From_Gene_to_Protein[1]

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Published on March 2, 2009

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From Genes to Proteins: From Genes to Proteins BIOLOGY Introduction: The DNA in an organism leads to specific traits by dictating the synthesis of proteins. Proteins are the links between genotype and phenotype. For example, Mendel’s dwarf pea plants lack a functioning gene that specifies the synthesis of gibberellins. Gibberellins stimulate the normal elongation of stems. Introduction Evidence that Genes Specify Proteins: In 1909, Archibald Gerrod was the first to suggest that genes dictate phenotype through enzymes by working with alkaptonuria, a hereditary disease. He was the first to use the phrase inborn errors of metabolism . Research conducted several decades later supported Gerrod’s hypothesis. Evidence that Genes Specify Proteins Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: In the 1930s, George Beadle and Boris Ephrussi speculated that each mutation affecting eye color in Drosophila blocks pigment synthesis by preventing production of the enzyme that catalyzes that step. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: In 1940, Beadle and Edward Tatum established the link between genes and enzymes in their exploration of the metabolism of a bread mold, Neurospora crassa . Most nutritional mutants survive on a medium with all 20 amino acids. One type of mutant required only the addition of arginine to the growth medium. Beadle and Tatum concluded that this mutant was defective somewhere in the biochemical pathway that normally synthesizes arginine. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: They identified three classes of arginine deficient mutants, each lacking a key enzyme at a different step in the synthesis of arginine. Lead to the one gene - one enzyme hypothesis. PowerPoint Presentation: It became clear that not all proteins are enzymes and yet their synthesis depends on specific genes. This changed to one gene - one protein. Later research demonstrated that many proteins are composed of several polypeptides, each of which has its own gene. Beadle and Tatum’s idea has been restated as the one gene - one polypeptide hypothesis . A chemical change in just one base pair of a gene causes a point mutation , which if these occur in gametes or cells producing gametes, they may be transmitted to future generations. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Example of the one gene-one polypeptide hypothesis:: Example of the one gene-one polypeptide hypothesis: Hemoglobin contains two types of polypeptide chains, alpha and beta. Only the beta chain is affected in persons with the sickle-cell disease; so there must be a gene for each type of chain. Sickle-cell disease results when the 6 th of 146 amino acids in the beta chain is changed from glutamate to valine. RNA : An Overview: Genes provide the instructions for making proteins. Between DNA and protein synthesis is RNA. RNA is chemically similar to DNA, except: 1. it contains ribose as its sugar 2. it substitutes the uracil for thymine 3. RNA molecules usually are single stranded. There are three major classes of RNA: messenger, ribosomal, and transfer. RNA : An Overview Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Functions of RNA: Functions of RNA Messenger RNA (mRNA) takes a message from DNA in the nucleus to the ribosomes in the cytoplasm. Ribosomal RNA (rRNA) along with proteins, makes up the ribosomes. Transfer RNA (tRNA) transfers amino acids to the ribosomes for protein synthesis. PowerPoint Presentation: To get from DNA, written in one chemical language, to protein, written in another, requires two major stages, transcription and translation . Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: During transcription , a DNA strand is used to synthesize a complementary RNA strand. process used to make any type of RNA from DNA. Transcription of a gene makes a messenger RNA ( mRNA ) molecule. During translation , the information contained in the order of nucleotides in mRNA is used to determine the amino acid sequence of a polypeptide. Translation occurs at ribosomes. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes. Since bacteria lack nuclei, ribosomes attach to the leading end of a mRNA molecule while transcription is still in progress . Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.2a PowerPoint Presentation: In a eukaryotic cell, almost all transcription occurs in the nucleus and translation occurs mainly at ribosomes in the cytoplasm. Before the primary transcript leaves the nucleus it is modified in during RNA processing To summarize: Genes program protein synthesis via mRNA. The molecular chain of command in a cell is : DNA --> RNA --> protein. This is also known as the Central Dogma of molecular biology. Nucleotide Triplets Specify Amino Acids: The genetic instructions for a polypeptide chain are written in DNA as a series of three-nucleotide words. Triplets of nucleotide bases are the smallest units of uniform length that can code for all 20 amino acids. Triplet code: Codons (3 consecutive bases) specify an amino acid, creating 4 3 (64) possible code words. Nucleotide Triplets Specify Amino Acids PowerPoint Presentation: During transcription, one DNA strand, the template strand , provides a template for the sequence of nucleotides in RNA transcript. The complementary RNA molecule is made according to base-pairing rules, except that uracil replaces thymine. During translation, blocks of three nucleotides, codons , are decoded into a sequence of amino acids . Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.3 PowerPoint Presentation: During translation, the codons are read in the 5’->3’ direction along the mRNA. Each codon specifies one of the 20 amino acids to be incorporated at the next position along the polypeptide. Because codons are base triplets, the number of nucleotides making up a genetic message must be three times the number of amino acids making up the protein product. It would take at least 300 nucleotides to code for a polypeptide that is 100 amino acids long. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: In 1961, Marshall Nirenberg and J. Heinrich Matthei determined the first match--that UUU coded for the amino acid phenylalanine. By the mid-1960s the entire code was deciphered. 61 of 64 triplets code for amino acids. AUG codes for methionine and starts translation. Three codons do not make amino acids but terminate translation. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: The genetic code is degenerate,with most amino acids having more than one codon. protects against the potentially harmful effects of mutations. For example, UUA, UUG, CUU, CUC, CUA and CUG all code for leucine. The code has start and stop signals. One start signal: AUG . There are three stop signals: UGA, UAG, and UAA. The genetic code is redundant but not ambiguous . Several different codons indicate a specific amino acid. Any one codon indicates only one amino acid. Both GAA and GAG specify glutamate, but no other amino acid. Codons synonymous for the same amino acid often differ only in the third codon position . The Genetic Code Must Have Evolved Very Early in the History of Life: The genetic code is nearly universal, shared by organisms from the simplest bacteria to the most complex plants and animals. A reminder of the kinship that bonds all life on Earth. Genes can be transcribed and translated after they are transplanted from one species to another. This tobacco plant is expressing a transpired firefly gene. The Genetic Code Must Have Evolved Very Early in the History of Life Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.5 PowerPoint Presentation: This and other similar applications are exciting developments in biotechnology, permitting bacteria to be programmed to synthesize certain human proteins after insertion of human genes. Exceptions to the universality of the genetic code exist in translation systems where a few codons differ from standard ones. These occur in certain single-celled eukaryotes like Paramecium . Other examples include translation in certain mitochondria and chloroplasts. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Transcription : A Closer Look: Messenger RNA is transcribed from the template strand of a gene. RNA polymerase separates the DNA strands and bonds the RNA nucleotides as they base-pair along the DNA template. Like DNA polymerases, RNA polymerases can add nucleotides only to the 3’ end of the growing polymer. Genes are read 3’->5’, creating a 5’->3’ RNA molecule. Transcription : A Closer Look PowerPoint Presentation: Specific sequences of nucleotides along the DNA mark where gene transcription begins and ends. RNA polymerase attaches and initiates transcription at the promotor , “upstream” of the information contained in the gene, the transcription unit . The terminator signals the end of transcription. Bacteria have a single type of RNA polymerase. In contrast, eukaryotes have three RNA polymerases (I, II, and III) in their nuclei. RNA polymerase II is used for mRNA synthesis. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: Transcription can be separated into three stages: initiation, elongation, and termination . Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.6a PowerPoint Presentation: Proteins called transcription factors recognize the promotor region, especially a TATA box , and bind to the promotor. After they have bound to the promotor, RNA polymerase binds to transcription factors to create a transcription initiation complex . RNA polymerase then starts transcription. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.7 PowerPoint Presentation: As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at time. The enzyme adds nucleotides to the 3’ end of the growing strand. Behind the point of RNA synthesis, the double helix re-forms and the RNA molecule peels away. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.6b PowerPoint Presentation: A single gene can be transcribed simultaneously by several RNA polymerases at a time, this increases the amount of mRNA transcribed from it. This helps the cell make the encoded protein in large amounts. Transcription proceeds until after the RNA polymerase transcribes a terminator sequence in the DNA. In eukaryotes, the polymerase continues for hundreds of nucleotides past the terminator sequence, AAUAAA. Figure 17.6 The stages of transcription: initiation, elongation, and termination (Layer 4): Figure 17.6 The stages of transcription: initiation, elongation, and termination (Layer 4) Eukaryotic Cells Modify RNA after Transcription: Enzymes in the eukaryotic nucleus modify pre-mRNA before the they are sent out. At the 5’ end of the pre-mRNA molecule, a modified form of guanine is added, the 5’ cap . This helps protect mRNA from hydrolytic enzymes. It also functions as an “attach here” signal for ribosomes. At the 3’ end, an enzyme adds 50 to 250 adenine nucleotides, the poly(A) tail . the poly(A) tail facilitates the export from the nucleus. The mRNA molecule also includes nontranslated leader and trailer segments. Eukaryotic Cells Modify RNA after Transcription Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.9 RNA splicing removes introns (noncoding segments) and joins exons (coding regions) to create an mRNA molecule with a continuous coding sequence. This splicing is accomplished by a spliceosome consisting of proteins and several small nuclear ribonucleoproteins ( snRNPs ) each about 150 nucleotides long. The snRNA acts as a ribozyme, an RNA molecule enzyme. PowerPoint Presentation: Split genes may also facilitate the evolution of new proteins. In many cases, different exons code for different domains, discrete structural and functional regions, of a protein. The presence of introns increases the probability of potentially beneficial crossing over between genes. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.11 Translations : A Closer Look: In the process of translation, a cell reads a series of codons along a mRNA molecule. Transfer RNA ( tRNA ) transfers amino acids from the cytoplasm’s pool to a ribosome. The ribosome adds each amino acid carried by tRNA to the growing end of the polypeptide chain. Translations : A Closer Look Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.12 PowerPoint Presentation: Each tRNA repeatedly carries a specific amino acid at one end and has a specific nucleotide triplet, an anticodon , at the other. The anticodon pairs with a complementary codon on mRNA. mRNA codon is UUU, then tRNA anticodon AAA carrying phenyalanine will bind to it. tRNAs deposit amino acids in the prescribed order and the ribosome joins them into a polypeptide chain. The anticodons of some tRNAs recognize more than one codon because of wobble rules: Anticodon U can bind with A or G in the 3 rd position. Some tRNA anticodons include a modified form of adenine, inosine, which can hydrogen bond with U, C, or A on the codon. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint Presentation: A tRNA molecule consists of a strand of about 80 nucleotides that folds back on itself to form a three-dimensional structure. It includes a loop containing the anticodon and an attachment site at the 3’ end for an amino acid. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.13 PowerPoint Presentation: Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules. The P site (for peptide) holds the tRNA carrying the growing polypeptide chain. The A site (for amino acid) carries the tRNA with the next amino acid. Discharged tRNAs leave the ribosome at the E site . Fig. 17.15b &c PowerPoint Presentation: Ribosomes facilitate the specific coupling of the tRNA anticodons with mRNA codons. Each ribosome has a large and a small subunit. These are composed of proteins and ribosomal RNA (rRNA), the most abundant RNA in the cell . Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 17.15a PowerPoint Presentation: Translation can be divided into three stages: initiation elongation termination Initiation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits. Elongation consists of a series of three step cycles as each amino acid is added to the proceeding one. Termination occurs when one of the three stop codons reaches the A site. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Figure 17.17 The initiation of translation: Figure 17.17 The initiation of translation Figure 17.18 The elongation cycle of translation: Figure 17.18 The elongation cycle of translation Figure 17.19 The termination of translation: Figure 17.19 The termination of translation Figure 17.25 A summary of transcription and translation in a eukaryotic cell: Figure 17.25 A summary of transcription and translation in a eukaryotic cell

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