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As we have seen in this chapter, regulatory DNA sequences control which cells in an organism will express a particular gene, and at what point during development that gene will be turned on. In eukaryotes, these regulatory sequences are frequently located upstream of the gene itself. One way to locate a regulatory DNA ... | {
"Header 1": "The Expression of Different Genes Can Be Coordinated by a Single Protein",
"Header 3": "Dissecting the DNA",
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Figure 8–17 Combinations of a few transcription regulators can generate many cell types during development. In this simple scheme, a "decision" to make a new transcription regulator (shown as a numbered circle) is made after each cell division. Repetition of this simple rule can generat... | {
"Header 1": "The Expression of Different Genes Can Be Coordinated by a Single Protein",
"Header 3": "Dissecting the DNA",
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We have seen that, in some cases, one type of differentiated cell can be experimentally converted into another type by the artificial expression of specific transcription regulators (see Figure 8–16). Even more surprising, transcription regulators can coax various differentiated cells to *de-differentiate* into **pluri... | {
"Header 1": "The Expression of Different Genes Can Be Coordinated by a Single Protein",
"Header 3": "Specialized Cell Types Can Be Experimentally Reprogrammed to Become Pluripotent Stem Cells",
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We have seen that a small number of transcription regulators can control the expression of whole sets of genes and can even convert one cell type into another. But an even more stunning example of the power of transcriptional control comes from studies of eye development in *Drosophila*. In this case, a single "master"... | {
"Header 1": "The Formation of an Entire Organ Can Be Triggered by a Single Transcription Regulator",
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Once a cell has become differentiated into a particular cell type, it will generally remain differentiated, and all its progeny cells will remain that same cell type. Some highly specialized cells, including skeletal muscle cells and neurons, never divide again once they have differentiated—that is, they are *terminall... | {
"Header 1": "The Formation of an Entire Organ Can Be Triggered by a Single Transcription Regulator",
"Header 3": "Epigenetic Mechanisms Allow Differentiated Cells to Maintain Their Identity",
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The more time an mRNA persists in the cell before it is degraded, the more protein it will produce. In bacteria, most mRNAs last only a few minutes before being destroyed. This instability allows a bacterium to adapt quickly to environmental changes. Eukaryotic mRNAs are generally more stable. The mRNA that encodes β-g... | {
"Header 1": "The Formation of an Entire Organ Can Be Triggered by a Single Transcription Regulator",
"Header 3": "Each mRNA Controls Its Own Degradation and Translation",
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MicroRNAs, or miRNAs, are tiny RNA molecules that control gene expression by base-pairing with specific mRNAs and reducing both their stability and their translation into protein. In humans, miRNAs are thought to regulate the expression of at least one-third of all protein-coding genes.
Like other noncoding RNAs, suc... | {
"Header 1": "Regulatory RNAs Control the Expression of Thousands of Genes",
"Header 3": "MicroRNAs Direct the Destruction of Target mRNAs",
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Some of the same components that process and package miRNAs also play another crucial part in the life of a cell: they serve as a powerful cell defense mechanism. In this case, the system is used to eliminate "foreign" RNA molecules—in particular, the double-stranded RNAs produced by many viruses and transposable genet... | {
"Header 1": "Regulatory RNAs Control the Expression of Thousands of Genes",
"Header 3": "Small Interfering RNAs Are Produced From Double-Stranded, Foreign RNAs to Protect Cells From Infections",
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At the other end of the size spectrum are the long noncoding RNAs, a class of RNA molecules that are more than 200 nucleotides in length. There are thought to be upwards of 8000 of these RNAs encoded in the human and mouse genomes. Yet, with few exceptions, their roles in the biology of the organism are not entirely cl... | {
"Header 1": "Regulatory RNAs Control the Expression of Thousands of Genes",
"Header 3": "Thousands of Long Noncoding RNAs May Also Regulate Mammalian Gene Activity",
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- • A typical eukaryotic cell expresses only a fraction of its genes, and the distinct types of cells in multicellular organisms arise because different sets of genes are expressed as cells differentiate.
