Bio Notes Ch 15-21 PDF

Chapter 15: The Chromosomal Basis of Inheritance. 0. Overview: Locating Genes Along Chromosomes. 1. Gregor Mendel’s “heredita...

Chapter 15: The Chromosomal Basis of Inheritance. 0. Overview: Locating Genes Along Chromosomes. 1. Gregor Mendel’s “hereditary factors” were purely an abstract concept when he proposed their existence in 1860. At that time, no cellular structures were know that could house these imaginary units. 2. Today, we can show that genes—Mendel’s “factors”--are located along chromosomes. 1. Mendelian inheritance has its physical basis in the behavior of chromosomes. 1. Using improved techniques of microscopy, cytologists worked out the process of mitosis in 1875 and meiosis in the 1890s. 2. Around 1902, Walter S. Sutton, Theodor Boveri, and others independently noted the parallels between the behavior of chromosomes and the behavior of Mendel’s proposed hereditary factors. The chromosome theory of inheritance began to take form. According to this theory Mendelian genes have specific loci (positions) along chromosomes, and it is the chromosomes that undergo segregation and independent assortment. Wild type: the phenotype for a 3. Thomas Hunt Morgan: character most commonly observed 1. He first mated fruit flies until he got a single male fruit fly with white eyes instead of the normal red eyes. in natural populations. 2. He then mated the white-eyed fly with a normal red-eyed fly. All the offspring had red eyes. Mutant phenotype: Traits that are 3. When these offspring mated, the new offspring had the ratio of 3-red-eyed: 1-white-eyed, Morgan noticed that all alternatives to the wild type. the white-eyed flies produced were male. 4. He concluded that a fly’s eye color was linked to its sex. 2. Sex-linked genes exhibit unique patterns of inheritance. 1. In humans and other mammals, there are two varieties of sex chromosomes, designated X and Y. A person who inherits two X chromosomes usually develops as a female. An XY person develops into a male. 2. Researchers have sequenced the human Y chromosome and have identified 78 genes, which code for about 25 proteins. About half of these genes are expressed only in the testis, and some are required for normal testicular function. Sex-linked gene: a gene located on 3. If a sex-linked trait is due to a recessive allele, a female will express the phenotype only if she is a homozygote. either sex chromosome. Because males have only one locus, the terms homozygous and heterozygous lack meaning for describing their sex- linked genes; the term hemizygous is used in such cases. 4. A number of of human sex-linked disorders are much more serious that color blindness. An example is Duchenne muscular dystrophy. The disease is characterized by a progressive weakening of the muscles and loss of coordination. Researchers have traced the disorder to the absence of a key muscle protein called dystrophin and have mapped the gene for this protein to specific locus on the X chromosome. 5. Hemophilia: a sex-linked recessive disorder defined by the absence of one or more of the proteins required for blood clotting. 6. X-inactivation in Female Mammals 1. One X chromosome in each cell in females becomes almost completely inactivated during embryonic development. The inactive X in each cell of a female condenses into a compact object called a Barr body, which lies along the inside of the nuclear envelope. 2. British geneticist Mary Lyon demonstrated that the selection of which X chromosome will form the Barr body occurs randomly and independently in each embryonic cell present at the time of X inactivation. As a consequence, females consist of a mosaic of two types of cells: those with the active X derived from the father and those with the active X derived from the mother. 3. Inactivation of an X chromosome involves modification to the DNA, including attachment of methyl groups to one of the nitrogenous bases of DAN nucleotides. Researchers also have discovered an X chromosome gene called XIST that is active only on the Barr-body chromosome. Multiple copies of the RNA product of this gene apparently attach to the X chromosome on which they are made, eventually almost covering it. 3. Linked genes tend to be inherited together because they are located near each other on the same chromosome. Linked genes: Genes located on the 1. When 50% of all offspring are recombinants, genetics say that there is a 50% frequency of recombination. A 50% same chromosome that tend to be frequency of recombination is observed for any two genes that are located on different chromosomes and are thus inherited together in genetic crosses. unlinked. Genetic recombination: the 2. Crossing over accounts for the recombination of linked genes. In crossing over, which occurs while the replicated production of offspring with homologous chromosomes are paired during prophase of meiosis I, a set of proteins orchestrates an exchange of combinations of traits that differ from corresponding segments of one maternal and one paternal chromatid. those found in either parent. 3. Genetic map: an ordered list of the genetic loci along a particular chromosome. Parental types: have phenotypes that 4. Alfred H. Sturtevant predicted that the farther apart two genes are, the higher the probability that a crossover will matches one of the parental occur between them and therefore the higher the recombination frequency. phenotypes. 5. Linkage map: A genetic map based on recombination frequencies. Sturtevant expressed the distances between genes in Recombinant types map units (centimorgans), defining one map unit as equivalent to a 1% recombination frequency. (recombinants): have phenotypes 6. Other methods enable geneticists to construct cytogenetic maps of chromosomes, which locate genes with respect to that differ from the parental chromosomal features. phenotypes. 4. Alterations of chromosome number or structure cause some genetic disorders 1. The phenotype of an organism can be affected by small-scale changes involving individual genes. Random mutations Nondisjunction: the members of a are the source of all new alleles, which can lead to new phenotypic traits. pair of homologous chromosomes do 2. Large-scale chromosomal changes can also affect an organism’s phenotype. They often lead to spontaneous abortion not move apart properly during (miscarriage) of a fetus. meiosis I or sister chromatids fail to 3. Aneuploidy: a condition in which a zygote has an abnormal number of chromosomes. Monosomic: the zygote only has separate during meiosis II. one copy of a chromosome. Trisomic: the zygote has three copies of a chromosome. 4. Polyploidy: More than two complete chromosome sets in all somatic cells. It is fairly common in the plant kingdom. Many of the plant species we eat are polyploid. In the animal kingdom, polyploid species are much less common, although they are known to occur among fishes and amphibians. In general, polyploids are more nearly normal in appearance than aneuploids. 5. Errors in meiosis or damaging agents such as radiation can cause breakage of a chromosome, which can lead to four types of of changes in chromosome structure. 1. Deletion: a chromosomal fragment is lost. 2. Duplication: a “deleted” fragment becomes attached as an extra segment to a sister chromatid. 3. Inversion: the fragment reattaches to the original chromosome but in reverse orientation. Shulin Ye pg 1 of 2 08/31/09 07:28:04 PM  Chapter 14: Mendel and the Gene Idea 4. Translocation: the fragment joins a non-homologous chromosome. 6. Down syndrome: an aneuploid condition that affects one about of every 700 children born in the United States. Down syndrome is usually the result of an extra chromosome 21. Down syndrome includes characteristic facial features, short stature, heart defects, susceptibility to respiratory infection, and mental retardation. The frequency of Down syndrome increases with the age of the mother. While the disorder occurs in just 0.04% of children born to women under age 30, the risk climbs to 0.92% for mothers at age 40 and is even higher for older mothers 7. Klinefelter syndrome: A condition in which a male has an extra X chromosome (XXY). People with this disorder have male sex organs, but the testes are abnormally small and the man is sterile. Some breast enlargement and other female body characteristics are common. Affected individuals may have subnormal intelligence. 