Genetics at the University of Florida

AGR 3303 (3 credits)
University of Florida - Fort Lauderdale
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Below is exam #2 for 2000, Molecular genetics
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AGR 3303 - Genetics 13 Nov 2000

University of Florida - Fort Lauderdale

Exam #2: MOLECULAR GENETICS

Multiple choice (54 pts., 3 pts each)

Please read these carefully. One and only one response (a, b, c, d, or e) completely and correctly answers the question, or completes the statement. Circle the appropriate response and turn in this exam. Make sure your circle is unambiguous. Take time to relax. (Suggestion: put the problem into gene symbols, if that helps you to visualize the problem and its solution.)  (Comments attempt to explain why the true answer is true, and the other answers are false.  Page numbers refer to pages in Klug and Cummings, 6th ed.)

  1. What can you say about an organism with the following base composition?
    The organism has DNA, because this sample contains thymine not uracil.  The base pair composition (see p. 298, and problem 31 on page 316) does not show any proportionality between A and T, or between G and C, as would be expected for double-stranded DNA (which has complementary bases on the strands).  Therefore the organism has single-stranded DNA.  Other choices are irrelevant, e.g., collinearity is not a feature of DNA, and mitochondria have double-stranded DNA.

    2. A (adenine)= 18%      T (thymine)= 31%     G (guanine)= 31%      C (cytosine)=20%
    1. Its genetic material is probably double-stranded RNA
    2. This organism must have single-stranded DNA
    3. This organism must have double-stranded DNA
    4. This organism has collinearity between the pyrimidines and the purines
    5. This is mitochondrial DNA

  2. If an experiment had used radioactively labeled human insulin DNA, in a microbial synthesis, what would you expect to find in the insulin protein produced (think carefully about this):
    The question does not indicate any radiolabelling of the protein or amino acids, thus there is no basis to expect that the insulin protein would be radioactive.  The classic experiment of Hershey and Chase (p. 291) detected radioactively labeled P in phage-infected bacteria, indicating that the genetic material was whichever material contained radioactive P, that is, the DNA.  But in this example it is only the DNA that is radiolabelled.
    1. radioactive P would occur in the insulin
    2. both radioactive P and S would occur in the insulin
    3. radioactive S would occur in the insulin
    4. neither radioactive P or S would occur in the insulin
    5. insulin would not be produced

  3. Frameshift mutations are observed because:
    Either a or b is correct.  Frameshift mutations occur both because of the absence of commas in the DNA code imposes a new reading frame on the frameshift mutant, and because stop codons will occur frequently (3 times out of 64) in a frameshift, causing premature polypeptide termination, a nonsense mutation.  Frameshift mutations were an elegant and simple demonstration of the triplet nature of the code (pp. 351-352).
    1. The DNA code is commaless
    2. The DNA code has stop codons
    3. The DNA code is antiparallel
    4. The DNA code is degenerate
    5. The DNA code is ambiguous

  4. Human insulin can be produced by bacteria, using human DNA, which proves:
    DNA doesn't contain S, so answer c is false.  The other four answers true statements, but only statement b is proven or even has any direct relationship with human insulin production.  DNA is the transforming principal, the molecule of heredity, as shown by Avery, MacLeod, and McCarty experiment while creating smooth (virulent) bacteria using DNA and rough (avirulent) bacteria (page 288).  But creating insulin in bacteria is a direct, cause-and-effect proof of DNA as the genetic material.  Insulin     was the first human gene product manufactured using recombinant DNA, and it was licensed in 1982 (page 593).
    1. DNA is a double helix
    2. human DNA is a transforming principal
    3. the DNA contains S, not P
    4. there is base pair complementarity
    5. bacteria are endosymbionts of people

  5. Which statement is true of the double helix?
    Only a is true (p. 302).  DNA base pairs are always purine-pyrimidine pairs, e.g., AT or GC, and they "melt" or "denature" under heat, and renature or anneal when they cool.
    1. T pairs involve two hydrogen bonds
    2. purine pairs with purine
    3. heating causes the strands to anneal
    4. G pairs with T
    5. U pairs with T

  6. Where would you expect to find the genetic information describing the potential characteristics of Tyrannosaurus rex?
    Darwin (p. 4) believed that there were gemmules which were physical units representing all the parts of the body and were gathered together by the blood into the semen, and which determined the respective nature or form of each body part.  This idea is inconsistent with the modern understanding of the cell, chromosomes, and DNA.  Every cell in an organism has (with few exceptions) the same complement of chromosomes (p. 6) and containing the same DNA.  Germ cells are specialized for gamete production and sexual reproduction, based on meiotic division, but other cells must also have DNA for normal function.
    1. In virtually every cell of its body.
    2. Depends on the characteristic; eye color genes would be found in its eyes, hemoglobin genes in its erythrocytes.
    3. In the ribosomes.
    4. Only in its germ cells, i.e., primary spermatocytes or oocytes.
    5. In a place in New Mexico called Roswell.