- • In principle, gene expression can be controlled at any of the steps between a gene and its ultimate functional ... | {
"Header 1": "Regulatory RNAs Control the Expression of Thousands of Genes",
"Header 3": "Essential Concepts",
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#### **QUESTION 8-11**
Figure 8–17 shows a simple scheme by which three transcription regulators are used during development to create eight different cell types. How many cell types could you create, using the same rules, with four different transcription regulators? As described in the text, MyoD is a transcripti... | {
"Header 1": "Regulatory RNAs Control the Expression of Thousands of Genes",
"Header 3": "Essential Concepts",
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For a given individual, the nucleotide sequence of the genome in virtually every one of its cells is the same. But compare the DNA of two individuals—even parent and child—and that is no longer the case: the genomes of individuals within a species contain slightly different information. And between members of different... | {
"Header 1": "How Genes and Genomes Evolve",
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For bacteria and unicellular organisms that reproduce mainly asexually, the inheritance of genetic information is fairly straightforward. Each individual duplicates its genome and donates one copy to each daughter cell when the individual divides in two. The family tree of such unicellular organisms is simply a branchi... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "In Sexually Reproducing Organisms, Only Changes to the Germ Line Are Passed On To Progeny",
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Despite the elaborate mechanisms that exist to faithfully copy and repair DNA sequences, each nucleotide pair in an organism's genome runs a small risk of changing each time a cell divides. Changes that affect a single nucleotide pair are called point mutations. These typically arise from rare errors in DNA replication... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Point Mutations Are Caused by Failures of the Normal Mechanisms for Copying and Repairing DNA",
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Mutations in the coding sequences of genes are fairly easy to spot because they change the amino acid sequence of the encoded protein in predictable ways. But mutations in regulatory DNA are more difficult to recognize, because they don't affect protein sequence and can be located some distance from the coding sequence... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Point Mutations Can Change the Regulation of a Gene",
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Point mutations can influence the activity of an existing gene, but how do new genes with new functions come into being? Gene duplication is perhaps the most important mechanism for generating new genes from old ones. Once a gene has been duplicated, each of the two copies is free to accumulate mutations that might all... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "DNA Duplications Give Rise to Families of Related Genes",
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The evolutionary history of the globin gene family provides a striking example of how gene duplication and divergence has generated new proteins. The unmistakable similarities in amino acid sequence and structure among the present-day globin proteins indicate that all the globin genes must derive from a single ancestra... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "The Evolution of the Globin Gene Family Shows How Gene Duplication and Divergence Can Produce New Proteins",
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Almost every gene in the genomes of vertebrates exists in multiple versions, suggesting that, rather than single genes being duplicated in a piecemeal fashion, the whole vertebrate genome was long ago duplicated in one fell swoop. Early in vertebrate evolution, it appears that the entire genome actually underwent dupli... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Whole-Genome Duplications Have Shaped the Evolutionary History of Many Species",
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As we discussed in Chapter 4, many proteins are composed of a set of smaller functional *domains*. In eukaryotes, each of these protein domains is usually encoded by a separate exon, which is surrounded by long stretches of noncoding introns (see Figures 7–17 and 7–18). This organization of eukaryotic genes can facilit... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Novel Genes Can Be Created by Exon Shuffling",
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*Mobile genetic elements*—DNA sequences that can move from one chromosomal location to another—are an important source of genomic change and have profoundly affected the structure of modern genomes. These parasitic DNA sequences can colonize a genome and then spread within it. In the process, they often disrupt the fun... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "The Evolution of Genomes Has Been Profoundly Influenced by the Movement of Mobile Genetic Elements",
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So far we have considered genetic changes that take place within the genome of an individual organism. However, genes and other portions of genomes can also be exchanged between individuals of different species. This mechanism of horizontal gene transfer is rare among eukaryotes but common among bacteria, which can exc... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Genes Can Be Exchanged Between Organisms by Horizontal Gene Transfer",
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We have seen how genomes can change over evolutionary time. The nucleotide sequences of present-day genomes provide a record of those changes that conferred biological success. By comparing the genomes of a variety of living organisms, we can thus begin to decipher our evolutionary history, seeing how our ancestors vee... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Reconstructing Life's Family Tree",
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Evolution is commonly thought of as progressive, but at the molecular level the process is random. Consider the fate of a point mutation that occurs in a germ-line cell. On rare occasions, the mutation might cause a change for the better. But most often it will either have no consequence or cause serious damage. Mutati... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Genetic Changes That Provide a Selective Advantage Are Likely to Be Preserved",
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For species that are closely related, it is often most informative to focus on selectively neutral mutations. Because they accumulate steadily at a rate that is unconstrained by selection pressures, these mutations provide a metric for gauging how much modern species have diverged from their common ancestor. Such compa... | {
"Header 1": "How Genes and Genomes Evolve",
"Header 3": "Closely Related Organisms Have Genomes That Are Similar in Organization As Well As Sequence",
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As we delve back further into our evolutionary history and compare our genomes with those of more distant relatives, the picture begins to change. The lineages of humans and mice, for example, diverged about 75 million years ago. These genomes are about the same size, contain practically the same genes, and are both ri... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
