule. Folding is also crucial to the function of a completed protein. This relationship between protein structure and function was hammered home in a set of classic experiments by Christina Anfinsen and colleagues during the 1950’s.

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Normal Folding is Crucial to Function

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Anfinsen studied a protein called ribonuclease that cleaves ribonucleic acid (RNa) polymers. He found that ribonuclease could be unfolded, or denatured, by treating it with compounds that break hydrogen bonds and disulfide bonds. The denatured ribonuclease was unable to function normally, it could no longer degrade nucleic acids. When the chemical denaturing agents were removed, however, ribonuclease refolded spontaneously and began to function normally again. These experiments confirmed that the primary sequence contained all the information required for folding and that fodling is essential for protein function.

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(left) Ribonuclease is functional when properly folded via hydrogen and disulfide bonds. (right) When the disulfide and various noncovalent bonds are broken, ribonuclease is no longer able to function. The double arrow indicates that in this case, the process is reversible.

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molecular chaperones

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More recent work has shown that cells contain special proteins called molecular chaperones that can facilitate protein folding. Many molecular chaperones belong to a family of molecules called the heat-shock proteins, because they are produced in large quantities after cells experience the denaturing effects of high temperatures. The name given to these proteins is a good indicator of their activity. The chaperones at a high school dance are responsible for blocking inappropriate interactions, and molecular chaperones do the same with unfolded proteins. As shown in Figure 3.13, the nonpolar side chains of unfolded polypeptides can clump together and disrupt the normal folding process. Molecular chaperones, such as the heat shock protein (Hsp90) shown at the start of this chapter, step in and attach t o these hydrophobic patches before aggregates can form, then release them to fold properly. In this way, chaperones help new proteins, and in some cases denatured proteins, fold into the shape specified by their primary sequence.

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Unfolded proteins can spontaneously clump into nonfunctional aggregates. Molecular chaperones prevent these detrimental interaction by reversibly binding to nonpolar (green) regions of unfolded proteins and allowing them to fold into functional proteins.

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Protein Shape Is Flexible

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Although each protein has a characteristic folded shape that is necessary for its function, most proteins are flexible and dynamic when they are not actively performing that function. OVer half of the proteins that have been analyzed to date have disordered regions lacking any apparent structure when they are in an inactive state. Each of these proteins will exist in an assortment of shapes until they are prompted to adopt a single folded and functional form. This step is often accomplished when the proteins interact with particular ions or molecules, or when they are chemically modified.

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Protein Folding is Often Regulated

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Since the function of a protein is dependent on its shape, controlling when or where it is folded into its active shape will regulate its activity. Proteins involved in cell signaling, for example, are often regulated in this way. Many of these proteins are disordered and do not complete their folding until after binding to other molecules or ions that are present only during a signaling event. This interaction induces the protein to fold into an ordered, active conformation. Such regulated folding plays a major role in controlling and coordinating cellular activities.

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Folding Can Be “Infectious”

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In 1982, Stanley Prusiner published what may be the most surprising result to emerge from research on protein folding: Certain normal proteins can be induced to fold into infectious, disease-causing agents. These proteins are called prions, or proteinaceous infectious particles. Infectious prions are alternately folded forms of normal proteins that are present in healthy individuals. The two versions of the protein have the same primary structure, but their shapes are radically different. Figure 3.14 illustrates the differences in shape observed between the normal and infectious forms of the prion protein (PrP) responsible for “mad cow disease”-- a disease in cattle that destroys the central nervous system. Figure 3.14a shows the normal folded form seen in healthy cattle cells. The infectious version of this protein is shown in Figure 3.14b.

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Ribbon diagrams of (a) normal, noninfectious prion protein with alpha-helices; and (b) infectious prion protein with beta-pleated sheets, which causes mad cow disease in cattle.

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mad cow disease

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Mad cow disease is one of a family of diseases caused by prions known as the spongiform encephalopathies literally, “ sponge-brain-illnesses”. Cows, sheep, goats, and humans afflicted with these diseases undergo massive degeneration of the brain. Although some spongiform encephalopathies can be inherited, in many cases the disease is transmitted when individuals eat tissues containing the infectious form of PrP. Infectious prions propagate by binding to normal prions and inducing conformational changes that cause the normal versions to adopt the alternate, infectious shape. This shape change stabilizes the interactions between prion proteins, resulting in the assembly of long fibrils that often leads to cell death. Prions are a particularly dramatic example of how a protein's function depends on its shape as well as how the final shape of a protein depends on folding.

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Protein Functions Are as Diverse as Protein Structures

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As a group, proteins perform more types of cell function than any other type of molecule. It makes sense to hypothesize that life began with proteins, simply because proteins are so vital to the life of today's cells. Consider the red blood cells that are moving through your veins and arteries right now. Each of these cells contains about 300 million copies of hemoglobin. Hemoglobin carries oxygen from your lungs to cells throughout the body. But every red blood cell also has thousands of copies of a protein called carbonic anhydrase, which is important for moving carbon dioxide from cells back to the lungs, where it can be breathed out. These are just two examples of the incredible variety of proteins in your body. Proteins are crucial to most tasks required for cells and organisms to exist. Catalysis Many proteins are specialized to catalyze or speed up chemical reactions. A protein that functions as a catalyst is called enzyme. The carbonic anhydrase molecules in red blood cells are enzymes. So is the salivary amylase protein in your mouth. Salivary amylase begins the digestion of starch into simple sugars. Most chemical reactions that make life possible depend on enzymes. Structure Structural proteins make up body components such as fingernails and hair, and form the internal “skeleton” of individual cells. Structural proteins keep red blood cells flexible and in their normal disc like shape. Movement Motor proteins and contractile proteins are responsible for moving the cell itself, or for moving large molecules and other types of cargo inside the cell. As you turn this page, for example, specialized proteins called actin and myosin will slide past one another to flex or extend muscle cells in your fingers and arm. Signaling Proteins are involved in carrying receiving signals from cell to cell inside the body. Many of them reside on the cells membrane to interact with neighboring cells. If sugar levels in your blood are low, a small peptide called glucagon will bind to receptor proteins on your liver cells, triggering enzymes inside to release sugar into your bloodstream. Transport proteins allow particular molecules to enter and exit cells or carry them throughout the body. Hemoglobin is a particularly well studied transport protein, but virtually every cell is studded with membrane proteins that control the passage of specific molecules and ions. Defense Proteins called antibodies attack and destroy viruses and bacteria that cause disease. Of all the functions that proteins perform in cells, catalysis may be the most important. The reason is speed. Life, at its most basic level, consists of chemical reactions. But most don’t occur fast enough to support life unless a catalyst is present. Enzymes are the most effective catalysts on Earth. Why is this so?

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Why Are Enzymes Good Catalysts?

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Catalyzed reactions involve one or more reactants, called substrates. Part of the reason enzymes are such effective catalysts is that they hold substrates in a precise orientation so they can react. The initial hypothesis for how enzymes work was proposed by Emil Fischer in 1894. According to Fischer’s “lock and key” model, enzymes are analogous to a lock and the keys are substrates that fit into the lock and then react. Several important ideas in this model have stood the test of time. For example, Fischer was correct in proposing that enzymes bring substrates into a precise orientation that makes reaction more likely. His model also accurately explained why most enzymes effectively catalyze one specific reaction. Enzyme specificity is a product of the geometry and types of functional group in the sites where substrates bind. As researchers began to test Fischer’s model, the location where substrates bind and react became known as the enzymes active site. The active site is where catalysis actually occurs. When techniques for determining the three dimensional structure of enzymes became available (see x-ray crystallography in BioSkills 6), the active sites were identified as clefts or cavities in the overall shapes. The digestive enzyme chymotrypsin, at work in your body now, is a good example. The active site in chymotrypsin contains three key amino acid residues, called a catalytic triad, with functional groups that catalyze the cleavage of peptide bonds in other proteins.

No other class of macromolecules can match proteins for their catalytic potential. The variety of reactive functional groups present in amino acid is much better suited for this activity than those found in nucleotides or sugars. The role of enzymes in catalyzing reactions is discussed in more detail in the next unit. There you will see that Fischer’s model had to be refined as research on enzyme action progressed.

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The active site in chymotrypsin, as in many enzymes, contains three key amino acid residues that bind substrates and catalyze a reaction.

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Did Life Arise from a Self-Replicating Enzyme?

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Based on several observations in the preceding sections, it could be argued that a protein catalyst was the first molecule capable of replication. Experimental studies have shown that amino acids were likely abundant during chemical evolution and that they could have polymerized to form small proteins. To date, however, attempts to simulate the origin of life with proteins alone have not been successful. Although it is too early to arrive at definitive conclusions, most origin-of-life researchers are skeptical that life began with a protein. To achieve the attributes of life, proteins would need to possess information, replicate, and evolve. The information carried in proteins is necessary for their function, but it cannot be used as a template or mold for their own replication. If they cannot replicate, then they cannot evolve on their own. Nucleic acids, in contrast, do carry this type of information. How they use it is the subject of the next chapter.

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What Is a Nucleic Acid?

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Nucleic acids are polymers, just as proteins are polymers. But instead of being assembled from amino acids, nucleic acids are made up of monomers called nucleotides. Figure 4.1a diagrams the three components of a nucleotide (1) a phosphate group, (2) a five carbon sugar, and (3) a nitrogenous (nitrogen containing) base. The phosphate group is bonded to the sugar molecule, which in turn is bonded to the base. Note that in the bases, the nitrogen (N) that bonds to the sugar is colored blue. The sugar is the central component of the nucleotide, much like the alpha-carbon in amino acids. The five carbons in this sugar are labeled with numbers and prime (‘) symbols to provide a frame of reference. For example, the base is attached to the 1’ carbon and the phosphate group is attached to the 5’ carbon. The monomers of ribonucleic acid (RNA) are referred to as ribonucleotides, and the monomers of deoxyribonucleic acid (DNA) are called deoxyribonucleotides. In ribonucleotides, the sugar is ribose; in deoxyribonucleotides, it is deoxyribose. As Figure 4.1b shows, bothe of these sugars have an -OH group bonded to the 3’ carbon, but ribose has an -OH group bonded to the 2’ carbon while deoxyribose has an H at the same location, a difference of just a single oxygen atom. Ribonucleotides and deoxyribonucleotides also differ in one of their nitrogenous bases. These bases, diagrammed in Figure 4.1c, belong to structural groups called purines and pyrimidines. The purines are adenine (A) and guanine (G); the pyrimidines are cytosine ( C), uracil (U), and thymine (T). Ribonucleotides use uracil (U) while deoxyribonucleotides use thymine (T). Note that purines consist of double rings formed from nin atoms, compared to the six atoms that make up the single ring in each pyrimidine. This makes identifying the structure of purines easy, since both adenine and guanine include “nine” in their names. To summarize: After the different sugars and bases are taken into account, eight different nucleotides are used to bind nucleic acids, four ribonucleotides (A, G, C, and U) and four deoxyribonucleotides (A, G, C, and T). See Making models 4.1 to learn how simple models are commonly used to represent nucleotides.

