The Structure of Proteins The Structure of Proteins. How Proteins are Made: Genetic Transcription, Translation, and Regulation

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1 How Proteins are Made: Genetic, Translation, and Regulation PLAY The Structure of Proteins 14.1 The Structure of Proteins Proteins - polymer amino acids - monomers Linked together with peptide bonds A string of amino acids is called a polypeptide chain. Copyright 2009 Pearson Education, Inc., publishing as Benjamin Cummings. 1

2 The Structure of Proteins The Structure of Proteins Primary structure Amino acid sequence Secondary structure Initial folding Alpha helices Beta sheets Tertiary structure 3 dimensional shape Combinations of alpha helices and beta sheets Quaternary structure Combinations of tertiary subunits Polypeptide chain Folded into its working three-dimensional shape Now functioning protein The Structure of Proteins The Structure of Proteins 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. 20 amino acids Hundreds of thousands of different proteins, all of them are put together from a starting set of 20 amino acids Sequence of amino acids dictates what protein is made (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). Figure

3 The Structure of Proteins Protein Structure Review PLAY 14.2 Protein Synthesis in Overview Copyright 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Stages of Protein Synthesis Stages of Protein Synthesis There are two principal stages in protein synthesis: Copying the genetic code Translation Changing the language from nucleic acid to protein First step Information encoded in DNA is copied onto a length of messenger RNA (mrna). mrna moves from nucleus to ribosome in the cytoplasm In eukaryotes 3

4 Stages of Protein Synthesis Translation Second step amino acids brought to a ribosome by transfer RNA (trna) Amino acid molecules are linked together within the ribosome in the order specified by the mrna sequence. Stages of Protein Synthesis 1. In transcription, a section of DNA unwinds and nucleotides on it form base pairs with nucleotides of messenger RNA, creating an mrna chain. 2. 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. 4. This segment of mrna then leaves the cell nucleus, headed for a ribosome in the cell s cytoplasm, where translation takes place. When the chain is finished and folded up, a protein has come into existence. nucleus cytosol mrna protein amino acids DNA ribosome Translation trna mrna Figure A Closer Look at DNA template Information is transferred to mrna through complementary base pairing. For instance: C nucleotide in DNA template results in a G nucleotide being added to mrna This continues down the template, one nucleotide at a time Uracil used in RNA instead of Thymine Therefore A-U, C-G Copyright 2009 Pearson Education, Inc., publishing as Benjamin Cummings. 4

5 RNA and DNA Compared (a) Comparison of RNA and DNA nucleotides RNA nucleotide phosphate group sugar ribose base uracil DNA nucleotide phosphate group (b) Comparison of RNA and DNA three-dimensional structure base thymine sugar deoxyribose Helicase unwinds the DNA sequence to be transcribed RNA polymerase strings together the chain of RNA nucleotides that is complementary to the DNA template RNA strand sugar-phosphate handrails DNA strand sugar-phosphate handrails bases: cytosine (C) guanine (G) adenine (A) uracil (U) bases: cytosine (C) guanine (G) adenine (A) thymine (T) Figure 14.3 RNA DNA RNA 1. RNA polymerase unwinds a region of the DNA double helix. RNA nucleotides 2. RNA polymerase begins assembling RNA nucleotides on the DNA template. 3. The completed portion of the RNA transcript separates from the DNA. Meanwhile, RNA polymerase unwinds more of the untranscribed region of the DNA. In all eukaryotes (including humans) Initial RNA chain transcribed from a DNA template is not the finished messenger RNA chain Called a primary transcript Must undergo some editing before becoming an mrna chain RNA 4. The RNA transcript is released from the DNA, and the DNA is rewound into its original form. is completed. Figure

6 Codon Set of three nucleotides in a row Each set of three (codon) codes for a specific amino acid Genetic code The linkages between base triplets (codons) and the amino acids they code for The secret decoder ring 14.4 A Closer Look at Translation PLAY Copyright 2009 Pearson Education, Inc., publishing as Benjamin Cummings. 6

7 Transfer RNA Transfer RNA Transfer RNA (trna) serves as a bridging molecule in protein synthesis ability to bind with both amino acids and nucleic acids in the form of mrna trna molecule binds with a specific amino acid in the cell s cytoplasm transfers that amino acid to a ribosome in which an mrna transcript is being read. Transfer RNA Translation 4. A polypeptide chain is produced trna and amino acids float freely in cytoplasm. trna links to an amino acid and transfers it to the ribosome. Anticodon Another portion of the trna molecule binds with the appropriate codon in the mrna chain Complimentary to mrna Therefore identical to the original DNA template 3. trna links to the appropriate mrna codon at the ribosome. mrna ribosome Figure

