Bisc 102 - Chapter 7: DNA Structure and Gene Function
Bisc 102 - Chapter 7: DNA Structure and Gene Function Bisc 102
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Date Created: 09/25/16
7.1 DNA Is a Double Helix Life depends on DNA (deoxyribonucleic acid), a molecule that stores the information each cell needs to produce proteins. In 1953 biochemist James Watson and English physicist Francis Crick used two lines of evidence to deduce DNA’s structure. Biochemist Erwin Chargaff had shown that the amount of guanine in a DNA molecule always equals the amount of cytosine, and the amount of adenine always equals the amount of thymine. English physicist Maurice Wilkins and chemist Rosalind Franklin used a technique called Xray diffraction to determine the threedimensional shape of the molecule. The Xray diffraction pattern revealed a regularly repeating structure of building blocks. Watson and Crick combined these clues to build a ballandstick model of the DNA molecule. The DNA double helix resembles a twisted ladder. The twin rails of the ladder, called sugarphosphate “backbones,” are alternating units of deoxyribose and phosphate joined with covalent bonds. The two chains are parallel to each other, but are oriented in opposite directions. The ladder’s rungs are AT and CG base pairs joined by hydrogen bonds. These base pairs arise from the chemical structures of the nucleotides. The two strands of a DNA molecule are c omplementary t o each other. The sequence of each strand determines the sequence of the other. An A on one strand means a T on the opposite, and a G on one means a C on the other. An organism's g enome i s all of the genetic material in its cells. In a eukaryotic cell, the majority of the genome is divided among multiple chromosomes housed inside the cell’s nucleus; each chromosome is a discrete package of DNA coiled around proteins. On the other hand, the genome of a bacterial cell typically consists of one circular chromosome. A gene is a sequence of DNA nucleotides that encodes a specific protein or RNA molecule; the human genome includes 20,00 to 25,000 genes scattered on its 23 pairs of chromosomes. A bacterial chromosome is also divided into multiple genes. 7.2 DNA Stores Genetic Information: An Overview In the 1940s, biologists deduced that each gene somehow controls the production of one protein. In the next decade, Watson and Crick described this relationship between nucleic acids and proteins as a flow of information the called the “central dogma”. First, in transcription, a cell “rewrites” a gene’s DNA sequence to a complementary RNA molecule. Then, in translation, the information in RNA is used to assemble a different class of molecule: a protein. Messenger RNA (mRNA) c arries the information that specifies a protein. The mRNA is divided into genetic “code words” called codons; a c odon is a group of three consecutive mRNA bases that corresponds to one amino acid. T ransfer RNA (tRNA) molecules are “connectors” that bind an mRNA codon at one end and a specific amino acid at the other. Their role is to carry each amino acid to the correct spot along the mRNA molecule. R ibosomal RNA (rRNA) c ombines with proteins to form a ribosome, the physical location where translation occurs. 7.3 Transcription Uses a DNA Template to Build RNA DNA is a double helix, but only one of the two strands contains the information encoding each protein. This strand, called the t emplate strand, contains the DNA sequence that is actually copied to RNA. The enzymes that carry out transcription recognize the promoter, a DNA sequence that not only signals a gene’s start but also indicates which of the two strands is the template. Transcription occurs in three stages. 1. Initiation: Enzymes unzip the DNA double helix corresponding to the gene, exposing the template strand. RNA polymerase, t he enzyme that builds an RNA chain, may then attach to the promoter. Often, however, proteins called transcription factors must also bind to the promoter for RNA polymerase to attach to the DNA. 2. longation: R NA polymerase moves along the DNA template strand, adding RNA nucleotides that are complementary to exposed bases on the DNA template strand. 3. ermination: A erminator sequence in DNA signals the end of the gene. Upon reaching the terminator, the RNA polymerase enzyme separates from the DNA template and released the newly produced RNA. The DNA molecule then resumes its usual double helix shape. As the RNA molecule forms, it curls into a threedimensional shape dictated by complementary base pairing within the molecule. The final shape determines whether the RNA functions as mRNA, rRNA, or rRNA. The phrase g ene expression can therefore mean the production of either a functional RNA molecule or a protein. In bacteria and archaea, ribosomes may begin translating mRNA to a protein before transcription is even complete. In eukaryotic cells, however, mRNA is usually altered before it leaves the nucleus to be translated. A short sequence of modified nucleotides, called a cap, is added to one end of the mRNA molecule. At the opposite end, 100 to 200 adenine are added, forming a “poly A tail.” Together, the cap and poly A tail help ensure that ribosomes attach to the correct end of the mRNA. Introns are portions of the mRNA that are removed before translation. The remaining portions, called exons, are spliced together to form the mature mRNA that leaves the nucleus to be translated. (Exons are the parts of the mRNA that are actually expressed or that exit the nucleus). 