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To determine a protein's structure using X-ray crystallography, you first need to coax the protein into forming crystals: large, highly ordered arrays of the pure protein in which every molecule has the same conformation and is perfectly aligned with its neighbors. Growing highquality protein crystals is still somethin... | {
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"Header 3": "X-rays",
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The trouble with X-ray crystallography is that you need crystals. And not all proteins like to form such orderly assemblies. Many have intrinsically disordered regions that wiggle around too much to stack neatly into a crystalline array. Others might not crystallize in the absence of the membranes in which they normall... | {
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#### (A) ION-EXCHANGE CHROMATOGRAPHY
Ion-exchange columns are packed with small beads carrying either positive or negative charges that retard proteins of the opposite charge. The association between a protein and the matrix depends on the pH and ionic strength of the solution passing down the column. These can be va... | {
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"Header 3": "solvent flow positively . charged bead bound negatively charged molecule free positively charged molecule",
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- • Living cells contain an enormously diverse set of protein molecules, each made as a linear chain of amino acids linked together by covalent peptide bonds.
- • Each type of protein has a unique amino acid sequence, which determines both its three-dimensional shape and its biological activity.
- • The folded structur... | {
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"Header 3": "Essential Concepts",
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Look at the models of the protein in Figure 4–12. Is the red α helix right- or left-handed? Are the three strands that form the large β sheet parallel or antiparallel? Starting at the N-terminus (the *purple* end), trace your finger along the peptide backbone. Are there any knots? Why, or why not?
#### Question 4–10 ... | {
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"Header 3": "Question 4–9",
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What common feature of α helices and β sheets makes them universal building blocks for proteins?
#### Question 4–12
Protein structure is determined solely by a protein's amino acid sequence. Should a genetically engineered protein in which the original order of all amino acids is reversed have the same structure as... | {
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"Header 3": "Question 4–11",
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An enzyme isolated from a mutant bacterium grown at 20°C works in a test tube at 20°C but not at 37°C (37°C is the temperature of the gut, where this bacterium normally lives). Furthermore, once the enzyme has been exposed to the higher temperature, it no longer works at the lower one. The same enzyme isolated from the... | {
"Header 1": "The Relatedness of Proteins Aids the Prediction of Protein Structure and Function",
"Header 3": "Question 4–18",
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Life depends on the ability of cells to store, retrieve, and translate the genetic instructions required to make and maintain a living organism. This hereditary information is passed on from a cell to its daughter cells at cell division, and from generation to generation in multicellular organisms through the reproduct... | {
"Header 1": "DNA and Chromosomes",
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Well before biologists understood the structure of DNA, they had recognized that inherited traits and the genes that determine them were associated with the chromosomes. Chromosomes (named from the Greek *chroma*, "color," because of their staining properties) were discovered in the nineteenth century as threadlike str... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "The Structure of DNA",
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A molecule of deoxyribonucleic acid (DNA) consists of two long polynucleotide chains. Each *chain*, or *strand*, is composed of four types of nucleotide subunits, and the two strands are held together by hydrogen bonds between the base portions of the nucleotides (Figure 5–2).
Figure 5–... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "A DNA Molecule Consists of Two Complementary Chains of Nucleotides",
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The case for DNA began to emerge in the late 1920s, when a British medical officer named Fred Griffith made an astonishing discovery. He was studying *Streptococcus pneumoniae* (pneumococcus), a bacterium that causes pneumonia. As antibiotics had not yet been discovered, infection with this organism was usually fatal. ... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "Messages from the dead",
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Griffith's remarkable finding set the stage for the experiments that would provide the first strong evidence that genes are made of DNA. The American bacteriologist Oswald Avery, following up on Griffith's work, discovered that the harmless pneumococcus could be transformed into a pathogenic strain in a culture tube by... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "Transformation",
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68-69) can be brought close together without perturbing the double helix. Two hydrogen bonds form between A and T, whereas three form between G and C. The bases can pair in this way only if the two polynucleotide chains that contain them are antiparallel—that is, oriented in opposite directions. (B) A short section of ... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "Transformation",
