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In this embryo we see antibodies tagged with a fluorescent label bound to proteins that are in the nuclei; each small sphere corresponds to one nucleus. Three different antibodies were used, each specific for a different protein and each giving a distinct color (yellow, green, or blue) in a fluorescence microscope. The... | {
"Header 1": "1",
"Header 2": "Genetics Reveals the Consequences of Damaged Genes",
"token_count": 2029,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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Using recombinant DNA techniques researchers can engineer specific genes to contain mutations that inactivate or increase production of their encoded proteins. Such genes can be introduced into the embryos of worms, flies, frogs, sea urchins, chickens, mice, a variety of plants, and other organisms, permitting the ef... | {
"Header 1": "1",
"Header 2": "Genetics Reveals the Consequences of Damaged Genes",
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"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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In this way, the genetic composition of a population of organisms can change over time.
#### **Human Medicine Is Informed by Research on Other Organisms**
Mutations that occur in certain genes during the course of our lives contribute to formation of various human cancers. The normal, wild-type forms of such "cance... | {
"Header 1": "1",
"Header 2": "Genetics Reveals the Consequences of Damaged Genes",
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"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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Polysaccharide chains on the surface of cellulose visualized by atomic force microscopy. [Courtesy of M. Miles from A. A. Baker et al., 2000, *Biophys J.* **79**:1139–1145.]
he life of a cell depends on thousands of chemical interactions and reactions exquisitely coordinated with one an... | {
"Header 1": "1",
"Header 2": "2 CHEMICAL FOUNDATIONS",
"token_count": 1015,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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Strong and weak attractive forces between atoms are the glue that holds them together in individual molecules and permits interactions between different biological molecules. Strong forces form a **covalent bond** when two atoms share one pair of electrons ("single" bond) or multiple pairs of electrons ("double" bond, ... | {
"Header 1": "1",
"Header 2": "2.1 Atomic Bonds and Molecular Interactions",
"token_count": 358,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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Hydrogen, oxygen, carbon, nitrogen, phosphorus, and sulfur are the most abundant elements found in biological molecules. These atoms, which rarely exist as isolated entities, readily form covalent bonds with other atoms, using electrons that reside in the outermost electron orbitals surrounding their nuclei. As a rule,... | {
"Header 1": "1",
"Header 2": "Each Atom Has a Defined Number and Geometry of Covalent Bonds",
"token_count": 1207,
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In many molecules, the bonded atoms exert different attractions for the electrons of the covalent bond, resulting in unequal sharing of the electrons. The extent of an atom's ability to attract an electron is called its **electronegativity**. A bond between atoms with identical or similar electronegativities is said to... | {
"Header 1": "1",
"Header 2": "Electrons Are Shared Unequally in Polar Covalent Bonds",
"token_count": 553,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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Covalent bonds are very stable because the energies required to break them are much greater than the thermal energy available at room temperature (25 °C) or body temperature (37 °C). For example, the thermal energy at 25 °C is approximately 0.6 kilocalorie per mole (kcal/mol), whereas the energy required to break the c... | {
"Header 1": "1",
"Header 2": "Covalent Bonds Are Much Stronger and More Stable Than Noncovalent Interactions",
"token_count": 316,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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as the energy required to break a particular type of linkage. Covalent bonds are one to two powers of 10 stronger than noncovalent interactions. The latter are somewhat greater than the thermal energy of the environment at normal room temperature (25 °C). Many biological processes are coupled to the energy released dur... | {
"Header 1": "1",
"Header 2": "➤ FIGURE 2-4 Relative energies of covalent bonds and noncovalent interactions. Bond energies are determined",
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A **hydrogen bond** is the interaction of a partially positively charged hydrogen atom in a molecular dipole (e.g., water) with unpaired electrons from another atom, either in the same (intramolecular) or in a different (intermolecular) molecule. Normally, a hydrogen atom forms a covalent bond with only one other atom.... | {
"Header 1": "1",
"Header 2": "Hydrogen Bonds Determine Water Solubility of Uncharged Molecules",
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Because nonpolar molecules do not contain charged groups, possess a dipole moment, or become hydrated, they are insoluble or almost insoluble in water; that is, they are hydrophobic. The covalent bonds between two carbon atoms and between carbon and hydrogen atoms are the most common nonpolar bonds in biological system... | {
