Chapter 11: From DNA to Proteins: Translation

problem 9: Compare and contrast the process of protein synthesis in in bacterial and eukaryotic cells, giving similarities and differences in the process of translation in these two types of cells.

1. Similarities: -Code is universal to both, so genes can be translated to each other -Both use aminoacyl-tRNA synthetases to attach amino acids -Elongation/Termination similar, in both mRNA's are translated multiple times and are simultaneously attached to several ribosomes 2. Differences: -In bacterial cells transcription and translation take place simultaneously, nuclear envelope separates theses processes in eukaryotic cells. -mRNA is short lived in bacterial cells, but mRNA in eukaryotic cells has longevity. -Ribosomal subunits differ in size and composition -In initiation in bacterial cells the small ribosomal subunit attaches directly to the region surrounding the stop codon (Shine-Delgarno consensus), in eukaryotes the small subunit first binds to a protein then migrates down the mRNA scanning for a start codon

problem 10: What are some types of posttranslated modification of proteins?

1.) proteins are synthesized as larger precursor proteins and must be cleaved and trimmed by enzymes 2.) Carbohydrates are attached to some for activation

Problem 13: How many codons would be possible in a triplet code if only three bases (A,C, and U) were used?

3^3 or 27 possible codons

problem 6: How are the tRNAs linked to their corresponding amino acids?

A tRNA molecule has an "L" structure held together by hydrogen bonds between bases in different parts of the tRNA sequence. One end of the tRNA binds to a specific amino acid (amino acid attachment site) and the other end has an anticodon that will bind to an mRNA codon.

problem 11: Explain how some antibiotics work by affecting the process of protein synthesis.

Antibiotics work by preventing new amino acids from being attached to the growing chain, misreading the mRNA to make the wrong protein, or preventing it from bringing in new amino acids.

Problem 3: What is the significance of the fact that many synonymous codons differ only in the third nucleotide position?

Synonymous codons code for the same amino acid, or, in other words, they have the same meaning. A nucleotide at the third position of a codon pairs with a nucleotide in the first position of the anticodon. Unlike the other nucleotide positions involved in the codon-anticodon pairing, this pairing is often weak, or "wobbles," and nonstandard pairings can occur. Because the "wobble," or nonstandard base pairing with the anticodons, affects the third nucleotide position, the redundancy of codons ensures that the correct amino acid is inserted in the protein when nonstandard pairing occurs

problem 16: A nontemplate strand of bacterial DNA has the following base sequence. What amino acid sequence will be encoded by this sequence? 5'-ATGATACTAAGGCCC-3'

The RNA strand that is made from the template strand is 5'-AUGAUACUAAGGCC-3' so the amino acid sequence is met-ile-leu-arg-pro

problem 5: How is the reading frame of a nucleotide sequence set?

The initiation codon on the mRNA sets the reading frame.

Problem 4: Define the following terms as they apply to the genetic code: reading frame overlapping code nonoverlapping code initiation codon termination codon sense codon nonsense codon universal code nonuniversal code

The reading frame refers to how the nucleotides in a nucleic acid molecule are grouped into codons, with each codon containing three nucleotides. Any sequence of nucleotides has three potential reading frames that have completely different sets of codons. In an overlapping code, a single nucleotide is included in more than one codon. The result for a sequence of nucleotides is that more than one type of polypeptide can be encoded within that sequence. In a nonoverlapping code, a single nucleotide is part of only one codon, which results in the production of a single type of polypeptide from one polynucleotide sequence. An initiation codon establishes the appropriate reading frame and specifies the first amino acid of the protein chain. Typically, the initiation codon is AUG; however, GUG and UUG also can serve as initiation codons. The termination codon signals the termination, or end, of translation and the end of the protein molecule. The three types of termination codons—UAA, UAG, and UGA—are also referred to as stop codons or nonsense codons. These codons do not encode amino acids. A sense codon is a group of three nucleotides that encode an amino acid. Sixty-one sense codons encode the 20 amino acids commonly found in proteins. A nonsense codon, or termination codon, signals the end of translation. Nonsense codons do not encode amino acids. In a universal code, each codon specifies the same amino acid in all organisms. The genetic code is nearly universal but not completely. Most of the exceptions are in mitochondrial genes. Although most codons are universal (or nearly universal) in that they specify the same amino acids in almost all organisms, there are exceptions in which a codon has different meanings in different organisms.

problem 8: What events bring about the termination of translation?

Translation termination begins when a stop codon is encountered in the A-site of the ribosome. Two "class I" release factors, RF1 (which recognize UAA and UAG) and RF2 (which recognizes UAA) together with the "class II" release factor RF3, release the completed polypeptide.

Problem 20: Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from this, determine which position of the codon (first, second, third nucleotide) in the mRNA must be altered for the change to result. a. Leu->Gln b. Phe->Ser c. Phe->Ile d. Pro->Ala e. Asn->Lys f. Ile->Asn

a could result from a change in the second base b could result from a change in the second base c could result from a change in the first base d could result from a change in the first base e could result from a change in the third base f could result from a change in the second base

Assume that the number of different types of bases in RNA is four. What would be the minimum codon size(number of nucleotides) required to specify all amino acids if the number of different types of amino acids in proteins (a) 2, (b) 8, (c) 17, (d) 45, (e) 75? Problem 12

a.) 1 b.) 2 c.) 3 d.) 3 e.) 4

Problem 19: The following anticodons are found in a series of tRNAs. Refer to the genetic code in figure 11.5 and give the amino acid carried by each of these tRNAs. a.) 5'-GUA-3' b.) 5'-AUU-3' c.) 5'-GGU-3' d.) 5'-CCU-3'

a.) Val b.) Ile c.) Gly d.) Pro

Problem 15: Referring to the genetic code presented in figure 11.5, give the amino acids specified by the following bacterial mRNA sequences, and indicate the amino acid and carboxyl ends of the polypeptide produced. Hint: Remember that AUG is the initiation codon a. 5'-AUGUUUAAAUUUAAAUUUUGA-3' b. 5'-AGGGAAAUCAGAUGUAUAUAUAUAUAUGA-3' c. 5'-UUUGGAUUGAGUGAAACGAUGGAUGAAAGAUUUCUCGCUUGA-3' d. 5'-GUACUAAGGAGGUUGUAUGGGUUAGGGGACAUCAUUUUGA-3'

a.) amino-met-phe-lys-phe-lys-phe-carboxyl b.) amino-met-tyr-ile-tyr-ile-carboxyl c.) amino-met-asp-glu-arg-phe-leu-ala-carboxyl d.) amino-met-gly-carboxyl

Problem 14: Using the genetic code presented in Figure 11.5, indicate which amino acid is encoded by each of the following mRNA codons a.) 5'-CCC-3' b.) 5'-UUG-3' c.)5'-CUG-3' d.)5'-AGA-3' e.)5'-UAA-3'

a.Pro b.Leu c.Leu d.Arg e.Stop

Problem 21: Arrange the following components of translation in the approximate order in which they would appear or be used in prokaryotic protein synthesis 70S initiation complex 30S initiation complex Release factor 1 Elongation factor Tu Initiation factor 3 Elongation factor G fMet-tRNA^fmet

the order is as follows: initiation factor 3 fMet-tRNA^fmet 30S initiation complex 70S initiation complex Elongation factor Tu Elongation factor G Release factor 1