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The need for genes to encode information that must be copied and transmitted accurately when a cell divides raised two fundamental questions: how can the information for specifying an organism be carried in chemical form, and how can the information be accurately copied? The discovery of the structure of the DNA double... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "The Structure of DNA Provides a Mechanism for Heredity",
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Large amounts of DNA are required to encode all the information needed to make even a single-celled bacterium, and far more DNA is needed to encode the information to make a multicellular organism like you. Each human cell contains about 2 meters (m) of DNA; yet the cell nucleus is only 5–8 μm in diameter. Tucking all ... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "The Structure of Eukaryotic Chromosomes",
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In eukaryotes, such as ourselves, the DNA in the nucleus is distributed among a set of different chromosomes. The DNA in a human nucleus, for example, contains approximately 3.2 × 109 nucleotides parceled out into 23 or 24 different types of chromosome (males, with their Y chromosome, have an extra type of chromosome t... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "Eukaryotic DNA Is Packaged into Multiple Chromosomes",
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The most important function of chromosomes is to carry the genes—the functional units of heredity (**Figure 5–12**). A **gene** is often defined as a
(A) (B)
Figure 5–11 Abnormal chromosomes are associated with some inherited genetic defects. (A) A pair of Chromosomes 12 from a patient with inherited ataxia, a gene... | {
"Header 1": "DNA and Chromosomes",
"Header 3": "Chromosomes Contain Long Strings of Genes",
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To form a functional chromosome, a DNA molecule must do more than simply carry genes: it must be able to be replicated, and the replicated copies must be separated and partitioned equally and reliably into the two daughter cells at each cell division. These processes occur through an ordered series of events, known col... | {
"Header 1": "Specialized DNA Sequences Are Required for DNA Replication and Chromosome Segregation",
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Inside the nucleus, the interphase chromosomes—although longer and finer than mitotic chromosomes—are nonetheless organized in various
Figure 5–16 A typical duplicated mitotic chromosome is highly compact. Because DNA is replicated during interphase, each duplicated mitotic chromosome c... | {
"Header 1": "Specialized DNA Sequences Are Required for DNA Replication and Chromosome Segregation",
"Header 3": "Interphase Chromosomes Are Not Randomly Distributed Within the Nucleus",
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As we have seen, all eukaryotic cells, whether in interphase or mitosis, package their DNA tightly into chromosomes. Human Chromosome 22, for example, contains about 48 million nucleotide pairs; stretched out end-to-end, its DNA would extend about 1.5 cm. Yet, during mitosis, Chromosome 22 measures only about 2 μm in l... | {
"Header 1": "Specialized DNA Sequences Are Required for DNA Replication and Chromosome Segregation",
"Header 3": "The DNA in Chromosomes Is Always Highly Condensed",
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The proteins that bind to DNA to form eukaryotic chromosomes are traditionally divided into two general classes: the **histones** and the *nonhistone chromosomal proteins*. Histones are present in enormous quantities (more than 60 million molecules of several different types in each cell), and their total mass in chrom... | {
"Header 1": "Nucleosomes Are the Basic Units of Eukaryotic Chromosome Structure",
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Although long strings of nucleosomes form on most chromosomal DNA, chromatin in the living cell rarely adopts the extended beads-on-a-string form seen in Figure 5–20B. Instead, the nucleosomes are further packed on top of one another to generate a more compact structure, such as the chromatin fiber shown in Figure 5–20... | {
"Header 1": "Nucleosomes Are the Basic Units of Eukaryotic Chromosome Structure",
"Header 3": "Chromosome Packing Occurs on Multiple Levels",
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Eukaryotic cells have several ways to adjust the local structure of their chromatin rapidly. One way takes advantage of chromatin-remodeling complexes, protein machines that use the energy of ATP hydrolysis to change the position of the DNA wrapped around nucleosomes (Figure 5–26A). The complexes, which attach to both ... | {
"Header 1": "Nucleosomes Are the Basic Units of Eukaryotic Chromosome Structure",
"Header 3": "Changes in Nucleosome Structure Allow Access to DNA",
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The localized alteration of chromatin packing by remodeling complexes and histone modification has important effects on the large-scale structure of interphase chromosomes. Interphase chromatin is not uniformly packed. Instead, regions of the chromosome that contain genes that are being expressed are generally more ext... | {
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"Header 3": "Interphase Chromosomes Contain Both Condensed and More Extended Forms of Chromatin",
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Mutations in a particular gene on the X chromosome result in color blindness in men. By contrast, most women carrying the mutation have proper color vision but see colored objects with reduced resolution, as though functional cone cells (the photoreceptor cells responsible for color vision) are spaced farther apart tha... | {
"Header 1": "Nucleosomes Are the Basic Units of Eukaryotic Chromosome Structure",
"Header 3": "Question 5–4",
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- • Life depends on the stable storage and inheritance of genetic information. ECB4 e5.30/5.30
- • Genetic information is carried by very long DNA molecules and is encoded in the linear sequence of four nucleotides: A, T, G, and C.