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Going back even further in evolution, we can compare our genome with those of more distantly related vertebrates. The lineages of fish and mammals diverged about 400 million years ago. This is long enough for random sequence changes and differing selection pressures to have obliterated almost every trace of similarity ... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Genome Comparisons Show That Vertebrate Genomes Gain and Lose DNA Rapidly",
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As we go back further still to the genomes of our even more distant relatives—beyond apes, mice, fish, flies, worms, plants, and yeasts, all the way to bacteria—we find fewer and fewer resemblances to our own genome. Yet even across this enormous evolutionary divide, purifying selection has maintained a few hundred fun... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Sequence Conservation Allows Us to Trace Even the Most Distant Evolutionary Relationships",
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The tree of life depicted in Figure 9–23 includes representatives from life's most distant branches, from the cyanobacteria that release oxygen into the atmosphere to the animals, like us, that use that oxygen to boost their metabolism. What the diagram does not encompass, however, are the parasitic genetic elements th... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "TRANSPOSONS AND VIRUSES",
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Mobile genetic elements, also called transposons, are typically classified according to the mechanism by which they move or *transpose*. In bacteria, the most common mobile genetic elements are the *DNA-only transposons*. The name is derived from the fact that the element moves from one place to another as a piece of D... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Mobile Genetic Elements Encode the Components They Need for Movement",
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The sequencing of human genomes has revealed many surprises, as we describe in detail in the next section. But one of the most stunning was the finding that a large part of our DNA is not entirely our own. Nearly half of the human genome is made up of mobile genetic elements, which number in the millions. Some of these... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "The Human Genome Contains Two Major Families of Transposable Sequences",
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Viruses are also mobile, but unlike the transposons we have discussed so far, they can actually escape from cells and move to other cells and organisms. Viruses were first categorized as disease-causing agents that, by virtue of their tiny size, passed through ultrafine filters that can hold back even the smallest bact... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Viruses Can Move Between Cells and Organisms",
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Although there are many similarities between bacterial and eukaryotic viruses, one important class of viruses—the retroviruses—is found only in eukaryotic cells. In many respects, retroviruses resemble the retrotransposons we just discussed. A key feature of the life cycle of both is a step in which DNA is synthesized ... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Retroviruses Reverse the Normal Flow of Genetic Information",
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When the DNA sequence of human Chromosome 22, one of the smallest human chromosomes, was completed in 1999, it became possible for the first time to see exactly how genes are arranged along an entire vertebrate chromosome (Figure 9–32). The subsequent publication of the whole human genome sequence—a first draft in 2001... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "The Nucleotide Sequences of Human Genomes Show How Our Genes Are Arranged",
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Mobile genetic elements, such as the *Alu* sequences, are found in many copies in human DNA. In what ways could the presence of an *Alu* sequence affect a nearby gene?
ECB4 e9.28/9.32 Figure 9–32 The sequence of Chromosome 22 shows how human chromosomes are organized. (A) Chromosome 22,... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Question 9–6",
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When the chimpanzee genome sequence became available in 2005, scientists began searching for DNA sequence changes that might account for the striking differences between us and them (Figure 9–35). With about 3 billion nucleotide pairs to compare between the two species, the task is daunting. But the search is made much... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Accelerated Changes in Conserved Genome Sequences Help Reveal What Makes Us Human",
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How many genes does it take to make a human? It seems a natural thing to wonder. If 6000 genes can produce a yeast and 13,000 a fly, how many are needed to make a human being—a creature curious and clever enough to study its own genome? Until researchers completed the first draft of the human genome sequence, the most ... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "COUNTING GENES",
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As always, the situation is simplest in bacteria and simple eukaryotes such as yeasts. In these genomes, genes that encode proteins are identified by searching through the entire DNA sequence looking for open reading frames (ORFs). These are long sequences—say, 100 codons or more—that lack stop codons. A random sequenc... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Signals and chunks",
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Of course, these estimates are based on what we think genes look like; to get around this bias, we must employ more direct, experiment-based methods for locating genes. Because genes are transcribed into RNA, the preferred strategy for finding genes involves isolating all of the RNAs produced by a particular cell type ... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Matching RNAs",
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Based on a combination of all of these computational and experimental techniques, current estimates of the number of human genes are now converging around 30,000. It could be many years, however, before we have the final answer to how many genes it takes to make a human. In the end, having an exact count will not be ne... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Human gene countdown",
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With the possible exception of some identical twins, no two people have exactly the same genome sequence. When the same region of the genome from two different humans is compared, the nucleotide sequences typically differ by about 0.1%. That might seem an insignificant degree of variation, but considering the size of t... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Genome Variation Contributes to Our Individuality—But How?",
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The finding that humans, chimps, and mice contain essentially the same protein-coding genes has raised a fundamental question: What makes these creatures so different from one another?