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Models of complex chemical structures may be drawn by using simple shapes for the different components. Nucleotides are often drawn using a circle for the phosphate group, a pentagon with an upright tail for the sugar, and a hexagon for the base. MODEL Using the shapes above ,draw to nucleotide models, one ribonucleotide and one deoxyribonucleotide. Use lines to represent covalent bonds connecting the different components. Label 2’,3’,, and 5’ carbons on the sugars and show what is bonded to each carbon. To see this model in action go the Study Area of Mastering Biology. If nucleic acids played any role in the chemical evolution of life, then at least some of these nucleotides must have been present in the prebiotic oceans. Is there any evidence to suggest that this was possible?

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Could Chemical Evolution Result in the Production of Nucleotides?

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Based on data from Stanley Miller and researchers who followed, most biologists accept the idea that amino acids could have been synthesized early in Earth’s history. The reactions behind the prebiotic synthesis of nucleotides, however, have been more difficult to identify. Miller-like laboratory simulations have shown that nitrogenous bases and many different types of sugars, including ribose, can be synthesized readily under conditions that mimic those in early Earth oceans. Recent work has focused on the conditions that exist in deep sea hydrothermal vent systems. What researchers have found is striking, reactive minerals on the surface of walls inside deep sea vents preferentially bind to ribose, effectively enriching and concentrating ribose from a pool of diverse sugars. Did this likewise occur in the ancient vents? If yes, the implications are exciting: A high concentration of ribose would have been present in the same deep-sea vent environment where the evolution of life may have taken place. The production of nucleotides has been a challenge for the theory of chemical evolution, but research on this issue continues. In the meantime, let’s consider the next question: Once nucleotides formed, how would they polymerize to form nucleic acids? This question has a definitive answer.

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How Do Nucleotides Polymerize to Form Nucleic Acids?

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As Figure 4.2 shows, nucleotides polymerize via condensation reaction between the hydroxyl on the sugar component of one nucleotide and the phosphate group of another nucleotide. The reaction forms a new covalent bond between the nucleotides, and a molecule of water is released. The bridge formed by the phosphate group is called a phosphodiester linkage, also frequently referred to as a phosophodiester bond.

The resulting phosphodiester linkage connects the 3’ carbon of one nucleotide and the 5’ carbon of another nucleotide. The two ester bonds connecting the nucleotides are highlighted in red. (Ribonucleotides are shown here, but the same reaction occurs between deoxyribonucleotides.) When phosphodiester linkages join ribonucleotides together, the polymer that is produced is RNA. Phosphodiester linkages between deoxyribonucleotides produce DNA.

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DNA and RNA Stands Are Directional

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FIgure 4.3 on page 98 shows how the chain of linked sugars and phosphates in a nucleic acid acts as a backbone, analogous to the peptide bonded backbone found in proteins. Identify the four bases in this RNA strand, using Figure 4.1 c as a key. Then write down the base sequence, starting at the 5’ end.Like the peptide-bonded backbone of a polypeptide, the sugar-phosphate backbone of a nucleic acid is directional. In a strand of RNA or DNA, one end has an unlinked 5’ phosphate while the other end has an unlinked 3’ hydroxyl, meaning the groups are not bonded to another nucleotide. The order of the different nucleotides forms the primary structure of the nucleic acid. When biologists write the primary structure of a stretch of DNA or RNA, they use shorthand and simply list the sequence of bases by their single letter abbreviations. For example, a DNA sequence consisting of six nucleotides might be ATTAGC. It would take roughly 6 billion of these letters to write the primary structure of the DNA in most of your cells. By convention the sequence of bases found in an RNA or DNA strand is always written in the 5’-> 3’ direction. This system is logical because in cells, RNA and DNA are always synthesized in this direction. Nucleotides are added only at the 3’ end of a growing nucleic acid molecule.

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Polymerization Requires an Energy Source

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As with other polymerization reactions, the joining of nucleotides into nucleic acids dramatically decreases entropy and is thus not spontaneous. An input of energy is needed to tip the energy balance in favor or polymerization. Nucleic acid polymerization can take place in cells (assisted by enzymes) because the potential energy of the nucleotide monomers is first raised by reactions that add two additional phosphate groups to the 5’ phosphates of ribonucleoside or deoxyribonucleoside monophosphates, creating nucleoside triphosphates. In the context of nucleic acid polymerization, researchers refer to the nucleoside triphosphate as “activated nucleotides”. Figure 4.4a shows an example of an activated ribonucleotide; this molecule is called adenosine triphosphate or ATP. The equivalent nucleotide for DNA synthesis would be deoxyadenosine triphosphate (dATP). A note about nomenclature: A molecule consisting of just a sugar and on of the bases in Figure 4.1c is called a nucleoside. A molecule consisting of a sugar and a base plus one or more phosphate groups is called a nucleotide. By convention, the phosphorylation state of a nucleotide is conveyed by using nucleoside, the appending mono-, di,or tri- to the word phosphate. For example, a sugar attached to a base and one phosphate group is called a nucleoside monophosphate;with three attached phosphates you have a nucleoside triphosphate.

The potential energy in activated nucleotides, such as ATP, is primarily stored in the bonds between the phosphates. When ATP reacts with water, one of the bonds between two phosphates is replaced with a lower potential energy bond, resulting in the release of energy, and either a monophosphate (Pi) or a diphosphate (PPi), usually called, for historical reasons, pyrophosphate. ( The subscript “i” signifies that the groups are inorganic; ie. not bonded to a carbon.) A similar release of potential energy occurs when activated nucleotides are used as substrates for polymerization of nucleic acids. How does adding phosphate groups raise the potential energy of a nucleotide? Recall that phosphates are negatively charged and that like charges repel. Linking two or more phosphates together generates covalent bonds that carry a large amount of potential energy due to strong repulsive forces. The energy is released when the phosphates form new, more stable bonds with other atoms. When activated nucleotides polymerize, the energy released from the condensation reaction compensates for the decrease in entropy, making the reaction spontaneous. You wil see in later chapters that potential energy stored in ATP is also used to drive other cellular activities, independent of nucleotide polymerization.

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DNA Structure and Function

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The primary structure of DNA is somewhat similar to the primary structure of proteins. Proteins have a peptide bonded backbone with a series of R-groups that extend from it. DNA molecules have a sugar-phosphate backbone, created by phosphodiester linkages, and a sequence of any of four nitrogenous bases that extend from it. Like proteins, DNA also has secondary structure. But while the alpha-helices and beta-pleated sheets of proteins are formed by hydrogen bonding between groups in the back bone, the secondary structure of DNA is formed in a very different way. Let’s look at details of this structure and how it relates to DNA’s function as an information carrying molecule.

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What is the Nature of DNA’s Secondary Structure

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the discovery of DNA’s secondary structure, announced in 1953, ranks among the great scientific breakthroughs of the twentieth century. James Watson and Francis Crick presented their celebrated model for the secondary structure of DNA in a single page that was published in the scientific journal Nature

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Early Data Provided Clues

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Watson and Crick’s model was a hypothesis based on a series of results from other laboratories. They were trying to propose a secondary structure that could explain several important observations about the DNA found in cells: Chemists had worked out the structure of nucleotides and knew that DNA polymerized through the formation of phosphodiester linkages. Thus, Watson and Crick knew that the molecule had a sugar phosphate backbone. By analyzing the nitrogenous bases in DNA samples from different organisms, Erwin Chargaff had established two empirical rules: (1) The number of purines in a given DNA molecule is equal to the number of pyrimidines, and (2) the DNA molecule has an equal number of T’s and A’s and it has an equal number of C’s and G’s By bombarding DNA with X-rays and analyzing how it scattered the radiation, Rosalind Franklin and Maurice Wilkins had calculated the distances between groups of atoms in the molecule. The technique they used is called X-ray crystallography. The scattering patterns showed that three distances were repeated many times: 0.34 nanometer (nm), 2.0 nm, and 3.4 nm. Because the measurements repeated, the researchers inferred that DNA molecules had regular and repeating structure. THe pattern of x-ray scattering suggested that the molecule was helical, or spiral, in nature. Based on this work, understanding DNA’s structure boiled down to understanding the nature of the helix involved. What type of helix would have a sugar phosphate backbone and explain both Chargaff’s rules and Franklin Wilkins measurements.

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DNA Strands Form an Antiparallel Double Helix

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Watson and Crick began by analyzing the size and geometry of the three nucleotide components: deoxyribose, phosphate, and base. The bond angles and measurements suggested that the distance of 2.0 nm represented the width of the helix and that 0.34 nm was likely to be the distance between bases stacked in a spiral. How could they make sense of Chargaff’s rules and the 3.4 nm distance, which appeared to be exactly 10 times the distance between a single pair of bases? To solve this problem, Watson and Crick constructed a series of physical models that allowed them to tinker with different types of helical configurations. After many false starts, certain things started to click: They arranged two strands of DNA side by side with the sugar phosphate backbones on the outside and the bases on the inside. If the bases extending from each backbone are to fit within the interior of a 2.0 nm wide structure, then they have to form purine-pyrimidine pairs. Purines-pyrimidine pairing allows hydrogen bonds to form only between certain bases, said to be complementary. Adenine will form two hydrogen bonds with thymine, and guanine will form three hydrogen bonds with cytosine. The third hydrogen bond in G-C pairs makes them slightly stronger than A-T pairs. The patterns of hydrogen bonding shown in Figure 4.5b could form only if the bases on opposite strands were flipped 180 degrees relative to one another. For this to happen, the two parallel strands of DNA must be orientated in opposite directions meaning that one strand runs in the 5’-->3’ direction while the other strand runs 3’-->5’. Strands with this orientation are said to be antiparallel. After these parameters were in place, the antiparallel strands were predicted to be twisted together to form a double helix.

By creating this model, Watson and Crick had discovered complementary base pairing between that A-T and G-C bases. In fact, the term Watson-Crick Pairing is now used interchangeably with the phrase “complementary base pairing.” This discovery explains the purine-pyrimidine ratios that Chargaff observed. As Figure 4.5c shows, DNA is put together like a ladder. The antiparallel sugar-phosphate backbones form the ladder side rails. The bases attached to the sugars are rotated and pair up via hydrogen bonding to form the ladder rungs. Although each base has polar groups involved in the hydrogen bonds, the bases carbon nitrogen rings are mostly nonpolar. This is a key point, because in aqueous solution ( the environment inside a cell) hydrophobic interaction cause double stranded DNA to twist into a heli to minimize contact between the hydrophobic bases and surrounding water molecules. The physical restraints posed by these interaction result in a full helical turn every 10 base, the 3.4 nm distance observed by Franklin and Wilkins.

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The schematic diagrams illustrate complementary base pairing (left) and how strands are twisted into a double helix (right). (Yellow bands represent hydrogen bonding.) (b) The space-filling model shows tight packing of the bses inside the double helix. The double helix structure explains the measurements inferred from X-ray analysis of DNA molecules.

The two strands are further stabilized by base stacking, which results from van der Waals interactions between the tightly packed base pairs allows the rings of adjacent bases to stack on top of one another like coins. This nonpolar interior is sandwiched between the negatively charged phosphate groups of the outward-facing backbone, which make the double helix hydrophilic overall and thus soluble in aqueous solutions. Additional features of DNA’s secondary structure are highlighted in Figure 4.6b. Its important to note that the outside of the helical DNA molecule forms two types of grooves. The wider of the two is known as the major groove, and the narrower one is known as the minor groove. This groove, and the narrower one is known as the minor groove. This groove asymmetry is vital for granting access to proteins that bind to particular base sequences in DNA.