"Header 1": "▲ FIGURE 2-8 Two oxygen molecules in van der Waals contact. In this space-filling model, red indicates negative charge and blue indicates positive charge. Transient dipoles in the electron clouds of all atoms give rise to weak attractive forces, called *van der Waals interactions*. Each type of atom ha... |
complementary shapes, charges, polarity, and hydrophobicity of two protein surfaces permit multiple weak interactions, which in combination produce a strong interaction and tight binding. Because deviations from molecular complementarity substantially weaken binding, any given biomolecule usually can bind tightly to on... | {
"Header 1": "▲ FIGURE 2-8 Two oxygen molecules in van der Waals contact. In this space-filling model, red indicates negative charge and blue indicates positive charge. Transient dipoles in the electron clouds of all atoms give rise to weak attractive forces, called *van der Waals interactions*. Each type of atom ha... |
The monomeric building blocks of proteins are 20 **amino acids**, all of which have a characteristic structure consisting of a central $\alpha$ **carbon atom** ( $C_{\alpha}$ ) bonded to four different chemical groups: an amino (NH<sub>2</sub>) group, a carboxyl (COOH) group, a hydrogen (H) atom, and one variable gro... | {
"Header 1": "▲ FIGURE 2-8 Two oxygen molecules in van der Waals contact. In this space-filling model, red indicates negative charge and blue indicates positive charge. Transient dipoles in the electron clouds of all atoms give rise to weak attractive forces, called *van der Waals interactions*. Each type of atom ha... |
Two types of chemically similar nucleic acids, **DNA** (deoxyribonucleic acid) and **RNA** (ribonucleic acid), are the principal information-carrying molecules of the cell. The monomers from which DNA and RNA are built, called **nucleotides**, all have a common structure: a phosphate group linked by a phosphoester bond... | {
"Header 1": "▲ FIGURE 2-8 Two oxygen molecules in van der Waals contact. In this space-filling model, red indicates negative charge and blue indicates positive charge. Transient dipoles in the electron clouds of all atoms give rise to weak attractive forces, called *van der Waals interactions*. Each type of atom ha... |
n-Mannose
n-Galactose
hyde group results in the formation of D-glucofuranose, a hemiacetal containing a five-member ring. Although all three forms of D-glucose exist in biological systems, the pyranose form is by far the most abundant.
Many biologically important sugars are six-carbon sugars that are structurally... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
Before considering phospholipids and their role in the structure of biomembranes, we briefly review the properties of **fatty acids**. Like glucose, fatty acids are an important energy source for many cells and are stored in the form of triacylglycerols within adipose tissue (Chapter 8). Fatty acids also are precursors... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
This is illustrated by **triacylglycerols**, which contain three acyl groups esterfied to glycerol:
| TABLE 2-3 | Fatty Acids That Predominate in Phospholipids |
|-----------|-----------------------------------------------|
| | |
| Common Name of<br>Acid (Ioni... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
In biological systems, nearly all sugars are D isomers, while nearly all amino acids are L isomers.
- Differences in the size, shape, charge, hydrophobicity, and reactivity of the side chains of amino acids determine the chemical and structural properties of proteins (see Figure 2-13).
- Amino acids with hydrophobic si... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
The equilibrium constant $K_{\rm eq}$ depends on the nature of the reactants and products, the temperature, and the pressure (particularly in reactions involving gases). Under standard physical conditions (25 °C and 1 atm pressure, for biological systems), the $K_{\rm eq}$ is always the same for a given reaction, w... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
Its $[H^+]$ is roughly a millionfold greater than that of cytoplasm with a pH of about 7.
Although the cytosol of cells normally has a pH of about 7.2, the pH is much lower (about 4.5) in the interior of lysosomes, one type of organelle in eukaryotic cells. The many degradative enzymes within lysosomes function opt... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
In general, an **acid** is any molecule, ion, or chemical group that tends to release a hydrogen ion $(H^+)$ , such as hydrochloric acid (HCl) and the carboxyl group (—COOH), which tends to dissociate to form the negatively charged carboxylate ion (—COO $^-$ ). Likewise, a **base** is any molecule, ion, or chemical gr... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
A growing cell must maintain a constant pH in the cytoplasm of about 7.2–7.4 despite the metabolic production of many acids, such as lactic acid and carbon dioxide; the latter reacts with water to form carbonic acid ( $H_2CO_3$ ). Cells have a reservoir of weak bases and weak acids, called **buffers**, which ensure tha... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
**Electric energy**—the energy of moving electrons or other charged particles—is yet another major form of kinetic energy.