- • Each molecule of DNA is a double helix composed of a pair of antiparallel, complemen... | {
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gene
A. The nucleotide sequence of one DNA strand of a DNA double helix is
5'-GGATTTTTGTCCACAATCA-3'.
What is the sequence of the complementary strand?
- B. In the DNA of certain bacterial cells, 13% of the nucleotides are adenine. What are the percentages of the other nucleotides?
- C. How many possible nucleo... | {
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"Header 3": "Question 5–5",
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The ability of a cell to survive and proliferate in a chaotic environment depends on the accurate duplication of the vast quantity of genetic information carried in its DNA. This duplication process, called *DNA replication*, must occur before a cell can divide to produce two genetically identical daughter cells. Maint... | {
"Header 1": "DNA Replication, Repair, and Recombination",
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In the preceding chapter, we saw that each strand of a DNA double helix contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. Each strand can therefore serve as a **template**, or mold, for the synthesis of a new complementary strand. In other words, if we de... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "**Base-Pairing Enables DNA Replication**",
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The DNA double helix is normally very stable: the two DNA strands are locked together firmly by the large numbers of hydrogen bonds between the bases on both strands (see Figure 5–2). As a result, only temperatures approaching those of boiling water provide enough thermal energy to separate the two strands. To be used ... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "DNA Synthesis Begins at Replication Origins",
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In 1953, James Watson and Francis Crick published their famous two-page paper describing a model for the structure of DNA (see Figure 5–2). In it, they proposed that complementary bases—adenine and thymine, guanine and cytosine—pair with one another along the center of the double helix, holding together the two strands... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "THE NATURE OF REPLICATION",
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To distinguish between the two models, Meselson and Stahl turned up the heat. When DNA is subjected to high temperature, the hydrogen bonds holding the two strands together break and the helix comes apart, leaving a collection of single-stranded DNAs. When the researchers heated their hybrid molecules before centrifu... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "THE NATURE OF REPLICATION",
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The movement of a replication fork is driven by the action of the replication machine, at the heart of which is an enzyme called DNA polymerase. This enzyme catalyzes the addition of nucleotides to the 3ʹ end of a growing DNA strand, using one of the original, parental DNA strands as a template. Base pairing between an... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "DNA Polymerase Synthesizes DNA Using a Parental Strand as Template",
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Look carefully at the micrograph and drawing 2 in Figure 6–9.
A. Using the scale bar, estimate the lengths of the DNA strands between the replication forks. Numbering the replication forks sequentially from the left, how long will it take until forks 4 and 5, and forks 7 and 8, respectively, collide with each other? ... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "Question 6–1",
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The 5'-to-3' direction of the DNA polymerization reaction poses a problem at the replication fork. As illustrated in Figure 5–2, the sugar-phosphate backbone of each strand of a DNA double helix has a unique chemical direction, or polarity, determined by the way each sugar residue is linked to the next, and the two str... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "The Replication Fork Is Asymmetrical",
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DNA polymerase is so accurate that it makes only about one error in every 10<sup>7</sup> nucleotide pairs it copies. This error rate is much lower than can be explained simply by the accuracy of complementary base-pairing. Although A-T and C-G are by far the most stable base pairs, other, less stable base pairs—for exa... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "**DNA Polymerase Is Self-correcting**",
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We have seen that the accuracy of DNA replication depends on the requirement of the DNA polymerase for a correctly base-paired 3ʹ end before it can add more nucleotides to a growing DNA strand. How then can the polymerase begin a completely new DNA strand? To get the process started, a different enzyme is needed—one th... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "Short Lengths of RNA Act as Primers for DNA Synthesis",
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DNA replication requires the cooperation of a large number of proteins that act in concert to open up the double helix and synthesize new DNA. These proteins form part of a remarkably complex replication machine. The first problem faced by the replication machine is accessing the
Figure 6–17 Multiple enzymes are requ... | {
"Header 1": "DNA Replication, Repair, and Recombination",
"Header 3": "Proteins at a Replication Fork Cooperate to Form a Replication Machine",
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Having discussed how DNA replication begins at origins and how movement of a replication fork proceeds, we now turn to the special problem
#### QUESTION 6-2
Discuss the following statement: "Primase is a sloppy enzyme that makes many mistakes. Eventually, the RNA primers it makes are disposed of and replaced with D... | {
"Header 1": "Telomerase Replicates the Ends of Eukaryotic Chromosomes",
