Chapter 11 From DNA to Proteins Translation 11 1 The Genetic Code Determines How the Nucleotide Sequence Specifies the Amino Acid Sequence of a Protein A One Gene one enzyme hypothesis suggested that genes function by encoding enzymes and that each gene encodes a separate enzyme 1 One gene one polypeptide hypothesis some proteins are composed of more than one polypeptide chain and that different polypeptide chains are encoded by separate genes B The Structure and Function of Proteins 1 Many proteins are enzymes the biological catalysts that drive the chemical reactions of the cell i Others are structural providing support for membranes filaments bone and hair ii Some help transport substances others have a regulatory communication or defense function 2 All are composed of amino acids consists of a central carbon atom bonded to an amino group a hydrogen atom a carboxyl group and a radical group that differs i Peptide bonds join the amino acids in proteins to form polypeptide chains ii Polypeptide have polarity with one end having a free amino NH3 group and the other a carboxyl COO group 3 Several Levels of Organization i Primary is its sequence of amino acids a Through its interactions with neighboring amino acids it folds and twists making the secondary structures ii Secondary Structures iii Tertiary Structures a pleated sheet and the helix which fold to form tertiary structures a Overall the three dimensional structure of a protein is determined by the secondary and tertiary structure iv Quaternary structure a Two or more polypeptide chains C Breaking the Genetic Code 1 How many nucleotides are necessary to specify a single amino acid i Codons contain a minimum of three nucleotides occupied by one of four bases a A triplet code requiring three nucleotides per codon is the most efficient way to encode all 20 amino acids 2 Marshall Nirenberg and Johann Heinrich Matthaei created synthetic RNAs to determine the amino acid sequence i Determined that the UUU codon specifies the amino acid phenylamine CCC encodes proline and AAA encodes lysine D Characteristics of the Genetic Code 1 The degeneracy of the code i One amino acid is encoded by three consecutive nucleotides in mRNA and each nucleotide can have one of four possible bases permitting 64 possible codons a Three are stop codons specifying the end of translation b Sense codons the other 61 that encode amino acids c Degenerate codon the code contains more information than is needed to specify amino acids 61 sense only 20 different amino acids Degenerate means that amino acids can be specified for more than one codon d Synonymous codons that specify the same amino acid e Isoaccepting tRNAs different tRNAs that accept amino acids but have different anticodons 1 There are more codons than anticodons because different condons can sometimes pair with the same anitcodon through flexibility in base pairing at the third position of the codon 2 The 5 pairs with the 3 base then the middle codon and anticodon 3 Wobble the third bases weakly pair and causes flexibility in their pair pairing 2 The reading frame and initiation codons i The genetic code is generally nonoverlapping overlapping code is one in which a single nucleotide may be included in more than one codon a Overlapping genes are found in viruses ii Reading frame each differe nt way of reading the sequence and any sequence of nucleotides has three potential reading frames a Three reading frames have completely different sets of codons and will therefore specify proteins with entirely different amino acid sequences b The correct reading frame is set by the initiation codon the first codon of the mRNA sequence to specify an amino acid 1 After the initiation codon the other codons are read as successive groups of three nucleotides 2 No bases are skipped between codons 3 The initiation codon is usually AUG although GUG and UUG are used on rare occasions 4 The initiation codon specifies an amino acid i In bacterial cells AUG encodes a modified type of methionine N formylmethionine ii When AUG is at an internal position in a gene encodes iii unformylate methionine In both archael and eukaryotic cells AUG specifies unformylated methionine both at the initiation position and at internal positions 3 Termination codons i UAA UAG and UGA do not encode amino acids they signal the end of the protein in both bacterial and eukaryotic cells called stop termination or nonsense codons ii No tRNA molecules have anticodons that pair with termination codons 4 The universality of the code i Universal meaning that each codon specifies the same amino acid in all organisms a Exceptions in termination codons in which one sense codon substitutes for another 11 2 Amino Acids Are Assembled into a Protein Through the Mechanism of Translation A The mechanism by which amino acids are assembled into proteins 1 Translation takes place on ribosomes that attaches near the 5 end of an mRNA strand and moves toward the 3 end translating as it goes 2 Synthesis begins at the amino end of the protein and the protein is elongated by the addition of new amino acids to the carboxyl end 3 Protein synthesis can be divided into four stages B The Binding of Amino Acids to Transfers RNAs 1 First stage of translation is the binding of tRNA molecules to their appropriate amino acids called tRNA charging i Each tRNA is specific for only one amino acid ii Aminoacyl tRNA synthetases The key to specificity between an amino acid and its tRNA is a set of a enzymes a A cell has 20 different ones one for each of the 20 amino acids as well as all the tRNAs that accept that amino acids 2 tRNA Charging the attachment of a tRNA to its appropriate amino acid It requires energy which is supplied by ATP C The Initiation of Translation 1 All the components necessary for protein synthesis assemble the small and large subunits of the ribosome i mRNA ii iii a set of three proteins called the imitation factors iv initiator tRNA with N formylmethionine attached v guanosine triphosphate GTP 2 A functional ribosome exists as two subunits the small 30S subunit and the large 50S subunit i When not actively translating the two subunits are joined ii Initiation factor 3 binds to small subunit of the ribosome and prevents the large subunit from binding during initiation Initiation factor 2 allows the initiator tRNA f Met tRNAf Met attaches to the initiation codon i 30S initiation complex consists of the small subunit of the ribosome the mRNA the initiator
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