Comprehensive Questions Chapter 11

Define the following terms as they apply to the genetic code: Sense codon

A group of three nucleotides that encode an amino acid. sixty-one sense codons encode the 20 amino acids commonly found in proteins.

Define the following terms as they apply to the genetic code: 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.

Define the following terms as they apply to the genetic code: 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.

Define the following terms as they apply to the genetic code: Nonuniversal codons

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.

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

Bacterial and eukaryotic cells share several similarities as well as have several differences in protein synthesis. Initially, bacteria and eukaryotes share the universal genetic code. However, the initiation codon, AUG, in eukaryotic cells codes for methionine, whereas in bacteria the AUG codon codes for N-formyl methionine. In eukaryotes, transcription takes place within the nucleus, whereas most translation takes place in the cytoplasm (although some translation does take place within the nucleus). Therefore, transcription and translation in eukaryotes are kept temporally and spatially separate. However, in bacterial cells transcription and translation occur nearly simultaneously. Stability of mRNA in eukaryotic cells and bacterial cells is also different. Bacterial mRNA is typically short-lived, lasting only a few minutes. Eukaryotic mRNA may last hours or even days. Charging of the tRNAs with amino acids is essentially the same in both bacteria and eukaryotes. The ribosomes of bacteria and eukaryotes are different as well. Bacteria and eukaryotes have large and small ribosomal subunits, but they differ in size and composition. The bacterial large ribosomal consists of two ribosomal RNAs, while the eukaryotic large ribosomal subunit consists of three. During translation initiation, the bacterial small ribosomal subunit recognizes the Shine-Dalgarno consensus sequence in the 5' UTR of the mRNA and to regions of the 16S rRNA. In most eukaryotic mRNAs, the small subunit binds the 5' cap of the mRNA and scans downstream until it encounters the first AUG codon. Finally, elongation and termination in bacterial and eukaryotic cells are functionally similar, although different elongation and termination factors are used.

Define the following terms as they apply to the genetic code: 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.

Define the following terms as they apply to the genetic code: 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 can also serve as initiation codons.

Define the following terms as they apply to the genetic code: Reading frame

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.

Define the following terms as they apply to the genetic code: Nonsense codon

Or termination codon, signals the end of translation. These codons do not code for amino acids.

Define the following terms as they apply to the genetic code: 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 code for amino acids.

Arrange the following components of translation in the approximate order in which they would appear or be used in protein synthesis:

The components are in order according to when they are used or play a key role in translation. The potential exception is initiation factor 3. Initiation factor 3 could possibly be listed first because it is necessary to prevent the 30s ribosome from associating with the 50s ribosome. It binds to the 30s subunit prior to the formation of the 30s initiation complex. However, during translation events the release of initiation factor 3, allows the 70s initiation complex to form, a key step in translation. initiation factor 3 fMet-tRNAfMet 30S initiation complex 70S initiation complex elongation factor Tu elongation factor G release factor 1

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

To determine the amino acid sequence, we need to know the mRNA sequence and the codons present. The nontemplate strand of the DNA has the same sequence as the mRNA, except that thymine containing nucleotides are substituted for the uracil containing nucleotides. So the mRNA sequence would be as follows: 5'-AUGAUACUAAGGCCC-3'. Assuming that the AUG indicates a start codon, then the amino acid sequence would be starting from the amino end of the peptide and ending with the carboxyl end: fMet-Ile- Leu-Arg-Pro.

Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from the alteration of a single base, determine which position of the codon (first, second, or third nucleotide) in the mRNA must be altered for the change to result.

a. b. c. d. e. Leu Gln Of the six codons that encode for Leu, only two could be mutated by the alteration of a single base to produce the codons for Gln: CUA (Leu)—Change the second position to A to produce CAA (Gln). CUG (Leu)—Change the second position to A to produce CAG (Gln). Phe Ser Both Phe codons (UUU and UUC) could be mutated at the second position to produce Ser codons: UUU (Phe)—Change the second position to C to produce UCU (Ser). UUC (Phe)—Change the second position to C to produce UCC (Ser). Phe Ile Both Phe codons (UUU and UUC) could be mutated at the first position to produce Ile codons: UUU (Phe)—Change the first position to A to produce AUU (Ile). UUC (Phe)—Change the first position to A to produce AUC (Ile). Pro Ala All four codons for Pro can be mutated at the first position to produce Ala codons: CCU (Pro)—Change the first position to G to produce GCU (Ala). CCC (Pro)—Change the first position to G to produce GCC (Ala). CCA (Pro)—Change the first position to G to produce GCA (Ala). CCG (Pro)—Change the first position to G to produce GCG (Ala). Asn Lys Both codons for Asn can be mutated at a single position to produce Lys codons: AAU (Asn)—Change the third position to A to produce AAA (Lys). AAU (Asn)—Change the third position to G to produce AAG (Lys). AAC (Asn)—Change the third position to A to produce AAA (Lys). AAC (Asn)—Change the third position to G to produce AAG (Lys). f. Ile Asn Only two of the three Ile codons can be mutated at a single position to produce Asn codons: AUU (Ile)—Change the second position to A to produce AAU (Asn). AUC (Ile)—Change the second position to A to produce AAC (Asn).

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 ́ Tyr b. 5 ́-AUU-3 ́ Asn c. 5 ́-GGU-3 ́ Thr d. 5 ́-CCU-3 ́ Arg

Using the genetic code presented in Figure 11.5, indicate which amino acid is encoded by the following codons on the mRNA.

a. 5′-CCC -3′ Pro b. 5′-UUG -3′ Leu c. 5′ -CUG-3′ Leu d. 5′ -AGA-5′ Arg e. 5′ -UAA-3′ no amino acid, stop codon