**Potential Energy** Several forms of potential energy are biologically significant. Central to biology is **chemical potential energy,** the energy stored in the bonds connecting atoms in mole... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
Because biological systems are generally held at constant temperature and pressure, it is possible to predict the direction of a chemical reaction from the change in the **free energy** G, named after J. W. Gibbs, who showed that "all systems change in such a way that free energy [G] is minimized." In the case of a che... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
A chemical mixture at equilibrium is already in a state of minimal free energy; that is, no free energy is being generated or released. Thus, for a system at equilibrium ( $\Delta G = 0$ , $Q = K_{\rm eq}$ ), we can write
$$\Delta G^{0'} = -2.3RT \log K_{\rm eq} = -1362 \log K_{\rm eq}$$
(2-8)
under standard condi... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
In the case of a substance moving into a cell, Equation 2-7 becomes
$$\Delta G = RT \ln \frac{[C_{in}]}{[C_{out}]}$$
(2-10)
where $[C_{\rm in}]$ is the initial concentration of the substance inside the cell and $[C_{\rm out}]$ is its concentration outside the cell. We can see from Equation 2-10 that $\Delta G$... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
Clearly, to continue functioning cells must constantly replenish their ATP supply. The initial energy source whose energy is ultimately transformed into the phosphoanhydride bonds of ATP and bonds in other compounds in nearly all cells is sunlight. In **photosynthesis**, plants and certain microorganisms can trap the e... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
Protons are soluble in aqueous solutions (as H<sub>3</sub>O<sup>+</sup>), but electrons are not and must be transferred di-
(a) (b) Oxidized: FAD Reduced: FADH2
Oxidized: NAD+
Reduced: NADH
$$H_3C$$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$H_3C$
$... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
To describe redox reactions, such as the reaction of ferrous ion $(Fe^{2+})$ and oxygen $(O_2)$ , it is easiest to divide them into two **half-reactions**:
Oxidation of
$$Fe^{2+}$$
: 2 $Fe^{2+} \longrightarrow 2 Fe^{3+} + 2 e^{-}$
Reduction of $O_2$ : 2 $e^{-} + \frac{1}{2} O_2 \longrightarrow O^{2-}$
In th... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
The lysosome is a subcellular organelle with a pH of about 5.0; the pH of cytoplasm is 7.0. What is the effect on the pH of the fluid content of lysosomes when cells are exposed to ammonia? *Note:* Protonated ammonia does not diffuse freely across membranes.
- 9. Consider the binding reaction $L + R \rightarrow LR$ ... | {
"Header 1": "**A FIGURE 2-16 Chemical structures of hexoses.** All hexoses have the same chemical formula (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) and contain an aldehyde or keto group. (a) The ring forms of p-glucose are generated from the linear molecule by reaction of the aldehyde at carbon 1 with the hydroxyl... |
Electron density map of the $F_1$ -ATPase associated with a ring of 10 c-subunits from the $F_0$ domain of ATP synthase, a molecular machine that carries out the synthesis of ATP in eubacteria, chloroplasts, and mitochondria. [Courtesy of Andrew Leslie, MRC Laboratory of Molecular Biol... | {
"Header 1": "3",
"Header 2": "PROTEIN STRUCTURE AND FUNCTION",
"token_count": 2006,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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#### **Secondary Structures Are the Core Elements of Protein Architecture**
The second level in the hierarchy of protein structure consists of the various spatial arrangements resulting from the folding of localized parts of a polypeptide chain; these arrangements are referred to as **secondary structures.** A sing... | {
"Header 1": "3",
"Header 2": "PROTEIN STRUCTURE AND FUNCTION",
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Tertiary structure refers to the overall conformation of a polypeptide chain—that is, the three-dimensional arrangement of all its amino acid residues. In contrast with secondary structures, which are stabilized by hydrogen bonds, tertiary structure is primarily stabilized by hydrophobic interactions between the nonpol... | {
"Header 1": "3",
"Header 2": "Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure",
"token_count": 2041,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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(a) Tertiary structure of each HA subunit constitutes the folding of its helices and strands into a compact structure that is 13.5 nm long and divided into two domains. The membrane-distal domain is folded into a globular conformation. The membrane-proximal domain has a fibrous, stemlike conformation owing to the align... | {
"Header 1": "3",
"Header 2": "Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure",
"token_count": 2026,
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The molecular revolution in biology during the last decades of the twentieth century also created a new scheme
#### ▲ FIGURE 3-10 Evolution of the globin protein family. (Left) A primitive monomeric oxygen-binding globin is thought to be the ancestor of modern-day blood hemoglobins, m... | {
"Header 1": "3",
"Header 2": "Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure",
"token_count": 2000,
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Proper folding of other proteins (*bottom*) depends on chaperonins such as the prokaryotic GroEL, a hollow, barrel-shaped complex of 14 identical 60,000-MW subunits arranged in two stacked rings.