8 The Structure of Transfer RNA (a) Transfer RNA binding (b) The 3-D shape of trna Ribosomes trna molecule arg amino acid attachment site anticodon mrna attachment site hydrogen bonds anticodon Ribosomes the complex workbenches of protein synthesis composed of proteins and ribosomal RNA (rrna) Each ribosome exists as two separate subunits in the cytoplasm come together only with the initiation of protein translation. codon mrna Figure 14.7 Ribosomes The Structure of Ribosomes (a) Large and small ribosomal units protein A, P, and E binding sites In each ribosome To which trna molecules bind large subunit small subunit E P A mrna Ribosomes are composed of two subunits that come together during translation. (b) Binding sites in the ribosome protein large subunit mrna small subunit E P A site site site A simplified cross section of the ribosome illustrates the E, P, and A sites where trna molecules bind during translation. Figure

9 Translation Translation The steps of translation Succession of trna molecules arriving at a ribosome bound to their specific amino acids then binding to their appropriate codon in the mrna transcript In this fashion, succession of amino acids linked together into polypeptide chains 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, start codon then binds this AUG codon. 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. 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 E P A P site, and moving a new mrna codon site site site into the A site. mrna E P A site site site E P A site site site polypeptide chain 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 Figure 14.9 Translation 14.5 Genetic Regulation PLAY Copyright 2009 Pearson Education, Inc., publishing as Benjamin Cummings. 9

10 Genetic Regulation Genetic Regulation Protein production 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 Less than 2 % of DNA in the human genome actually codes for protein Genetic Regulation Junk DNA noncoding segments of DNA may be junk that never had a function That we know of Enabling DNA Other segments seem to have served an enabling function; they have enabled organisms to become more complex Regulatory DNA Still other segments are regulatory, meaning they help regulate the production of proteins Enhancers Promoters Promoters and Enhancers Promoter Noncoding sequence of DNA bases that lies just upstream from a gene sequence Aligns RNA polymerase on the template All gene transcription requires that RNA polymerase be properly aligned 10

11 Promoters and Enhancers Promoters and Enhancers Enhancer A second noncoding segment of DNA lies at some distance from the promoter sequence. factors Separate groups of proteins bind to both the promoter and enhancer sequences. Thus, they facilitate the alignment of RNA polymerase at the promoter Genetic Regulation Genetic Regulation (a) Chicken enhancer proteins DNA (b) Mouse enhancer proteins low transcription rate Hoxc8 gene RNA polymerase transcription complex Better alignment of transcription complex by enhancer proteins 7 thoracic vertebrae 13 thoracic vertebrae factors Proteins that 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 high transcription rate Hoxc8 gene DNA RNA polymerase results in a higher transcription rate Figure

12 Alternative Splicing Alternative Splicing Primary transcript Initial RNA chain produced during transcription undergoes editing by means of some sequences being cut out of it In all eukaryotes Remaining sequences are spliced back together Using the enzyme ligase The result is a completed mrna Introns The sequences that are removed from the primary transcript Exons The sequences that are retained Introns do not code for protein, but most exons do Alternative Splicing Alternative Splicing exon 1 intron exon 2 exon 3 intron enzyme enzymes cut out the introns messenger RNA primary transcript Some relatively simple organisms have nearly as many genes as human beings (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. Figure

13 Alternative Splicing Alternative Splicing Through alternative splicing, a single primary transcript can result in different messenger RNA chains. These in turn can result in different proteins. Figure Alternative Splicing RNA in Genetic Regulation DNA codes for several different forms of RNA. Only mrna then goes on to code for proteins. exon 1 intron exon 2 intron exon 3 primary transcript exon 4 intron intron exon edited mrna transcripts protein A protein B Figure

14 RNA in Genetic Regulation The Importance of Regulation Micro-RNAs Several varieties of regulatory RNA coded for by DNA 1,500 micro-rna sequences discovered to date all have the effect of reducing the production of particular proteins usually by targeting their mrnas for destruction Gene regulation (or expression) May be more responsible for differences among organisms than the genes themselves There is little relation between the number of genes an organism has and the complexity of that organism Importance of non-coding DNA What is Central in Genetics? Correlation between complexity and amount of non-coding DNA The more non-coding DNA present, the more complex the organism Non-coding DNA makes up only about 10 percent of the prokaryote genome...but more than 98 percent of the human genome. Percent of DNA not coding for protein bacterium baker s yeast mustard plant roundworm fruit fly mouse human Figure

15 What is Central in Genetics? While genetic regulation and noncoding DNA may be more important to genetics than has traditionally been assumed 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. 15