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When you’re drawing models of DNA, the molecular details of the structure are not necessary. The sugar-phosphate backbones can be simplified to single lines with arrowheads to identify the 3’ ends. Base pairing is drawn as short lines between the backbones and, if the sequence is part of the model, nucleotides are represented by letters. MODEL Draw a double-stranded DNA molecule with the sequence A-G-C-T. Label the 5’ and 3’ ends, one of the sugar phosphate backbones, and the hydrogen bonds involved in base pairing. To see this model in action, go to the Study Area of Mastering Biology Since Watson and Crick’s model of the double helix was published, experimental tests have shown that the hypothesis is correct in almost every detail. To summarize: DNA’s secondary structure consists of two antiparallel strands twisted into a double helix. The double helix is shaped and stabilized by hydrogen bonding between the complementary base pairs, hydrophobic interactions, and van der Waals interactions. So far, the focus of this chapter has been on DNA’s secondary structure. Does the DNA double helix also form tertiary structures?

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The Tertiary Structure of DNA

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Recall that the secondary structure of a protein often leads to a more compact tertiary structure when the polypeptide folds on itself. It turns out that the DNA in cells is also normally found in more compact three-dimensional structures. The need for this compaction is evident, when you consider that the total length of DNA in each of your cells is roughly six feet long. Compared to proteins, tertiary structure in DNA is less dependent on primary structure, and so it is far less variable between different sequences. Two forms of DNA tertiary structure are commonly found in cells. When DNA becomes wound too tightly or loosely with respect to the number of base pairs per helical turn, it can twist on itself to form compact, three-dimensional structures called supercoils. In addition, DNA in the cells of eukaryotes and certain archaea will from tertiary structures by wrapping around specialized DNA- binding proteins called histones. The resulting DNA protein complexes compact the DNA into discrete, movable units during cell division ( ie. condensed chromosomes, contribute to DNA’s ability to store and transmit information). Now let’s take a closer look at how the structure of DNA is involved in storing biological information.

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DNA Functions as an Information-Containing Molecule

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Watson and Crick’s model created a sensation for a simple reason: It revealed the role of DNA as a biological reservoir of information. In literature, information consists of letters on a page. In music, information is composed of the notes on a staff. But inside cells, information consists of a sequence of nucleotides in a nucleic acid. The four nitrogenous bases function like letters of the alphabet. A sequence of bases is like the sequence of letters in a word, it has meaning. In all organisms that have been examined to date, from tiny bacteria to gigantic redwood trees, DNA stores the information required for the organisms growth and reproduction. Exploring how hereditary information is encoded and translated into action is the heart of several later chapters. Here, however, our focus is on DNA structure and how this structure relates to its function and, possibly, how life began. The theory of chemical evolution holds that life began once a molecule emerged that could make a copy of itself. Does the structure of DNA allow it to be replicated? Watson and Crick ended their paper on the double helix with one of the classic understatements in the scientific literature: “ It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism”. Here’s the key insight: DNA’s primary structure serves as a template for the synthesis of a complementary strand, meaning that DNA contains the information required for a copy of itself to be made.

copy of the DNA molecule can be produced. When double-stranded DNA is heated to 95 degrees celsius, the bonds between complementary base pairs break and single stranded DNA results. Considering this observation, is the reaction shown in step 1 spontaneous?Step 1: The two strands of a DNA double helix can be separated by breaking the hydrogen bonds that hold them together using either heat or enzyme catalyzed reactions. Step 2: Free deoxyribonucleotides form hydrogen bonds with complementary bases on the original strand of DNA, also called a template strand. As they do, their sugar-phosphate groups form phosphodiester linkages to create a new strand, also called a complementary strand. Note that the 5’-->3’ directionality of the complementary strand is the opposite to that of the template strand. Step 3: Complementary base pairing allows each strand of a DNA double helix to be copied exactly, producing two identical daughter molecules. Making copies of DNA represents one of the five characteristics of life: replication. But can DNA catalyze the reactions needed to self replicate? In today's cells and in laboratory experiments, the answer is no. Instead, the molecule is copied through a complicated series of reactions that are catalyzed by enzymes. Why cant DNA catalyze these reactions itself?

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The DNA Double Helix Is a Stable Structure

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The DNA double helix is highly structured. It is regular, symmetric, and held together by phosphodiester linkages, hydrogen bonding, and hydrophobic interactions. In addition, the double helix has few functional groups exposed that can participate in chemical reactions, making the molecule particularly stable and resistant to degradation. Intact stretches of DNA have been recovered from fossils that are tens of thousands of years old. The molecules have the same sequence of bases as the organisms had when they were alive, despite death and exposure to a wide array of pH, temperature, and chemical conditions. DNA’s stability is the key to its effectiveness as a reliable information storage molecule. DNA’s structure is consistent with its function in cells. The orderliness and stability that make DNA such a dependable information repository also make it inept at catalysis. Recall that enzymes function by forming a structure that will specifically bind to a substrate and catalyze a reaction. A wide variety of catalytic activities can be generated in protein enzymes thanks to variation in the reactivity among R-groups in amino acids and the enormous diversity of shapes found in proteins. In comparison, the structure of DNA is simple and nonreactive. Its not surprising then that DNA has never been observed to catalyze any reaction in any organism. In short, DNA furnishes an extraordinarily stable template for storing information encoded in a sequence of bases. But owing to DNA’s inability to act as an effective catalyst and therefore to self replicate, there is virtually no support for the hypothesis that the first life form consisted of DNA alone. Instead, most biologists who are working on the origin of life support the hypothesis that life began with RNA.

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RNA Structure and Function

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The first living molecule would have needed to perform two key functions: carry information and catalyze reaction that promoted its own replication. At first glance, these two functions appear to conflict. Information storage requires regularity and stability; catalysis requires variation in chemical composition and flexibility in shape. How is it possible for a molecule to do both? The answer lies in structure.

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Primary Structure

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Like DNA, RNA has a primary structure consisting of for types of nitrogenous bases extending from a sugar-phosphate backbone. But it’s important to recall two significant differences between these nucleic acids: The sugar in the sugar-phosphate backbone of RNA is ribose, not deoxyribose as in DNA. The pyrimidine base thymine does not exist in RNA. Instead, RNA contains the closely related pyrimidine base uracil. The first point is critical. Look back at Figure 4.1b and compare the functional groups attached to ribose and deoxyribose. Notice the hydroxyl is much more reactive than the hydrogen atom on the 2’ carbon of deoxyribose. When RNA molecules fold in certain ways, the hydroxyl group can attack the phosphate linkage between nucleotides, which would generate a break in the sugar phosphate backbone. This -OH group makes RNA much less stable than DNA, but as you will see later, it can also support other catalytic activities.

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Secondary Structure

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Like DNA, most RNA molecules have secondary structure that results from complementary base pairing between purine and pyrimidine bases. In RNA, adenine forms two hydrogen bonds with uracil, and guanine again forms three hydrogen bonds with cytosine. (other non watson crick base pairs can occur, although less frequently.) This hydrogen bonding should seem familiar, since DNA bonds in a similar manner --so how do the secondary structures of RNA and DNA differ? In the vast majority of cases, the purine and pyrimidine bases in RNA undergo hydrogen bonding with complementary bases on the same strand, rather than forming hydrogen bonds with complementary bases on a different strand, as in DNA. FIgure 4.8 shows how within strand base pairing works. The key is that when bases on one part of an RNA strand fold over and align with bases on another part of the same stand, the two sugar phosphate strands are antiparallel. In this orientation hydrogen bonding between complementary bases results in a helical structure that resembles the double helix of DNA, but unlike DNA, RNA structure forms form s single nucleic acid strand.

If the section where the fold occurs includes unpaired bases, then the stem and loop configuration shown in FIgure 4.8 results. Several other types of RNA secondary structures are possible, each involving a different length and arrangement of base paired segments. Like the alpha-helices and beta-pleated sheets observed in many proteins, RNA secondary structures will form spontaneously. The bases are brought together by hydrophobic interaction and stabilized by hydrogen bonding and base stacking interactions.

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This RNA molecule has secondary structures in the form of a double helical “stem” and unpaired “loop”. Note that in secondary structures, the bases participating in hydrogen bonding are antiparallel.

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Tertiary Structure

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RNA molecules can also have tertiary structure, which arises when secondary structures fold into more complex shapes. The pseudoknot structure in Figure 4.9 is an example of how three dimensional shapes can be formed by base pairing between distant regions of folded RNA molecules. As a result, RNA molecules with different base sequences can have very different overall shapes and chemical properties. RNA molecules are much more diverse in size, shape, , and reactivity than DNA molecules. Base pairing between different regions of an RNA molecule causes it to fold into a more complex tertiary structure. Note that in tertiary structures, as in secondary structures, the bases participating in hydrogen bonding are antiparallel. Table 4.1 summarizes the similarities and differences in the structures of RNA and DNA.

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RNA’s Versatility

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In cells, RNA molecules are highly versatile, like a pocket tool with an array of functions. In terms of structure, you’ve seen that RNA is a nucleic acid like DNA, but RNA folds into complex three dimensional shapes much like proteins. The structural flexibility of RNA molecules allows them to perform many different tasks. The central dogma introduced RNA as an intermediate between DNA and protein. This intermediate, called messenger RNA, transmits information needed to synthesize polypeptides. Further research has brought new insights into the diversity of roles that RNAs play in cells. RNA molecules also help regulate the production of messenger RNA from DNA, process and edit information stored in these messages, and even catalyze the synthesis of proteins, among other things. For this chapter, let’s focus on the roles that RNA may have played in the origin of life, as a catalyst and as an information containing entity.

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RNA Can Function as a Catalytic Molecule

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In terms of diversity in shape and chemical reactivity, the four types of nucleotides in RNA molecules are no match for the 20 different amino acid residues in proteins. Nevertheless, because RNA has a degree of structural and chemical complexity, its capable of forming structures that catalyze a number of chemical reactions. Sidney Altman and Thomas Cech shared the 1989 Nobel Prize in Chemistry for showing that organisms have catalytic RNAs. These RNAs are called ribozymes, or RNA enzymes, because they catalyze reaction similar to protein enzymes.

Figure 4.10 shows the structure of a ribozyme Cech isolated from a single celled eukaryote called Tetrahymena. This ribozyme catalyzes both the hydrolysis and condensation of phosphodiester linkages in RNA. Researchers have since discovered a variety of ribozymes that catalyze several important reactions in cells. For example, ribozymes are responsible for the catalytic activity of the ribosomes that polymerize amino acids to form polypeptides. Ribozymes are at work in your cells right now.

The three dimensional nature of ribozymes is vital to their catalytic activity. To catalyze a chemical reaction, substrates must be brought together in an environment that will promote the reaction. As with protein enzymes, the region of the ribozyme that is responsible for this activity is called the active site. When the Tetrahymena ribozyme was compared to enzymes that catalyze similar reactions, their active sites were found to be similar in structure. This observation about two very different molecules demonstrates the critical relationship between structure and function. The discovery of ribozymes was a watershed event in origin of life research. Before Altman and Cech published their results, most biologists thought that the only molecules capable of catalyzing reactions in cells were proteins. The fact that a ribozyme could catalyze the formation of a phosphodiester bond raised the possibility that an RNA molecule could polymerize a copy of itself. Such a molecule could qualify as the first living entity. Is there any experimental evidence to support this hypothesis.