One end of GroEL is transiently blocked by the cochaperonin GroES, an assembly of 10,000-MW subunits. (b) In the absence o... | {
"Header 1": "3",
"Header 2": "Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure",
"token_count": 520,
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Nearly every protein in a cell is chemically modified after its synthesis on a ribosome. Such modifications, which may alter the activity, life span, or cellular location of proteins, entail the linkage of a chemical group to the free $-\mathrm{NH}_2$ or $-\mathrm{COOH}$ group at either end of a protein or to a rea... | {
"Header 1": "3",
"Header 2": "Many Proteins Undergo Chemical Modification of Amino Acid Residues",
"token_count": 1780,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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After their synthesis, some proteins undergo irreversible changes that do not entail changes in individual amino acid residues. This type of post-translational alteration is sometimes called *processing*. The most common form is enzymatic cleavage of a backbone peptide bond by proteases, resulting in the removal of res... | {
"Header 1": "3",
"Header 2": "Peptide Segments of Some Proteins Are Removed After Synthesis",
"token_count": 297,
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In addition to chemical modifications and processing, the activity of a cellular protein depends on the amount present, which reflects the balance between its rate of synthesis and rate of degradation in the cell. The numerous ways that cells regulate protein synthesis are discussed in later chapters. In this section, ... | {
"Header 1": "3",
"Header 2": "Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes",
"token_count": 1995,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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#### **KEY CONCEPTS OF SECTION 3.2**
#### **Folding, Modification, and Degradation of Proteins**
- The amino acid sequence of a protein dictates its folding into a specific three-dimensional conformation, the native state.
- Protein folding in vivo occurs with assistance from molecular chaperones (Hsp70 proteins)... | {
"Header 1": "3",
"Header 2": "Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes",
"token_count": 1322,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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In contrast with antibodies, which bind and simply present their ligands to other components of the immune system, enzymes promote the chemical alteration of their ligands, called **substrates**. Almost every chemical reaction in the cell is catalyzed by a specific enzyme. Like all catalysts, enzymes do not affect the ... | {
"Header 1": "3",
"Header 2": "Enzymes Are Highly Efficient and Specific Catalysts",
"token_count": 2030,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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Mutations in the glycine lid that inhibit its flexibility slow catalysis by protein kinase A even further.
Phosphoryl Transfer by Protein Kinases After substrates have bound and the catalytic core of protein kinase A has assumed the closed conformation, the phosphorylation of a serine or threonine residue on the targ... | {
"Header 1": "3",
"Header 2": "Enzymes Are Highly Efficient and Specific Catalysts",
"token_count": 462,
"source_pdf": "datasets/websources/biochem/s-molecularcellbiology.pdf"
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ADP and a peptide with a phosphorylated serine or threonine
side chain. The catalytic mechanism of other protein kinases is
similar.
▲ FIGURE 3-18 Mechanism of phosphorylation by protein
enzyme-catalyzed reaction are determined from plots of the initia... | {
"Header 1": "**kinase A.** (*Top*) Initially, ATP and the target peptide bind to the active site (see Figure 3-17a). Electrons of the phosphate group are delocalized by interactions with lysine side chains and $Mg^{2+}$ . Colored circles represent the residues in the kinase core critical to substrate binding and ph... |
These mechanochemical enzymes convert energy released by the hydrolysis of ATP or from ion gradients into a mechanical force.
