19.E: Review of Molecular Genetics (Exercises)

These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.

19.1: Polypeptides and Proteins

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1. Describe an amino acid and state what all amino acids have in common. (ans)
2. State what makes one amino acid different from another. (ans)
3. Describe how amino acids are joined by peptide bonds. (ans)
4. Compare the terms peptide, polypeptide, and protein. (ans)
5. Due to hydrogen bonds that form between the oxygen atom of one amino acid and the nitrogen atom of another, this gives the protein or polypeptide the two-dimensional form of an alpha-helix or a beta-pleated sheet. This best describes:
   1. the primary structure of a protein (ans)
   2. the secondary structure of a protein (ans)
   3. the tertiary structure of a protein (ans)
   4. the quaternary structure of a protein (ans)
6. In some cases, such as with antibody molecules and hemoglobin, several polypeptides may bond together to form a quaternary structure. This best describes:
   1. the primary structure of a protein (ans)
   2. the secondary structure of a protein (ans)
   3. the tertiary structure of a protein (ans)
   4. the quaternary structure of a protein (ans)
7. The actual order of the amino acids in the protein that is determined by DNA. This best describes:
   1. the primary structure of a protein (ans)
   2. the secondary structure of a protein (ans)
   3. the tertiary structure of a protein (ans)
   4. the quaternary structure of a protein (ans)
8. In globular proteins such as enzymes, the long chain of amino acids becomes folded into a three-dimensional functional shape. This is because certain amino acids with sulfhydryl or SH groups form disulfide (S-S) bonds with other amino acids in the same chain. Other interactions between R groups of amino acids such as hydrogen bonds, ionic bonds, covalent bonds, and hydrophobic interactions also contribute to this structure. This best describes:
   1. the primary structure of a protein (ans)
   2. the secondary structure of a protein (ans)
   3. the tertiary structure of a protein (ans)
   4. the quaternary structure of a protein (ans)
9. Define gene. (ans)
10. Describe how the order of nucleotide bases in DNA ultimately determines the final three-dimensional shape of a protein or polypeptide. (ans)

19.2: Enzymes

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1. Define enzyme and state how enzymes are able to speed up the rate of chemical reactions. (ans)
2. Fill in the blanks.

   Many enzymes require a nonprotein cofactor to assist them in their reaction. In this case, the protein portion of the enzyme, called an _______________ (ans), combines with the cofactor to form the whole enzyme or ____________ (ans). Some cofactors are ions such as Ca⁺⁺, Mg⁺⁺, and K⁺; other cofactors are organic molecules called _____________ (ans) which serve as carriers for chemical groups or electrons. Anything that an enzyme normally combines with is called a _____________ (ans).

3. Briefly describe a generalized enzyme-substrate reaction, state the function of an enzyme's active site, and describe how an enzyme is able to speed up chemical reactions. (ans)
4. State four characteristics of enzymes. (ans)
5. State how the following will affect the rate of an enzyme reaction.
   1. increasing temperature (ans)
   2. decreasing temperature (ans)
   3. pH (ans)
   4. salt concentration (ans)

19.3: Deoxyribonucleic Acid (DNA)

Questions

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1. State the 3 basic parts of a deoxyribonucleotide. (ans)
2. State which nitrogenous bases are purines.
   1. cytosine and thymine (ans)
   2. adenine and guanine (ans)
3. In the complement base pairing of nucleotides, adenine can form hydrogen bonds with ____________ (ans) and guanine can form hydrogen bonds with ____________ (ans).
4. State what is meant by the 3' (3-prime) and 5' (5-prime) ends of a DNA strand. (ans)
5. State why DNA can only be synthesized in a 5' to 3' direction. (ans)
6. What is a nucleosome? (ans)
7. State whether the following characteristics are seen in prokaryotic or eukaryotic DNA.
   1. linear chromosomes (ans)
   2. no nuclear membrane (ans)
   3. presence of nucleosomes (ans)
   4. no mitosis (ans)
   5. produce gametes through meiosis (ans)

19.4: DNA Replication in Prokaryotic Cells

Questions

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1. Briefly describe the process of DNA replication. (ans)
2. State what enzyme carries out the following functions during DNA replication.
   1. Unwinds the helical DNA by breaking the hydrogen bonds between complementary bases. (ans)
   2. Synthesizes a short RNA primer at the beginning of each origin of replication. (ans)
   3. Adds DNA nucleotides to the RNA primer. (ans)
   4. Digests away the RNA primer and replaces the RNA nucleotides of the primer with the proper DNA nucleotides. (ans)
   5. Links the DNA fragments of the lagging strand together. (ans)
3. The DNA strand replicated in short fragments called Okazaki fragments is called the:
   1. lagging strand (ans)
   2. leading strand (ans)