  7. Parent plants with the genotypes AABBCC and aabbcc were crossed, and their F1 progeny were backcrossed to a homozygous recessive tester. The 1000 backcross progeny had the phenotypic distribution:
    Phenotype ABC abc AbC aBc Abc aBC ABc abC
    Number 355 355 5 5 95 95 45 45
    What is the map distance between A and C?

    8. The problem involves a trihybrid cross, and the parental gametes are ABC and abc.  The double-crossover gametes are the least frequent classes, AbC and aBc, therefore the gene locus in the middle is the one which is "odd" compared with its neighbor, hence the B gene must be in the middle.  Meanwhile the classes Abc and aBC must represent single crossovers in the region A-B, and the rate of crossing over is their sum, plus the doubles, or 95+95+5+5=200 out of 1000, or 20%, or 20 map units.  In the same way, the distance B-C must be 45+45+5+5=100 out of 1000, or 10%, or 10 map units.  Therefore, the distance A-C is the sum, 20+10=30.
    1. 1 map unit
    2. 10 map units
    3. 20 map units
    4. 30 map units
    5. 40 map units

  8. Which sentence describes the general relationship between the sequences of a polypeptide and its respective mRNA?
    The collinear relationship between DNA and polypeptide is based (p 397) on the triplet nature of the code, three nucleotides for each amino acid.  While answer e is false (the code is not ambiguous), answer a is false (has got it backwards), and answer d is false (there are no amino acids in mRNA), answer c is clearly also false, because there is a numerical relationship between the polypeptide subunits and the mRNA subunits.
    1. The number of amino acids in the polypeptide is three times the number of nucleotide pairs.
    2. The number of bases in mRNA is three times the number of amino acids.
    3. The presence of wobble makes it impossible to predict a numerical relationship between the units in a polypeptide and its respective mRNA.
    4. The number of amino acids in mRNA is three times the number of bases in the polypeptide.
    5. The code is ambiguous, which makes it impossible to predict a numerical relationship between a polypeptide and its respective mRNA.

  9. A single piece of single-stranded DNA reads 5' CGGCATTAC 3'. Which of the following pieces of single-stranded DNA could form a normal, complimentary double helix with the original piece?
    DNA strands are antiparallel, which is one of the basic features proposed by Watson and Crick (p. 299), also, G pairs with C and T pairs with A.
    1. 5' GTAATCGGC 3'
    2. 5' GTAATGCCG 3'
    3. 5' CGGCTAATG 3'
    4. 5' GCCGTAATG 3'
    5. 5' GTATACGGC 3'

  10. Watson and Crick (1953) proposed:
    Their article (p. 303), "Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid" only referred to DNA as having a "possible copying mechanism for the genetic material," but the thrust was the structure.  They did not deal with the mechanism of gene expression, and even the implication of DNA as the genetic material (which is the ultimate outcome, was not part of the proposal).
    1. the genetic code
    2. that DNA is the hereditary molecule
    3. the Central Dogma
    4. the structure of DNA
    5. genetic engineering

  11. What has molecular biology added to the knowledge of genetics?
    Mendel had already proven b and c, while a was never proven, and d was proven in the 1930s by McClintock.  The only thing left for the molecular biologists was c.
    1. proof of the inheritance of acquired characteristics
    2. proof that genes act as particles
    3. proof that genes are made of chemicals
    4. proof that genes are located in the chromosomes
    5. proof that both the female and the male parent contribute to the characteristics of the offspring

  12. The bacteria of Avery et al. (1944) were transformed by a substance which was inactivated by:
    Only DNase (p. 288).
    1. 32P
    2. 35S
    3. polymerase
    4. RNase
    5. DNase