Motor proteins generate either linear or rotary motion (Table 3-2). Some motor proteins are components of macroinfer three general properties that they possess:
- The ability to transduce a ... | {
"Header 1": "**kinase A.** (*Top*) Initially, ATP and the target peptide bind to the active site (see Figure 3-17a). Electrons of the phosphate group are delocalized by interactions with lysine side chains and $Mg^{2+}$ . Colored circles represent the residues in the kinase core critical to substrate binding and ph... |
As shown in Figure 3-25, myosin undergoes a series of events during each step of movement. In the course of one cycle, myosin must exist in at least three conformational states: an ATP state unbound to actin, an ADP-Pi state bound to actin, and a state after the power-generating stroke has been completed. The major q... | {
"Header 1": "**kinase A.** (*Top*) Initially, ATP and the target peptide bind to the active site (see Figure 3-17a). Electrons of the phosphate group are delocalized by interactions with lysine side chains and $Mg^{2+}$ . Colored circles represent the residues in the kinase core critical to substrate binding and ph... |
In the preceding examples, oxygen, cAMP, and ATP cause allosteric changes in the activity of their target proteins (hemoglobin, protein kinase A, and GroEL, respectively). Two additional allosteric ligands, ${\rm Ca^{2+}}$ and GTP, act through two types of ubiquitous proteins to regulate many cellular processes.
Ca... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
Extracellular signals are often instrumental in inducing changes in the rates of protein synthesis and degradation (Chapters 13–15). Such regulated changes play a key role in the cell cycle (Chapter 21) and in cell differentiation (Chapter 22).
#### **KEY CONCEPTS OF SECTION 3.5**
#### **Common Mechanisms for Regul... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
▲ **EXPERIMENTAL FIGURE 3-31 Centrifugation techniques separate particles that differ in mass or density.** (a) In differential centrifugation, a cell homogenate or other mixture is spun long enough to sediment the denser particles (e.g., cell organelles, cells), which collect as a pellet at the bottom of the tube (ste... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
(c) In antibody-affinity chromatography, a specific antibody is covalently attached to beads packed in a column. Only protein with high affinity for the antibody is retained by the column; all the nonbinding proteins flow through. The bound protein is eluted with an acidic solution, which disrupts the antigen–antibody ... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
A sensitive method for tracking a protein or other biological molecule is by detecting the radioactivity emitted from radioisotopes introduced into the molecule. At least one atom in a radiolabeled molecule is present in a radioactive form, called a **radioisotope**.
Radioisotopes Useful in Biological Research Hundre... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
In both instruments, the time of flight is inversely proportional to a protein's mass and directly proportional to its charge. As little as 1 10<sup>15</sup> mol (1 femtomole) of a protein as large as 200,000 MW can be measured with an error of 0.1 percent.
#### **Protein Primary Structure Can Be Determined by Chemi... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
X-ray crystallography provides the most detailed structures but requires protein crystallization. Cryoelectron microscopy is most useful for large protein complexes, which are difficult to crystallize. Only relatively small proteins are amenable to NMR analysis.
#### **P E R S P E C T I V E S F O R T H E F U T U R E*... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
#### Web Sites
Entry site into the proteins, structures, genomes, and taxonomy: http://www.ncbi.nlm.nih.gov/Entrez/
The protein 3D structure database: http://www.rcsb.org/
Structural classifications of proteins: http://scop.mrclmb.cam.ac. uk/scop/
Sites containing general information about proteins: http://ww... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
Electron micrograph of DNA (green arrow) being transcribed into RNA (red arrow). [O. L. Miller, Jr., and Barbara R. Beatty, Oak Ridge National Laboratory.]
he extraordinary versatility of proteins as molecular machines and switches, cellular catalysts, and components of cellular struct... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
Like polypeptides, polynucleotides can twist and fold into three-dimensional conformations stabilized by noncovalent bonds. Although the primary structures of DNA and RNA are generally similar, their three-dimensional conformations are quite different. These structural differences are critical to the different function... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
Indeed, the percentage of G·C base pairs in a DNA sample can be estimated from its *T*<sup>m</sup> (Figure 4-6b). The ion concentration also influences the *T*<sup>m</sup> because the negatively charged phosphate groups in the
two strands are shielded by p... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
In this chapter, we focus on the functions of mRNA, tRNA, and rRNA in gene expression. In later chapters we will encounter other RNAs, often associated with proteins, that participate in other cell functions.