8. Males with an extra Y chromosome (XYY) do not exhibit any well-defined syndrome, but they tend to be taller than average. 9. Females with trisomy X (XXX), which occurs once in approximately 1,000 live births, are healthy and cannot be distinguished from XX females except by karyotype. 10. Turner syndrome (monosomy X): The only viable monosomy in humans. It occurs about once in every 5,000 births. Although these X0 individuals are phenotypically female, they are sterile because their sex organs do not mature. 11. Many deletions in human chromosomes, even in a heterozygous state, cause severe problems. Cri du chat (“cry of the cat”), results from a specific deletion in chromosome 5. A child born with this deletion is mentally retarded, has a small head with unusual facial features, and has a cry that sounds like the mewing of a distressed cat. 12. Chromosomal translocations have been implicated in certain cancers, including chronic myelogenous leukemia (CML). In these cells, the exchange of a large portion of chromosome 22 with a small fragment from a top of chromosome 9. 5. Some inheritance patterns are exceptions to the standard chromosome theory. 1. Geneticists have identified two or three dozen traits in mammals that depend on which parent passed along the alleles for those traits. This is called genomic imprinting. 1. Genomic imprinting occurs during the formation of gametes and results in the silencing of one allele of certain genes. This imprints are transmitted to all the body cells during development, so either the maternal or paternal allele of a give imprinted gene is expressed in every cell of that organism. In each generation, the old imprints are “erased” in gamete-producing cells, and the chromosomes of the developing gametes are newly imprinted according to the sex of the individuals forming the gametes. 2. Consider, for example, the mouse gene for insulin-like growth factor 2 (Igf2), one of the first imprinted genes to be identified. Although this growth factor is required for normal prenatal growth, only the parental allele is expressed. Although heavily methylated genes are usually inactive, methylation of certain cytosines on the paternal chromosome leads to expression of the parental Igf2 allele. In experiments with mice, embryos engineered to inherit both copies of certain chromosomes from the same parent usually die before birth, whether that parent is male or female. Apparently, normal development requires that embryonic cells have exactly one active copy—not zero, not two—of certain genes. 2. Some genes are located in organelles in the cytoplasm; because they are outside the nucleus, these genes are sometimes called extracellular genes or cytoplasmic genes. 1. In 1909, German scientist Karl Correns observed that the coloration of offspring was determined only by the maternal parent and not by the paternal parent when it came to yellow or white patches of the leaves of otherwise green plants. In most plants, a zygote receives all its plastids from the cytoplasm of the egg and none from the pollen. 2. Similar maternal inheritance is also the rule for mitochondrial genes in most animals and plants, because almost al the mitochondria passed on to the a zygote come from the cytoplasm of the egg. Shulin Ye pg 2 of 2 08/31/09 07:28:04 PM  Chapter 15: The Chromosomal Basis of Inheritance. 0. Overview: Life’s Operating Instructions 1. In April 1953, James Watson and Francis Crick shook the scientific world with an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA. 2. Of all of nature’s molecules, nucleic acids are unique in their ability to direct their own replication from monomers. 1. Dna is the Genetic Material. 1. Once T. H. Morgan’s group showed that genes are located along chromosomes, the two chemical components of chromosomes—DNA and proteins—became the candidates for the genetic material. 2. Until the 1940s, the case for proteins seemed stronger, especially since biochemists had identified them as a class of macromolecules with great heterogeneity of specificity of function, essential requirements for the hereditary material. In addition, little was known about nucleic acids. 3. We can trace the discovery of the genetic role of DNA back to 1928. While attempting to develop a vaccine against pneumonia, a British medical officer named Frederick Griffith studied Streptococcus pneumoniae, a bacterium that causes pneumonia in mammals. He was surprised to find that when he killed the pathogenic bacteria with heat and then Transformation: a change in mixed the cell remains with living bacteria of the nonpathogenic strain, some of the living cells become pathogenic. genotype and phenotype due to the 4. Griffith’s work set the stage for a 14-year search by American bacteriologist Oswald Avery for the identity of the assimilation of external DNA by a transforming substance. Avery focused on the three main candidates: DNA, RNA, and protein. Avery broke open the cell. heat-killed pathogenic bacteria and extracted the cellular contents. In separate samples, he used specific treatments that inactivated each of the three types of molecules. He then tested each treated ample for its ability to transform live Bacteriophages (phages): viruses nonpathogenic bacteria. Only when DNA was allowed to remain active did transformation occur. However, his results that infect bacteria. were met with skepticism. 5. In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA in the genetic material of a phage known as T2. They devised an experiment showing that only one of the two components of T2 actually enters E. coli cell during infection by using radioactive isotopes to tag proteins and DNA. They found that the phage DNA entered the host cells but the phage protein did not. 6. Further evidence that DNA is the genetic material came from the laboratory of biochemist Erwin Chargaff. He noticed a peculiar regularity in the ratios of nucleotide bases within a single species. 7. Once most biologists were convinced that DNA was the genetic material, the challenge was to determine how the structure of DNA could account for its role in inheritance. By the early 1950s, the arrangement of covalent bonds in a nucleic acid polymer was well established. While visiting the laboratory of Maurice Wilkins, Watson saw an X-ray diffraction image of DNA produced by Wilkins’s accomplished colleague Rosalind Franklin. Watson was familiar with the types of patterns that helical molecules produce. A careful study of Franklin’s X-ray diffraction photo of DNA not only told him that DNA was helical in shape, but also enabled him to approximate the width of the helix and the spacing of the nitrogenous bases along it. The presence of two strands accounts for the now-familiar term double helix. 8. Franklin had concluded that the sugar-phosphate backbones were on the outside of the double helix. This arrangement was appealing because it put the relatively hydrophobic nitrogenous bases in the molecule’s interior and thus away from the surrounding aqueous solution. Franklin’s X-ray data indicated that the helix makes one full turn every 3.4 nm along its length. With the bases stacked just 0.34 nm apart, there are ten layers of base pairs, or rungs of the ladder, in each full turn of the helix. 9. Because the helix has the same diameter for its entire length, Watson and Crick reasoned that pyrimidines were paired with purines and vis-versa. 2. Many Proteins Work Together in Dna Replication and Repair. 1. Watson and Crick: “Now, our model for deoxyribonucleic acid is, in effect, a pair of templates, each of which is complementary to the other. We imagine that prior duplication the hydrogen bonds are broken, and the two chains unwind and separate. Each chain then acts as a template for the formation onto itself of a new companion chain, so that eventually we shall have two pairs of chains, where we only had one before. Moreover, the sequence of the pairs of bases will have been duplicated exactly. 2. Semiconservative model: Each of the two daughter molecules will have one old strand, derived from the parent molecule, and one newly made strand. 