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Biology A Guide to the Natural World Chapter 14 • Lecture Outline How Proteins are Made: Genetic Transcription, Translation, and Regulation Fifth Edition David Krogh © 2011 Pearson Education, Inc. 14.1 The Structure of Proteins © 2011 Pearson Education, Inc. The Structure of Proteins • Proteins are composed of building blocks called amino acids. • A string of amino acids is called a polypeptide chain. © 2011 Pearson Education, Inc. The Structure of Proteins • Once a polypeptide chain has folded into its working three-dimensional shape, it is a protein. © 2011 Pearson Education, Inc. glycine (gly) isoleucine (ile) (a) Amino acids The building blocks of proteins are amino acids such as glycine and isoleucine, which differ only in their side-chain composition (light colored squares). (b) Polypeptide chain These amino acids are strung together to form polypeptide chains. Pictured is one of the two polypeptide chains that make up the unusually small protein insulin. (c) Protein Polypeptide chains function as proteins only when folded into their proper three-dimensional shape, as shown here for insulin. Note the position of the glycine and isoleucine amino acids in one of the insulin polypeptide chains (colored light green). © 2011 Pearson Education, Inc. Figure 14.1 The Structure of Proteins • Although there are hundreds of thousands of different proteins, all of them are put together from a starting set of 20 amino acids. © 2011 Pearson Education, Inc. The Structure of Proteins • It is the order in which the amino acids are linked in a polypeptide chain that determines which protein will be produced. © 2011 Pearson Education, Inc. The Structure of Proteins • Proteins often are composed of two or more linked polypeptide chains. © 2011 Pearson Education, Inc. The Structure of Proteins Animation 14.1: Structure of Proteins © 2011 Pearson Education, Inc. 14.2 Protein Synthesis in Overview © 2011 Pearson Education, Inc. Stages of Protein Synthesis • There are two principal stages in protein synthesis: • Transcription • Translation © 2011 Pearson Education, Inc. Stages of Protein Synthesis • The first stage is transcription, in which the information encoded in DNA is copied onto a length of messenger RNA (mRNA). • In eukaryotes, mRNA moves from the cell nucleus to a structure in the cytoplasm called a ribosome. © 2011 Pearson Education, Inc. Stages of Protein Synthesis • The second stage is translation, in which amino acids brought to a ribosome by transfer RNA (tRNA) molecules are linked together within the ribosome in the order specified by the mRNA sequence. © 2011 Pearson Education, Inc. Transcription 1. In transcription, a section of DNA unwinds and nucleotides on it form base pairs with nucleotides of messenger RNA, creating an mRNA chain. DNA Transcription mRNA 2. This segment of mRNA then leaves the cell nucleus, headed for a ribosome in nucleus the cell’s cytoplasm, where translation takes place. Translation 3. Joining the mRNA chain at the ribosome are amino acids, brought there by transfer RNA molecules. The length of messenger RNA is then “read” within the ribosome. The result? A chain of amino acids is linked together in the order specified by the mRNA sequence. cytosol amino acids tRNA mRNA ribosome protein Translation 4. When the chain is finished and folded up, a protein has come into existence. © 2011 Pearson Education, Inc. Figure 14.2 14.3 A Closer Look at Transcription © 2011 Pearson Education, Inc. Transcription • The information in DNA is transferred to messenger RNA through complementary base pairing. • Each “C” nucleotide in a segment of DNA being transcribed results in a “G” nucleotide being added to a segment of RNA, and so forth. © 2011 Pearson Education, Inc. (a) Comparison of RNA and DNA nucleotides DNA nucleotide RNA nucleotide base thymine base uracil phosphate group sugar ribose phosphate group sugar deoxyribose (b) Comparison of RNA and DNA three-dimensional structure RNA strand sugar-phosphate handrails DNA strand bases: cytosine (C) guanine (G) adenine (A) uracil (U) © 2011 Pearson Education, Inc. sugar-phosphate handrails bases: cytosine (C) guanine (G) adenine (A) thymine (T) Figure 14.3 Transcription • The enzyme RNA polymerase unwinds the DNA sequence to be transcribed and then strings together the chain of RNA nucleotides that is complementary to it. © 2011 Pearson Education, Inc. Figure 14.4 1. RNA polymerase unwinds a region of the DNA double helix. RNA nucleotides RNA 2. RNA polymerase begins assembling RNA nucleotides on the DNA template. DNA RNA 3. The completed portion of the RNA transcript separates from the DNA. Meanwhile, RNA polymerase unwinds more of the untranscribed region of the DNA. RNA 4. The RNA transcript is released from the DNA, and the DNA is rewound into its original form. Transcription is completed. © 2011 Pearson Education, Inc. Transcription • In all eukaryotes (including humans), the initial RNA chain transcribed from a DNA sequence is not the finished messenger RNA