#### **KEY CONCEPTS OF SECTION 4.1**
#### **Structure of Nucleic Acids**
- Deoxyribonucleic acid (DNA),... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
During transcription of DNA, one DNA strand acts as a *tem-plate*, determining the order in which ribonucleoside triphosphate (rNTP) monomers are polymerized to form a complementary RNA chain. Bases in the template DNA strand base-pair with complementary incoming rNTPs, which then are joined in a polymerization reactio... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
Rather, eukaryotic genes devoted to a single pathway are most often physically separated in the DNA; indeed such genes usually are located on different chromosomes. Each gene is transcribed from its own promoter, producing one mRNA, which generally is translated to yield a single polypeptide (Figure 4-12b).
When rese... | {
"Header 1": "▲ FIGURE 3-27 Ligand-induced activation of protein kinase A (PKA). At low concentrations of cyclic AMP (cAMP), the PKA is an inactive tetramer. Binding of cAMP to the regulatory (R) subunits causes a conformational change in these subunits that permits release of the active, monomeric catalytic (C) sub... |
▲ FIGURE 4-14 Overview of RNA processing to produce functional mRNA in eukaryotes. The β-globin gene contains three protein-coding exons (coding region, red) and two intervening noncoding introns (blue). The introns interrupt the protein-coding sequence between the codons for amino acids ... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
In contrast to bacterial and archaeal genes, the vast majority of genes in higher, multicellular eukaryotes contain multiple introns. As noted in Chapter 3, many proteins from
▲ **FIGURE 4-15 Cell type–specific splicing of fibronectin pre-mRNA in fibroblasts and hepatocytes.** The ≈75-k... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
When no lactose is present, binding of the *lac* repressor to a sequence called the *lac* **operator,** which overlaps the transcription start site, blocks transcription initiation by the polymerase (Figure 4-16a). When lactose is present, it binds to specific binding sites in each subunit of the tetrameric *lac* repre... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Most *E. coli* promoters interact with $\sigma^{70}$ -RNA polymerase, the major form of the bacterial enzyme. Transcription of certain groups of genes, however, is carried out by *E. coli* RNA polymerases containing one of several alternative sigma factors that recognize different consensus promoter sequences than $\... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
When the activator and 54–RNA polymerase interact, the DNA between their binding sites forms a loop (see Figure 4-17).
■ In two-component regulatory systems, one protein acts as a sensor, monitoring the level of nutrients or other components in the environment. Under appropriate conditions, the -phosphate of an ATP i... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
As a result, the same nucleotide sequence specifies different amino acids during translation. Although they are rare, many instances of such overlaps have been discovered in viral and cellular genes of prokaryotes and eukaryotes. It is theoretically possible for the mRNA to have a third reading frame.
*shifting.* In ... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
If perfect Watson-Crick base pairing were demanded between codons and anticodons, cells would have to contain exactly 61 different tRNA species, one for each codon that specifies an amino acid. As noted above, however, many cells contain fewer than 61 tRNAs. The explanation for the smaller number lies in the capability... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
This consistency is another reflection of the common evolutionary origin of the most basic constituents of living cells.
The sequences of the small and large rRNAs from several thousand organisms are now known. Although the primary nucleotide sequences of these rRNAs vary considerably, the same parts of each type of ... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The previous sections have introduced the major participants in protein synthesis—mRNA, aminoacylated tRNAs, and ribosomes containing large and small rRNAs. We now take a detailed look at how these components are brought together to carry out the biochemical events leading to formation of polypeptide chains on ribosome... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
During the first stage of translation, a ribosome assembles, complexed with an mRNA and an activated initiator tRNA, which is correctly positioned at the start codon. Large and small ribosomal subunits not actively engaged in translation are kept apart by binding of two **initiation factors**, designated eIF3 and eIF6 ... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
With the initiating Met-tRNAi Met at the P site and the second aminoacyl-tRNA tightly bound at the A site, the amino group of the second amino acid reacts with the "activated" (ester-linked) methionine on the initiator tRNA, forming a peptide bond (Figure 4-26, step 3; see Figures 4-19 and 4-21). This *peptidyltransf... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
#### Polysomes and Rapid Ribosome Recycling Increase the Efficiency of Translation
As noted earlier, translation of a single eukaryotic mRNA molecule to yield a typical-sized protein takes 30–60 seconds. Two phenomena significantly increase the overall rate at which cells can synthesize a protein: the simultaneous ... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
After 1.9 generations, approximately half the DNA had the density of H-L DNA; the other half had the density of L-L DNA. With additional generations, a larger and larger fraction of the extracted DNA consisted of L-L duplexes; H-H duplexes never appeared. These results match the predicted pattern for the semiconservati... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
As illustrated in Figure 4-34b, PCNA is a homotrimeric protein that has a central hole through which the daughter duplex DNA passes, thereby preventing the PCNA-Rfc–Pol complex from dissociating from the template.