3. The bacterium E. coli has a single chromosome about 4.6 million nucleotide pairs. In a favorable environment, an E. coli cell can copy all this DNA and divide to form two genetically identical daughter cells in less than an hour. 4. More than a dozen enzymes and other proteins participate in DNA replication. Much more is known about how this “replication machine” works in bacteria than in eukaryotes. 5. The replication of a DNA molecule begins at special sites called origins of replication, short stretches of DNA having a specific sequence of nucleotides. At each end of a replication bubble a replication fork, a Y-shaped region where the parental strands of DNA are being unwound. Several kinds of proteins participate in the unwinding. 1. Helicases: enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands. 2. After parental strand separation, single-strand binding proteins bind to the unpaired DNA strands, stabilizing them. 3. The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork. Topoisomerase helps relieve this strain by breaking, swiveling, and rejoining DNA strands. 6. The initial nucleotide chain that is produced during DNA synthesis is actually a short stretch of RNA, not DNA. This RNA is called a primer and is synthesized by the enzyme primase. 7. Enzyme called DNA polymerase catalyze the synthesis of new DNA by adding nucleotides to a pre-existing chain. Most DNA polymerase require a primer and a DNA template strand, along which complementary DNA nucleotides line up. Each nucleotide added to a growing DNA strand comes from a nucleotide triphosphate, which is a nucleoside with three phosphate groups. As each monomer joins the growing end of a DNA strand, two phosphate groups are lost as a molecular of pyrophosphate. Subsequent hydrolysis of the pyrophosphate to two molecules of inorganic phosphate is a coupled exergonic reaction that helps drive the polymerization reaction. 8. Because of their structure, DNA polymerases can add nucleotides only to the free 3´ end of a primer or growing DNA strand, never to the 5´ end. Along one template strand, DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5´→3´ direction. 9. The DNA strand made by this mechanism is called the leading strand. 10. To elongate the other new strand of DNA in the mandatory 5´→3´ direction, DNA pol III must work along the other template strand in the direction away from the replication fork. The DNA strand elongating in this direction is called the lagging strand. The lagging strand is elongated in segments called Okazaki fragments. Whereas only one primer is required on the leading strand, each Okazaki fragment on the ladding strand must be primed separately. Another DNA Shulin Ye pg 1 of 2 08/31/09 07:28:04 PM  Chapter 14: Mendel and the Gene Idea polymerase I, replaces the RNA nucleotides of the primers with DNA versions, adding them one by one onto the 3´ end of the adjacent Okazaki fragment. Another enzyme, DNA ligase, accomplishes this task, joining the sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand. 11. It is traditional—and convenient—to represent DNA polymerase molecules as locomotives moving along a DNA “railroad track,” but such a model is inaccurate in two important ways. First, the various proteins that participate in DNA replication actually form a single large complex, a “DNA replication machine.” 12. Second, the DNA replication complex does not move along the DNA; rather, the DNA moves through the complex during the replication process. In eukaryotic cells, multiple copies of the complex, perhaps grouped into “factories,” may be anchored to the nuclear matrix. 13. Although errors in the completed DNA molecule amount to only one in 10 billion nucleotides, initial pairing errors between incoming nucleotides and those in the template strand are 100,000 times more common—an error rate of one in 100,000 nucleotides. During DNA replication, DNA polymerases proofread each nucleotide against its template as soon as it is added to the growing strand. 14. In mismatch repair, enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors. 15. Incorrectly paired or altered nucleotides can also arise after replication. DNA molecules are constantly subjected to potentially harmful chemical and physical agents. In addition, DNA bases undergo spontaneous chemical changes under normal cellular conditions. However, these changes in DNA are usually corrected before they become mutations perpetuated through successive replications. Many different DNA repair enzymes have evolved. Often, a segment of the strand containing the damage is cut out (excised) by a DNA-cutting enzyme—a nuclease—and the resulting gap is then filled in with nucleotides. One such DNA repair system is called nucleotide excision repair. 16. In spite of the impressive capabilities of DNA polymerases, there is a small portion of the cell’s DNA that DNA polymerases can neither replicate nor repair. For linear DNA, such as the DNA of eukaryotic chromosomes, the fact that a DNA polymerase can add nucleotides only to the 3´ end of a pre-existing poly-nucleotide leads to an apparent problem. Repeated rounds of replication produce shorter and shorter DNA molecules with uneven ends. However, eukaryotic chromosomal DNA molecules have special nucleotide sequences called telomeres at their ends. In addition, specific proteins associated with telomeric can prevent the staggered ends of the daughter molecule from activating the cell’s systems for monitoring DNA damage. Telomeres do not prevent the shortening of DNA molecules due to successive rounds of replication; they just postpone the erosion of genes near the ends of DNA molecules. 3. A Chromosome Consists of a Dna Molecule Packed Together with Proteins 1. Stretched out, the DNA of an E. coli cell would measure about a millimeter in length, 500 times longer than the cell. Within a bacterium, however, certain proteins cause the chromosome to coil and “supercoil,” densely packing it so that it fills only part of the cell. 2. Together, a complex of DNA and protein, called chromatin, fits into the nucleus through an elaborate, multilevel system of DNA packing. 1. DNA, the double helix, is about 2 nm apart. 2. Histones are responsible for the first level of DNA packing in chromatin. They consist of about 100 amino acids each, and have a many positively charged amino acids that bind tightly to the negatively charged DNA. H2A, H2B, H3, and H4 are the four most common types of histones. 3. Nucleosomes, or “beads on a string” (10nm fiber): In electron micrographs, unfolded chromatin is 10 nm in diameter. Such chromatin resembles beads on a string. Each “bed” is a nucleosome, the basic unit of DNA packaging; the “string” between beads is called linker DNA. A nucleosome consists of DNA wound twice around a protein core composed of two molecules each of the four main histone types. The N-terminus of each histone (the histone tail) extends outward from the nucleosome. In the cell cycle, histones leave the DNA only briefly during replication and gene expression. 4. 30-nm fiber: Interactions between the histone tails of one nucleosome and the linker DNA and nucleosomes on either side cause the 10-nm fiber to coil into a 30-nm fiber. A fifth histone, H1, is involved. 5. Looped domains (300-nm fiber). The 30-nm fiber, in turn, forms loops called looped domains attached to a chromosome scaffold made of proteins, thus making up a 300-nm fiber. The scaffold is rich in one type of topoisomerase, and H1 molecules also appear to be present. 6. Metaphase chromosome: In the mitotic chromosome, the looped domains themselves coil and fold in a manner not yet fully understood, further compacting all the chromatin to produce the characteristic metaphase chromosome. The width of one chromatid is 700 nm. Particular genes always end up located at the same places in metaphase chromosomes, indicating that the packing steps are highly specific and precise. 3. Even during interphase, the centromeres and telomeres of chromosomes, as well as other chromosomal regions in some cells, exist in a highly condensed state similar to that seen in a metaphase chromosome. This type of interphase chromatin, visible as irregular clumped with a light microscope, visible as irregular clumps with a light microscrope, is called heterochromatin, to distinguish it from the less compacted, more dispersed euchromatin. Shulin Ye pg 2 of 2 08/31/09 07:28:04 PM  Chapter 17: From Gene to Protein