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The diversity of living organisms and their success in colonizing almost every part of the Earth's surface depend on genetic changes accumulated gradually over millions of years. Some of these changes allow organisms to adapt to changing conditions and to thrive in new habitats. However, in the short term, and from the... | {
"Header 1": "Telomerase Replicates the Ends of Eukaryotic Chromosomes",
"Header 3": "DNA Repair",
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Just like any other molecule in the cell, DNA is continually undergoing thermal collisions with other molecules, often resulting in major chemical changes in the DNA. For example, during the time it takes to read this sentence, a total of about a trillion (10<sup>12</sup>) purine bases (A and G) will be lost from DNA i... | {
"Header 1": "Telomerase Replicates the Ends of Eukaryotic Chromosomes",
"Header 3": "DNA Damage Occurs Continually in Cells",
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The thousands of random chemical changes that occur every day in the DNA of a human cell—through thermal collisions or exposure to reactive metabolic by-products, DNA-damaging chemicals, or radiation—are repaired by a variety of mechanisms, each catalyzed by a different set of enzymes. Nearly all these repair mechanism... | {
"Header 1": "Telomerase Replicates the Ends of Eukaryotic Chromosomes",
"Header 3": "Cells Possess a Variety of Mechanisms for Repairing DNA",
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Although the high fidelity and proofreading abilities of the cell's replication machinery generally prevent replication errors from occurring, rare mistakes do happen. Fortunately, the cell has a backup system—called mismatch repair—which is dedicated to correcting these errors. The replication machine makes approximat... | {
"Header 1": "Telomerase Replicates the Ends of Eukaryotic Chromosomes",
"Header 3": "A DNA Mismatch Repair System Removes Replication Errors That Escape Proofreading",
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The repair mechanisms we have discussed thus far rely on the genetic redundancy built into every DNA double helix. If nucleotides on one strand are damaged, they can be repaired using the information present in the complementary strand.
But what happens when both strands of the double helix are damaged at the same ti... | {
"Header 1": "Double-Strand DNA Breaks Require a Different Strategy for Repair",
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The problem with repairing a double-strand break, as we mentioned, is finding an intact template to guide the repair. However, if a double-strand break occurs in one double helix shortly after a stretch of DNA has been replicated, the undamaged double helix can readily serve as a template to guide the repair of the bro... | {
"Header 1": "Homologous Recombination Can Flawlessly Repair DNA Double-Strand Breaks",
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On occasion, the cell's DNA replication and repair processes fail and give rise to a mutation. This permanent change in the DNA sequence can have profound consequences. A mutation that affects just a single nucleotide pair can severely compromise an organism's fitness if the change occurs in a vital position in the DNA... | {
"Header 1": "Homologous Recombination Can Flawlessly Repair DNA Double-Strand Breaks",
"Header 3": "Failure to Repair DNA Damage Can Have Severe Consequences for a Cell or Organism",
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Although the majority of mutations do neither harm nor good to an organism, those that have harmful consequences are usually eliminated from the population through natural selection; individuals carrying the altered DNA may die or experience decreased fertility, in which case these changes will be lost. By contrast, fa... | {
"Header 1": "Homologous Recombination Can Flawlessly Repair DNA Double-Strand Breaks",
"Header 3": "A Record of the Fidelity of DNA Replication and Repair Is Preserved in Genome Sequences",
"token_count": 389,
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- • Before a cell divides, it must accurately replicate the vast quantity of genetic information carried in its DNA.
- • Because the two strands of a DNA double helix are complementary, each strand can act as a template for the synthesis of the other. Thus DNA replication produces two identical, double-helical DNA mole... | {
"Header 1": "Homologous Recombination Can Flawlessly Repair DNA Double-Strand Breaks",
"Header 3": "Essential Concepts",
"token_count": 1989,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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Once the double-helical structure of DNA (deoxyribonucleic acid) had been determined in the early 1950s, it became clear that the hereditary information in cells is encoded in the linear order—or *sequence*—of the four different nucleotide subunits that make up the DNA. We saw in Chapter 6 how this information can be p... | {
"Header 1": "From DNA to Protein: How Cells Read the Genome",
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Transcription and translation are the means by which cells read out, or *express*, the instructions in their *genes*. Many identical RNA copies can be made from the same gene, and each RNA molecule can direct the synthesis of many identical protein molecules. This successive amplification enables cells to rapidly synth... | {
"Header 1": "From DNA to Protein: How Cells Read the Genome",
"Header 3": "From DNA to RNA",
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The first step a cell takes in expressing one of its many thousands of genes is to copy the nucleotide sequence of that gene into RNA. The process is called **transcription** because the information, though copied into another chemical form, is still written in essentially the same language—the language of nucleotides.... | {
"Header 1": "From DNA to Protein: How Cells Read the Genome",
"Header 3": "Portions of DNA Sequence Are Transcribed into RNA",