To a large extent, the instructions needed to produce a multicellular animal from a fertilized egg are provided by the regulatory DNA... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Differences in Gene Regulation May Help Explain How Animals With Similar Genomes Can Be So Different",
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- • By comparing the DNA and protein sequences of contemporary organisms, we are beginning to reconstruct how genomes have evolved in the billions of years that have elapsed since the appearance of the first cells.
- Genetic variation—the raw material for evolutionary change—arises through a variety of mechanisms that ... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Essential Concepts",
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But how can this be demonstrated? One approach is to compare several genes from the same two species, as shown for rat and human in the table above. Two measures of rates of nucleotide substitution are indicated in the table. Nonsynonymous changes refer to single-nucleotide changes in the DNA sequence that alter the en... | {
"Header 1": "Functionally Important Genome Regions Show Up As Islands of Conserved DNA Sequence",
"Header 3": "Essential Concepts",
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Since the turn of the century, biologists have amassed an unprecedented wealth of information on the genes that direct the development and behavior of living things. Thanks to advances in our ability to rapidly determine the nucleotide sequence of entire genomes, we now have access to the complete molecular blueprints ... | {
"Header 1": "Modern Recombinant DNA Technology",
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DNA sequencing of your own two β-globin genes (one from each of your two Chromosome 11s) reveals a mutation in one of the genes. Given this information alone, should you worry about being a carrier of an inherited disease that could be passed on to your children? What other information would you like to have to assess ... | {
"Header 1": "Modern Recombinant DNA Technology",
"Header 3": "Question 10–1",
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Humans have been experimenting with DNA, albeit without realizing it, for millennia. The roses in our gardens, the corn on our plate, and the dogs in our yards are all the product of selective breeding that has taken place over many, many generations (Figure 10–1). But it wasn't until the development of recombinant DNA... | {
"Header 1": "Modern Recombinant DNA Technology",
"Header 3": "Manipulating and Analyzing DNA Molecules",
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Like many of the tools of recombinant DNA technology, restriction nucleases were discovered by researchers trying to understand an intriguing biological phenomenon. It had been observed that certain bacteria always degraded "foreign" DNA that was introduced into them experimentally. A search for the mechanism responsib... | {
"Header 1": "Modern Recombinant DNA Technology",
"Header 3": "Restriction Nucleases Cut DNA Molecules at Specific Sites",
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Target sequences are often palindromic (that is, the nucleotide sequence is symmetrical around a central point). Here, both strands of the DNA double helix are cut at specific points within the target sequence (orange). Some enzymes, such as Haelll, cut straight across the double helix and leave two blunt-ended DNA mol... | {
"Header 1": "Gel Electrophoresis Separates DNA Fragments of Different Sizes",
"Header 3": "Figure 10–2 Restriction nucleases cleave DNA at specific nucleotide sequences.",
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The separated DNA bands on an agarose or polyacrylamide gel are not, by themselves, visible. To see these bands, the DNA must be labeled or stained in some way. One sensitive method involves exposing the gel to a dye that fluoresces under ultraviolet (UV) light when it is bound to DNA. When the gel is placed on a UV li... | {
"Header 1": "Bands of DNA in a Gel Can Be Visualized Using Fluorescent Dyes or Radioisotopes",
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Under normal conditions, the two strands of a DNA double helix are held together by hydrogen bonds between the complementary base pairs (see Figure 5–6). But these relatively weak, noncovalent bonds can be fairly easily broken. Such *DNA denaturation* will release the two strands from each other, but does not break the... | {
"Header 1": "Hybridization Provides a Sensitive Way to Detect Specific Nucleotide Sequences",
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Whole genomes, even small ones, are too large and unwieldy to be handled easily in the laboratory. Thus the first step in cloning any gene is to break the genome into smaller, more manageable pieces. These fragments can then be joined together, or recombined, to produce the DNA molecules that will be amplified. Our abi... | {
"Header 1": "DNA Cloning Begins with Genome Fragmentation and Production of Recombinant DNAs",
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To introduce recombinant DNA into a bacterial cell, investigators take advantage of the fact that some bacteria naturally take up DNA molecules present in their surroundings. The mechanism that controls this uptake is called transformation, because early observations suggested it could "transform" one bacterial strain ... | {
"Header 1": "DNA Cloning Begins with Genome Fragmentation and Production of Recombinant DNAs",
"Header 3": "Recombinant DNA Can Be Copied Inside Bacterial Cells",
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Thus far, we have described the amplification of a single DNA fragment. In reality, when a genome is cut by a restriction nuclease, millions of different DNA fragments are generated. How can the single fragment that contains the DNA of interest be isolated from this collection? The solution involves introducing all of ... | {
"Header 1": "DNA Cloning Begins with Genome Fragmentation and Production of Recombinant DNAs",
"Header 3": "Genes Can Be Isolated from a DNA Library",
"token_count": 716,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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For many applications—for example, when attempting to clone a protein-coding gene, it is advantageous to obtain the gene in a form that contains only the coding sequence; that is, a form that lacks the intron DNA. For some genes, the complete genomic clone—including introns and exons—is too large and unwieldy to handle... | {
"Header 1": "cDNA Libraries Represent the mRNAs Produced by Particular Cells",
"token_count": 1410,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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The success of PCR depends on the exquisite selectivity of DNA hybridization, along with the ability of DNA polymerase to copy a DNA template