 Overview The Flow of Genetic Information 1. Gene expression: the process by which DNA directs the synthesis of proteins (or, in some cases, just RNAs).  Genes Specify Proteins Via Transcription and Translation 1. In 1909, British physician Archibald Garrod was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell. Garrod may have been the first person to recognize that Mendel’s principles of heredity apply to humans as well as peas. 2. Using a treatment shown in the 1920s to cause genetic changing, George Beadle and Edward Tatum bombarded Neurospora crassa, a bread mold, with X-rays and then looked among the survivors for mutants that differed in their nutritional needs from the wild-type mold. Wild-type Neurospora can survive in the laboratory on a moist support medium called agar, mixed only with inorganic salts, glucose and the vitamin biotin. Beadle and Tatum identified mutants that could not survive on minimal medium, apparently because they were unable to synthesize certain essential molecules from the minimal ingredients. To ensure survival of these nutritional mutants, Beadle and Tatum allowed them to grow on a complete growth medium. They then took samples from each mutant and distributed them to a number of different vials, each containing minimal medium plus a single additional nutrient. Afterwards, they pinned Transcription: the synthesis of RNA down each mutant’s defect more specifically. Their results provided strong support for the one-gene—one enzyme under the direction of DNA. hypothesis: the function of a gene is to dictate the production of a specific enzyme. Messenger RNA carries a genetic 3. However, many eukaryotic genes can code for a set of closely related polypeptides in a process called alternative message from the DNA to the splicing. Also, quite a few genes code for RNA molecules that have important function sin cells even though they are ribosomes. never translated into protein. Translation: the synthesis of a 4. In prokaryotes, the lack of segregation between DNA and ribosomes means that translation of mRNA begins while polypeptide under the direction of transcription is still in progress. RNA. Occurs at the ribosomes. 5. In eukaryotes, the initial RNA transcript from any gene, including those coding for RNA that is not translated into protein, is more generally called a primary transcript. 6. Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids. The flow of information from gene to protein is based on a triplet code: The genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words. For each gene, only one of the two DNA strands is transcribed. This strand is called the template strand. The mRNA base triplets are called codons, and they are customarily written in the 5´→3´ direction. The three codons that do not designate amino acids are “stop” signals, or termination codons, marking the end of translation. The codon AUG has a dual function: It codes for the amino acid methionine (Met) and also functions as a “start” signal, or initiation codon. There is redundancy in the genetic code, but no ambiguity. 7. Our ability to extract the intended message from a written language depends on reading the symbols in the correct groupings—that is, in the correct reading frame. 8. The genetic code is nearly universal, shared by organism from the simplest bacteria to the most complex plants and animals. Exceptions to the universality of the genetic code include translation systems in which a few codons differ from the standard ones. There are also exceptions in which stop codons can be translated into one of two amino acids not found in most organism. One of them, pyrrolysine, has only been detected so far in archaea; the other, selenocysteine is a component of some bacterial proteins and even some human enzymes. 2. Transcription is the DNA#Directed Synthesis of RNA a closer look 1. An enzyme called an RNA polymerase pries the two strands of DNA apart and joins the RNA nucleotides as they base- pair along the DNA template. 2. The DNA sequence where RNA polymerase attaches and initiates transcription is known as the promoter; in bacteria, the sequence that signals the end of transcription is called the terminator. The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit. 3. Bacteria only have a single type of RNA polymerase. Eukaryotes have at least three types of RNA polymerase. The one used for mRNA synthesis is called RNA polymerase II. 4. Certain sections of a promoter are especially important for binding RNA polymerase. A collection of proteins called TATA box: a crucial promoter DNA transcription factors mediate the binding of RNA polymerase and the initiation of transcription, and they are required sequence. for RNA polymerase II to bind to the promoter. The whole complex of transcription factors and RNA polymerase II bound to the promoter is called a transcription initiation complex. 5. As RNA polymerase moves along the DNA, it continues to untwist the double helix, exposing about 10 to 20 DNA bases at a time. The enzyme add nucleotides to the 3´ end of the growing RNA molecule, and the new RNA molecule peels away from its DNA template and the DNA double helix re-forms. A single gene can be transcribed simultaneously by several molecules of RNA polymerase following each other like trucks in a convoy. 6. The mechanism of termination differs between bacteria and eukaryotes. In bacteria, a terminator sequence causes the the polymerase to detach from the DNA and release the transcript, which available for immediate use as mRNA. In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which does for a polyadenylation signal (AAUAAA) in the pre-mRNA. Then, at a point about 10 to 35 nucleotides downstream from the AAUAAA signal, proteins associated with the growing RNA cut it free from the polymerase. However, the polymerase continues transcribing DNA for hundreds of nucleotides. The RNA produced by this continued transcription is digested by an enzyme that moves along the RNA. When the enzyme reaches the polymerase, transcription is terminated and the polymerase falls off the DNA. & Eukaryotic cells modify RNA after transcription 1. RNA processing: The 5′ end receives a 5′ cap, a modified form of a guanine nucleotide with three phosphate groups. The 3′ end, an enzyme adds 50 to 250 more adenine (A) nucleotides, forming a poly-A tail. These two modifications facilitate the export of the mature mRNA from the nucleus, protect the mRNA from hydrolytic enzymes, and help ribosomes attach to the 5′ end of the mRNA. 2. RNA splicing: the removal of large portions of the RNA molecule. The average length of a transcription unit along a human DNA molecule is about 27,000 base pairs; however, it takes only 1,200 nucleotides in RNA to doe for the average-sized protein of 400 amino acids. Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides. Most of these noncoding sequences are interspersed between coding segments of the gene. The noncoding segments of nucleic acid that lie between coding regions are called intervening sequences, or introns. The other regions are called exons. The introns are cut out from the molecules and the exons joined together, forming an mRNA molecule with a continuous coding sequence. The signal for RNA splicing is a short nucleotide sequence at each end of an intro. Particles called small nuclear ribonucleoproteins, abbreviated snRNPs, recognize these splice sites. Several different snRNPs join with additional proteins to form an even lager assembly called a spliceosome, which is almost as big as a ribosome. The spliceosome interacts with certain sites along an intron, releasing the iron and joining together the two exons. 3. The idea of a catalytic role for snRNA arose from the discovery of riboenzymes, RNA molecules molecules that function as enzymes. In some organisms, RNA splicing can occur without proteins or even additional RNA molecules: Shulin Ye pg 1 of 3 08/31/09 07:28:04 PM  Chapter 17: From Gene to Protein The intron RNA functions as a riboenzyme and catalyzes its own excision. 