19.5: DNA Replication in Eukaryotic Cells and the Eukaryotic Cell Cycle

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1. Briefly describe the process of DNA replication. (ans)
2. State which cell type has multiple origins of replication in its genome.
   1. prokaryotic (ans)
   2. eukaryotic (ans)
3. Identify the following stages of mitosis.
   1. During this final stage of mitosis, the nuclear membrane and nucleoli reform, cytokinesis is nearly complete, and the chromosomes eventually uncoil to chromatin. (ans)
   2. Refers to all stages of the cell cycle other than mitosis. During this phase, cellular organelles double in number, the DNA replicates, and protein synthesis occurs. The chromosomes are not visible and the DNA appears as uncoiled chromatin. (ans)
   3. During this phase of mitosis, the nuclear membrane fragmention is complete and the duplicated chromosomes line up along the cell's equator. (ans)
   4. During the first stage of mitosis, the chromatin condenses and the chromosomes become visible. Also the nucleolus disappears, the nuclear membrane fragments, and spindle fibers are assembled. (ans)
   5. During this phase of mitosis, diploid sets of daughter chromosomes move toward opposite poles of the cell and cytokinesis (cytoplasmic cleavage) begins. (ans)

19.6: Ribonucleic Acid (RNA)

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1. State the 3 basic parts of a ribonucleotide. (ans)
2. State 3 ways RNA differs from DNA. (ans)
3. Copies the genetic information in the DNA by complementary base pairing and carries this "message" to the ribosomes where the proteins are assembled. This best describes:
   1. tRNA (ans)
   2. mRNA (ans)
   3. rRNA (ans)
4. Picks up specific amino acids, transfers the amino acids to the ribosomes, and insert the correct amino acids in the proper place according to the mRNA message. This best describes:
   1. tRNA (ans)
   2. mRNA (ans)
   3. rRNA (ans)

19.7: Polypeptide and Protein Synthesis

Questions: Transcription

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1. Define transcription. (ans)
2. Match the following with their role in transcription.

   _____ The end of a strand of nucleic acid that has a hydroxyl (OH) group on the number 3 carbon of the deoxyribose or ribose and is not linked to another nucleotide. (ans)
   _____ The covalent bond that links ribonucleotides together to form RNA. (ans)
   _____ The portion of DNA that contains the actual message for protein synthesis. (ans)
   _____ A molecule synthesized by complementary base pairing of ribonucleotides with deoxyribonucleotides to match a portion of one strand of DNA coding for a polypeptide or protein. (ans)
   _____ A series of three consecutive mRNA bases coding for one specific amino acid. (ans)
   _____ A segment of DNA that determines what region of the DNA and which strand of DNA will be transcribed into RNA. (ans)
   _____ The enzyme that initiates transcription, joins the RNA nucleotides together, and terminates transcription. (ans)
   _____ A "stop" signal at the end of a gene that causes the completed mRNA to drop off the gene. (ans)

   1. mRNA
   2. 3' end
   3. 5' end
   4. RNA polymerase
   5. phosphodiester bond
   6. promoter
   7. leader sequence
   8. coding sequence
   9. transcription terminator
   10. codon
3. Match the following with their role in transcription in eukaryotic cells.

   _____ The RNA synthesized after RNA polymerase copies both the exons and the interons of a gene. (ans)
   _____ The RNA produced after non-protein coding regions (introns) are excised and coding regions (exons) are joined together by complexes of ribonucleoproteins called spliceosomes. (ans)
   _____ An unusual nucleotide, 7-methylguanylate, that is added to the 5' end of the pre-mRNA early in transcription. It helps ribosomes attach for translation. (ans)
   _____ Non-protein coding regions of DNA that are not part of the code for the final protein that are interspersed among the coding regions of DNA in most genes of higher eukaryotic cells. (ans)
   _____ The coding regions of DNA in most genes of higher eukaryotic cells that actually code for the final protein. (ans)
   _____ A series of 100-250 adenine ribonucleotides that is added to the 3' end of the pre-mRNA. This series of nucleotides is thought to help transport the mRNA out of the nucleus and may stabilize the mRNA against degradation in the cytoplasm. (ans)

   1. introns
   2. exons
   3. precurser mRNA
   4. cap
   5. poly-A tail
   6. mature mRNA
4. What amino acid sequence would the DNA base sequence 5' ATAGCCACC 3'code for? Hint: see Figure 8. (ans)

Questions: Translation

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1. Define translation. (ans)
2. Match the following with their role in translation.