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All the RNA in a cell is made by transcription, a process that has certain similarities to DNA replication (discussed in Chapter 6). Transcription begins with the opening and unwinding of a small portion of the DNA double helix to expose the bases on each DNA strand. One of the two strands of the DNA double helix then ... | {
"Header 1": "Transcription Produces RNA That Is Complementary to One Strand of DNA",
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The vast majority of genes carried in a cell's DNA specify the amino acid sequences of proteins. The RNA molecules encoded by these genes—which
Figure 7–7 DNA is transcribed into RNA by the enzyme RNA polymerase. RNA
polymerase (pale blue) moves stepwise along the DNA, unwinding the D... | {
"Header 1": "Transcription Produces RNA That Is Complementary to One Strand of DNA",
"Header 3": "Cells Produce Various Types of RNA",
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The initiation of transcription is an especially critical process because it is the main point at which the cell selects which proteins or RNAs are to be produced. To begin transcription, RNA polymerase must be able to recognize the start of a gene and bind firmly to the DNA at this site. The way in which RNA polymeras... | {
"Header 1": "Transcription Produces RNA That Is Complementary to One Strand of DNA",
"Header 3": "Signals in DNA Tell RNA Polymerase Where to Start and Finish Transcription",
"token_count": 1430,
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Many of the principles we just outlined for bacterial transcription also apply to eukaryotes. However, transcription initiation in eukaryotes differs in several important ways from that in bacteria:
- The first difference lies in the RNA polymerases themselves. While bacteria contain a single type of RNA polymerase, ... | {
"Header 1": "Initiation of Eukaryotic Gene Transcription Is a Complex Process",
"token_count": 676,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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The initial finding that, unlike bacterial RNA polymerase, purified eukaryotic RNA polymerase II could not initiate transcription on its own in a test tube led to the discovery and purification of the general transcription factors. These accessory proteins assemble on the promoter, where they position the RNA polymeras... | {
"Header 1": "Initiation of Eukaryotic Gene Transcription Is a Complex Process",
"Header 3": "Eukaryotic RNA Polymerase Requires General Transcription Factors",
"token_count": 402,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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Could the RNA polymerase used for transcription be used as the polymerase that makes the RNA primer required for DNA replication (discussed in Chapter 6)?
Figure 7–13 TATA-binding protein (TBP) binds to the TATA box (indicated by letters) and bends the ... | {
"Header 1": "Initiation of Eukaryotic Gene Transcription Is a Complex Process",
"Header 3": "Question 7–3",
"token_count": 1447,
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Most eukaryotic pre-mRNAs have to undergo an additional processing step before they are functional mRNAs. This step involves a far more radical modification of the pre-mRNA transcript than capping or polyadenylation, and it is the consequence of a surprising feature of most eukaryotic genes. In bacteria, most proteins ... | {
"Header 1": "In Eukaryotes, Protein-Coding Genes Are Interrupted by Noncoding Sequences Called Introns",
"token_count": 262,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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Figure 7–15 Phosphorylation of the tail of RNA polymerase II allows RNA-processing proteins to assemble there. Note that the phosphates shown here are in addition to the ones required for transcription initiation (see Figure 7–12). Capping, polyadenylation, and splicing are all modifica... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"token_count": 336,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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To produce an mRNA in a eukaryotic cell, the entire length of the gene, introns as well as exons, is transcribed into RNA. After capping, and as RNA polymerase II continues to transcribe the gene, the process of RNA splicing begins, in which the introns are removed from the newly synthesized RNA and the exons are stitc... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "Introns Are Removed From Pre-mRNAs by RNA Splicing",
"token_count": 1457,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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We have seen how eukaryotic pre-mRNA synthesis and processing take place in an orderly fashion within the cell nucleus. However, these events create a special problem for eukaryotic cells: of the total number of pre-mRNA transcripts that are synthesized, only a small fraction—the mature mRNAs—will be useful to the cell... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "Mature Eukaryotic mRNAs Are Exported from the Nucleus",
"token_count": 470,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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Because a single mRNA molecule can be translated into protein many times (see Figure 7–2), the length of time that a mature mRNA molecule persists in the cell affects the amount of protein it produces. Each mRNA molecule is eventually degraded into nucleotides by ribonucleases (RNAses) present in the cytosol, but the l... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "mRNA Molecules Are Eventually Degraded in the Cytosol",
"token_count": 298,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The process of transcription is universal: all cells use RNA polymerase and complementary base-pairing to synthesize RNA from DNA. Indeed, bacterial and eukaryotic RNA polymerases are almost identical in overall structure and clearly evolved from a shared ancestral polymerase. It may therefore seem puzzling that the re... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "The Earliest Cells May Have Had Introns in Their Genes",
"token_count": 941,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