4. Three properties of RNA enable some RNA molecules to function as enzymes: 1. A region of a RNA molecule may base-pair with a complementary region elsewhere in the same molecule, which gives the molecule a particular three-dimensional structure. 2. Some of the bases in RNA contain functional groups that may participate in catalysis. 3. The ability of RNA to hydrogen-bond with other nucleic acid molecules adds specificity to its catalytic activity. 5. Alternative RNA splicing: when a gene can give rise to two or more different polypeptides, based on which segments are treated as introns during RNA processing. 6. Proteins often have a modular architecture consisting of discrete structural and functional regions called domains. 7. The presence of introns in a gene my facilitate the evolution of new potentially useful proteins as a result a process known as exon shuffling. 4. Translation Is the RNA#directed synthesis of a polypeptide a closer look 1. Transfer RNA interprets mRNA. Molecules of tRNA are not all identical. As a tRNA molecule arrives at a ribosome, it bears a specific amino acid at one end. At the other end of the tRNA is a nucleotide triplet called an anticodon. Translation is simple in principle by complex in its biochemistry and mechanics, especially in the eukaryotic cell. 2. Like mRNA and other types of cellular RNA, transfer RNA molecules are transcribed from DNA templates. In a eukaryotic cell, tRNA, like mRNA, is made in the nucleus and must travel from the nucleus to the cytoplasm, where translation occurs. 3. A tRNA molecule consist of a single RNA strand that is only about 80 nucleotide long. This single strand can fold back upon itself and form a molecule with a three-dimensional structure that is roughly L-shaped. The loop extending from one end of the L includes the anticodon. From the other end of the L-shaped tRNA molecule protrudes its 3´ end, which is the attachment site for an amino acid. 4. A tRNA that binds to an mRNA codon specifying a particular amino acid must carry that amino acid, and no other, to the ribosome. The correct matching up of tRNA and amino acid is carried out by a family of related enzymes called aminoacyl-tRNA synthetases. 5. There are 20 different synthetases, one for each amino acid; each synthetase is able to bind all the different tRNAs that code for its particular amino acids. 6. Some tRNAs are able to bind to more than one codon. Such versatility is possible because the rules for base pairing between the third base of a codon and the corresponding base of a tRNA anticodon are relaxed compared to those at other codon positions. The flexible base pairing at this codon position is called wobble. 7. Ribosomes facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis. A ribosome is made up of two subunits, called the large and small subunits. The ribosomal subunits are constructed of proteins and RNA molecules named ribosomal RNAs, or rRNAs. In eukaryotes, the subunits are made in the nucleolus. 8. In both bacteria and eukaryotes, large and small subunits join to form a functional ribosome only when they attach to an mRNA molecule. About two-third of the mass of a ribosome consists of rRNAs, either three molecules (in bacteria) or four (in eukaryotes). 9. Although the ribosomes of bacteria and eukaryotes are very similar in structure and function, those of eukaryotes are slightly larger and differ somewhat from bacterial ribosomes in their molecular composition. 10. In addition to a binding site for mRNA, each ribosome has three binding sites for tRNA. The P site holds the tRNA carrying the growing polypeptide, while the A site holds the tRNA carrying the next amino acid to be added to the chain. Discharged tRNAs leave the ribosome from the E site. 11. As the polypeptide becomes longer, it passes through an exit tunnel in the ribosome’s large subunit. 12. Recent research strongly supports the hypothesis that rRNA, not protein, is primarily responsible for both the structure and function of the ribosome. 13. We can divide translation, the synthesis of a polypeptide chain, into three stages: initiation, elongation, and termination. 1. Initiation: The initiation stage of translation brings together mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome. 1. First, a small ribosomal unit binds to both mRNA and a specific initiator tRNA, which carries the amino acid methionine. 1. In bacteria, the small subunit can bind these two in either order. 2. In eukaryotes, the small subunit, with the initiator tRNA already bound, binds to the 5´ cap of the mRNA and then scans downstream along the mRNA until it reaches the start codon. 2. The attachment of a large ribosomal subunit completes the translation initiation complex. 3. Proteins called initiation factors are required to bring all these components together. A GTP molecule is also required. A polypeptide is always synthesized from the N-terminus to the C-terminus. 2. Elongation: Amino acids are added one by one to the preceding amino acid. Each addition involves the participation of several proteins called elongation factors. 1. Codon recognization: The anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysis of GTP increases the accuracy and efficiency of this step. 2. Peptide bond formation: An rRNA molecule of the large ribosomal subunit catalysed the formation of a peptide bond between the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site. 3. Translocation: The ribosome translocates the tRNA in the A site to the P site. The empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bond tRNAs, bringing the next codon to be translated into the A site. A GTP molecule is required. 3. Termination: A stop codon in the mRNA reaches the A site of the ribosome. A protein called a release factor binds directly to the stop codon in the A site. The release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain. The translation assembly breaks apart, a process that requires 2 GTP. 4. Multiple ribosomes translate an mRNA at the same time. Such strings of ribosomes are called polyribosomes or polysomes. 14. Post-translational modifications may be required before the protein can begin doing its particular job. Certain amino acids may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additions. Enzymes may remove one or more amino acids from the leading (amino) end of the polypeptide chian. A polypeptide chian may be enzymatically cleaved into two or more pieces. Two or more polypeptides may come together, becoming the subunits of a protein that has quaternary structure. 15. Polypeptide synthesis always begins in the cytosol, when a free ribosome starts to translate an mRNA molecule. The growing polypeptide itself may cue the ribosome to attach to the ER. A segment of the polypeptide, called the signal polypeptide, is recognized as it emerges from the ribosome by a protein-RNA complex called a signal-recognization particle (SRP). Shulin Ye pg 2 of 3 08/31/09 07:28:04 PM  Chapter 17: From Gene to Protein ) Point mutations can affect protein structure and function 1. Mutations are responsible for the huge diversity of genes found among organisms because mutations are the ultimate source of new genes. 2. Point mutation: chemical changes in a single base pair of a gene. 1. Base-pair substitution: the replacement of one nucleotide and its partner with another pair of nucleotides. 1. Silent mutations have no effect on the encoded protein. 2. Missense mutations exchange one amino acid to another one. 3. Nonsense mutation change a codon for an amino acid to a stop codon. 2. Insertions and deletions are additions or losses of nucleotide pairs in a gene. 1. Frameshift mutation: Insertion or deletion of nucleotides may alter the reading frame of the genetic message. 3. Errors during DNA replication or recombination can lead to base-pair substitutions, insertions, or deletions, as well as to mutation affecting longer stretches of DNA. A number of physical and chemical agents, called mutagens, interact with DNA in ways that cause mutations. 1. Chemical mutagens: 1. Base analogs: chemicals that are similar to normal DNA bases but pair incorrectly during DNA replication. 2. Some other chemical mutagens interfere with correct DNA replication by inserting themselves into the DNA and istorting the double helix. 