Significant changes made to the Problem Book, 20th edition, re-revised (2014) to convert it to the 21st edition (2015)

This is what you need if you have the 20^th edition, re-revised (2014). If you have the 21^st edition (2015), all these changes have already been made.

Below are the significant additions or changes. (Corrections to typos or formatting that do not change the meaning in any way are not listed.)  The added questions are listed below. The answers are at prob-book-fix-ans-for20r-r.html.

1. There are 4 more pp. in the 21^st edition.  The page numbers for the problem section are the same, but some of the numbers in the answer section are changed.  The major differences are the insertion of 2 pp after the key to Prob. Set 7R ( pp. 183-184 in 21^st ed) , and 2 pp at the end of the key to Prob. Set 13 ( pp. 227-228 in 21^st ed).  For most purposes, the page numbers do not matter as long as you have all the problems. (The 'problems to do' page lists the problem numbers, not the page numbers.) All the new problems are given below -- item 3.

If you have the 20^th ed (unrevised, revised, or re-revised),  and you want to match the page numbers in the 21^st edition, here is what you should do: Pages 183-224 should be renumbered 185-226. Pages 225-238 should be renumbered 229-242. (You will be missing pages 183-184, and 227-228. Those pages contain the answers to some of the new problems. See prob-book-fix-ans-for20r-r.html for what should be on those pages.)

2. The following questions were added: 7-19, 7R-3, 7R-4, 8-16, 12R-5 (old 12R-5 is now 12R-6), & 13-17.  13-3, part B was updated, and 13-16 was replaced with a new problem. All the added questions are below.

3. Questions:

7-19. Two parts were added to problem 7-19.

B. Consider the approximate ΔG^o for (a) the hydrolysis of met-tRNA and for (b) hydrolysis of a peptide bond. Both values are negative. Which ΔG^o has the largest absolute value?
 (a) (b) (neither – they’re the same) (can’t predict).  Explain your reasoning briefly in words. Please do not reproduce the class handout.

C. For parts C-1 & C-2, consult a genetic code table and the wobble rules as needed.
   C-1. A normal cell would be expected to contain tRNA(s) with the anticodon(s)
(UAG) (AUC) (AUG) (UAC) (none of these). All sequences are written 3' to 5'.
Circle all correct answers, and explain briefly.  

    C-2.  If a cell contains the minimum number of different tRNAs, it is likely to contain tRNA(s) with the anticodon(s) (CUA) (CUG) (CUI) (none of these). All sequences are written 3' to 5'.
Circle all correct answers and explain briefly.

Problem Set 7R. Two questions (7R-3 & 7R-4) were added to problem set 7R. To fit the answers to 7R-3 & 7R-4 in, two pages were added to the key to 7R (183 & 184). 

7R-3. You have a double stranded DNA. One strand looks like this:  

5’ GAAC…………………GGAG……………CATT ………………….ATGA 3’

    |------------- Gene A --------------| ß--P --à |----------------- Gene B -----------|

The DNA contains two genes and one promoter as indicated. The promoter is a so-called divergent promoter – it can be used to transcribe in either direction. Depending on how RNA polymerase binds, either gene A or gene B can be transcribed. Assume the promoter itself is not transcribed, and that the sequences shown represent the ends of the transcribed regions.

    A-1. If transcription occurs to the right, the 5’ end of the transcript will be ___________________.
    A-2. If transcription occurs to the left, the 5’ end of the transcript will be ___________________.
Fill in each blank with the correct 4 base sequence, label the ends of each sequences, and explain.  

    B-1. For gene A, the sense strand of the DNA is (the strand shown) (complement of strand shown) (either strand).
    B-2.  Suppose gene B contains the sequence TAC in the strand shown, written left to right, and the triplet is in the correct reading frame. Then the corresponding protein will have the amino acid (tyr) (his) (met) (val)  (none of these).  

C. Consider the piece of double stranded DNA consisting only of the strand shown above and its complement. Suppose this DNA is replicated in bacteria, and replication is bidirectional from a single origin to the left of the promoter.
    C-1. In the region of the promoter, the complement to the strand shown should be made (continuously) (discontinuously) (either way) (part continuously & part discontinuously). |
    C-2. When DNA synthesis is finished, which of the sequences shown are likely to be single stranded, that is, have no complement? (GAAC) (GGAG) (CATT) (ATGA) (none of these).  Explain both answers. 