By the end of the 1950s, biologists had demonstrated that the information encoded in DNA is copied first into RNA and then into protein. The debate then shifted to the "coding problem": How is the information in a linear sequence of nucleotides in an RNA molecule translated into the linear sequence of a chemically quit... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "From RNA to Protein",
"token_count": 840,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Transcription as a means of information transfer is simple to understand: DNA and RNA are chemically and structurally similar, and DNA can act as a direct template for the synthesis of RNA through complementary basepairing. As the term transcription signifies, it is as if a message written out by hand were being conver... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "An mRNA Sequence Is Decoded in Sets of Three Nucleotides",
"token_count": 720,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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By the beginning of the 1960s, the *central dogma* had been accepted as the pathway along which information flows from gene to protein. It was clear that genes encode proteins, that genes are made of DNA, and that mRNA serves as an intermediary, carrying the information from DNA to the ribosome, where the RNA is transl... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "CRACKING THE GENETIC CODE",
"token_count": 274,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Before researchers could test their synthetic mRNAs, they needed to perfect a cell-free system for protein synthesis. This would allow them to translate their messages into polypeptides in a test tube. (Generally speaking, when working in the laboratory, the simpler the system, the easier it is to interpret the results... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "Losing the cells",
"token_count": 365,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Producing a synthetic polynucleotide with a defined sequence was not as simple as it sounds. Again, it would be years before chemists and bioengineers developed machines that could synthesize any given string of nucleic acids quickly and cheaply. Nirenberg decided to use polynucleotide phosphorylase, an enzyme that wou... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "Faking the message",
"token_count": 834,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
These final ambiguities in the code were resolved when Nirenberg and a young medical graduate named Phil Leder discovered that RNA fragments that were only three nucleotides in length—the size of a single codon could bind to a ribosome and attract the appropriate amino-acid-containing tRNA molecule to the proteinmaking... | {
"Header 1": "RNA capping and polyadenylation coding sequence sequence AAAAA<sub>150-250</sub> RNA poly-A tail (A)",
"Header 3": "Trapping the triplets",
"token_count": 1708,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
For a tRNA molecule to carry out its role as an adaptor, it must be linked or charged—with the correct amino acid. How does each tRNA molecule recognize the one amino acid in 20 that is its right partner? Recognition and attachment of the correct amino acid depend on enzymes called aminoacyl-tRNA synthetases, which cov... | {
"Header 1": "Specific Enzymes Couple tRNAs to the Correct Amino Acid",
"token_count": 514,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The recognition of a codon by the anticodon on a tRNA molecule depends on the same type of complementary base-pairing used in DNA replication and transcription. However, accurate and rapid translation of mRNA into protein requires a molecular machine that can move along the mRNA, capture complementary tRNA molecules, h... | {
"Header 1": "Specific Enzymes Couple tRNAs to the Correct Amino Acid",
"Header 3": "The mRNA Message Is Decoded by Ribosomes",
"token_count": 475,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
In a clever experiment performed in 1962, a cysteine already attached to its tRNA was chemically converted to an alanine. These "hybrid" tRNA molecules were then added to a cellfree translation system from which the normal cysteine-tRNAs had been removed. When the resulting protein was analyzed, it was found that alani... | {
"Header 1": "Question 7–4",
"token_count": 1444,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The ribosome is one of the largest and most complex structures in the cell, composed of two-thirds RNA and one-third protein by weight. The determination of the entire three-dimensional structure of its large and small subunits in 2000 was a major triumph of modern biology. The structure confirmed earlier evidence that... | {
"Header 1": "Question 7–4",
"Header 3": "The Ribosome Is a Ribozyme",
"token_count": 493,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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In the test tube, ribosomes can be forced to translate any RNA molecule (see How We Know, pp. 240–241). In a cell, however, a specific start signal is required to initiate translation. The site at which protein synthesis begins on an mRNA is crucial, because it sets the reading frame for the whole length of the message... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"token_count": 1542,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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The synthesis of most protein molecules takes between 20 seconds and several minutes. But even during this short period, multiple ribosomes usually bind to each mRNA molecule being translated. If the mRNA is being translated efficiently, a new ribosome hops onto the 5′ end of the mRNA molecule almost as soon as the pre... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "Proteins Are Made on Polyribosomes",
"token_count": 281,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The ability to translate mRNAs accurately into proteins is a fundamental feature of all life on Earth. Although the ribosome and other molecules that carry out this complex task are very similar among organisms, we
Figure 7–39 Proteins are synthesized on p... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "Inhibitors of Prokaryotic Protein Synthesis Are Used as Antibiotics",