chain. • Instead it is a sequence, called a primary transcript, that must undergo some editing before becoming an mRNA chain. © 2011 Pearson Education, Inc. Transcription • Each three coding bases of DNA pair with three RNA bases, but each group of three mRNA bases then codes for a single amino acid. © 2011 Pearson Education, Inc. Transcription • Each triplet of mRNA bases that codes for an amino acid is called a codon. © 2011 Pearson Education, Inc. Transcription • The inventory of linkages between base triplets and the amino acids they code for is called the genetic code. © 2011 Pearson Education, Inc. 14.4 A Closer Look at Translation © 2011 Pearson Education, Inc. Transfer RNA • Transfer RNA serves as a bridging molecule in protein synthesis thanks to its ability to bind with both amino acids on the one hand and nucleic acids on the other (in the form of mRNA). © 2011 Pearson Education, Inc. Transfer RNA • A given tRNA molecule binds with a specific amino acid in the cell’s cytoplasm, and then transfers that amino acid to a ribosome in which an mRNA transcript is being “read.” © 2011 Pearson Education, Inc. Transfer RNA 1. tRNA and amino acids float freely in cytoplasm. 2. tRNA links to an amino acid and transfers it to the ribosome. 4. A polypeptide chain is produced. 3. tRNA links to the appropriate mRNA codon at the ribosome. mRNA ribosome © 2011 Pearson Education, Inc. Figure 14.6 Translation • There, another portion of the tRNA molecule, called an anticodon, binds with the appropriate codon in the mRNA chain. © 2011 Pearson Education, Inc. arg amino acid attachment site tRNA molecule mRNA attachment site G C U anticodon C G A codon © 2011 Pearson Education, Inc. mRNA Figure 14.7 Ribosomes • Ribosomes, the complex “workbenches” of protein synthesis, are composed of proteins and ribosomal RNA (rRNA). © 2011 Pearson Education, Inc. Ribosomes • Each ribosome exists as two subunits in the cytoplasm that come together only with the initiation of protein translation. © 2011 Pearson Education, Inc. Ribosomes • Each ribosome bears A, P, and E binding sites to which tRNA molecules bind. Thus, it facilitates the synthesis of an amino acid chain. © 2011 Pearson Education, Inc. (a) Large and small ribosomal units protein large subunit mRNA Ribosomes are composed of two subunits that come together during translation E PA small subunit (b) Binding sites in the ribosome protein large subunit mRNA E P A site site site small subunit A simplified cross section of the ribosome illustrates the E, P, and A sites where tRNA molecules bind during translation © 2011 Pearson Education, Inc. Figure 14.8 Protein Synthesis Suggested Media Enhancement: Meiosis To access this animation go to folder C_Animations_and_Video_Files and open the BioFlix folder. © 2011 Pearson Education, Inc. Translation • Translation works by means of a succession of tRNA molecules arriving at a ribosome, bound to their appropriate amino acids, and then binding to their appropriate codon in the mRNA transcript. © 2011 Pearson Education, Inc. Translation • As this process takes place, the succession of amino acids is linked together into a polypeptide chain. © 2011 Pearson Education, Inc. Translation The steps of translation met 1. A messenger RNA transcript binds to the small subunit of a ribosome as the first transfer RNA is arriving. The mRNA codon AUG is the “start” sequence for most polypeptide chains. The tRNA, with its methionine (met) amino acid attached, then binds this AUG codon. AUG mRNA start codon © 2011 Pearson Education, Inc. Figure 14.9 Translation continues 2. The large ribosomal subunit joins the ribosome, as a second tRNA arrives, bearing a leucine (leu) amino acid. The second tRNA binds to the mRNA chain, within the ribosome’s A site. met leu met CUG E P A site site site 3. A bond is formed between the newly arrived leu amino acid and the met amino acid, thus forming a polypeptide chain. The ribosome now effectively shifts one codon to the right, relocating the original P site tRNA to the E site, the A site tRNA to the P site, and moving a new mRNA codon into the A site. 4. The E site tRNA leaves the ribosome, even as a new tRNA binds with the A site mRNA codon, and the process of elongation continues. E P A site site site met leu met leu E P A site site site E P A site site site polypeptide chain met leu E P A site site site © 2011 Pearson Education, Inc. Figure 14.10 14.5 Genetic Regulation © 2011 Pearson Education, Inc. Genetic Regulation • Protein production is carefully controlled or “regulated” in living things. • Most genes do not simply stay “on,” but instead are transcribed in accordance with the needs of an organism. © 2011 Pearson Education, Inc. Genetic Regulation • Less than 2 percent of the DNA in the human genome codes for proteins. © 2011 Pearson Education, Inc. Genetic Regulation • Some noncoding segments of DNA may be “junk” that never had a function. • Other segments seem to have served an enabling function; they have enabled organisms to become more complex. • Still other segments