  13. In the lac operon,
    It is the repressor protein that binds with the DNA (p. 416.)
    1. lactose binds with the DNA, preventing transcription
    2. lactose binds with a protein, preventing translation
    3. a protein binds with the DNA, preventing transcription
    4. there are three regulatory genes and one structural gene
    5. translation results in lactose

  14. Which of the following is a nucleotide of DNA:
    Nucleic acid terminology is illustrated on p. 296.
    1. deoxyribose + uracil + phosphate group
    2. deoxyribose + thymine + phosphate group
    3. deoxyribose + nitrogenous base
    4. ribose + pyrimidine + phosphate group
    5. ribose + ATP

  15. What molecule is transcribed from the DNA template, is single stranded, is typically a large molecule, and has a short half-life (high turnover)?
    That's the messenger (p. 8).
    1. ribosome
    2. mRNA
    3. rRNA
    4. enzyme
    5. polypeptide

  16. Based on the Watson-Crick model of the double helix:
    All are true (p. 299).
    1. if you know the content of one nitrogenous base (e.g, A) then you know the content of the other three (e.g., T, G, and C)
    2. nitrogenous bases of antiparallel strands are paired by hydrogen bonds
    3. the structure explains the function
    4. for every purine there must be a pyrimidine
    5. all of the above

  17. Among this group, who proved that DNA is the genetic material?
    See p. 288.
    1. Avery, MacLeod, and McCarty - transforming principle
    2. Darwin - evolution by natural selection
    3. Mendel - unit factors of inheritance
    4. Watson and Crick - double helix
    5. McClintock -jumping genes

  18. The normal human metabolic pathway makes substance Z from substance X, as shown below.
    If both Enzyme A and B were functional, what would be the most probable consequence.
    There's nothing complicated going on.
       
    Enzyme A Enzyme B
    A >-----> B >-----> C
  1. Substance Y would accumulate in the body
  2. Substance X would accumulate in the body
  3. Enzyme B would accumulate in the body
  4. Enzyme A would not be produced
  5. Enzyme B would go ahead and complete the synthesis of Z

Fill in the blank (21 pts., 1 pt. each).

In each of the following twenty-one blank spaces, insert the correct word or phrase.

 

19. The form of the DNA molecule, as proposed by Watson and Crick
double helix

 

20. The three-nucleotide "word" in mRNA, which specifies a single amino acid
codon

 

21. An oligomeric protein which is important in the blood.
hemoglobin

 

22.A method for artificially replicating short sequences of DNA segments to large number of copies
polymerase chain reaction (PCR)

 

23.A type of mutation involving a deletion or an insertion of one or more nucleotides, resulting in a garbled message
frameshift

 

24. "Wobble" in the third nucleotide of tRNA's anticodon is believed to result in inexact complementarity. This permits what key characteristic of the genetic code?
redundancy or degeneracy

 

25. The correspondence between the sequence of nucleotides and the sequence of amino acids resulting from translation
collinearity

 

26.A cutter enzyme
restriction endonuclease

 

27. The place in a protein where structural integrity is required for function; mutations which disrupt the protein here usually result in defective protein
active site

 

28. An organelle which is believed to have been an ancient cellular invader; a possible endosymbiont
mitochondrion

 

29. The regulatory gene which binds with a repressor protein, preventing RNA polymerase from binding with the promoter, thus preventing transcription
operator

 

30.A nitrogenous base present in RNA, but not in DNA (spell it out)
uracil

 

31. Virus which attacks bacteria; often used in genetic studies
phage

 

32. An organism lacking a nucleus
prokaryote

 

33.A process of sudden genetic change, the source of most alleles
mutation

 

34. When two enzymes contribute to a metabolic pathway, Mendelian 9:3:3:1 phenotypic ratios are sometimes altered; the genetic phenomenon is:
epistasis

 

35. The level of protein structure that involves the actual sequence of amino acids
primary

 

36. A type of organism in which transcription and translation are separated in space:
eukaryote

 

37. The kind of evidence for DNA as the genetic material that is provided by the UV action spectrum:
circumstantial

 

38. The number of possible codons:
64

 

39. A ribonucleoprotein organelle that is the site of translation of mRNA codons into amino acids.
ribosome

 

Short answer (25 pts, 5 pts each)

Attach extra pages as necessary

40. Describe in chemical terms how a mutation can affect the phenotype. Make sure to say what a mutation is and mention factors and mechanisms that will lead to a trait being expressed or not expressed.
(Pertinent terminology is:  redundancy, regulatory gene, active site, dominance, heterozygosity, and oligomeric proteins.)