7.4 Translation Builds the Protein Genetic code is the set of “rules” by which a cell uses the codons in mRNA to to assemble amino acids into a protein. Translation Requires mRNA, tRNA and Ribosomes Translation the actual construction of a protein requires three main types of participants. The first type is mRNA, the molecule that carries the genetic information encoding a protein. The second type of participant is tRNA. This “bilingual” molecule carries amino acids from the cytoplasm to the mRNA being translated. tRNA interacts with mRNA via its anticodon, a threebase loop on tRNA that is complementary to one mRNA codon. The remaining participant in translation is the ribosome, the site of translation. Each cell has many ribosomes, which may be free in the cytosol or attached to the rough endoplasmic reticulum. Translation Occurs in Three Steps The process of translation is divided into three stages, during which mRNA, tRNA molecules, and ribosomes come together, link amino acids into a chain, and then dissociate again. Initiation brings together the ribosomal subunits, mRNA, and the tRNA carrying the first amino acid. Elongation begins, and a tRNA molecule bearing the second amino acid binds to the second codon. The first amino acid forms a covalent bond with the second amino acid. Additional tRNAs bring subsequent amino acids encoded in the mRNA. Termination occurs when a release factor binds to the stop codon. All components of the translation machine are released, along with the completed polypeptide. The cell maximizes efficiency by producing multiple copies of each mRNA; moreover, many ribosomes may simultaneously translate the same mRNA molecule. Proteins Must Fold Correctly after Translation Regions of the amino acid chain attract or repel other parts, contorting the polypeptide overall shape. Enzymes catalyze the formation of chemical bonds, and “chaperone” proteins stabilize partially folded regions. Proteins can fold incorrectly if the underlying DNA sequence is altered because the encoded protein may have the wrong sequence of amino acids. In addition to folding, some proteins must be altered in other ways before they become functional. 7.5 Protein Synthesis is Highly Regulated Producing proteins costs tremendous amounts of energy. Considering the high cost of making a protein, it makes sense that cells save energy by not producing unneeded proteins. Operons Are Groups of Bacterial Genes that Share One Promoter An operon is a group of related genes plus a promoter and an operator that control the transcription of the entire group at once. The promoter, as described earlier, is the site to which RNA polymerase attaches to begin transcription. The operator is a DNA sequence located between the promoter and the proteinencoding regions. If a protein called a r epressor binds to the operator, it prevents the transcription of the genes. Eukaryotic Organisms Use Many Methods to Regulate Gene Expression In multicellular eukaryotes, the control of protein synthesis is more complex than in bacteria, because different cell types express different combinations of genes. (REFER TO FIGURE 7.11 IN BOOK FOR FOLLOWING:) DNA Availability Transcription Factors mRNA processing mRNA Exit from Nucleus mRNA Degradation Protein Processing and Degradation 7.6 Mutations Change DNA A mutation is any change in a cell’s DNA sequence. The change may occur in a gene or in a regulatory region such as a promoter. Although some mutations do cause illness, they also provide the variation that makes life interesting and evolution possible. Mutations Range from Silent to Devastating A mutation may change one or a few base pairs or affect large portions of a chromosome. A substitution mutation is the replacement of one DNA base with another. Such a mutation is “silent” if the mutated gene encodes the same protein as the original version. Mutations can be silent because more than one codon encodes most amino acids. An insertion mutation a dds one or more nucleotides to a gene; a d eletion mutation removes nucleotides. In a frameshift mutation, nucleotides are added or deleted by a number other than a multiple of three. What Causes Mutations? Some mutations occur spontaneously with outside causes, a DNA replication error, or during meiosis. A mutagen is any external agent that induces mutations. Alleles are variants of genes. The importance of mutations in evolution became clear with the discovery of homeotic genes, which encode transcription factors that are expressed during the development of an embryo. Mutations can also be enormously useful in science and agricultures. Geneticists frequently induce mutations to learn how genes normal function. Viruses Are Genes Wrapped in a Protein Coat A virus is a small, infectious agent that is simply genetic information enclosed in a protein coat. Viruses Are Smaller and Simpler than Cells A typical virus is much smaller than a cell. Viruses are simple structures that lack many of the characteristics of cells. All viruses, however, have g enetic information and a rotein coat. Some viruses have a lipidrich e nvelope, an outer layer derived from the host cell’s membrane. Bacteriophages a re viruses that infect bacteria. Viral Replication Occurs in Five Stages Attachment: A virus attaches to a host cell by adhering to a receptor molecule on the cell’s surface. Penetration: Animal cells engulf virus particles and bring them into the cytoplasm via endocytosis. Viruses that infect plants often enter their host cells by hitching a ride on the mouthparts of insects that munch on leaves. Synthesis: The host cell produces multiple copies of the viral genome. Assembly: The subunits of the protein coat join, and then genetic information is packed inside. Release: Once the virus particles are assembled, they are ready to leave the cell. The cell may die as enveloped viruses carry off segments of the cell membrane. 7.8 Viruses Infect All Cell Types Following attachment to the host cell and penetration of the viral genetic material, viruses may or may not immediately cause cell death. The two viral replication strategies in bacteriophages are called lytic and lysogenic infections. In the lytic pathway, the host cell bursts (lyses) when particles leave the cell. In lysogeny, viral DNA replicates along with the cell, but new viruses are not produced. Stress in the host cell may trigger a lysogenic virus to switch to the lytic pathway. Bacteriophages May Kill Cells Immediately or “Hide” in a Cell In a lytic infection, a virus enters a bacterium, immediately replicates, and causes the host cell to burst (lyse) as it releases a flood of new viruses. The newly released viruses infect other bacteria, repeating the process until all of the cells are dead. In a lysogenic infection, the genetic material of a virus is replicated along with the bacterial chromosome, but the cell is not immediately destroyed. At some point, however, the virus reverts to a lytic cycle, releasing new viruses and killing the cell. A prophage is the DNA of a lysogenic bacteriophage that is inserted into the host chromosome. During a lysogenic stage, the viral DNA does not damage the host cell. At some signal, such as stress from DNA damage or cell starvation, these viral proteins trigger a lytic infection cycle that kills the cell and releases new viruses that infect other cells. The next
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