reliably, through repeated rounds of replication *in vitro*. The enzyme works by adding nucleotides to the 3' end of a growing strand of DNA (see Figure 6–11). To initiate the ... | {
"Header 1": "PCR Uses a DNA Polymerase to Amplify Selected DNA Sequences in a Test Tube",
"token_count": 219,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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PCR is an iterative process in which the cycle of amplification is repeated dozens of times. At the start of each cycle, the two strands of the double-stranded DNA template are separated and a unique primer is annealed to each. DNA polymerase is then allowed to replicate each strand independently (Figure 10–14). In sub... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"token_count": 800,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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In addition to its use in gene cloning, PCR is frequently employed to amplify DNA for other, more practical purposes. Because of its extraordinary sensitivity, PCR can be used to detect invading microorganisms at very early stages of infection. In this case, short sequences complementary to a segment of the infectious ... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "PCR is Also Used for Diagnostic and Forensic Applications",
"token_count": 531,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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The procedures we have described thus far enable biologists to obtain large amounts of DNA in a form that is easy to work with in the laboratory. Whether present as fragments stored in a DNA library in bacteria or as a collection of PCR products nestled in the bottom of a test tube, this DNA also provides the raw mater... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "Exploring and Exploiting Gene function",
"token_count": 929,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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In the late 1970s, researchers developed several schemes for determining, simply and quickly, the nucleotide sequence of any purified DNA fragment. The one that became the most widely used is called **dideoxy sequencing** or **Sanger sequencing** (after the scientist who invented it). The technique uses DNA polymerase,... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "Whole Genomes Can Be Sequenced Rapidly",
"token_count": 451,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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molecules. To determine the complete sequence of a single-stranded fragment of DNA (gray), the DNA is first hybridized with a short DNA primer (orange) that is labeled with a fluorescent dye or radioisotope. DNA polymerase and an excess of all four normal deoxyribonucleoside triphosphates (blue A, C, G, and T) are adde... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "Figure 10–20 The Sanger method produces four sets of labeled DNA",
"token_count": 574,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pd... |
The Sanger method has made it possible to sequence the genomes of humans and of many other organisms including most of those discussed in this book. But newer methods, developed since 2005, have made genome sequencing even more rapid—and very much cheaper. With these so-called *second-generation sequencing methods*, th... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "Next-Generation Sequencing Techniques Make Genome Sequencing Faster and Cheaper",
"token_count": 584,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biolo... |
When DNA sequencing techniques became fully automated, determining the order of the nucleotides in a piece of DNA went from being an elaborate Ph.D. thesis project to a routine laboratory chore. Feed DNA into the sequencing machine, add the necessary reagents, and out comes the sought-after result: the order of As, Ts,... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "SEQUENCING THE HUMAN GENOME",
"token_count": 240,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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The most straightforward approach to sequencing a genome is to break it into random fragments, separate and sequence each of the single-stranded fragments, and then use a powerful computer to order these pieces using sequence overlaps to guide the assembly (Figure 10–24). This approach is called the shotgun sequencing ... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "Shotgun sequencing",
"token_count": 581,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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In this approach, researchers started by preparing a genomic DNA library. They broke the human genome into overlapping fragments, 100–200 kilobase pairs in size. They then plugged these segments into bacterial artificial chromosomes (BACs) and inserted them into *E. coli.* (BACs are similar to the bacterial plasmids di... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "Clone-by-clone",
"token_count": 567,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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The clone-by-clone approach produced the first draft of the human genome sequence in 2000 and the completed sequence in 2004. As the set of instructions that specify all of the RNA and protein molecules needed to build a human being, this string of genetic bits holds the secrets to human development and physiology. But... | {
"Header 1": "Multiple Cycles of Amplification *In Vitro* Generate Billions of Copies of the Desired Nucleotide Sequence",
"Header 3": "All together now",
"token_count": 345,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
In this example, mRNA is collected from two different cell samples—for example, cells treated with a hormone and untreated cells of the same type—to allow for a direct comparison of the specific genes expressed under both conditions. The mRNAs are converted to cDNAs that are labeled with a red fluorescent dye for one s... | {
"Header 1": "Figure 10–27 DNA microarrays are used to analyze the production of thousands of different mRNAs in a single experiment.",
"token_count": 266,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Strings of nucleotides, at first glance, reveal nothing about how that genetic information directs the development of a living organism—or even what type of organism it might encode. One way to learn something about the function of a particular nucleotide sequence is to compare it with the multitude of sequences availa... | {
"Header 1": "Comparative Genome Analyses Can Identify Genes and Predict Their Function",
"token_count": 319,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
As we discussed in Chapter 8, a cell expresses only a subset of the thousands of genes available in its genome. This subset differs from one cell type to another. One way to determine which genes are being expressed in a population of cells or in a tissue is to analyze which mRNAs are being produced.