D. Consider the ds DNA containing the strand shown above. Suppose you want to use PCR to make copies of the ds DNA. You want the PCR product to be the full length.
    D-1. Consider the 4 sequences shown, and assume (for exam purposes) that they are long enough to serve as primers. Of the sequences given above, which can serve as primers to make a full length PCR product? (GAAC) (GGAG) (CATT) (ATGA) (none of these). Circle all correct answers.
    D-2. Ligase will be needed to complete synthesis of (the strand shown) (the complement to the strand shown) (both strands) (neither strand) (one strand or the other, but can't predict which). Explain both answers briefly. Include enough details to support your answers, but please do not reproduce the entire class handout. 

7R-4. Suppose bacteria have a gene (say Gene Q) that codes for an mRNA with only one CUA leucine codon in the translated part. You have 3 mutant bacteria with different mutant versions of gene Q. In each case, the leucine codon is altered by addition, removal, or change of a single base pair. (You have to decide which case it is.)
   A. Fill in the blanks and/or chose the best answer below. (In each case, if there is more than one possibility for the blank, pick one.) Explain each answer, and be as specific as possible.      
     A-1. In Mutant 1, peptide Q (encoded by gene Q), is unchanged. The codon in the mRNA (must be unchanged) (must be changed) (could be changed or not). 
     A-2. In Mutant 2, peptide Q has a change of one amino acid from leu to val. The codon in the mRNA could be changed to  ___________,  AND this mutation is best classified as (mis-sense) (nonsense) (silent) (a frameshift).
     A-3. In Mutant 3, peptide Q has a change of one amino acid from leu to arg. The codon in the mRNA could be changed to  ___________,  AND this mutation is a (substitution) (deletion) (insertion) (deletion or insertion) (any of these).

   B.  Suppose peptide Q is needed for drug resistance. Which mutant is most likely to be drug sensitive?
(1) (2) (3) (1 or 2) (2 or 3) (1 or 3) none of these -- all are equally likely to be drug sensitive) (none of these – all are likely to be drug resistant). Consult a text or handout with amino acid structures, and explain briefly.

*8-16. There are established lines of lilies that are fertile polyploids. The gametes of tetraploid lilies contain 24 chromosomes, and approximately 10 pg (picograms) of DNA. Answer the following questions about diploid lilies, and explain your answers.

  A-1. In a diploid lily plant, the # of pairs of homologous chromosomes in prophase I of meiosis   should be (0)  (1)  (2)  (3)  (4)  (5)  (6)  (10)  (12)  (18)  (20)  (24)  (36)  (48)  (96).
  A-2. In a diploid lily plant, the value of C (in correct units) should be   (0)  (1)  (2)  (3)  (4)  (5)  (6)  (10)  (12) (18)  (20)  (24)  (36)  (48)  (96).
  A-3. Which of the following should contain approximately 10 pg (picograms) of DNA?
  __ (somatic cell of a diploid in G1)                   __ (somatic cell of a diploid in G2)     
  __ (spores of a diploid)                                    __ (germ cells of a diploid in pro I)    
  __ (zygote of a diploid line before S)                __ (gametes of a diploid)
  __ (none of these). 
  Check off all correct choices – there may be more than one.

B. Suppose a cell in a diploid lily plant goes through the first div. of meiosis to produce 2 daughter cells, but 2^nd division has not occurred yet. You examine the daughter cells. What do you expect to find in each cell? Assume your answers to part A are correct, and put a real number in each blank, not a multiple of N or C.

 B-1. The # of chromosomes per cell should be ____________.
 B-2. The # of chromatids per chromosome should be _________________.

Problem Set 12R. A new 12R-5 (below) was added to Prob. Set 12R. The old 12R-5 is now 12R-6.

12R-5. You have two batches of normal E. coli cells. The cells are the same in each batch, but the growth conditions are different.
     Batch L was grown with lactose present as the only carbon source.
     Batch W was grown w/o lactose on a different carbon source (not glucose). 

You have three separate preparations isolated from each batch of E. coli cells. You have 
     1. Polysomes isolated from cells of either batch -- from batch L or W.   
     2. Loaded tRNAs – all types. Loaded tRNAs were isolated from cells of either batch.   
     3. Cell supernatant – isolated from cells of either batch. The cell supernatant contains all necessary small molecules & soluble proteins of the cell.
If you mix all 3 preparations together, in vitro (in a test tube), protein synthesis will occur.  It doesn’t matter which batch each of the preparations came from – but you need all 3 components.    

Here is the question: You want your in vitro system to make beta galactosidase, encoded by the lac operon. Suppose you mix all 3 preparations together in a test tube, and then measure the production of beta galactosidase in vitro (in the test tube).

A. To get maximum production of beta-galactosidase in vitro, which preparation(s) must come from batch L? (1) (2) (3) (none of these). Circle all correct answers.