3. Other mutagens cause chemical changes in bases that change their pairing properties. * While gene expression differs among the domains of life, the concept of a gene is universal Gene: a region of DNA that can be 1. Bacterial and eukaryotic RNA polymerases differ significantly from each other. The single RNA polymerase of archaea expressed to produce a final resembles the three eukaryotic RNA polymerases, and archaea and eukaryotes use a complex set of transcription functional product that is either a factors, unlike bacteria. polypeptide or an RNA molecule. 2. Archaeal ribosomes are the same size as bacterial ribosomes, but their sensitivity to chemical inhibitors most closely matches that of eukaryotic ribosomes. The archaeal process of initiation of translation is more like that of bacteria. 3. The most important differences between bacteria and eukaryotes with regard to gene expression arise from the bacterial cell’s relative absence of compartmental organization. In the absence of a nucleus, a bacterial cell can simultaneously transcribe and translate the same gene. In contrast, the eukaryotic cell’s nuclear envelope segregates transcription from translation and provided a compartment for extensive RNA processing. 4. A given type of cell expresses only a subset of its genes. Gene expression is precisely regulated. Shulin Ye pg 3 of 3 08/31/09 07:28:04 PM  Chapter 18: Regulation of Gene Expression 0. Overview: Conducting the Genetic Orchestra 1. Cells intricately and precisely regulated their gene expression. Gene expression in eukaryotes, as in bacteria, is often regulated at the stage of transcription, but control at other levels of gene expression is also important. 1. Bacteria often respond to environmental change by regulating transcription. 1. Metabolic control occurs on two levels. First, cells can adjust the activity of enzymes already present. Second, cells can adjust the production level of certain enzymes. 2. A key advantage of grouping genes of related function into one transcription unit is that a single on-off “switch” can control the who cluster of functionally related genes; in other words, these genes are under coordinate control. The switch is a segment of DNA called an operator. All together, the operator, the promoter, and the genes they control constitute and operon. 3. Regulation of both the trp and lac operons involves the negative control of genes, because the operons are switched off by the active form of the repressor protein. 1. For the trp operon, the entire operon can be switched off by a protein called the trp repressor. The trp repressor is the product of a regulatory gene called trpR, which is located some distance from the operon it controls and has its own promoter. Regulatory genes are expressed continuously, although at a low rate. 1. Trytophan functions in this system as a corepressor, a small molecule that cooperates with a repressor protein to switch an operon off. 2. The trp operon is said to be a repressible operon because its transcription is usually on but can be inhibited (repressed) when a specific small molecule binds allosterically to a regulatory protein. 3. Repressible enzymes generally function in anabolic pathways, which synthesize essential end products from raw materials. 2. An inducible operon is usually off but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein. The specific small molecule, called an inducer, inactivates the repressor. For the lac operon, the inducer is is allolactose. 1. The enzymes of the lactose pathway are referred to as inducible enzymes because their synthesis is induced by a chemical signal. 4. Positive gene regulation: When glucose and lactose are both present in its environment, E. coli preferentially uses glucose. Only when lactose is present and glucose is in short supply does E. coli use lactose as an energy source. The mechanism depends on the interaction of an allosteric regulatory protein with a small organic molecule, in this cAMP, which accumulates when glucose is scarce. The regulatory protein, called catabolite activator protein (CAP), is an activator, a protein that binds to DNA and stimulates transcription of a gene. By facilitating the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription, the attachment of CAP to the promoter directly stimulates gene expression. Therefore, this mechanism qualifies as positive regulation. 2. Eukaryotic gene expression can be regulated at any stage. 1. A typical human cell probably expresses about 20% of its genes at any given time. Highly differentiated cells, such as Differential gene expression: the muscle or nerve cells, express an even smaller fraction of their genes. expression of different by cells with 2. Only a small amount of the DNA—about 1.5% in humans—codes for protein. The rest of the DNA either codes for the same genome. RNA products, such as tRNAs, or isn’t transcribed at all. 3. The structural organization of chromatin not only packs a cell’s DNA into a compact form that fits inside the nucleus but also helps regulate gene expression in several ways. Genes within heterochromatin, which is highly condensed, are usually not expressed. 4. In histone acetylation, acetyl groups (-COCH3) are attached to lysine in histone tails; deacetylation is the removal of acetyl groups. When lysines are acetylated, their positive charges are neutralized and the histone tails no longer bind to neighboring nucleosomes. The addition of methyl groups (-CH3) to histone tails (methylation) can promote condensation of the chromatin. The addition of a phosphate group to an amino acid (phosphorylation) next to a methylated amino acid can have the opposite effect. 1. Some activators recruit proteins that acetylate histones near the promoters of specific genes, thus promoting transcription. 5. Inactive DNA, such as that of inactivated mammalian X chromosomes, is generally more methylated than DNA that is actively transcribed, although there are exceptions. 1. At least in some species, DNA methylation seems to be essential for the long-term inactivation of genes that occurs during normal cell differentiation in the embryo. 2. Once methylated, genes usually stay that way through successive cell divisions in a given individual. At DNA sites where one stand is already methylated, methylation enzymes correctly methylate the daughter strand after each round of DNA replication. 3. A methylation pattern maintained in this way also accounts for genomic imprinting in mammals. 4. Alterations in normal patterns of DNA methylation are seen in some cancers, where they are associated with inappropriate gene expression. 6. Epigenetic inheritance: inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence. 7. The REGULATION OF TRANSCRIPTION INITIATION in eukaryotes involves proteins that bind to DNA and either facilitate or inhibit binding of RNA polymerase. 1. A cluster of proteins called a transcription initiation complex assembles on the promoter sequence at the “upstream” end of the gene. 2. Associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that help regulate transcription by binding certain proteins. 3. To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors. Only a few general transcription factors independently bind a DNA sequence, such as the TATA box within the promoter; the others primarily bind proteins, including each other and RNA polymerase II. 4. Proximal control elements are located close to the promoter. Distal control elements, groupings of which are called enhancers, may be thousands of nucleotides upstream or downstream of a gene or even within an intron. 5. Protein-mediated bending of the DNA is thought to bring the bond activators in contact with a group of so-called mediator proteins, which in turn interact with proteins at the promoter. These multiple protein-protein interactions help assemble and position the initiation complex on the promoter. 