After parental DNA is separated into single-stranded templates at the replication fork, it is bound by m... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The simplest viruses contain only enough RNA or DNA to encode four proteins; the most complex can encode 100–200 proteins. In addition to their obvious importance as causes of disease, viruses are extremely useful as research tools in the study of basic biological processes.
#### **Most Viral Host Ranges Are Narrow**... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
In each infected cell, about 100–200 T4 progeny virions are produced and released by lysis.
The lytic cycle is somewhat more complicated for DNA viruses that infect eukaryotic cells. In most such viruses, the DNA genome is transported (with some associated proteins) into the cell nucleus. Once inside the nucleus, the... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Finally, the integrated DNA, called a provirus, is transcribed by the cell's own machinery into RNA, which either is translated into viral proteins or is packaged within virion coat proteins to form progeny virions that are released by budding from the host-cell membrane. Because most retroviruses do not kill their hos... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
In contrast, a related, smaller protein is secreted from the cell and functions to bind available growth factor circulating in the blood, thus inhibiting the downstream signaling pathway. Speculate on how the cell synthesizes these disparate proteins.
- **7.** Describe the molecular events that occur at the *lac* opero... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Acta* **1493**:1–11.
Ramakrishnan, V. 2002. Ribosome structure and the mechanism of translation. *Cell* **108**:557–572.
Sonenberg, N., J. W. B. Hershey, and M. B. Mathews, eds. 2000. *Translational Control of Gene Expression*. Cold Spring Harbor Laboratory Press.
#### DNA Replication
Bullock, P. A. 1997. The i... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Atomic force microscopy reveals sphyingomyelin rafts (orange) protruding from a dioleoylphosphatidylcholine background (black) in a mica-supported lipid bilayer. Placental alkaline phosphatase (yellow peaks), a glycosylphosphatidylinositol-anchored protein, is shown to be almost exclusiv... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Phospholipids of the composition present in cells spontaneously form sheetlike **phospholipid bilayers**, which are two molecules thick. The hydrocarbon chains of the phospholipids in each layer, or *leaflet*, form a **hydrophobic** core that is 3–4 nm thick in most biomembranes. Electron microscopy of thin membrane se... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
(a) Most phosphoglycerides are derivatives of glycerol 3-phosphate (red) containing two esterified fatty acyl chains, constituting the hydrophobic "tail" and a polar "head group" esterified to the phosphate. The fatty acids can vary in length and be saturated (no double bonds) or unsaturated (one, two, or three double ... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
A typical cell contains myriad types of membranes, each with unique properties bestowed by its particular mix of lipids and proteins. The data in Table 5-1 illustrate the variation in lipid composition among different biomembranes. Several phenomena contribute to these differences. For instance, differences between mem... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
A characteristic of all membranes is an asymmetry in lipid composition across the bilayer. Although most phospholipids are present in both membrane leaflets, they are commonly more abundant in one or the other leaflet. For instance, in plasma membranes from human erythrocytes and certain canine kidney cells grown in cu... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The density and complement of proteins associated with biomembranes vary, depending on cell type and subcellular location. For example, the inner mitochondrial membrane is 76 percent protein; the myelin membrane, only 18 percent. The high phospholipid content of myelin allows it to electrically insulate a nerve cell fr... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The side chains of the helix in one monomer are shown in red; those in the other monomer, in gray. Residues depicted as space-filling structures participate in intermonomer van der Waals interactions that stabilize the coiled-coil dimer. [Part (b) adapted from K. R. MacKenzie et al., 1997, *Science* **276**:131.]