"token_count": 671,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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After a protein is released from the ribosome, a cell can control its activity and longevity in various ways. The number of copies of a protein in a cell depends, like the human population, not only on how quickly new individuals are made but also on how long they survive. So controlling the breakdown of proteins into ... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "Controlled Protein Breakdown Helps Regulate the Amount of Each Protein in a Cell",
"token_count": 983,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"... |
We have seen that many types of chemical reactions are required to produce a protein from the information contained in a gene. The final concentration of a protein in a cell therefore depends on the rate at which each of the many steps is carried out (Figure 7–42). In addition, many proteins—once they leave the ribosom... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "There Are Many Steps Between DNA and Protein",
"token_count": 1074,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
We have seen that complementary base-pairing enables one nucleic acid to act as a template for the formation of another. Thus a single strand of RNA or DNA can specify the sequence of a complementary polynucleotide, which, in turn, can specify the sequence of the original molecule, allowing the original nucleic acid to... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "RNA Can Both Store Information and Catalyze Chemical Reactions",
"token_count": 962,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The first cells on Earth would presumably have been much less complex and less efficient in reproducing themselves than even the simplest present-day cells. They would have consisted of little more than a simple membrane enclosing a set of self-replicating molecules and a few other components required to provide the ma... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "RNA Is Thought to Predate DNA in Evolution",
"token_count": 458,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Discuss the following: "During the evolution of life on Earth, RNA lost its glorious position as the first selfreplicating catalyst. Its role now is as a mere messenger in the information flow from DNA to protein."
glucose and other simple carbohydrates, is readily formed from formaldehyde (HCHO), which is one of the... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "Question 7–6",
"token_count": 582,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
- • The flow of genetic information in all living cells is DNA → RNA → protein. The conversion of the genetic instructions in DNA into RNAs and proteins is termed gene expression.
- • To express the genetic information carried in DNA, the nucleotide sequence of a gene is first transcribed into RNA. Transcription is cat... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "Essential Concepts",
"token_count": 954,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
#### Question 7–7
Which of the following statements are correct? Explain your answers.
- A. An individual ribosome can make only one type of protein.
- B. All mRNAs fold into particular three-dimensional structures that are required for their translation.
- C. The large and small subunits of an individual ribosome ... | {
"Header 1": "Specific Codons in mRNA Signal the Ribosome Where to Start and to Stop Protein Synthesis",
"Header 3": "Questions",
"token_count": 1613,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
An organism's DNA encodes all of the RNA and protein molecules that are needed to make its cells. Yet a complete description of the DNA sequence of an organism—be it the few million nucleotides of a bacterium or the few billion nucleotides in each human cell—does not enable us to reconstruct that organism any more than... | {
"Header 1": "Control of Gene Expression",
"token_count": 731,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The evidence that cells have the ability to change which genes they express without altering the nucleotide sequence of their DNA comes from experiments in which the genome from a differentiated cell is made to direct the development of a complete organism. If the chromosomes of the differentiated cell were altered irr... | {
"Header 1": "Control of Gene Expression",
"Header 3": "The Different Cell Types of a Multicellular Organism Contain the Same DNA",
"token_count": 522,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The extent of the differences in gene expression between different cell types may be roughly gauged by comparing the protein composition of cells in liver, heart, brain, and so on. In the past, such analysis was performed by two-dimensional gel electrophoresis (see Panel 4–5, p. 167). Nowadays, the total protein conten... | {
"Header 1": "Control of Gene Expression",
"Header 3": "Different Cell Types Produce Different Sets of Proteins",
"token_count": 380,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The specialized cells in a multicellular organism are capable of altering their patterns of gene expression in response to extracellular cues. For example, if a liver cell is exposed to the steroid hormone cortisol, the production of several proteins is dramatically increased. Released by the adrenal gland during perio... | {
"Header 1": "Control of Gene Expression",
"Header 3": "A Cell Can Change the Expression of Its Genes in Response to External Signals",
"token_count": 209,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
If differences among the various cell types of an organism depend on the particular genes that the cells express, at what level is the control of gene expression exercised? As we saw in the last chapter, there are many steps in the pathway leading from DNA to protein, and all of them can in principle be regulated. Thus... | {
"Header 1": "Control of Gene Expression",
"Header 3": "Gene Expression Can Be Regulated at Various Steps from DNA to RNA to Protein",