   _____ A series of three tRNA bases complementary to a mRNA codon. (ans)
   _____ The ribozyme that forms peptide bonds between amino acids during translation. (ans)
   _____ The ribosomal subunit that binds to mRNA to form the initiation complex. (ans)
   _____ The ribosomal site where an aminoacyl-tRNA first attaches during translation. (ans)
   _____ The ribosomal site where the growing amino acid chain is temporarily being held by a tRNA as the next codon in the mRNA is being read. (ans)
   _____ A complex of an amino acid and a tRNA molecule. (ans)
   _____ The sequence of bases on mRNA to which a 30S or 40S ribosomal subunit first attaches. (ans)
   _____ A series of three mRNA bases coding for no amino acid and thus terminates the protein chain: UAA, UAG, UGA. (ans)
   _____ A complex consisting of a 30S or 40S ribosomal subunit, a tRNA having the anticodon UAC and carrying an altered form of the amino acid methionine (N-formylmethionine or f-Met), and proteins called initiation factors. (ans)
   _____ A three-dimensional, inverted cloverleaf-shaped molecule about 70 nucleotides long to which a specific amino acid can be attached; transports amino acids to the ribosome during translation. (ans)

   1. 30S or 40S ribosomal subunit
   2. ribosome binding site
   3. initiation complex
   4. 50S or 60S ribosomal subunit
   5. tRNA
   6. aminoacyl-tRNA
   7. anticodon
   8. P-site of ribosome
   9. A-site of ribosome
   10. peptidyl transferase
   11. nonsense (stop) codon
   12. release factors
   13. start cocon
3. What amino acid sequence would the DNA base sequence AAAGAGCCT code for? Hint: see Fig. 2. (ans)

19.8: Enzyme Regulation

Questions

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1. Matching

   _____ Regulatory proteins that block transcription of mRNA by binding to a portion of DNA called the operator that lies downstream of a promoter. (ans)

   _____ A molecule that alters the shape of the regulatory protein in a way that blocks its binding to the operator and thus permits transcription. (ans)

   _____ Regulatory proteins that promote transcription of mRNA. (ans)

   _____ A molecule that alters the shape of the regulatory protein to a form that can bind to the operator and block transcription. (ans)

   _____ Producing antisense RNA that is complementary to the mRNA coding for the enzyme. When the antisense RNA binds to the mRNA by complementary base pairing, the mRNA cannot be translated into protein and the enzyme is not made. (ans)

   _____ The induction or repression of enzyme synthesis by regulatory proteins that can bind to DNA and either block or enhance the function of RNA polymerase. (ans)

   _____ The inhibitor is the end product of a metabolic pathway that is able to bind to a second site (the allosteric site) on an enzyme. Binding of the inhibitor to the allosteric site alters the shape of the enzyme's active site thus preventing binding of the first substrate in the metabolic pathway. (ans)

   _____ The inhibitor is the end product of an enzymatic reaction. That end product is also capable of reacting with the enzyme's active site and prevents the enzyme from binding its normal substrate. (ans)

   1. activators
   2. competitive inhibition
   3. corepressors
   4. genetic control
   5. inducer
   6. noncompetitive inhibition
   7. repressors
   8. translational control
2. Describe how the lac operon in E. coli functions as an inducible operon. (ans)

19.9: Mutation​​​​​​​

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1. Match the following:

   _____The sequence of deoxyribonucleotide bases in the genes that make up a organism's DNA. (ans)
   _____ An error during DNA replication that results in a change in the sequence of deoxyribonucleotide bases in the DNA. (ans)
   _____ Alternate forms of a gene. (ans)
   _____ Mutations caused by mutagens, substances that cause a high rate of mutation. (ans)
   _____ The physical characteristics of an organism. (ans)

   1. genotype
   2. phenotype
   3. allele
   4. mutation
   5. spontaneous mutation
   6. induced mutation
2. Describe 2 different mechanisms of spontaneous mutation. (ans)
3. Match the following:

   _____ This is usually seen with a single substitution mutation and results in one wrong codon and one wrong amino acid (ans)
   _____ If the change in the deoxyribonucleotide base sequence results in transcription of a stop, the protein is terminated at that point in the message. (ans)
   _____ This is sometimes seen with a single substitution mutation when the change in the DNA base sequence results in a new codon still coding for the same amino acid. (ans)
   _____ This is seen when a number of DNA nucleotides not divisible by three is added or deleted and all of the codons and all of the amino acids after that addition or deletion are usually wrong. (ans)

   1. sense mutation
   2. nonsense mutation
   3. frameshift mutation
   4. missense mutation
4. Briefly describe 3 ways chemical mutagens work. (ans)
5. Compare ultraviolet radiation and gamma radiation in terms of how they induce mutation. (ans)
6. As a result of a substitution mutation, a DNA base triplet AGA is changed to AGG. State specifically what effect this would have on the resulting protein (see Figure 9). (ans)
7. A third triplet in a bacterial gene is TTT. A substitution mutation changes it to ATT. State specifically what effect this would have on the resulting protein (see Figure 9). (ans)