![]... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
As already discussed, PLAP is concentrated in lipid rafts, the more ordered bilayer microdomains that are enriched in sphingolipids and cholesterol (see Figure 5-10). Although PLAP and other GPI-anchored proteins lie in the opposite membrane leaflet from acyl-anchored proteins, both types of membrane proteins are con... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The enzyme binds with greatest affinity to bilayers composed of negatively charged phospholipids (e.g., phosphotidylethanolamine). This finding suggests that a rim of positively charged lysine and arginine residues around the entrance catalytic channel is particularly important in interfacial binding (Figure 5-17a). Bi... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Such static pictures of the cell reveal the organization of the cytoplasm into compartments and the stereotypic location of each type of organelle within the cell. In this section, we describe the basic structures and functions of the major organelles in animal and plant cells (Figure 5-19). Plant and fungal cells cont... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
❚
▲ **FIGURE 5-21 Electron micrograph showing various organelles in a rat liver cell.** Two peroxisomes (P) lie in close proximity to mitochondria (M) and the rough and smooth endoplasmic reticulum (ER). Also visible are accumulations of glycogen, a polysaccharide that is the primary gl... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Sci USA* **98**:2399.]
carry soluble or membrane proteins to lysosomes or other organelles. How intracellular transport vesicles "know" with which membranes to fuse and where to deliver their contents is also discussed in Chapter 17.
#### **Plant Vacuoles Store Small Molecules and Enable a Cell to Elongate Rapidly*... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The thylakoid membranes contain green pigments
▲ **FIGURE 5-27 Electron micrograph of a plant chloroplast.**
The internal membrane vesicles (thylakoids) are fused into stacks (grana), which reside in a matrix (the stroma). All the chlorophyll in the cell is contained in the thylakoid... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
For example, in the absorptive epithelial cells that line the lumen of the intestine, actin microfilaments are abundant in the apical region, where they are associated with cell–cell junctions and support a dense carpet of microvilli (Figure 5-30a). Actin filaments are also present in a narrow zone adjacent to the plas... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The strength and flexibility of the erythrocyte plasma membrane depend on a dense cytoskeletal network that underlies the entire membrane and is attached to it at many points. The primary component of the erythrocyte cytoskeleton is *spectrin,* a 200-nm-long fibrous protein. The entire cytoskeleton is arranged in a spo... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Step 1: A concentrated suspension of labeled cells is mixed with a buffer (the sheath fluid) so that the cells pass single-file through a laser light beam. Step 2: Both the fluorescent light emitted and the light scattered by each cell are measured; from measurements of the scattered light, the size and shape of the ce... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
#### **Organelle-Specific Antibodies Are Useful in Preparing Highly Purified Organelles**
Cell fractions remaining after differential and equilibrium density-gradient centrifugation may still contain more than one type of organelle. Monoclonal antibodies for various organelle-specific membrane proteins are a powerf... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Modern cell biologists have many more-powerful tools for revealing cell architecture. For example, variations of standard light microscopy permit scientists to view objects that were undetectable several decades ago. Electron microscopy, which can reveal extremely small objects, has yielded much information about subce... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
All microscopes produce a magnified image of a small object, but the nature of the images depends on the type of microscope employed and on the way in which the specimen is prepared. The compound microscope, used in conventional bright-field light microscopy, contains several lenses that magnify the image of a specimen... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
Evans.]
in thick specimens (e.g., an intact *Caenorhabditis elegans* roundworm) can be observed in a series of such optical sections, and the three-dimensional structure of the object can be reconstructed by combining the individual DIC images.
#### **Fluorescence Microscopy Can Localize and Quantify Specific Molec... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
By examining cells continuously in the fluorescence microscope and measuring rapid changes in the ratio of fura-2 fluorescence at these two wavelengths, one can quantify rapid changes in the fraction of fura-2 that has a bound Ca<sup>2+</sup> ion and thus in the concentration of cytosolic Ca<sup>2+</sup> (Figure 5-47).... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
The very low temperature (196 -C) keeps water from evaporating, even in a vacuum, and the sample can be observed in detail in its native, hydrated state without fixing or heavy metal
0.5 µm
▲ **EXPERIMENTAL FIGURE 5-51 Gold particles coated with protei... | {
"Header 1": "▲ FIGURE 4-13 Structure of the 5' methylated cap of eukaryotic mRNA. The distinguishing chemical features are the 5'→5' linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and the methyl group on the 2' hydroxyl of the ribose of the first nucleotide (base 1). Both these features... |
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