"token_count": 489,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Control of transcription is usually exerted at the step at which the process is initiated. In Chapter 7, we saw that the **promoter** region of a gene binds the enzyme *RNA polymerase* and correctly orients the enzyme to begin its task of making an RNA copy of the gene. The promoters of both bacterial and eukaryotic ge... | {
"Header 1": "Transcription Regulators Bind to Regulatory DNA Sequences",
"token_count": 948,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The simplest and best understood examples of gene regulation occur in bacteria and in the viruses that infect them. The genome of the bacterium $E.\ coli$ consists of a single circular DNA molecule of about $4.6\times10^6$ nucleotide pairs. This DNA encodes approximately 4300 proteins, although only a fraction of t... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"token_count": 1087,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The tryptophan repressor, as its name suggests, is a **transcriptional repressor** protein: in its active form, it switches genes off, or *represses* them. Some bacterial transcription regulators do the opposite: they switch genes on, or *activate* them. These **transcriptional activator** proteins work on promoters th... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"Header 3": "Repressors Turn Genes Off and Activators Turn Them On",
"token_count": 261,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
In many instances, the activity of a single promoter is controlled by two different transcription regulators. The *Lac operon* in *E. coli*, for example,
is controlled by both the *Lac repressor* and the CAP activator that we just discussed. The *Lac* op... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"Header 3": "An Activator and a Repressor Control the Lac Operon",
"token_count": 589,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Explain how DNA-binding proteins can make sequence-specific contacts to a double-stranded DNA molecule without breaking the hydrogen bonds that hold the bases together. Indicate how, through such contacts, a protein can distinguish a T-A from a C-G pair. Indicate the parts of the nucleotide base pairs that could form n... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"Header 3": "Question 8–2",
"token_count": 271,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Eukaryotes, too, use transcription regulators—both activators and repressors—to regulate the expression of their genes. The DNA sites to which eukaryotic gene activators bind are termed *enhancers*, because their presence dramatically enhances the rate of transcription. It was surprising to biologists when, in 1979, it... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"Header 3": "Eukaryotic Transcription Regulators Control Gene Expression from a Distance",
"token_count": 449,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Initiation of transcription in eukaryotic cells must also take into account the packaging of DNA into chromosomes. As discussed in Chapter 5, eukaryotic DNA is packed into nucleosomes, which, in turn, are folded into higher-order structures. How do transcription regulators, general transcription factors, and RNA polyme... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"Header 3": "Eukaryotic Transcription Regulators Help Initiate Transcription by Recruiting Chromatin-Modifying Proteins",
"token_count": 681,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biolo... |
All cells must be able to switch genes on and off in response to signals in their environment. But the cells of multicellular organisms have evolved this capacity to an extreme degree and in highly specialized ways to form organized arrays of differentiated cell types. In particular, once a cell in a multicellular orga... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"Header 3": "The Molecular Mechanisms That Create Specialized Cell Types",
"token_count": 281,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Because eukaryotic transcription regulators can control transcription initiation when bound to DNA many base pairs away from the promoter, the nucleotide sequences that control the expression of a gene can be spread over long stretches of DNA. In animals and plants, it is not unusual to find the regulatory DNA sequence... | {
"Header 1": "Transcriptional Switches Allow Cells to Respond to Changes in Their Environment",
"Header 3": "Eukaryotic Genes Are Controlled by Combinations of Transcription Regulators",
"token_count": 535,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
In addition to being able to switch individual genes on and off, all cells—whether prokaryote or eukaryote—need to coordinate the expression of different genes. When a eukaryotic cell receives a signal to divide, for example, a number of hitherto unexpressed genes are turned on together to set in motion the events that... | {
"Header 1": "The Expression of Different Genes Can Be Coordinated by a Single Protein",
"token_count": 366,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The ability to regulate gene expression is crucial to the proper development of a multicellular organism from a fertilized egg to a fertile adult. Beginning at the earliest moments in development, a succession of transcriptional programs guides the differential expression of genes that allows an animal to form a proper... | {
"Header 1": "The Expression of Different Genes Can Be Coordinated by a Single Protein",
"Header 3": "gene regulation—the story of *eve*",
"token_count": 227,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
*Even-skipped*—*Eve*, for short—is a gene whose expression plays an important part in the development of the *Drosophila* embryo. If this gene is inactivated by mutation, many parts of the embryo fail to form and the fly larva dies early in development. But *Eve* is not expressed uniformly throughout the embryo. Instea... | {
"Header 1": "The Expression of Different Genes Can Be Coordinated by a Single Protein",
"Header 3": "Seeing *Eve*",
"token_count": 217,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
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