are regulatory, meaning they help regulate the production of proteins. © 2011 Pearson Education, Inc. Promoters and Enhancers • All gene transcription requires that RNA polymerase be properly aligned at a noncoding sequence of DNA bases, called a promoter, that lies just “upstream” from a gene sequence. © 2011 Pearson Education, Inc. Promoters and Enhancers • There is usually a second noncoding segment of DNA, called an enhancer, that lies at some distance from the promoter sequence. © 2011 Pearson Education, Inc. Promoters and Enhancers • Separate groups of proteins, called transcription factors, bind to both the promoter and enhancer sequences. Thus, they facilitate the alignment of RNA polymerase at the promoter. © 2011 Pearson Education, Inc. Genetic Regulation (a) Chicken enhancer proteins 7 thoracic vertebrae low transcription rate Hoxc8 gene DNA RNA polymerase transcription complex (b) Mouse enhancer proteins Better alignment of transcription complex by enhancer proteins… 13 thoracic vertebrae high transcription rate Hoxc8 gene DNA RNA polymerase …results in a higher transcription rate © 2011 Pearson Education, Inc. Figure 14.12 Genetic Regulation • Transcription factors are themselves produced through normal transcription and translation. • They are coded for by DNA, but then feed back on it, helping control its transcription. • Thus, the entire system is self-regulating. © 2011 Pearson Education, Inc. Alternative Splicing • In all eukaryotes, the initial RNA chain produced during transcription—the primary transcript—undergoes editing by means of some sequences being cut out of it. • Then, the remaining sequences are spliced back together. • The result is a completed messenger RNA chain. © 2011 Pearson Education, Inc. Alternative Splicing • The sequences that are removed from the primary transcript are called introns, while the sequences that are retained are called exons. • Introns do not code for protein, but most exons do. © 2011 Pearson Education, Inc. Alternative Splicing intron exon 2 enzyme intron primary transcript enzymes cut out the introns messenger RNA © 2011 Pearson Education, Inc. Figure 14.15 Alternative Splicing • Some relatively simple organisms have nearly as many genes as human beings do (20,000–25,000). • Human beings are able to be much more complex than these organisms, thanks in part to a form of genetic regulation called alternative splicing, in which a primary transcript can be edited in different ways. © 2011 Pearson Education, Inc. Alternative Splicing © 2011 Pearson Education, Inc. Figure 14.14 Alternative Splicing • Through alternative splicing, a single primary transcript can result in different messenger RNA chains. • These in turn can result in different proteins. © 2011 Pearson Education, Inc. Alternative Splicing protein A primary transcript edited mRNA transcripts protein B © 2011 Pearson Education, Inc. Figure 14.16 RNA in Genetic Regulation • DNA codes for several different forms of RNA. • Of these, only messenger RNA then goes on to code for proteins. © 2011 Pearson Education, Inc. RNA in Genetic Regulation • DNA also codes for several varieties of regulatory RNA that go under the collective name of micro-RNAs. © 2011 Pearson Education, Inc. RNA in Genetic Regulation • Of the 1,500 micro-RNA sequences discovered to date, all have the effect of reducing the production of particular proteins, usually by targeting their messenger RNAs for destruction. © 2011 Pearson Education, Inc. The Importance of Regulation • A case can be made that it is not genes, but instead the regulation of genes, that is the most important factor in bringing about the differences among organisms. © 2011 Pearson Education, Inc. The Importance of Regulation • In a similar vein, there seems to be little relation between the number of genes an organism has and the complexity of that organism. © 2011 Pearson Education, Inc. The Importance of DNA That Doesn’t Code for Protein • There does seem to be correlation between the complexity of an organism and the proportion of its DNA that does not code for protein. © 2011 Pearson Education, Inc. 100 . . . but more than 98 percent of the human genome Non-coding DNA makes up only about 10 percent of the prokaryote genome . . . 75 50 25 0 bacterium baker’s yeast mustard plant roundworm fruit fly © 2011 Pearson Education, Inc. mouse Percent of DNA not coding for protein What Is Central in Genetics? human Figure 14.17 What Is Central in Genetics? • Genetic regulation and noncoding DNA may be more important to genetics than has traditionally been assumed. © 2011 Pearson Education, Inc. What Is Central in Genetics? • We have no definitive answers about these questions, however, because research on genetic regulation and noncoding DNA lies at the cutting edge of contemporary genetic research. © 2011 Pearson Education, Inc. 14.6 Genetics and Life © 2011 Pearson Education, Inc. Genetics and Life • Life is made possible by the fantastic ability of genetic systems to store, use, and pass on information. © 2011 Pearson Education, Inc.