Biology 111B

Study Questions 15

TRANSCRIPTION AND TRANSLATION
Answers

1. What do the following terms mean?

transcription - the process of making mRNA from a gene in the DNA
translation
- the process of making a protein from the mRNA
codon
- a three base sequence in mRNA that codes for a particular amino acid
mRNA
- messenger RNA; the RNA that carries information from the DNA to the cytoplasm to be translated into a protein
tRNA
- transfer RNA; the RNA that connects a particular codon with a specific amino acid
rRNA
- ribosomal RNA; the RNA contained in the ribosome that does the base recognition and catalysis jobs of the ribosome
anticodon
- the triplet sequence on the tRNA that is complementary to the codon in the mRNA

2. What is RNA, and how is it different from DNA? What are the three kinds of RNA, and what is the purpose of each? RNA is ribonucleic acid. It differs from DNA in that it has ribose rather than deoxyribose as the sugar, it is usually single-stranded, and it incorporates uracil (U) in place of thymine (T). The three kinds of RNA are explained above, so if you did them there, no need to also answer here...but if you didn't do it in the definitions above, explain the purposes here.

3. How does the mRNA copy differ from the DNA template from which it is made? mRNA has the three differences specified in question 2 for all RNA, but it also differs from the DNA template in polarity (because it is antiparallel), and it is only as long as the gene.

4. How is mRNA made from DNA? What enzyme catalyzes this reaction? mRNA is transcribed from DNA by RNA polymerase. The RNA polymerase separats the two DNA strands, and adds RNA nucleotides in a 5'->3' direction, (following a template 3'->5'), following the same pairing rules as in DNA, except that a U is paired with a template A. As the RNA is made, it is displaced by the DNA strands reannealing, and the completed section of RNA is freed from the DNA.

5. How does the enzyme know where to start and stop transcription? RNA polymerase recognizes an initiation site -- a promoter sequence (usually containing a "TATA" box) -- in the DNA. Elongation of the RNA continues until a termination sequence has been transcribed. Then transcription is teminated and the entire RNA polymer is freed from the DNA.

6. How is a eukaryotic primary transcript different from finished mRNA? What about a prokaryotic primary transcript? A eukaryotic primary transcript undergoes three processing steps before it leaves the nucleus. It has a cap placed on the 5' end, a poly A tail added to the 3' end, and introns spliced out of the interior of the primary transcript. For a prokaryotic primary transcript, no processing is possible because there is no separation of nucleus and cytoplasm. Ribosomes attach to the transcript and begin translation before transcription has even finished.

7. How is protein made from mRNA? What raw materials must be present for this process to occur? Why is it important for translation that ribosomes contain three sites for tRNA and not just one? The small subunit of a eukaryotic ribosome recognizes the 5' cap and finds the start codon. The initiator tRNA carrying MET binds its anti-codon to the start codon. Then the large subunit of the ribosome attaches to the small subunit, surrounding the mRNA, and nestling the intiator tRNA into the P site. The tRNA bearing the anti-codon for the next codon (and bringing the correct amino acid for that codon) then binds at the ribosomal A site, the rRNA in the ribosome catalyzes the peptide bond between the two amino acids, and the ribosome assembly moves one codon downstream. The free initiator tRNA now occupies the E site, and from there leaves the ribosome to get recharged. This elongation continues down the mRNA (5' ->3') until the stop codon is encountered. At that point, no tRNA has an anticodon that fits, but a termination signal protein binds to the A site of the ribosome and lyses the finished polypeptide from the remaining tRNA in the P site. The whole translation assembly then dissociates. The three sites on the ribosome essentially form an active site where the two tRNAs, one carrying the growing polypeptide chain and the other carrying the new amino acid to be added, are held in position for the peptide bond to be formed. The third site, the E or Exit site, allows the now uncharged tRNA a smoot exit.

8. Why can transcription and translation be simultaneous in prokaryotes but not in eukaryotes? Transcription and translation are simultaneous in prokaryotes because there is no separation between cytoplasm and nucleus. In eukaryotes, the separation prevents simultaneous transcription and translation, introducing a time lag, but also allowing processing of RNA transcripts.

9. What is the function of the 5' cap on an mRNA? What about the 3' poly A tail? The cap on a eukaryotic mRNA helps the small ribosomal subunit find the start codon and protects the 5' end of the mRNA from degradation by exonucleases. The 3' poly A tail also delays degredation of the coding sequence of the mRNA by exonucleases.

10. What is a polyribosome? A polyribosome is the structure formed when many ribosomes are simultaneously translating an individual mRNA strand.

11. All of the following are directly involved in translation except ...

a. mRNA

b. tRNA

c. DNA

d. ribosomes

e. all of the above are involved

12. A protein contains 30 amino acids. How many N-bases code for this protein? 90 (or 93 if you include the stop codon).

13. What tells the ribosome where to start translation and stop translation? start and stop codons

14. Which of the molecules in the list on the right function to transfer information in the processes on the left? (Write the correct answer(s) on the blank line.)

Information transfer...

_c, d, g____ from nucleus to cytoplasm

a. proteins

e. rRNA

___g (a)___ from DNA to mRNA

b. tRNA

f. DNA polymerase

_a, b, e (d)_ from mRNA to protein

c. DNA

g. RNA polymerase

d. mRNA

h. ligase

15. Refer to the double stranded DNA molecule with the sequence below to answer parts a - d.

a. Which strand functions as the transcription template, the top one or the bottom one? Explain your reasoning. The bottom strand is the template. It contains TAC, the complement of the start codon (AUG).

b. What is the mRNA transcript and polypeptide from this strand? In the space below, copy the DNA strand that is transcribed, and write the mRNA transcript and polypeptide chain below it. Align the mRNA and polypeptide so that it is clear which DNA bases they came from.

DNA strand:

TA TAC ACC AGA GCT ATC CCG ACA AAA GAG GCC GG

mRNA:

AU AUG UGG UCU CGA UAG GGC UGU UUU CUC CGG CC

amino acid sequence:

MET - TRP - SER - ARG

c. How would the amino acid sequence differ if...

the DNA base pair 22 were changed from G/C to A/T? That change would not alter the polypeptide because that base pair is beyond the stop codon.

the DNA base pair 12 were changed from C/G to T/A? That change would introduce a premature stop codon. The protein would be shorter than normal (by one amino acid).

the DNA base pair 4 were changed from T/A to C/G? That change would destroy the start codon and no protein would be formed because the ribosome would not find a start codon to begin translation.

d. How would the amino acid sequence differ if an extra A/T base pair were inserted between base pairs 8 and 9? That change would alter the reading frame. All codons after that would be incorrect:

AU AUG UGG UUC UCG AUA GGG CUG UUU UCU CCG GCC

MET - TRP - PHE - SER - ILE - GLY - LEU - PHE - SER - PRO - ALA - ...