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7 introduction

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The cell theory states that all organisms consist of cells, and all cells are derived from preexisting cells. Since this theory was initially developed and tested in the 1850’s, an enormous body of research has confirmed that the cell is the fundamental structural and functional unit of life. Life on Earth is cellular. Previous chapters (Unit 1) delved into the fundamental attributes of life by looking at biologists current understanding of how the cell evolved, from the early chemistry to the assembly and replication of a protocell. As the first cells left their deep sea incubators in the oceans of Earth, they took with them characteristics that are now shared among all known life forms: Proteins that perform most of the cells functions Nucleic acids that store, transmit,and process information Carbohydrates that provide chemical energy, carbon, support, and identity A plasma membrane that serves as a selectively permeable barrier Thanks to the selective permeability of phospholipid bilayers and the activity of membrane transport proteins, the plasma membrane creates an internal environment that differs from conditions outside the cell. Our task now is to explore the structures contained within this membrane to understand how the properties of life emerged form their collaboration. Cells are divided into two fundamental types: eukaryotes and prokaryotes. This division is mostly based on cell morphology eukaryotic cells have a membrane bound compartment called a nucleus and prokaryotic cells do not.But according to phylogeny (“tribe-source”), or evolutionary history, organisms are divided into three broad domains called (1) Bacteria, (2) Archaea, and (3) Eukarya. Members of the Bacteria and Archaea are prokaryotic; members of the Eukarya, including algae, fungi, plants, and animals are eukaryotic. Let’s begin by analyzing how the parts inside a cell function individually and then exploring how they work as a unit. This approach in analogous to studying individual organs in the body and then learning about how they work together to form the nervous system or digestive system. As you study this material, keep asking yourself this key question: How does the structure of this part or group of parts correlate with its function?

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Bacterial and Archaeal Cell Structures and Their Functions

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Until the mid-twentieth century, biologists thought that prokaryotic cells had a simple morphology and that little structural diversity existed among species. This conclusion was valid at the time, given the resolution of the microscopes that were available and the number of species that had been studied. But our view of prokaryotes changed dramatically in 1931 with the invention of the transmission electron microscope, which passes a beam of electrons through extremely thin sections of cells to visualize their internal structure. Recent improvements in microscopy and other research tools are changing our view even more.

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A Revolutionary New View

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A Revolutionary New View Biologists are now convinced that prokaryotic cells, among which bacteria are the best understood, have an array of distinctive structures and functions found among millions of species. Discovering this diversity among prokaryotes was one of the most exciting developments in cell biology.To start with the basics, Figure 7.1 offers a low magnification electron micrograph and a stripped down diagram of prokaryotic cell. This electron micrograph, along with others in this chapter, was generated using a transmission electron microscope.Prokaryotic cells are identified by a negative trait, the absence of a membrane bound nucleus. Common characteristics among all bacterial and archaeal cells include a plasma membrane, chromosome, and protein synthesizing ribosomes.

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Prokaryotic Cell Structures: A Parts List

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Figure 7.1 highlights the components common to most prokaryotes studied to date, they all have at least one chromosome and many protein synthesizing ribosomes enclosed within a plasma membrane (for more about membranes, see CH. 6 sections 6.1 and 6.2. The phospholipid components of archaeal and bacterial membranes, however, have different structures. Bacterial phospholipids consist of fatty acids bound to glycerol while archaeal phospholipids use highly branched isoprenoid chains bound to glycerol. These molecules also vary in the structure of their hydrocarbon chains and the types of linkages used to join the hydrocarbon tails to glycerol heads. Because these variations, the archaeal membrane is more stable in the extreme environments that are inhabited by certain species in this domain. All the contents of a cell inside the membrane (excluding the nucleus in eukaryotes) are collectively termed the cytoplasm. Let’s explore these parts one by one, starting from the inside and working out, and then look to more specialized structures found in particular species

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The Chromosome Is Organized into a Nucleoid

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The most prominent structure inside a prokaryotic cell is the chromosome. Most bacterial and archaeal species have a single, circular chromosome that consists of a large DNA molecule associated with proteins. The DNA molecule contains information, and the proteins give the DNA structural support. Recall that the information in DNA is encoded in its sequence of nitrogenous bases. Segments of DNA that contain information for building functional RNA’s, some of which may be used to make polypeptides, are called genes. The synthesis of RNA based on information stored in DNA is the step in the central dogma, which describes the flow of genetic information in cells. Thus, chromosomes contain DNA, which contains genes that code for RNA. In the well studied bacterium Escherichia coli, the circular chromosome would be over 1 mm long if it were linear 500 times longer than the cell itself. This situation is typical in prokaryotes. To fit into the cell, the DNA double helix could on itself with the aid of enzymes to form a compact “supercoiled” structure. Supercoiled regions of DNA resemble a rubber band that has been held at either end and then twisted until it coils back onto itself.

The region of the cell where the circular chromosome is located is called the nucleoid.The genetic material in the nucleoid is often organized by clustering loops of DNA into distinct domains, but it is not separated from the rest of the cell interior by a membrane. There is currently intense research into the functional role of these domains and how it changes over time. Besides their chromosomes, prokaryotic cells may contain from one to about 100 small, usually circular, supercoiled DNA molecules called plasmids. Plasmids contain genes but are physically independent of the cellular chromosome. In many cases the genes carried by plasmids are not required under normal conditions; instead they help cells adapt to unusual circumstances, sich as the sudden presence of a poison in the environment. As a result, plasmids can be considered auxiliary genetic elements.

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(A) chromosomes of bacteria and archaea are often over 500times the length of the cell, as shown in this micrograph of E. coli that has been treated to release its DNA. To fit inside cells, this DNA must be highly compacted by supercoiling. (b) A colorized electron micrograph showing the effect of supercoiling on the DNA of isolated plasmids (colored green).

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Ribosomes Manufacture Proteins

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Ribosomes are observed in all prokaryotic cells and are found throughout the cell interior. It is not unusual for a single cell to contain 10,000 ribosomes, each functioning as a protein manufacturing center. Ribosomes are complex structures composed of large and small subunits, each of which contains RNA and protein molecules. Biologists often refer to ribosomes, along with other multicomponent complexes that perform specialized tasks, as “macromolecular machines” . These tiny machines are responsible for the second step of the central dogma, where the information stored in RNA may be used to direct the synthesis of protein. While the ribosomes in bacteria and archaea are similar in size and function, the primary structures of their RNA and protein components are different.

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The Cytoskeleton Structures the Cell’s Interior and Its Shape

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Researchers have also observed long, thin protein filaments in the cytoplasm of bacteria and archaea that serve a variety of roles. All bacterial species, for example, contain cytoplasmic protein filaments that are essential for cell division to take place. Some species also have internal filaments that help maintain cell shape. Protein filaments such as these form the basis of the cytoskeleton. Recent research has revealed a much more complex cytoskeletal network in prokaryotes than previously thought. Researchers are working to identify how these different filaments participate in cell morphology, growth, and division.

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Photosynthetic Species Have Internal Membrane Complexes

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Photosynthesis is the set of chemical reactions responsible for converting the energy in sunlight into chemical energy stored in sugars. In bacteria that perform photosynthesis, it is common to observe multiple membranes passing through the internal region of the cells. The photosynthetic membranes observed in bacteria develop as infoldings of the plasma membrane and contain the enzymes and pigment molecules required for these reactions to occur. In some cases, membrane-bound vesicles pinch off as the plasma membrane folds in. In other cases, flattened stacks of photosynthetic membrane remain connected to the plasma membrane, like those shown in Figure 7.3. These internal membranes provide an extensive surface area that allows more photosynthetic reaction to occur and thus increase the cells abilit to make food.

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Certain Species Have Organelles for Specialized Functions

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Several bacterial species have internal compartments classified as organelles. An organelle is a compartment inside the cell, often bonded by a membrane, that contains enzymes or structures specialized for a particular function. Bacterial organelles perform specialized tasks including, Storing calcium ions Holding crystals of the mineral magnetite, which function like compass needles to help cells swig in a directed way; and Concentrating enzymes responsible for synthesizing complex carbon compounds from carbon dioxide.

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The Cell Wall Forms a Protective “Exoskeleton”

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Because the cytoplasm contains a high concentration of solutes, it is hypertonic relative to the surrounding environment in most habitats. Under these conditions, water enters the cell via osmosis and makes the cells volume expand. In most bacteria and archaea, this pressure is resisted by a stiff cell wall. Bacterial and archaeal cell walls are a tough, fibrous layer that surrounds the plasma membrane. This structure protects the organisms and gives them shape and rigidity, much like the exoskeleton (external skeleton) of a crab or insect. In prokaryotes, the osmotic pressure that pushes the plasma membrane against the cell wall has a force similar to the pressure in an automobile tire. The molecular structure of cell walls differs between bacteria and archaea. In most bacteria, the primary structural component of the cell wall is the modified polysaccharide peptidoglycan. Some bacterial cell walls are also surrounded by an outer membrane consisting of glycolipids. The cell walls of archaea are highly variable among the different species, but peptidoglycan is markedly absent among those studied to date.

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Certain Species Have External Structures for Movement or Attachment

Certain Species Have External Structures for Movement or Attachment

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Many prokaryotes interact with their environment via structures that grow from the plasma membrane. The flagella and fimbriae shown in Figure 7.4 are structures commonly found on bacterial surfaces. Archaea also have flagella and appendages similar to fimbriae, but they are structurally distinct from those found on bacteria.

A prokaryotic flagellum (plural: flagella) is assembled from many different proteins at the cell surface of certain species. The feature that is common to both archaeal and bacterial flagella is a molecular motor embedded in the plasma membrane. The proteins that make up these motors and filaments differ between the two groups, but their functions are the sme, to rotate a long rigid filament that propels the cell through water. At top speed, flagella can drive a bacterial cell at 60 cell lengths per second. In contrast the fastest animal in the ocean the sail fish can swim at a mere 10 body lengths per second. A fimbria is a needle like projection that extends from the plasma membrane of some bacteria and promotes attachment to other cells or surfaces. Similar but unrelated structures are also found in archaea. These structures tend to be more numerous than flagella and are often distributed over the cell's entire surface. Fimbriae are not involved in cell motility, but their ability to glue bacteria to the surface of tissues makes them crucial in establishing many infections.

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7.2 Eukaryotic Cell Structures and Their Functions

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The domain Eukarya includes species that range for microscopic algae to 100-meter-tall redwood trees. Protists, fungi, plants and animals are all eukaryotic. Although multicellularity has evolved several times among eukaryotes many species are unicellular. The first thing that strikes biologists about eukaryotic cells is how much larger they are on average than bacteria and archaea. Most prokaryotic cells measure 1 to 10 micro meters in diameter, while most eukaryotic cell range from about 5 to 100 micro meters in diameter. A micrograph of an average eukaryotic cell, at the same scale as the bacterial cell in Figure 7.1 would fill this page. For many species of unicellular eukaryotes, this size difference allows them to make a living by ingesting bacteria and archaea whole. Large size has a downside, however. As a cell increases in diameter, its volume increases more than its surface area. In other words, the relationship between them, the surface area to volume ratio, changes. Since the surface is where the cell exchanges substances with its environment, the reduction in this ratio decreases the rate of exchange: Diffusion only allows for rapid movement across a very small distances. Prokaryotic cells tend to be small enough so that ions and small molecules arrive where they are needed via diffusion. The random movement of diffusion alone, however, is insufficient for this type of transport as the cells diameter increases. How do eukaryotic cells overcome the problems associated with a low surface-area-to- volume ratio? The answer lies in their many organelles.