The first tool t... | {
"Header 1": "Analysis of mRNAs By Microarray or RNA-Seq Provides a Snapshot of Gene Expression",
"token_count": 441,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Although microarrays and RNA-Seq provide a list of genes that are being expressed by a cell or tissue, they do not reveal exactly where in the cell or tissue those mRNAs are produced. To see where a particular RNA is made, investigators use a technique called *in situ* hybridization (from the Latin *in situ*, "in place... | {
"Header 1": "Analysis of mRNAs By Microarray or RNA-Seq Provides a Snapshot of Gene Expression",
"Header 3": "*In Situ* Hybridization Can Reveal When and Where a Gene Is Expressed",
"token_count": 263,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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For a gene that encodes a protein, the location of the protein within the cell, tissue, or organism yields clues to the gene's function. Traditionally, the most effective way to visualize a protein within a cell or tissue involved using a labeled antibody. That approach requires the generation of an antibody that speci... | {
"Header 1": "Analysis of mRNAs By Microarray or RNA-Seq Provides a Snapshot of Gene Expression",
"Header 3": "Reporter Genes Allow Specific Proteins to be Tracked in Living Cells",
"token_count": 1036,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Although it may seem counterintuitive, one of the best ways to determine a gene's function is to see what happens to an organism when the gene is inactivated by a mutation. Before the advent of gene cloning, geneticists
#### (B) USING A REPORTER GENE TO STUDY GENE X REGULATORY SEQUENCE... | {
"Header 1": "Analysis of mRNAs By Microarray or RNA-Seq Provides a Snapshot of Gene Expression",
"Header 3": "The Study of Mutants Can Help Reveal the Function of a Gene",
"token_count": 542,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Recombinant DNA technology has made possible a more targeted genetic approach to studying gene function. Instead of beginning with a randomly generated mutant and then identifying the responsible gene, a gene of known sequence can be inactivated deliberately and the effects on the cell or organism's phenotype can be ob... | {
"Header 1": "Analysis of mRNAs By Microarray or RNA-Seq Provides a Snapshot of Gene Expression",
"Header 3": "RNA Interference (RNAi) Inhibits the Activity of Specific Genes",
"token_count": 825,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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Despite its usefulness, RNAi has some limitations. Non-target genes are sometimes inhibited along with the gene of interest, and certain cell types are resistant to RNAi entirely. Even for cell types in which the mechanism functions effectively, gene inactivation by RNAi is often temporary, earning the description "gen... | {
"Header 1": "A Known Gene Can Be Deleted or Replaced With an Altered Version",
"token_count": 1047,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Technically speaking, transgenic approaches could be used to alter genes in the human germ line. For ethical reasons, such manipulations are unlawful. But transgenic technologies are widely used to generate animal models of human diseases in which mutant genes play a major part.
With the explosion of DNA sequencing t... | {
"Header 1": "A Known Gene Can Be Deleted or Replaced With an Altered Version",
"Header 3": "Mutant Organisms Provide Useful Models of Human Disease",
"token_count": 328,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Although we tend to think of recombinant DNA research in terms of animal biology, these techniques have also had a profound impact on the study of plants. In fact, certain features of plants make them especially amenable to recombinant DNA methods.
When a piece of plant tissue is cultured in a sterile medium containi... | {
"Header 1": "A Known Gene Can Be Deleted or Replaced With an Altered Version",
"Header 3": "Transgenic Plants Are Important for Both Cell Biology and Agriculture",
"token_count": 730,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
One of the most important contributions of DNA cloning and genetic engineering to cell biology is that they make it possible to produce any protein, including the rare ones, in nearly unlimited amounts. Such highlevel production is usually accomplished by using specially designed vectors known as *expression vectors*. ... | {
"Header 1": "Even Rare Proteins Can Be Made in Large Amounts Using Cloned DNA",
"token_count": 555,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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- • Recombinant DNA technology has revolutionized the study of cells, making it possible to pick out any gene at will from the thousands of genes in a cell and to determine its nucleotide sequence.
