chapter 4
Triple entendre. The RNA transcript of a region of T4 phage DNA contains the sequence 5'-AAAUGAGGA-3'. This sequence encodes three different polypeptides. What are they?
A peptide terminating with Lys (UGA is a stop codon), another containing -Asn-Glu-, and a third containing -Met-Arg-.
Flowing information. What is meant by the phrase gene expression?
Gene expression is the process of expressing the information of a gene in its functional molecular form. For many genes, the functional information is a protein molecule. Thus, gene expression includes transcription and translation.
Essential degradation. Reverse transcriptase has ribonuclease activity as well as polymerase activity. What is the role of its ribonuclease activity?
The ribonuclease serves to degrade the RNA strand, a necessary step in forming duplex DNA from the RNA-DNA hybrid.
The composition (in mole fraction units) of one of the strands of a double-helical DNA molecule is [A]= 0.30 and [G]=0.24. (a) what can you say about [T] and [C] for the same strand? (b) what can you say about [A],[G],[T], and [C] the complementary strand?
(a) 0.46 (b) [A] 0.30, [G] 0.24, [T] 0.30 [C] 0.24
To bring together as associates. Match the components in the right-hand column with the appropriate process in the left-hand column. (a) Replication_______ (b) Transcription____________ (c) Translation______________ 1. RNA polymerase 2. DNA polymerase 3. Ribosome 4. dNTP 5. tRNA 6. NTP 7. mRNA 8. primer 9. rRNA 10. promoter
(a) 2, 4, 8; (b) 1, 6, 10; (c) 3, 5, 7, 9.
36. A lively contest. Match the components in the righthand column with the appropriate process in the left-hand column. (a) fMet 1. continuous message (b) Shine-Dalgarno 2. removed (c) intron 3. the first of many (d) exon 4. uniter (e) pre-mRNA 5. joined (f) mRNA 6. locate the start (g) spliceosome 7. discontinuous message
(a) 3; (b) 6; (c) 2; (d) 5; (e) 7; (f ) 1; (g) 4.
Encoded sequences. (a) Write the sequence of the mRNA molecule synthesized from a DNA template strand having the following sequence. 5'-ATCGTACCGTTA-3' (b) What amino acid sequence is encoded by the following base sequence of an mRNA molecule? Assume that the reading frame starts at the 5'end. 5'-UUGCCUAGUGAUUGGAUG-3' (c) What is the sequence of the polypeptide formed on addition of poly(UUAC) to a cell-free protein-synthesizing system?
(a) 59-UAACGGUACGAU-39 (b) Leu-Pro-Ser-Asp-Trp-Met (c) Poly(Leu-Leu-Thr-Tyr)
Back to the bench. A protein chemist told a molecular geneticist that he had found a new mutant hemoglobin in which aspartate replaced lysine. The molecular geneticist expressed surprise and sent his friend scurrying back to the laboratory. (a) Why did the molecular geneticist doubt the reported amino acid substitution? (b) Which amino acid substitutions would have been more palatable to the molecular geneticist?
(a) A codon for lysine cannot be changed to one for aspartate by the mutation of a single nucleotide. (b) Arg, Asn, Gln, Glu, Ile, Met, or Thr.
Key polymerases. Compare DNA polymerase and RNA polymerase from E. coli in regard to each of the following features: (a) activated precursors, (b) direction of chain elongation, (c) conservation of the template, and (d) need for a primer.
(a) Deoxyribonucleoside triphosphates versus ribonucleosidetriphosphates. (b) 59 n 39 for both. (c) Semiconserved for DNA polymerase I; conserved for RNA polymerase. (d) DNA polymerase I needs a primer, whereas RNA polymerase does not.
(a) suppose that you want to radioactively label DNA but not RNA in dividing and growing bacteria cell, which radioactively molecule would you add to the culture medium? (b) suppose that you want to prepare DNA in which the backbone phosphorus atoms are uniformly labeled with 33P. Which precursors should be added to a solutions containing DNA polymerase and primed template DNA? Specify the position of radioactive atoms in these precursors.