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The Benefits of Organelles

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Organelles compartmentalize the volume inside a eukaryotic cell into many small bins. Because eukaryotic cells are subdivided, the cytosol the fluid portion between the plasma membrane and these organelles, is only a fraction of the total cell volume. This relatively small volume of cytosol offsets the effects of a low cell surface area to volume ratio with respect to the exchange of nutrients and waste products. Compartmentalization also offers two key advantages: Incompatible chemical reaction can be separated. For example, new fatty acids can be synthesized in one organelle while excess or damaged fatty acids are degraded and recycled in a different organelle. Chemical reaction become more efficient. First, the substrates required for particular reaction can be localized and maintained at high concentrations within organelles. When substrates are used up in a particular part of the organelle, they can be replaced by substrates that have only a short distance to diffuse. Second groups of enzymes that work together can be clustered within or on the membranes of organelles instead of floating free in the cytosol. When the product of one reaction is the substrate of a second reaction, clustering the two enzymes increases the speed and efficiency of both reactions. The complex internal organization of eukaryotic cells resembles a sprawling industrial park. The organelles and other structures found in eukaryotes are like highly specialized buildings that act as administrative centers, factories, transportation corridors, waste and recycling factories, warehouses and power stations. Let's now dig a little deeper into eukaryotic cells to investigate how their internal structures perform these different roles.

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Eukaryotic Cell structures: A Parts List

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Figure 7.5 provides simplified views of a typical animal cell and a typical plant cell. The artist has removed most of the cytoskeletal elements to make the organelles and other cellular parts easier to see. As you read about each cell component in the pages that follow focus on identifying how its structure correlates with its function. Then use Table 7.1 at the end of this section (page 157) as a study guide. As with bacterial cells, lets start from the inside and move to the outside.

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Generalized images of (a) an animal and (b) a plant cell that illustrate the cellular structures in the “typical” eukaryote. The structures have been colo coded for clarity. Compare wit the prokarotic cell, shown at true relative size.

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THe

Nucleus

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While prokaryotic chromosomes are in a loosely defined nucleoid region, eukaryotic chromosomes are enclosed within a membrane bound compartment called the nucleus. Among the largest and most highly organized of all organelles, the nucleus function as an administrative center for information storage and processing. It is enclosed by a unique double membrane structure called the nuclear envelope. As Section 7.4 will detail, then nuclear envelope is studded with pore like openings, and the inside surface is linked to fibrous proteins that form a lattice like sheet called the nuclear lamina. The nuclear lamina stiffens the double membrane and maintains organelle shape.

Chromosomes do not float freely inside the nucleus, instead, each chromosome occupies adistinct area, which may vary in different cell types and over the course of cell replication. Thechromosomes are arranged in the nucleus with densely packed section concentrated at theperiphery and loosely packed sections toward the interior.The nucleus is the site where the first step of the central dogma takes place, the synthesis ofRNA form information encoded in DNA. The nucleus also contains specific sites where RNAmolecules are processed into their functional form. One of these regions called the nucleolus,is responsible for manufacturing and processing the RNA molecules that assemble into largeand small ribosomal subunits.

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The nucleus houses genetic, or heredity, information encoded in DNA, which is a component ofthe chromosomes inside the nucleus.

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Ribosomes

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Scattered throughout the cytosol of eukaryotic cells are millions of ribosomes. Like bacterialribosomes, eukaryotic ribosomes are complex macromolecular machines that use theinformation in RNA to manufacture proteins. Note that ribosomes are not compartments insidea cell, so they are not classified as organelles.

Eukaryotic ribosomes are not only scattered free in the cytosol, but are also associated with thesurface of an organelle called the endoplasmic reticulum. Proteins manufactured by freeribosomes either remain in the cytosol or are imported into other organelles, such as thenucleus. Those made at the surface of the endoplasmic reticulum have a different fate. Letstake a closer look at this organelle to learn more.

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Eukaryotic ribosomes are larger than bacterial and archaeal ribosomes, but similar in overallstructure and function.

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Endoplasmic Reticulum

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Portions of the nuclear envelope extend into the cytoplasm to form an extensive membraneenclosed factory called the endoplasmic reticulum(ER). As figure 7.5 shows, the ERmembrane is continuous with the nuclear envelope. Although the ER is a single organelle, ithas two regions that are distinct in structure and function. Lets consider each region in turn.The Rough Endoplasmic Reticulum (RER) or simply rough ER, is named for its appearancein transmission electron micrographs. The dark, knobby looking structures lining the perimeterof the rough ER are ribosomes that are attached to its membrane. The membrane forms anetwork of flattened sacs and tubules.

The ribosomes associated with the surface of the rough ER synthesize proteins that move intothe interior of the organelle. The inside compartment of the rough ER, like the interior of any saclike structure is a cell or body, is called the lumen. In the rough ER lumen newly manufacturedproteins undergo folding and other types of processing.After the proteins are processed in the rough ER, they will either function in the ER or bepackaged into vesicles and transported as cargo to other destinations, such as a differentorganelle, the plasma membrane, or the cell exterior. The proteins that are exported playvarious roles for the cell. Some carry messages to other cells; some act as membrane transportproteins or pumps; others catalyze reactions.In electron micrographs, parts of the ER that are free of ribosomes appear smooth and even.Appropriately, these regions of the ER are called the smooth endoplasmic reticulum (SER)or smooth ER.The smooth ER contains enzymes that catalyze reactions involving lipids. Depending on thetype of cell, these enzymes may synthesize lipids needed by the organisms (such asphospholipids) or modify lipids and other molecules that are toxic. In addition, the smooth ERfunctions as a reservoir for calcium ions (Ca2+) that can be released to trigger a wide array ofactivities inside the cell.The structure of the endoplasmic reticulum correlates closely with its function. The rough ERhas ribosomes and functions primarily as a protein manufacturing center; the smooth ER lacksribosomes and functions primarily as a lipid processing center.

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The ER is continuous with the nuclear envelope and possesses two distinct regions: The roughER is a system of membrane bound sacs and tubules with ribosomes attached; the smooth ERis a system of membrane bound sacs and tubules that lacks ribosomes.

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Golgi Apparatus

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Most of the proteins that leave the rough ER must pass through the Golgi apparatus beforereaching their final destination. The Golgi apparatus consists of a set of membranouscompartments called cisternae ( singular: cisterna). Each cisterna varies in function based onthe distribution of different enzymes across the set of compartments. In most eukaryotes, thesecompartments are flattened sacs that are stacked on top of each other like pancakes. When thecisternae are arranged in this way, the Golgi apparatus has a distinct polarity or sidedness. Thecis (“on this side”) surface is closest to the nucleus and the trans (“across”) surface is orientaedtoward the plasma membrane.

The cis side of a Golgi apparatus receives the vesicles containing rough ER products, referredto as cargo, and the trans side ships them out to other organelles or the cell surface. As thecargo moves through the Golgi apparatus from the cis to trans surfaces, it is sequentriallyprocessed by the enzymes resident in each compartment and then packaged for delivery.Micrographs often show “bubbles” on either side of a Golgi stack. These are membrane boundtransport vesicles that carry proteins or other products to and from the organelle.

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Lysosomes

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Animal cells contain organelles called lysosomes that function as recycling centers.Lysosomes contain about 40 different enzymes, each specialized for hydrolyzing different typesof macromolecules, proteins, nucleic acids, lipids, or carbohydrates. The amino acids,nucleotides, sugars and other molecules that result from hydrolysis are exported from thelysosome via transport proteins in the organelles membrane. Once in the cytosol, they can beused as sources of energy or building blocks for new molecules.

The digestive enzymes inside lysosomes are collectively called acid hydrolases because underacidic conditions ( a pH of 5.0) they use water to break monomers from macromolecules. In thecytosol, where the pH is about 7.2 acid hydrolases would be less active. Proton pumps in thelysosomal membrane maintain an acidic pH in the lumen of the lysosome by importinghydrogen ions.Even though lysosomes are physically separated from the Golgi apparatus and theendoplasmic reticulum, these various organelles jointly form a key functional grouping referredto as the endomembrane system. The endomembrane (“inner-membrane”) system is a centerfor producing, processing and transporting proteins, carbohydrates, and lipids in eukaryoticcells. For example, acid hydrolases are synthesized in the ER, processed in the Golgiapparatus, and then shipped to the lysosome. Section 7.5 analyzes the intracellular movementof molecules through the endomembrane system in more detail.

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Lysosomes are oval or globular organelles that contain enzymes to digest macromolecules.

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Vacuoles

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The cells of plants, fungi and certain eukaryotes contain a prominent organelle called avacuole. Compared with the organelles of animal cells, vacuoles of plant and fungal cells arelarge, in plants, sometimes taking up as much as 80 percent of a cells volume

Propose a hypothesis to explain why toxins like nicotine, cocaine, and caffeine are stored invacuoles instead of the cytosol.The cellular role of a vacuole can vary between organisms and even between cells of the samemulticellular organism. Some vacuoles are known to contain hydrolases to digest and recyclemacromolecules which has led to their being classified as functionally equivalent to thelysosomes of animal cells.A more common role of vacuoles is to serve as storage depots. In many cases, ions such aspotassium (K+) and chloride(Cl-), among other solutes, are stored at such high concentrationsthey draw water in from the environment. As the vacuole expands in volume, it pushes thecytoplasm and plasma membrane against the cell wall. The effect of this change in volume isobserved when wilted green plants regain their rigid structure after water is added to the soil.In certain plant cells, vacuoles can include more specialized storage functions:● In seeds, cells may contain a large vacuole filled with proteins. When theembryonic plant inside the seed begins to grow, enzymes begin digesting theseproteins to provide amino acids for the growing individual.● In flower petals or fruits, cells may contain vacuoles that are filled with colorfulpigments.● Elsewhere, vacuoles may be packed with noxious compounds that protectleaves and stems from being eaten by predators. The type of chemical involvedvaries by species ranging from bitter tasting tannins to toxins such as nicotine,morphine, caffeine, or cocaine.

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Vacuoles vary in size and function. Some contain digestive enzymes and serve as recyclingcenters; most are large storage containers.

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Peroxisomes

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Virtually all eukaryotic cells contain globular organelles called peroxisomes. These organellesoriginate when empty vesicles from the ER are loaded with peroxisome-specific enzymes fromthe cytosol. Once peroxisomes are formed, they do not exchange materials with otherorganelles, so they are not considered part of the endomembrane system.

Although different types of cells from the same individual may have distinct types ofperoxisomes, these organelles all share a common function: Peroxisomes are centers forreduction -oxidation (redox) reactions. For example, the peroxisomes in your liver cells containenzymes that oxidize fatty acids to form a compound that can be used to store energy for thecell.In animals and plants, these reactions often include hydrogen peroxide (H2O2), which is highlyreactive. If hydrogen peroxide escaped from the peroxisome, it would quickly react wit anddamage DNA, proteins, and cellular membranes. This event is rare, however, because insidethe peroxisome, it would quickly react with and damage DNA, proteins, and cellularmembranes. This event is rare, however, because inside the peroxisome, the enzyme catalasequickly detoxifies hydrogen peroxide to form water and oxygen. The enzymes found inside theperoxisome make a specialized set of oxidation reaction possible and safe for the cell.