A mutation is a sudden genetic change, which can be either a "point" mutation (a nucleotide substitution) or a chromosome variation.  Nucleotide substitutions may affect either a structural or a regulatory gene.  In the latter case, a mutant regulatory gene may be unable to control production of an enzyme, in which case it is constitutive.  In the case of structural genes, they may have no effect due to redundancy (and no change in the amino acid), or no effect due to the fact that they are not in the active site of the enzyme (where amino acid substitutions would not be tolerated), or due to the fact that the organism is heterozygous (and the mutation is recessive, as most are).

41. How can knowing the genetic code be applied to inherited diseases?  What are some obvious ethical issues involving this information?
Intervention through stem cell replacement or the use of nonsense mRNA, the selection of surrogate donors, and development of targeted detection techniques.  Genetic diseases can also be avoided by detection in the fetus followed by abortion, or by selection of eggs and possibly even sperm before conception, and artificial insemination or even embryo transplantation.  Numerous ethical issues surround the use of genetics on humans.  All human cultures place an ethical value on human life, thus if a technique leads to the ending human life, at whatever stage (before or after conception), one ethical argument is that genetic intervention is also wrong.  This is supported by the viewpoint that there is not a precise definition of human life, and that wherever a line is drawn, some people will want to move the line, especially with new genetic methods.  Another ethical point of view is that humanity has a special relationship with the will of the deity, and that any form of intervention is "messing with Mother Nature" or "Playing God."  This view is consistent with the fact that the vast majority of abortions are natural, and represent chromosome aberrations and other genetic defects that are corrected naturally.  Another argument against genetic intervention in humans is that some parents will undoubtedly use genetics to engineer "beautiful" or "intelligent" offspring, both of which may be arbitrary styles.  Some genetic abnormalities, such as Down Syndrome, involve happy, loving children who often find jobs and are productive contributing members of their community.  While they are not necessarily "designer children," they have just as much right to be here as anybody else.  Another ethical argument is that unnecessary human suffering should be reduced, and that parents are responsible for the health of their children, even unborn children.  While it may be theoretically possible to keep anybody alive, the toll on parents in dealing with severely impaired childen can wreck numerous lives, without ever providing a quality life to those impaired, and can take scarce medical resources away from others.  Consequently, genetics is our best hope of preventing genetic abnormalities.  It should be added that whenever a new medical practice becomes available, whether it be immunization or blood transfusion, there will be some holdouts who refuse even to protect their own children, which would seem like the ultimate ethical responsibility, and there will be others who will rush to push the envelope.  But those extremes should not preclude the majority of people from the medical use of genetics within the ethical doctrine, "Cause no harm."

Just to liven up the argument, what if someone had an exact copy of the genome of, say, Zsa-Zsa Gabor or Adolf Hitler or the latest supermodel or rock star?  Would there be any ethical problems in parents choosing to bring another Zsa-Zsa Gabor into the world?  In a test tube?  Is Zsa-Zsa's genome an intellectual property, that she alone owns?  Who says the so-called parents are even parents if their only contribution was to find a test tube and some DNA?

42. Explain the simple idea behind the expression, "one-gene, one-enzyme," which connects Mendelism with molecular genetics. And how may the expression "one-gene, one-enzyme" be incomplete?
Some of this is answered in #40, involving regulatory genes (may not even produce an enzyme) and by the fact that genes produce a polypeptide, which must often be worked on to produce an enzyme.  Also, some gene products are proteins which are not necessarily enzymes, and there may be functional subunits.  For example, the protein hemoglobin has four subunits produced from two polypeptides, hence two genes involved.

43. Why are microorganisms so useful in molecular genetic experiments? In what situations may microorganisms be inadequate or inappropriate for genetic studies.
They're fast and the don't whine.

Problem is, they don't have half the complexity of humans, e.g., regulatoriy cascade, hormones, multicellurar architecture.  How would you feel if your life depended on a genetic therapy that was developed successfully in microbes?

44. Give some examples of the basic laboratory procedures used in studying DNA and describe their purpose or function.
UV (DNA detection), gel electrophoresis (separate large particles), centrifugation (separation), heating (denaturation) and hybridization kinetics (repetitive DNA).

 
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