8. In eukaryotes, the precise control of transcription depends largely on the binding of activators to DNA control elements. The particular combinations of control elements in an enhancer associated with a gene turns out to be more important than the presence of a single unique control element in regulating transcription of the gene. 9. Analysis of the genomes of several eukaryotic species has revealed some co-expressed genes that are clustered near one another on the same chromosome. However, each gene in such a cluster usually has its own promoter and is individually transcribed. Sometimes, however, several related genes do share a promoter and are transcribed into a single pre- mRNA, which is then processed into separate mRNAs. More commonly, co-expressed eukaryotic genes, such as genes Shulin Ye pg 1 of 3 08/31/09 07:28:04 PM  Chapter 17: From Gene to Protein Alternative RNA splicing: different coding for the enzymes of a metabolic pathway, are found scattered over different chromosomes. Coordinate control of mRNA molecules are produced from dispersed genes in a eukaryotic cell often occurs in response to chemical signals from outside the cell. the same primary transcript, 10. The life span of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell. depending on which RNA segments mRNA breakdown begins with the enzymatic shortening of the poly-A tail. Enzymes later remove the 5` cap. Once the are treated as exons and which as cap is removed, nuclease enzymes rapidly chew up the RNA. introns. 11. Translation presents another opportunity for regulating gene expression; such regulation occurs most commonly at the initiation stage. 1. Some mRNAs can be blocked by regulatory proteins that bind to specific sequences or structures within the 5' UTR of the mRNA. 2. Some stored mRNAs initially lack poly-A tails of sufficient length to allow translation initiation. A cytoplasmic protein adds adenine nucleotides to prompt translation. 12. Translation of all the mRNAs in a cell may be regulated simultaneously. In an eukaryotic cell, such “global” control usually involves the activation or inactivation of one more of the protein factors required to initiate translation. 13. The final opportunities for controlling gene expression occur after translation. Often, eukaryotic polypeptides must be processed to yield functional protein molecules. Many proteins undergo chemical modifications that make them functional. 14. Finally, the length of time each protein functions in the cell is strictly regulated by means of selective degradation. To mark a particular protein for destruction, the cell commonly attaches molecules of a small protein called ubiquitin to the protein. Giant protein complexes called proteasomes then recognize the ubiquitin-tagged proteins and degrade them 3. Noncoding RNAs play multiple roles in controlling gene expression. 1. Only 1.5% of the human genome codes for proteins. A significant amount of the genome may be transcribed into non- protein-coding RNAs, including a variety of small RNAs. 2. Regulation by noncoding RNAs is known to occur at two points in the pathway of gene expression: mRNA translation and chromatin configuration. 3. Since 1993, a number of research studies have uncovered small single-stranded RNA molecules, called microRNAs (miRNAs), that are capable of binding to complementary sequences in mRNA molecules. The miRNAs are formed from longer RNA precursors that fold back on themselves, forming one or more short double-stranded hairpins structures, each held together by hydrogen bonds. After each hairpin is cut away from the precursor, it is trimmed by an enzyme (Dicer) into a short double-stranded fragment of about 20 nucleotide pairs. One of the two strands is degraded, while the other strand, the miRNA, forms a complex with one or more proteins; the miRNA allows the complex to bind to any mRNA molecule with the complementary sequence. The miRNA-protein complex then either degrades the target mRNA or blocks its translation. 4. Researchers had found that that injecting double-stranded RNA molecules into a cell somehow turned off expression of a gene with the same sequence as the RNA (RNA interference, RNAi), which was later shown to be due to small interfering RNAs (siRNAs), which are similar in size and functions to miRNAs. 5. The distinction between miRNAs and siRNAs is based on the nature of the precursor molecule for each. While an miRNA is usually formed from a single hairpin in a precursor RNA, siRNAs are formed from much longer double- stranded RNA molecules, each of which gives rise to many siRNAs. 6. In addition to affect mRNAs, small RNAs can cause remodelling of chromatin structure. siRNAs produced by yeast cells appear to be crucial for the formation of heterochromatin at the centromeres of chromosomes. 4. A program of differential gene expression leads to the different cell types in a multicellular organism. Cell differentiation: the process by 1. In the embryonic development of multicellular organisms, a fertilized egg (a zygote) gives rise to cells of many different which cells become specialized in types, each with a different structure and corresponding function. structure and function. 2. The specific genes expressed in any particular cell of a developing organism determine its path. Morphogenesis: the physical 3. It turns out that materials placed into the egg by the mother set up a sequential program of gene regulation that is carried processes that give an organism its out as cells divide. One important source of information early in development is the egg’s cytoplasm. The cytoplasm of shape. an unfertilized egg is not homogeneous. Proteins, mRNA, other substances, and organelles, are distributed unevenly in Cytoplasmic determinates: maternal the unfertilized egg, and this unevenness has a profound impact on the development of the future embryo in many substances in the egg that influence species. the course of early development. 4. The other major source of developmental information, which becomes increasingly important as the number of Induction: the process in which embryonic cells increases, is the environment around a particular cell. Most influential are the signals impinging on an signals cause changes in target cells. embryonic cell from other embryonic cells in the vicinity, including contact with cell-surface molecules on neighboring cells and the binding of growth factors secreted by neighboring cells. Determination: the events that lead 5. Once it has undergone determination, an embryonic cell is irreversibly committed to its final fate. Differentiated cells to the observable differentiation of a are specialists at making tissue-specific proteins. cell. 6. MyoD is the protein that transforms an embryonic precursor cell to a myoblast, a cell that is committed to becoming a Pattern formation: The muscle cell. MyoD stimulates the production of certain proteins, as well as itself. development of a spatial organization 7. Positional information: the molecular cues that control pattern formation. in which the tissues and organs of an 8. In the 1940s, scientists began using the genetic approach—the study of mutants—to investigate Drosophila organism are all in their characteristic development. In Drosophila, cytoplasmic determinates that are localized in the unfertilized egg provide positional places. information for the placement of anterior-posterior and dorsal-ventral axes even before fertilization. Homeotic genes: control pattern 9. In the 1940s, Edward B. Lewis first showed the value of the genetic approach to studying embryonic development in formation in the late embryo, larva, Drosophila. Lewis studied bizarre mutant flies with developmental defects that led to extra wings or legs in the wrong and adult. places. Embryonic lethals: mutations with 10. In the 1970s, two researchers in Germany, Christiane Nüsslein-Volhard and Eric Wieschaus, set out to identify all the phenotypes causing death at the genes that affect segment formation in Drosophila. There were three major difficulties: embryonic or larval stage. 