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Peroxisomes are globular organelles that contain enzymes involved in detoxifying reactivemolecules, such as hydrogen peroxide.

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Mitochondria

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Most of the work required to maintain the structure and function of a cell depends on thechemical energy stored in adenosine triphosphate (ATP). The organelle primarily responsiblefor supplying ATP in animals, plants, and virtually all other eukaryotic cells is the mitochondrion(plural: mitochondria).As Figure 7.13 shows, each mitochondrion has two membranes. The outer membrane definesthe organelles surface, while the inner membrane forms a series of sac-like cristae ( singular:crista). The solution enclosed within the inner membrane is called the mitochondrial matrix. Ineukaryotes, the chemical energy in carbohydrates and fats is used to produce ATP. Most of theenzymes and molecular machines responsible for synthesizing ATP are embedded in the innermembrane or suspended in the matrix

Mitochondria are typically drawn as small bean-shaped organelles, but in cells, theirmorphology is often much more dynamic. These organelles are prone to fusion and fission,resulting in either elongated and branched structures, called mitochondrial networks, or multipleindividual organelles. Depending on the type of cell, the number of mitochondria can range fromone to more than a million.Each mitochondrion has many copies of small, circular or in some species linear, chromosomecalled mitochondrial DNA (mtDNA) that is independent of the nuclear chromosomes. Themitochondrial DNA contains only a tiny fraction of the genes responsible for the function of theorganelle the other genes reside in the nuclear DNA.Among the genes present in mitochondrial DNA are those that encode RNA’s for mitochondrialribosomes. These ribosomes are smaller than those found in the cytosol, yet they still functionto produce some of the mitochondrial proteins. (Most of the proteins found in mitochondria areproduced from ribosomes in the cytosol and imported into the organelle.)

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Mitochondria vary in size and shape, but all have two membranes with sac-like cristae formedfrom the inner membrane that are involved in producing ATP.

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Chloroplasts

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Most algal and plant cells possess an organelle called the chloroplast, in which sunlight isconverted to chemical energy during photosynthesis. Then Number of chloroplasts per cellvaries from one to several dozen.

Like the mitochondrion, the chloroplast is surrounded by a double membrane. Unlikemitochondria, however, chloroplasts have no cristae extending from the inner membrane intothe interior. Instead, a third membrane forms an independent network of hundreds of flattenedsac like structures called thylakoid throughout the interior. Most thylakoids are arranged ininterconnected stacks called grana (singular: granum).Many of the pigments, enzymes, and macromolecular machines responsible for converting lightenergy into chemical energy are embedded in the thylakoid membranes. The fluid filled spacesurrounding grana, called stroma, contain enzymes that use this chemical energy to producesugars.Like mitochondria, each chloroplast contains copies of its own circular chromosome and smallribosomes that manufacture some, but not all, of the organelles proteins. And like mitochondria,chloroplasts also grow and divide independently of cell division.Because these attributes are odd compared with those of other organelles, biologists proposethat mitochondria and chloroplasts were once free living bacteria. According to theendosymbiosis theory, these bacteria were engulfed by the ancestors of modern eukaryotes,but were not destroyed; instead, a mutually beneficial relationship evolved.

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Many of the enzymes and other molecules required for photosynthesis are located inmembranes inside the chloroplast. These membranes form thylakoids that consist of discsstacked into grana.

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Cytoskeleton

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The final major structural feature common to all eukaryotes is the cytoskeleton. This extensivesystem of protein fibers gives the cell its shape and structural stability. It is also involved inmoving materials within the cell as well as the cell itself. In essence, the cytoskeleton organizesall the organelles and other cellular structures into a cohesive whole. Recall that prokaryotesalso have a cytoskeleton, but it is far less extensive. Section 7.6 will analyze the structure andfunctions of the eukaryotic cytoskeleton in detail.

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The Eukaryotic Cell Wall and Extracellular Matrix

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In fungi, algae, and plants, cells have an outer cell wall in addition to their plasma membrane.Like the cell wall in bacteria and archaea, a eukaryotic cell wall is located outside the plasmamembrane and furnishes a durable outer layer that gives structural support to the cell. The cellsof animals lack a cell wall, but are often supported by a more diffuse mixture of secretedproteins and polysaccharides that form the extracellular matrix or ECM.Although the composition of the eukaryotic cell wall and ECM varies among species and evenamong types of cells in the same individual, the general plan is similar: Rods or fibers runthrough s stiff matrix made of polysaccharides and proteins. This organization of extracellularmolecules provides cells with structural support and may be used to attach cells to one another.To summarize: Within a cell, the structure of each component correlates with its function. Asyou will see in the next section, the overall size, shape and composition of a cell similarlycorrelate with its function.

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7.5 Cell Systems II:

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The Endomembrane System Manufacturers, Ships, and RecyclesCargoThe nuclear membrane is not the only place in cells where cargo moves in a regulated andenergy demanding fashion. Most of the proteins found in peroxisomes, mitochondria, andchloroplasts are also actively imported after being manufactured by ribosomes that are free inthe cytosol.If you think about it for a moment, the need to sort proteins and ship them to specific destinationshould be clear. Proteins are produced by ribosomes that are either free in the cytosol or on thesurface of the ER. Many of these proteins must be transported to a compartment inside theeukaryotic cell. Acid hydrolases must be shipped to lysosomes and catalase to peroxisomes.To get to the right location, each protein must have a specific zip code and delivery system.To get a better understanding of protein sorting and transport in eukaryotic cells, let's considerperhaps the most intricate of all manufacturing and shipping complexes: the endomembranesystem. In this system proteins that are synthesized on the rough ER move to the Golgiapparatus for processing, and from there they travel to the cell surface or other destinations.

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Studying the Pathway through the Endomembrane System

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extensive rough ER is shown). This correlation led to the idea that these organelles mayparticipate in a “secretory pathway” that starts in the rough ER and ends with products leavingthe cell. How does this hypothesized pathway work?

This hypothesis proposes that proteins intended for secretion from the cell are synthesized andprocessed in a highly prescribed series of steps. Note that proteins are packaged into vesiclesin order to move them from the rough ER to the Golgi and from the Golgi to the cell surface.

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Tracking Protein Movement via Pulse-Chase Assay

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George Palade and colleagues did pioneering research on the secretory pathway using apulse-chase experiment to track protein movement. This strategy is based on two steps:1. The “Pulse” Expose experimental cells to a high concentration of modified aminoacid for a short time. For example, if a cell is briefly exposed to a large amount ofradioactivity labeled amino acid, virtually all the proteins synthesized during thatinterval will be radiolabeled.2. The “Chase” End the pulse by washing away the modified amino acid andreplacing it with the normal version of the same molecule. The time following theend of the pulse is referred to as the chase. The proteins synthesized during thechase period will not be radiolabeled.The idea is to mark a population of molecules at a particular interval (the pulse) and then followtheir fate over time (the chase). This approach is analogous to adding a small amount of dye toa stream and then following the movement of the dye to track the pattern of water flow.To understand why the chase requires unlabeled amino acids in these experiments, imaginewhat would happen if you added dye to a stream continuously. Soon the entire stream would bedyed, you could no longer track a specific population of dye molecules.In testing the secretory pathway hypothesis, Parade's team focused on pancreatic cells.Pancreatic cells are specialized for secreting digestive enzymes into the small intestine and arepacked with rough ER and Golgi. The cells for the experiment were grown in culture or in vitro.The basic experimental approach was to pulse the cells for 3 minutes with radiolabeled versionof the amino acid leucine, followed by a long chase period with nonradioactive leucine. Thepulse produced a population of proteins that were related to one another by the timing of theirsynthesis. At different points during the chase, the researchers tracked the movement of theseproteins by preparing samples of the cells for autoradiography and electron microscopy. Thedrawings in Figure 7.19a illustrate what the researchers observed from electron micrographstaken at the end of the pule and at different times during the chase.

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Part (a) shows how newly synthesized proteins are labeled during the pulse when exposed tomedium containing radioactive amino acids (red). At the start of the chase, this medium isreplaced with medium containing non radioactive amino acids (yellow) so only proteins labeledin the pulse will be tracked (red dots). (b) A graph plots the relative abundance of radiolabeledproteins in three different organelles during the chase.

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Results of the Pulse Chase Experiment

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The graph in Figure 7.19b was based on the electron microscopy results, which revealed that proteins are trafficked through the secratory pathway in a highly organized and directed amnner. Track the movement of proteins through the cell during the chase by covering the graph with a piece of paper and then slowly sliding it off from left to right. Notice what is happeing to each line at the follwing time points

0 minutes Immediately after the pulse, most of the newly synthesized proteins are inside this cell’s rough ER. 37 minutes During the chase, the situation Changes. At this time, most of the labeled proteins have left the rough ER and entered the Golgi apparatus, and some of them have accumulated inside structures called secretory vesicles. 117 minutes By the end of the chase, most of the labeled proteins have left the Golgi and are either in secretory vesicles or were secreted from the cells.

0 0 minutes Immediately after the pulse, most of the newly synthesized proteins are inside this cell’s rough ER. 37 minutes During the chase, the situation Changes. At this time, most of the labeled proteins have left the rough ER and entered the Golgi apparatus, and some of them have accumulated inside structures called secretory vesicles. 117 minutes By the end of the chase, most of the labeled proteins have left the Golgi and are either in secretory vesicles or were secreted from the cells. Over a period of two hours, the labeled population of proteins moved along a defined trail through the tough ER, Golgi apparatus, and secretory vesicles to teach the exterior of the cell Jamieson and Palade’s results support the hypotheses that a secretory pathway exists and that the tough ER and Golgi apparatts function together as parts of an integrated endomembrane system Next, let’s examine four of this pathway's steps in mote detait 1. How do proteins enter the then of the rough ER? 2. How do the proteins move from the ER to the Golgi apparatus? 3. Once proteins are inside the Golgi apparatus, what happens to them? 4. And finally, how does the Golgi appaatus sat out the proteins so each one goes to the appropriate place?

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How do Proteins Enter the Endomembrane system d

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The synthesis of proteins destined to be secreted or embedded in membranes begins in ribosomes free in the cytosol. Gunter Blobel and colleagues proposed that at some point these ribosomes become attached to the outside of the ER. But what directs ribosomes t0 the ER sudace? The “signal hypothesis” predicts that proteins bound for the endomembrane system have a molecular zip code that serves a similar role to the nuclear localization signal in nucleoplasmin Blobel proposed that the [itst amino acid residues of the growing protein act as a signal that marks the ribosome for trampott to the ER membrane. Blobel's group went on to produce convincing data that supported the hypothesis: They identified a “send-to-ER” signaL or ER signal gquence, that guides the growing protein and associated ribosorne to the rough ER. The ER signal sequence typically is present in the first 20 amino acid residues and is removed when pmtein synthesis '5 complete. More recent work has documented the mechan'sms responsible for receiving this send-to-ER signal and inserting the protein into the tough ER. Eguxe 7.20 on page L63 illustrates the key steps involved for a protein that will eventually be shipped to the inside of an organelle or secreted fmm the cell.