- • A crucial element in this technology is the ability to cut a large DNA molecule into a specific and reproducible set o... | {
"Header 1": "Even Rare Proteins Can Be Made in Large Amounts Using Cloned DNA",
"Header 3": "Essential Concepts",
"token_count": 860,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
After decades of work, Dr. Ricky M. isolated a small amount of attractase—an enzyme that produces a powerful human pheromone—from hair samples of Hollywood celebrities. To take advantage of attractase for his personal use, he obtained a complete genomic clone of the attractase gene, connected it to a strong bacterial p... | {
"Header 1": "Even Rare Proteins Can Be Made in Large Amounts Using Cloned DNA",
"Header 3": "Question 10–7",
"token_count": 2030,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
A living cell is a self-reproducing system of molecules held inside a container. That container is the plasma membrane—a protein-studded, fatty film so thin that it cannot be seen directly in the light microscope. Every cell on Earth uses such a membrane to separate and protect its chemical components from the outside ... | {
"Header 1": "Membrane Structure",
"token_count": 873,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
ECB4 e11.04/11.04 The lipids in cell membranes combine two very different properties in a single molecule: each lipid has a hydrophilic ("water-loving") head and a hydrophobic ("water-fearing") tail. The most abundant lipids in cell membranes are the phospholipids, which have a phosphate-containing, hydrophilic head li... | {
"Header 1": "Membrane Structure",
"Header 3": "Membrane Lipids Form Bilayers in Water",
"token_count": 1301,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
#### Question 11–1
Water molecules are said "to reorganize into a cagelike structure" around hydrophobic compounds (e.g., see Figure 11–9). This seems paradoxical because water molecules do not interact with the hydrophobic compound. So how could they "know" about its presence and change their behavior to interact di... | {
"Header 1": "Membrane Structure",
"Header 3": "water δ<sup>+</sup> δ<sup>+</sup> δ HC CH3 CH3 CH3 HC CH3 CH3 CH3 2-methylpropane in water 2-methylpropane H H O",
"token_count": 404,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The aqueous environment inside and outside a cell prevents membrane lipids from escaping from the bilayer, but nothing stops these molecules from moving about and changing places with one another within the plane of the bilayer. The membrane therefore behaves as a two-dimensional fluid, a fact that is crucial for membr... | {
"Header 1": "Membrane Structure",
"Header 3": "The Lipid Bilayer Is a Flexible Two-dimensional Fluid",
"token_count": 679,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
The fluidity of a cell membrane—the ease with which its lipid molecules move within the plane of the bilayer—is important for membrane function and has to be maintained within certain limits. Just how fluid a lipid bilayer is at a given temperature depends on its phospholipid composition and, in particular, on the natu... | {
"Header 1": "Membrane Structure",
"Header 3": "The Fluidity of a Lipid Bilayer Depends on Its Composition",
"token_count": 1143,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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In eukaryotic cells, new phospholipids are manufactured by enzymes bound to the cytosolic surface of the *endoplasmic reticulum* (*ER*; see Figure 11–3). Using free fatty acids as substrates (see Panel 2–4, pp. 72–73), the enzymes deposit the newly made phospholipids exclusively in the cytosolic half of the bilayer.
... | {
"Header 1": "Membrane Structure",
"Header 3": "Membrane Assembly Begins in the ER",
"token_count": 453,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Most cell membranes are asymmetrical: the two halves of the bilayer often include strikingly different sets of phospholipids. But if membranes emerge from the ER with an evenly scrambled set of phospholipids, where does this asymmetry arise? It begins in the Golgi apparatus. The Golgi membrane contains another family o... | {
"Header 1": "Membrane Structure",
"Header 3": "Certain Phospholipids Are Confined to One Side of the Membrane",
"token_count": 1340,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Although the lipid bilayer provides the basic structure of all cell membranes and serves as a permeability barrier to the hydrophilic molecules on either side of it, most membrane functions are carried out by membrane proteins. In animals, proteins constitute about 50% of the mass of most plasma membranes, the remainde... | {
"Header 1": "Membrane Structure",
"Header 3": "Membrane Proteins",
"token_count": 775,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Proteins can be associated with the lipid bilayer of a cell membrane in any one of the ways illustrated in **Figure 11–20**.