(a) Tritiated thymine or tritiated thymidine. (b) dATP, dGTP, dCTP, and TTP labeled with 32P in the innermost (a) phosphorus atom.
Write the complementary sequence (in the standard 5'--> 3' notation) for (a) GATCAA (b)TCGAAC (c)ACGCGT, and (d) TACCAT
(a)TTGATC (b)GTTCGA (c)ACGCGT (d)ATGGTA
Family resemblance. Differentiate among mRNA, rRNA and tRNA.
- Messenger RNA encodes the information that, on translation,yields a protein. -Ribosomal RNA is the catalytic component of ribosomes, the molecular complexes that synthesize proteins. -Transfer RNA is an adaptor molecule, capable of binding a specificamino acid and recognizing a corresponding codon. TransferRNAs with attached amino acids are substrates for the ribosome.
Retrograde. What is a retrovirus and how does information flow for a retrovirus differ from that for the infected cell?
A retrovirus is a virus that has RNA as its genetic material. However, for the information to be expressed, it must first be converted into DNA, a reaction catalyzed by the enzyme reverse transcriptase. Thus, at least initially, information flow is opposite that of a normal cell: RNA n DNA rather than DNA n RNA.
If the forces-hydrogen bonds and stacking forces-holding a helix together are weak, why is it difficult to disrupt a double helix?
Although the individual bonds are weak, the population of thousands to millions of such bonds provides much stability. There is strength in numbers.
Sometimes it is not so bad. What is meant by the degeneracy of the genetic code?
Degeneracy of the code refers to the fact that most amino acids are encoded by more than one codon.
3 is greater than 2. The adjoining illustration graphs the relation between the percentage of GC base pairs in DNA and the melting temperature. Account for these results. ***Refer to graph on page 138***
GC base pairs have three hydrogen bonds compared with two for AT base pairs. Thus, the higher content of GC means more hydrogen bonds and greater helix stability.
Valuable synonyms. Proteins generally have low contents of Met and Trp, intermediate contents of His and Cys, and high contents of Leu and Ser. What is the relation between the number of an amino acid's codons and the frequency with which the amino acid is present in proteins? What might be the selective advantage of this relation?
Highly abundant amino acid residues have the most codons (e.g., Leu and Ser each have six), whereas the least-abundant amino acids have the fewest (Met and Trp each have only one). Degeneracy (1) allows variation in base composition and (2) decreases the likelihood that a substitution for a base will change the encoded amino acid. If the degeneracy were equally distributed, each of the 20 amino acids would have three codons. Both benefits (1 and 2) are maximized by the assignment of more codons to prevalent amino acids than to less frequently used ones.
In fact, it can be good. What is the biological benefit of a degenerate genetic code?
If only 20 of the 64 possible codons encoded amino acids, then a mutation that changed a codon would likely result in a nonsense codon, leading to termination of protein synthesis. With degeneracy, a nucleotide change might yield a synonym or a codon for an amino acid with similar chemical properties.
What result would Meselson and Stahl have obtained if the replication of DNA were conservative (ex: the parental double helix stayed together)?Give the expected distribution of DNA molecules after 1.0 and 2.0 generations for conservative replication.
In conservative replication, after 1.0 generation, half of the molecules would be 15N-15N, the other half 14N-14N. After 2.0 generations, one-quarter of the molecules would be 15N-15N, the other three-quarters 14N-14N. Hybrid 14N-15N molecules would not be observed in conservative replication.
A solution contains DNA polymerase and the Mg2+ salts of dATP, dGTP, dCTP, and TTP. The following GNA molecules are added to aliquots of this solution. Which of them would lead to DNA synthesis? (A) a single-stranded closed circle containing 1000 nucleotide units. (B) a double-stranded closed circle containing 1000 nucleotide pair.(C)(c) A single-stranded closed circle of 1000 nucleotides base-paired to a linear strand of 500 nucleotides with a free 39-OH terminus. (d) A doublestranded linear molecule of 1000 nucleotide pairs with a free 39-OH group at each end.