The synthesis of proteins destined to be secreted or embedded in membranes begins in ribosomes free in the cytosol. Gunter Blobel and colleagues proposed that at some point these ribosomes become attached to the outside of the ER. But what directs ribosomes t0 the ER sudace? The “signal hypothesis” predicts that proteins bound for the endomembrane system have a molecular zip code that serves a similar role to the nuclear localization signal in nucleoplasmin Blobel proposed that the [itst amino acid residues of the growing protein act as a signal that marks the ribosome for trampott to the ER membrane. Blobel's group went on to produce convincing data that supported the hypothesis: They identified a “send-to-ER” signaL or ER signal gquence, that guides the growing protein and associated ribosorne to the rough ER. The ER signal sequence typically is present in the first 20 amino acid residues and is removed when pmtein synthesis '5 complete. More recent work has documented the mechan'sms responsible for receiving this send-to-ER signal and inserting the protein into the tough ER. Eguxe 7.20 on page L63 illustrates the key steps involved for a protein that will eventually be shipped to the inside of an organelle or secreted fmm the cell. 1. Step 1 Protein synthesis begins on a free ribosome in the cytosol. The tibosome synthesizes the ER signal sequence, using information carried in an mRNA. 2. Step 2 The signal sequence binds to a signal recognition particle (S&H-a complex of RNA and protein. The attached SRP causes protein synthesis to stop. 3. Step 3 The ribosome + signal sequence + SRP complex moves to the rough ER membrane, where it attaches to the SRP receptor. Think of the SRP as a key that ‘5 activated by an ER signal sequence. The SRP receptorin the ER membtane is the lock. 4. Step 4 Once the lock (the receptor) and key (the SRP) connect, the SRP is released and protein synthesis continues through a channel called the translocon. 5. Step 5 The growing protein is fed into the ER lumen, and the ER signal sequence is removed After cleavage of the signal sequence, the protein may be completely released into the ER lumen. Some proteins, hawewr, remain associated with the membrane as integral membrane proteins. How do such proteins get inserted into the ER membrane? Cunent models propose that the uanslocon has molecular "gates" that divert stretches of nonpolar amino acids in the growing protein into the phospholipid bilayer. Recall that nansmembtane ponions of integral membrane pmteirs consist of nonpolar amino acids (m, Section 641). After pushing these regions into the membrane, the test of the protein continues to be made in the cytosol or the ER lumen. Once proteins are imide the tough ER or inserted into its membrane, they fold into their thtee-dimensional shape with the help of chapemne proteins Ch 3, Secuon 3 3). In addition, proteins that enter the ER lumen interact with enzymes that catalyze the addition of carbohydrate side chains (see Ltgme 718). Because catbohydtates ate polymers of sugar monomers, the addition of one or more carbohydrate groups is called glvconm ("sugar-together"). The resulting molecule is a glycopm (“sugar-protein"; QLE), Secuon 5.3). The structure of these carbohydrates changes as the proteins are folded. serving as an indicator for shipment to the next destination -the Golgi apparatus.

The synthesis of proteins destined to be secreted or embedded in membranes begins in ribosomes free in the cytosol. Gunter Blobel and colleagues proposed that at some point these ribosomes become attached to the outside of the ER. But what directs ribosomes t0 the ER sudace? The “signal hypothesis” predicts that proteins bound for the endomembrane system have a molecular zip code that serves a similar role to the nuclear localization signal in nucleoplasmin Blobel proposed that the [itst amino acid residues of the growing protein act as a signal that marks the ribosome for trampott to the ER membrane. Blobel's group went on to produce convincing data that supported the hypothesis: They identified a “send-to-ER” signaL or ER signal gquence, that guides the growing protein and associated ribosorne to the rough ER. The ER signal sequence typically is present in the first 20 amino acid residues and is removed when pmtein synthesis '5 complete. More recent work has documented the mechan'sms responsible for receiving this send-to-ER signal and inserting the protein into the tough ER. Eguxe 7.20 on page L63 illustrates the key steps involved for a protein that will eventually be shipped to the inside of an organelle or secreted fmm the cell. 1. Step 1 Protein synthesis begins on a free ribosome in the cytosol. The tibosome synthesizes the ER signal sequence, using information carried in an mRNA. 2. Step 2 The signal sequence binds to a signal recognition particle (S&H-a complex of RNA and protein. The attached SRP causes protein synthesis to stop. 3. Step 3 The ribosome + signal sequence + SRP complex moves to the rough ER membrane, where it attaches to the SRP receptor. Think of the SRP as a key that ‘5 activated by an ER signal sequence. The SRP receptorin the ER membtane is the lock. 4. Step 4 Once the lock (the receptor) and key (the SRP) connect, the SRP is released and protein synthesis continues through a channel called the translocon. 5. Step 5 The growing protein is fed into the ER lumen, and the ER signal sequence is removed After cleavage of the signal sequence, the protein may be completely released into the ER lumen. Some proteins, hawewr, remain associated with the membrane as integral membrane proteins. How do such proteins get inserted into the ER membrane? Cunent models propose that the uanslocon has molecular "gates" that divert stretches of nonpolar amino acids in the growing protein into the phospholipid bilayer. Recall that nansmembtane ponions of integral membrane pmteirs consist of nonpolar amino acids (m, Section 641). After pushing these regions into the membrane, the test of the protein continues to be made in the cytosol or the ER lumen. Once proteins are imide the tough ER or inserted into its membrane, they fold into their thtee-dimensional shape with the help of chapemne proteins Ch 3, Secuon 3 3). In addition, proteins that enter the ER lumen interact with enzymes that catalyze the addition of carbohydrate side chains (see Ltgme 718). Because catbohydtates ate polymers of sugar monomers, the addition of one or more carbohydrate groups is called glvconm ("sugar-together"). The resulting molecule is a glycopm (“sugar-protein"; QLE), Secuon 5.3). The structure of these carbohydrates changes as the proteins are folded. serving as an indicator for shipment to the next destination -the Golgi apparatus.

The synthesis of proteins destined to be secreted or embedded in membranes begins in ribosomes free in the cytosol. Gunter Blobel and colleagues proposed that at some point these ribosomes become attached to the outside of the ER. But what directs ribosomes t0 the ER sudace? The “signal hypothesis” predicts that proteins bound for the endomembrane system have a molecular zip code that serves a similar role to the nuclear localization signal in nucleoplasmin Blobel proposed that the [itst amino acid residues of the growing protein act as a signal that marks the ribosome for trampott to the ER membrane. Blobel's group went on to produce convincing data that supported the hypothesis: They identified a “send-to-ER” signaL or ER signal gquence, that guides the growing protein and associated ribosorne to the rough ER. The ER signal sequence typically is present in the first 20 amino acid residues and is removed when pmtein synthesis '5 complete. More recent work has documented the mechan'sms responsible for receiving this send-to-ER signal and inserting the protein into the tough ER. Eguxe 7.20 on page L63 illustrates the key steps involved for a protein that will eventually be shipped to the inside of an organelle or secreted fmm the cell. 1. Step 1 Protein synthesis begins on a free ribosome in the cytosol. The tibosome synthesizes the ER signal sequence, using information carried in an mRNA. 2. Step 2 The signal sequence binds to a signal recognition particle (S&H-a complex of RNA and protein. The attached SRP causes protein synthesis to stop. 3. Step 3 The ribosome + signal sequence + SRP complex moves to the rough ER membrane, where it attaches to the SRP receptor. Think of the SRP as a key that ‘5 activated by an ER signal sequence. The SRP receptorin the ER membtane is the lock. 4. Step 4 Once the lock (the receptor) and key (the SRP) connect, the SRP is released and protein synthesis continues through a channel called the translocon. 5. Step 5 The growing protein is fed into the ER lumen, and the ER signal sequence is removed After cleavage of the signal sequence, the protein may be completely released into the ER lumen. Some proteins, hawewr, remain associated with the membrane as integral membrane proteins. How do such proteins get inserted into the ER membrane? Cunent models propose that the uanslocon has molecular "gates" that divert stretches of nonpolar amino acids in the growing protein into the phospholipid bilayer. Recall that nansmembtane ponions of integral membrane pmteirs consist of nonpolar amino acids (m, Section 641). After pushing these regions into the membrane, the test of the protein continues to be made in the cytosol or the ER lumen. Once proteins are imide the tough ER or inserted into its membrane, they fold into their thtee-dimensional shape with the help of chapemne proteins Ch 3, Secuon 3 3). In addition, proteins that enter the ER lumen interact with enzymes that catalyze the addition of carbohydrate side chains (see Ltgme 718). Because catbohydtates ate polymers of sugar monomers, the addition of one or more carbohydrate groups is called glvconm ("sugar-together"). The resulting molecule is a glycopm (“sugar-protein"; QLE), Secuon 5.3). The structure of these carbohydrates changes as the proteins are folded. serving as an indicator for shipment to the next destination -the Golgi apparatus.

1. Step 1 Protein synthesis begins on a free ribosome in the cytosol. The tibosome synthesizes the ER signal sequence, using information carried in an mRNA. 2. Step 2 The signal sequence binds to a signal recognition particle (S&H-a complex of RNA and protein. The attached SRP causes protein synthesis to stop. 3. Step 3 The ribosome + signal sequence + SRP complex moves to the rough ER membrane, where it attaches to the SRP receptor. Think of the SRP as a key that ‘5 activated by an ER signal sequence. The SRP receptorin the ER membtane is the lock. 4. Step 4 Once the lock (the receptor) and key (the SRP) connect, the SRP is released and protein synthesis continues through a channel called the translocon. 5. Step 5 The growing protein is fed into the ER lumen, and the ER signal sequence is removed After cleavage of the signal sequence, the protein may be completely released into the ER lumen. Some proteins, hawewr, remain associated with the membrane as integral membrane proteins. How do such proteins get inserted into the ER membrane? Cunent models propose that the uanslocon has molecular "gates" that divert stretches of nonpolar amino acids in the growing protein into the phospholipid bilayer. Recall that nansmembtane ponions of integral membrane pmteirs consist of nonpolar amino acids (m, Section 641). After pushing these regions into the membrane, the test of the protein continues to be made in the cytosol or the ER lumen. Once proteins are imide the tough ER or inserted into its membrane, they fold into their thtee-dimensional shape with the help of chapemne proteins Ch 3, Secuon 3 3). In addition, proteins that enter the ER lumen interact with enzymes that catalyze the addition of carbohydrate side chains (see Ltgme 718). Because catbohydtates ate polymers of sugar monomers, the addition of one or more carbohydrate groups is called glvconm ("sugar-together"). The resulting molecule is a glycopm (“sugar-protein"; QLE), Secuon 5.3). The structure of these carbohydrates changes as the proteins are folded. serving as an indicator for shipment to the next destination -the Golgi apparatus.

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according to the signal hypothesis proteins destined for secretion contain a short stretch of amino acids that interact with a signal recognition particle (SRP) in the cytosol. This interaction directs the synthesis of the remaining protin into the rough ER lumen.

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Moving from the ER ro the Golgi Apparatus

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How do pmteim travel from the ER t0 the Golgi apparatus? In Palade’s pulse-chase experiment, labeled proteins were obsetved in small membrane-bound structures between the rough ER and the Golgi apparatus. Based on these observations, Palade’s group suggested that proteins are transported in vesicles that bud off from the ER and move to the cis face of the Golgi apparatus. This hypothes’s was supported when other researchers used differential centrifugation to isolate and characterize the vesicles that contained the pube-labeled proteins. They found that a distinctive type of vesicle carries proteins from the rough ER to the Golgi apparatus. Ensuring that only appropriate cargo '5 loaded into these vesicles and that the vesicles dock and fuse only with the cis face of the Golgi apparatus involves a complex series of events and is an area of active research.