- 1. Many membrane proteins extend through the bilayer, with part of their mass on either side (Figure 11–20A). Like their lipid neighbors, these *transmembrane proteins* are amphipathic, havin... | {
"Header 1": "Membrane Proteins Associate with the Lipid Bilayer in Different Ways",
"token_count": 387,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
All membrane proteins have a unique orientation in the lipid bilayer, which is essential for their function. For a transmembrane receptor protein, for example, the part of the protein that receives a signal from the environment must be on the outside of the cell, whereas the part that passes along the signal must be in... | {
"Header 1": "A Polypeptide Chain Usually Crosses the Lipid Bilayer as an $\\alpha$ Helix",
"token_count": 1377,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
To understand a protein fully, one needs to know its structure in detail. For membrane proteins, this presents special problems. Most biochemical procedures are designed for studying molecules in aqueous solution. Membrane proteins, however, are built to operate in an environment that is partly aqueous and partly fatty... | {
"Header 1": "A Polypeptide Chain Usually Crosses the Lipid Bilayer as an $\\alpha$ Helix",
"Header 3": "Membrane Proteins Can Be Solubilized in Detergents",
"token_count": 684,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
For many years, much of what we knew about the structure of membrane proteins was learned by indirect means. The standard method for determining a protein's three-dimensional structure directly is X-ray crystallography (see Figure 4–52), but this requires ordered crystalline arrays of the molecule. Because membrane pro... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"token_count": 1049,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
A cell membrane by itself is extremely thin and fragile. It would require nearly 10,000 cell membranes laid on top of one another to achieve the thickness of this paper. Most cell membranes are therefore strengthened and supported by a framework of proteins, attached to the membrane via transmembrane proteins. For plan... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"Header 3": "The Plasma Membrane Is Reinforced by the Underlying Cell Cortex",
"token_count": 1063,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Because a membrane is a two-dimensional fluid, many of its proteins, like its lipids, can move freely within the plane of the lipid bilayer. This lateral diffusion was initially demonstrated by experimentally fusing a mouse cell with a human cell to form a double-sized hybrid cell and then monitoring the distribution o... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"Header 3": "A Cell Can Restrict the Movement of Its Membrane Proteins",
"token_count": 726,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
We saw earlier that some of the lipids in the outer layer of the plasma membrane have sugars covalently attached to them. The same is true for most of the proteins in the plasma membrane. The great majority of these proteins have short chains of sugars, called oligosaccharides, linked to them; they are called *glycopro... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"Header 3": "The Cell Surface Is Coated with Carbohydrate",
"token_count": 351,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
An essential feature of the lipid bilayer is its fluidity, which is crucial for cell membrane integrity and function. This property allows many membrane-embedded proteins to move laterally in the plane of the bilayer, so that they can engage in the various protein–protein interactions on which cells depend. The fluid n... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"Header 3": "MEASURING MEMBRANE FLOW",
"token_count": 235,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
One such technique, called fluorescence recovery after photobleaching (FRAP), involves uniformly labeling the components of the cell membrane—its lipids or, more often, its proteins—with some sort of fluorescent marker. Labeling membrane proteins can be accomplished by incubating living cells with a fluorescent antibod... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"Header 3": "The FRAP attack",
"token_count": 265,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
One drawback to the FRAP approach is that the technique monitors the movement of fairly large populations of proteins—hundreds or thousands—across a relatively
Figure 11–34 Photobleaching techniques can be used to measure the rate of lateral diffusion of... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"Header 3": "One-by-one",
"token_count": 1933,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Describe the different methods that cells use to restrict proteins to specific regions of the plasma membrane. Is a membrane with many of its proteins restricted still fluid?
#### Question 11–8
Which of the following statements are correct? Explain your answers.
- A. Lipids in a lipid bilayer spin rapidly around ... | {
"Header 1": "We Know the Complete Structure of Relatively Few Membrane Proteins",
"Header 3": "Question 11–7",
"token_count": 1311,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
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To survive and grow, cells must be able to exchange molecules with their environment. They must import nutrients such as sugars and amino acids and eliminate metabolic waste products. They must also regulate the concentrations of a variety of inorganic ions in their cytosol and organelles. A few molecules, such as CO2 ... | {
"Header 1": "Transport Across Cell Membranes",
"token_count": 888,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Given enough time, virtually any molecule will diffuse across a lipid bilayer. The rate at which it diffuses, however, varies enormously depending on the size of the molecule and its solubility properties. In general, the smaller the molecule and the more hydrophobic, or nonpolar, it is, the more rapidly it will diffus... | {
"Header 1": "Lipid Bilayers Are Impermeable to Ions and Most Uncharged Polar Molecules",
"token_count": 451,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Because cell membranes are impermeable to inorganic ions, living cells are able to maintain internal ion concentrations that are very different from the concentrations of ions in the media that surrounds them. These differences in ion concentration are crucial for a cell's survival and function. Among the most importan... | {
"Header 1": "The Ion Concentrations Inside a Cell Are Very Different from Those Outside",
"token_count": 316,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
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