B. To get maximum production of beta-galactosidase in vitro, after you mix your 3 preparations, what do you need to add to, or remove from, your test tube? You need to (add lactose)   (omit lactose) (do neither – the level of lactose doesn't matter)   (add or omit lactose, but I'm not sure which).

13-3. The choices in problem 13-3, part B, were updated, and the answer adjusted to fit. Here are the current version of part B:

B.  People with hemoglobin C have pro‑lys‑glu in the corresponding place in the beta chain. Which of the following are likely to work to distinguish the beta‑S and beta-C alleles?
        i)     the size of the pieces after Dde treatment
        ii)    number of pieces after Dde treatment
        iii)   SDS gels of the gene products
        iv)   electrophoresis without SDS of the native gene products
        v)    gel filtration of the gene products
        vi)   ultracentrifugation of the gene products
        vii)   PCR followed by electrophoresis of product
        viii)  PCR followed by hybridization of product to probe
Explain why your choices are good, AND why the others are not so good.

Problem Set 13. 13-16 was replaced with a new 13-16, and an additional 13-17 was added. 

*13-16. You have mRNA from eukaryotic gene G. The mRNA has no poly A tail. Gene G codes for a protein 294 AA long. You make single stranded cDNA using reverse transcriptase. The cDNA is the same length as the mRNA.

A. The cDNA should hybridize to which of the following? (the sense strand of gene G) (the template strand of gene G) (the primary transcript of gene G) (the protein encoded by gene G)
(none of these) (can’t predict -- depends on the length of the mRNA).

B. You use PCR to make many copies of gene G. Then you cut up the DNA using the restriction enzyme, Rest5, and separate the pieces by gel electrophoresis. If you stain the gel for DNA, you get 12 separate bands. If you do a Southern blot, using the cDNA (labeled with a fluorescent tag) as a probe, you get 11 fluorescent bands on the blot. Which of the following is the most reasonable explanation of your result? (two of the pieces are the same size) (1 piece contains no introns) (1 piece contains no exons) (two pieces stick to the same molecule of probe) (1 piece contains no coding sequences, only a UTR).

C. The number of bases in the mRNA from gene G should be about (200) (300) (600) (900) ( >900) (<200) AND the number of base pairs in the transcribed part of gene G should be (about the same) (much larger) (much smaller) (can’t predict).   

*13-17. Protein P is synthesized in many tissues, including the kidney. Gene P, the gene that codes for protein P, has 11 exons. In most tissues, including kidney, protein P is 150 amino acids long, and exon #6 is skipped.

A.  In normal kidney cells, splicing should connect the 5’ donor site of intron #5 to the 3’ acceptor site of intron (#4) (#5) (#6) (#7) (#8) (#4 or #5) (#5 or #6) (none of these) (any of these). Draw the relevant introns & exons and show how the splicing should go in the kidney.

B. In the photoreceptor cells of the eye, exon #6 is not skipped. Exon #6 is 30 nucleotides long, and is in frame. 
     B-1. In normal people, how long should the protein P be in the photoreceptor cells? The number of amino acids should be (< 150) (150) (156) (160) (166) (165) (180) (>180) (can’t predict).
     B-2. Consider the primary transcript of gene P in eye cells. In normal people, the primary transcript of gene P in kidney cells should be (longer) (shorter) (the same length) (can’t predict).
     B-3. Consider the number of lariats formed during splicing of the primary transcript in eye cells. In normal people, the number of lariats in kidney cells should be (larger) (smaller) (the same) (can’t predict). Show how you get protein P of the length in B-1 in the eye.

C. You take mRNA from normal photoreceptor cells and from normal kidney cells. You run the mRNAs in separate lanes on a gel, blot, and hybridize to two labeled probes – one for exon 5 of gene P (probe 5) and one for exon 6 (probe 6). What will you see on the blot?
     C-1. If you use probe 5, you will see one or more labeled bands if you use mRNA from (eye cells) (kidney cells) (both) (neither) (can’t predict). 
     C-2. If you use probe 6, you will see one or more labeled bands if you use mRNA from (eye cells) (kidney cells) (both) (neither) (can’t predict).  Explain briefly.
     C-3. Suppose in at least one case, you find a labeled band corresponding to a size of 900 nucleotides. This means that 900 nt is the length of (the probe) (the mRNA) (both) (neither). Explain briefly.
     C-4. If you compare lanes on the blot, which of the following will get you the same results --same # of labeled bands, in the same place? You will get the same results if you use (probe 5 with either mRNA) (probe 6 with either mRNA) (mRNA from kidney cells with either probe) (mRNA from eye cells with either probe) (none of these). Explain briefly. You don’t need to repeat anything you said above, but it might help to draw all relevant blots.

The answers to these problems are at prob-book-fix-ans-for20r-r.html.