How do pmteim travel from the ER t0 the Golgi apparatus? In Palade’s pulse-chase experiment, labeled proteins were obsetved in small membrane-bound structures between the rough ER and the Golgi apparatus. Based on these observations, Palade’s group suggested that proteins are transported in vesicles that bud off from the ER and move to the cis face of the Golgi apparatus. This hypothes’s was supported when other researchers used differential centrifugation to isolate and characterize the vesicles that contained the pube-labeled proteins. They found that a distinctive type of vesicle carries proteins from the rough ER to the Golgi apparatus. Ensuring that only appropriate cargo '5 loaded into these vesicles and that the vesicles dock and fuse only with the cis face of the Golgi apparatus involves a complex series of events and is an area of active research.

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What Happens inside the Golgi Apparatus

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Section 7.2 described th’s organelle as a stack of flattened compartments called c'stemae, with cargo entering one side of the organelle and exiting the other. Recent research has shown that the composition of the Golgi apparatus is dynamic. New c‘stemae constantly form at the cis face of the Golgi apparatus, while old cistemae break apart at the trans face, to be replaced by the cistemae behind it. By separating individual cistemae and analyzing their contents, researchers found that c‘sternae at van'ous stages of maturation contain different suites of enzymes. As a result, the cargo gets modified in a stepwise manneras it moves within compartments at different stages of maturation. If the tough ER ’5 like a foundry and stamping plant where mugh pans are manufactured, then the Golgi apparatus can be considered a finishing area where products are polished, painted, and readied for shipping.

Section 7.2 described th’s organelle as a stack of flattened compartments called c'stemae, with cargo entering one side of the organelle and exiting the other. Recent research has shown that the composition of the Golgi apparatus is dynamic. New c‘stemae constantly form at the cis face of the Golgi apparatus, while old cistemae break apart at the trans face, to be replaced by the cistemae behind it. By separating individual cistemae and analyzing their contents, researchers found that c‘sternae at van'ous stages of maturation contain different suites of enzymes. As a result, the cargo gets modified in a stepwise manneras it moves within compartments at different stages of maturation. If the tough ER ’5 like a foundry and stamping plant where mugh pans are manufactured, then the Golgi apparatus can be considered a finishing area where products are polished, painted, and readied for shipping.

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How Do proteins reach their proper destinations

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The mugh ER and Golgi apparatts constitute an impressive assembly line. Certain proteins manufactured by this process remain in these organelles, replacing wom-out resident molecules. But those proteins that are simply passing through as cargo must be sorted and sent to their intended destination as the trans cistema breaks up into vesicles. How is cargo put into the right shipping containers, and how are the containers addressed for Hanspon to different locations? Studies on hydrolytic enzymes that are shipped to lysosomes have provided some am'ers to both questions. A key finding was tha lysosome-bound proteins have a phosphate group attached to a specific sugar on their surface. forming the compound mannose-Gphosphate. lf th‘s phosphorylated sugar is removed fmm these pmteins, they are not transported to a lysosome. The mannose-G-phosphate tag serves as a zip code, like the nuclear localization and ER signal sequences dBcussed earlier Data indicate that a receptor protein in the membrane of the trans-Golgi cisterna binds to th's tag. Regions that are enriched with these teceptor-(argo complexes will form cargo-fllled vesicles. Besides these receptors, the vesicles also include specific membrane pmteins that direct their transport to pre-lysosomal compartments. In this way. the presence of mannose-G-phosphate targets proteins to organelles tha eventually become lysosomes. Eigure 7.21 presens a simplified model of how cargo is sorted and loaded into specific vesicles that are shipped to different destinations. Eadt cargo protein has a molecular tag that directs it to particular vesicle budding sites by interacting with receptors in the trans cisterna. These receptors, along with other membrane and cytosolic pmteins that ate not shown, ditect the transpon vesicles to the correct destinations. Take a moment to observe how the vesicles shown in the middle of figure 7.21 {me with the pre-lysosomal compartment membrane and deliver their contents.

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Next, notice that the transport vesicle shown on the right of Ejgumlll is bound for the plasma membrane, where it will secrete its contents to the outside. This process is called exocytos's (“outside-cell-act"). When exocytosis occurs, the vesicle membrane and plasma membrane make contact. As the two membranes fuse, the interior of the vesicle ‘5 exposed to the outside of the cell The vesicle’s contents then diffuse into the space outside the cell Th’s is how cells in your pancreas deliver digestive enzymes to the duct that leads to your small intestine, where food ‘5 digested. When illustrating the process of cargo transport through the endomembrane system, biolog’sts often use arrows to represent different processes. To learn more about how to model the secretory pathway using arrows and simplitied structures, see Making Models on page 16_6_.

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Recycling Material in the Lysosome

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Now that you have seen how the endomembrane system transports cargo to differentdestmations in the celL let’s look at how cargo tramport contributes to protein recycling. Recall that large molecules, such as proteins, do not readily pass through membranes (Ch. 6 Section 6.2). Th‘s means that to get amino acid monomers back into the cytosol for new protein synthes's, ex'sting proteins must tirstbe digested in the lysosome-but how do they get there? There are three pathways that animal cells commonly use to recycle material in the lysosome (see Bgum 2.2;). Two of these three pathways involve pinching off the plasma membrane to take up material from outside the cell-a process called endocyto_s'5 (“insidecell-act"). The third pathway targets materials already inside the cell.

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Recepbr-mediard endocytosis and phagocytnsis involve bringing in maurid from the ouside and surrounding it wit: a lipii hilayer from the plasma menbrme. Endosomes mature inn lysosomes or, like phqosomes, wil fuse with existing lysosomes. In autaphagy, matetial within the cybplasm is encapmlaed with an internal menbtane before fusing with the lysosome.

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Receptor Mediated Endocytosis

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As its name inplies, mpwr-mediated endocytosis is a sequence of evens that begins when particles outside me cell bind b receptors on the plasma menbrane. Mate than 25 distinct cago receptms have now been chaacter‘ned, each specialized for b'nd'ng I) differem molecules. Once receptor bind'ng ocmls, the plasma menbrme folds in and pindles off to form at endocytic vesicle. These vesicles then drop off their cargo in an organelle caled the ggiy endosome (“inside-body"). Tin activiy of ptoton punps in the menbrme of this organelle ac‘difies is lumen, which causes the cargo to be released fmm dle‘t receptors. Many of these emptied cago receptors are then repackaged 'nto vesicles and letu'ned to the plasma menbrate. As proton punps cont'nue to lower the early endosome’s pH, it undergoes a series of ptooessing steps that cause i to maure into a lag gndosomg. The late endosome is the pre-lysosomal companmem immduced earlier (Eigmglll), where acid hydolases from the Golgi apparaus are dropped off. As before, the enptied cargo receptors tramponed from the Golgi apparaus are removed from the lae endosome as it matures inn a fuly active lysosome.

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phagocytosis

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A second pathway that involves recycling material brought in from the outside of the cell is called phagocytosis (“eat-cell-act”). In phagocytosis, the plasma membrane of a cell surrounds a smaller cell or food particle and engulfs it, forming a structune called a phagosome. This structure is delivened to a lysosome, where the phagosome and lysosome membranes fuse and the contents of the phagosome ate digested.

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Autophagy

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Cells are also involved in recycling large structures and organelles that exist within the cytoplasm through a pmcess called mng (“same-eating”). During autophagy, portions of the cytoplasm, including damaged organelles marked for destruction, are enclosed within an internal membrane to form an autophagosome. Like the phagosome, the membrane of the autophagosome fuses with the lysosome and the contents are digested. Regardless of whether the materials digested by lysosomes originate via autophagy, phagocytosis, or neceptor-mediated endocytosis, the result is similar: Molecules are hydrolyzed and the products are transported across the lysosomal membrane into the cytosol for Iecycling. Throughout this section, vesicles have been key to the transport of cargo. If these transport steps depended on the random movement of diffusion alone, however, then the vesicles and their cargo might never reach their intended destinations. Instead, there are defined tracks that direct the movement of these shipping containers. What are these tracks, and what molecule or molecules function to transport the vesicles along them? Let’s delve into these questions in the next section.

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Diffusion

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A thought experiment can help explain how substances can cross membranes spontaneously. Suppose you rack up a set of billiard balls in the middle of a pool table and then begin to vibrate the table. 1. Because of the vibration, the billiard balls will move about randomly. They will also bump into one another. 2. After these collisions, some balls will move outward-away from their original position. 3. As movement and collisions continue, the overall or net movement of balls will be outward. This occurs because the random motion of the balls disrupts their original, nonrandom position. As the balls move at random, they are more likely to move away from one another than to stay together. 4. Eventually, the balls will be distributed randomly across the table. The entropy of the billiard balls has increased. The second law of thermodynamics states that in an isolated system, entnopy always increases (Ch. 2, Section 2.3).

This hypothetical example illustrates how vibrating billiard balls move at random. More to the point, it also explains how substances located on one side of a lipid bilayer can move to the other side spontaneously-because like the billiard balls, dissolved solutes are in constant random motion due to their thermal energy. Spontaneous movement of molecules and ions is known as diffusion. A difference in solute concentrations creates what is called a concentration gradient. Solutes move randomly in all directions, but when a concentration gradient exists, there is a net movement from regions of high concentrau'on to regions of low concentration. Diffusion down a concentration gradient, or away from the higher concentration, is a spontaneous process because it results in an increase in entropy. Once the molecules or ions are randomly distributed throughout a solution, an equilibrium is established. For example, consider two aqueous solutions separated by a lipid-like the situation shown in step 1 of Eigure 6.13 on page m. Steps 2 and 3 of the figure show how solutes that can pass through the bilayer diffuse to the other side. When substances diffuse across a membrane in the absence of an outside energy source, it is known as Mpg.

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osmosis

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What about water? As the data in Eigiue 6.9 show, water moves across lipid bilayers relatively quickly. The movement of water is a special case of diffusion that is given its own name: osmosis. Osmosis occurs only when solutions are separated by a membrane that permits water to cross, but holds back some or all of the solutes-that is, a selectively permeable membrane. To drive this point home, let’s suppose the concentration of a particular solute is higher on one side of a selectively permeable membrane than it is on the other side (_F_igure 6.14, step 1). Also suppose that this solute cannot diffuse through the membrane to establish equilibrium. What happens? Water will move from the side with a lower concentration of solute to the side with a higher concentration of solute (P_igure 6.14, step 2).

It’s also important to note that the solute affects the movement of water across a membrane. Recall that water molecules interact with charged particles and form hydrogen bonds with polar molecules (see m, Section 2.2). If a solute can’t cross the membrane, then any associated water molecules are also prevented from crossing. Thus, only unbound water molecules are able to diffuse across the membrane during osm0513. The overall result is that osmosis dilutes the higher concentration of solute as water diffuses across the membrane. This directional movement is spontaneous because entropy will increase as the difference in solute concentrations decreases. When water moves by osmosis, the solutions on both sides of the membrane experience a change in volume as well as a change in solute concentration. The greater the initial difference in solute concentration, the greater the volume change will be. However, opposing forces, such as the pressure resulting from the downward pull of gravity, exert resistance to the directional movement of water. THIN K CAREFULLY If you understand what forces contribute to osmosis, you should be able to predict whether or not the concentration of the solute in Eigure 6.14 would be the same across the membrane after reaching equilibrium. Explain your answer.

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