Molecules in parts a and b would not lead to DNA synthesis, because they lack a 39-OH group (a primer). The molecule in part d has a free 39-OH group at one end of each strand but no template strand beyond. Only the molecule in part c would lead to DNA synthesis.
A single strand of RNA is 20% U. What can you predict about the percentages of the remaining bases?
Nothing, because the base-pair rules do not apply to single stranded nuclei acid
Differentiate between a nucleoside and a nucleotide?
Nucleoside= ribose sugar + base Nucleotide= sugar + base + phosphate
what does it mean to say that the DNA chains in a double helix have opposite polarity?
One end of a nucleic acid polymer ends with a free 59-hydroxyl group (or a phosphoryl group esterified to the hydroxyl group), and the other end has a free 39-hydroxyl group. Thus, the ends are different. Two chains of DNA can form a double helix only if the chains are running in different directions—that is, have opposite polarity.
Silent RNA. The code word GGG cannot be deciphered in the same way as can UUU, CCC, and AAA, because poly(G) does not act as a template. Poly(G) forms a triple-stranded helical structure. Why is it an ineffective template?
Only single-stranded RNA can serve as a template for protein synthesis.
Why are GC and AT the only base pairs permissible in the double helix?
Stable hydrogen bonding occurs only between GC and AT pairs. Moreover, two purines are too large to fit inside the double helix, and two pyrimidines are too small to form base pairs with each other.
Biochemist Erwin Chargaff was the first to note that, in DNA, [A]= [T] and [G]=[C], equalities now called Chargraff's rules. Using this rule, determine the percentages of all the bases in DNA that is 20% thymine.
T= 20% A= 20% C= 30% G= 30%
Eons apart. The amino acid sequences of a yeast protein and a human protein having the same function are found to be 60% identical. However, the corresponding DNA sequences are only 45% identical. Account for this differing degree of identity.
The genetic code is degenerate. Of the 20 amino acids, 18 are specified by more than one codon. Hence, many nucleotide changes (especially in the third base of a codon) do not alter the nature of the encoded amino acid. Mutations leading to an altered amino acid are usually more deleterious than those that do not and hence are subject to more stringent selection.
The human genome contains 3 billions nucleotides arranged in a vast array of sequences. What is the minimum length of a DNA sequences that will, in all probability, appears only once in the human genome? you need consider only one strand and may assume that all four nucleotides have the same probability of appearance.
The probability that any sequence will appear is 4n, where 4 is the number of nucleotides and n is the length of the sequence.The probability of any 15-base sequence appearing is 1/415, or 1/1,073,741,824. Thus, a 15-nucleotide sequence would be likely to appear approximately three times (3 billion 3 probability of appearance). The probability of a 16-base sequence appearing is 1/416, which is equal to 1/4,294,967,296. Such a sequence will be unlikely to appear more than once.
Why does heat denature or melt, DNA in solution?
The thermal energy causes the chains to wiggle about, which disrupts the hydrogen bonds between base pairs and the stacking forces between bases and thereby causes the strands to separate.
Describe the three forms that a double helix can assume.
The three forms are the A-DNA, the B-DNA and the Z-DNA, with B-DNA being the most common. There are many differences (see Table 4.2). Some key differences are: A-DNA and B-DNA are right-handed, whereas Z-DNA is left-handed.A-DNA forms in less-hydrated conditions than does B-DNA. The A form is shorter and wider than the B form.
DNA in the form of a double helix must be associated with cations, usually Mg2+. Why is this requirement the case?
There would be too much charge repulsion from the negative charges on the phosphoryl groups. These charges must be countered by the addition of cations.
What is watson-crick base pair?
hydrogen bond pairs between A & T and G & C in DNA