1. Drosophila has about 13,700 genes. The genes affecting segmentation might be just a few needles in a haystack or might be so numerous and varied that scientists would be unable to make sense of them. Maternal effect gene: a gene that, 2. Mutations affecting a process as fundamental as segmentation would be embryonic lethals. when mutant in the mother, results in 3. Cytoplasmic determinates in the egg were known to play a role in axis formation, and therefore the researchers a mutant phenotype in the offspring, knew they would have to study the mother’s genes as well as those of the embryo. regardless of the offspring’s own 11. Nüsslein-Volhard and Wieschaus began their search for segmentation genes by exposing flies to a mutagenic chemical genotype. Because they control the that affected the flies’ gametes. They mated the mutagenized flies and then scanned their descendants for dead embryos orientation (polarity) of the egg and or larvae with abnormal segmentation or other defects. Using this approach, they eventually identified about 1,200 consequently of the fly, maternal genes essential for pattern formation during embryonic development. effect genes are also called egg- 12. An embryo whose mother has a mutant bicoid gene lacks the front half of its body and has posterior structures at both polarity genes. ends. 13. Morphogen gradient hypothesis: Gradients of substances called morphogens establish an embryo’s axes and other features of its form. 14. Bicoid mRNA is highly concentrated at the extreme anterior end of the mature egg. The mRNA is produced in nurse Shulin Ye pg 2 of 3 08/31/09 07:28:04 PM  Chapter 18: Regulation of Gene Expression cells, transferred to the egg via cytoplasmic bridges, and anchored to the cytoskeleton at the anterior end of the egg. 15. Scientists injected pure bicoid mRNA into various regions of early embryos. The protein that resulted from its translation caused anterior structures to form at the injection sites. 5. Cancer results from genetic changes that affect cell cycle control. 1. The genes that normally regulate cell growth and division during the cell cycle include genes for growth factors, their receptors, and the intracellular molecules of signaling pathways. 2. An early breakthrough in understanding cancer came in 1911, when Peyton Rous, an American pathologist, discovered a virus that causes cancer in chickens. 3. Tumor viruses cause cancer in various animals. The Epstein-Barr virus, which causes infections mononucleosis, has been linked to several types of cancer, notably Burkitt’s lymphoma. Papillomaviruses are associated with cancer of the cervix, and a virus called HTLV-1 causes a type of adult leukemia. 4. Research on tumor viruses led to the discovery of cancer-causing genes called oncogenes in certain retroviruses. The normal versions of the cellular genes, called proto-oncogenes, code for proteins that stimulate normal cell growth and division. 5. The genetic changes that convert proto-oncogenes to oncogenes fall into three main categories: movement of DNA within the genome, amplification of a proto-oncogene, and point mutations in a control element or in the proto- oncogene itself. 1. Cancer cells frequently contain chromosomes that have broken and rejoined incorrectly, translocating fragments from one chromosome to another. If a translocated proto-oncogene ends up near an especially active promoter (or other control element), its transcription may increase, making it an oncogene. 2. Amplification increases the number of copies of the proto-oncogene in the cell. 3. A point mutation either (1) in the promoter or an enhancer that controls a proto-oncogene, causing an increase in its expression, or (2) in the coding sequence, changing the gene’s product to a protein that is more active or more resistant to degradation than the normal protein. 6. Tumor-suppressor genes code for proteins that help prevent uncontrolled cell growth. They have various functions: 1. Repair damaged DNA, a function that prevents the cell from accumulating cancer-causing mutations. 2. Control the adhesion of cells to each other or to the extracellular matrix; proper cell anchorage is crucial in normal tissues—and often absent in cancers. 3. Components of cell-signaling pathways that inhibit the cell cycle. 7. The Ras protein, encoded by the ras gene, is a G protein that relays a signal from a growth factor receptor on the plasma membrane to cascade of protein kinases. The cellular response at the end of the pathway is the synthesis of a protein that stimulates the cell cycle. 8. The p53 gene, named for the 53,000-dalton molecular weight of its protein product, is a tumor-suppressor gene. The protein it encodes is a specific transcription factor that promotes the synthesis of cell-cycle inhibiting proteins. The p53 gene has been called the “guardian angel of the genome.” Once activated, for example by DNA damage, the p53 protein functions as an activator for several genes. Often, it activates a gene called p21, whose product halts the cell cycle by binding to cyclin-dependent kinases, allowing time for the cell to repair the DNA; the p53 protein can also turn on genes directly involved in DNA repair. When DNA damage is irreparable, p53 activates “suicide” genes. 9. More than one somatic mutation is generally needed to produce all the changes characteristic of a full-fledged cancer cell. The model of a multistep path to cancer is well supported by studies of one of the best-understood types of human cancer, colorectal cancer. 10. About a half dozen changes must occur at the DNA level for a cell to become fully cancerous. These usually include the appearance of at least one active oncogene and the mutation or loss of several tumor-suppressor genes. Mutations must knock out both alleles in a cell’s genome to block tumor suppression. Most oncogenes behave as dominate alleles. The gene for telomerase is usually activated, allowing the cancer cells to be “immortal.” 11. About 15% of colorectal cancers involve inherited mutations. Many of these affect the tumor-suppressor gene called adenomatous polyposis coli, or APC. This gene has multiple functions in the cell, including regulation of cell migration and adhesion. There is evidence of a strong inherited predisposition in 5-10% of patients with breast cancer. Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers. Both genes are considered tumor- suppressor genes because their wild-type alleles protect against breast cancer and their mutant alleles are recessive. Both function in the cell’s DNA damage repair pathway. Shulin Ye pg 3 of 3 08/31/09 07:28:04 PM  Chapter 19: Viruses 0. Overview: A Borrowed Life 1. Lacking the structures and metabolic machinery found in cells, most viruses are little more than genes packaged in protein coats. Viruses cannot reproduce or carry out metabolic activities outside of a host cell. Most biologists studying viruses today would probably agree that they are not alive but exist in a shady area between life-forms and chemicals. 1. A Virus Consists of a Nucleic Acid Surrounded by a Protein Coat. 1. In 1883, Adolf Mayer, a German scientist, discovered that he could transmit mosaic disease from plant to plant by rubbing sap extracted from diseased leaves onto healthy plants. Mayer suggested that the disease was caused by unusually small bacteria that were invisible under a microscope. 2. Dimitri Ivanowsky, a Russian biologist, passed same from infected tobacco leaves through a filter designed to remove bacteria. After filtration, the sap still produced mosaic disease. 3. Dutch botanist Martinus Beijerinck carried out a classic series of experiments that showed that the infectious agent in the filtered sap could reproduce. He showed that the mysterious agent of mosaic disease could not be cultivated on nutrient media in test tubes or petri dishes. 4. In 1935, American scientist Wendell Stanley crystallized the infectious particle. Capsid: the protein shell enclosing 5. The tiniest viruses are only 20 nm in diameter—smaller than a ribosome. the viral genome. The capsid may be 6. Their genomes may consist of a double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded rod-shaped, polyhedral, or more RNA, depending on the kind of virus. The smallest viruses known have only four genes in their genome, while the complex in shame. Capsids are built largest have several hundred to a thousand. from a large number of protein 7. Rod-shaped viruses are commonly called helical viruses. subunits called capsomeres, but the 8. Some viruses have accessory structures that help them infect their hosts. number of different kinds of proteins 9. Viral envelopes are derived from the membranes of the host cell and contain phospholipids and membra