Blog Assignment 4: Chapters 6 and 7 Practice Questions

Chapter 6 Practice Questions
1. During cell division in eukaryotic cells (mitosis), the mitotic spindle makes sure each daughter cell gets a copy of each chromosome. How is this accomplished in binary fission?

Binary fission is the process of cell division in bacteria wherein the cell duplicates its components and divides into two cells. The chromosome is replicated before the cell divides into daughter cells.

2. Which type of microbe mostly utilizes budding for reproduction?

Yeast microbes utilize budding for reproduction wherein small, new cells grow on the surface of its parent cell and then separate from it.

3. How does the rate of growth of microbes differ in each phase: lag, log, stationary, decline?

Microbes have fur major phases of growth: (1) the lag phase, (2) the log (logarithmic) phase, (3) the stationary phase and (4) the decline phase.

The lag phase is the period in which microbes have little or no cell division occurs. However, the cells are not dormant and undergo metabolic activities – growth in size, synthesis of enzymes and production of large quantities of energy in the form of ATP. The log phase is the period when the microbes divide and actively grow at a logarithmic rate. The stationary phase is when cell growth slows down and microbial death balances the number of new cells. The growth of new cells and death of old cells are produced at the same rate. The decline phase is the period when microbes lose their ability to divide. The number of cell deaths exceeds the number of formation of new cells at this phase.

4. What is the difference between synchronous growth and nonsynchronous growth?

Synchronous growth is when the rate of cell division is directly proportional to the time resulting to a constant number of cells produced. This will appear like a ladder if placed in a graph because the microbes double their number each time. Nonsynchronous growth is when the pattern for cell growth is not constant.

5. You want to calculate the concentration of microbes in a sample so you perform a serial dilution to dilute the sample by a factor of 10³ and then plate it. It forms 15 colonies. What should you do next?

dilution sample 1:1000
plating 1:10,000 (15 colonies are formed)

The resulting number is used to estimate the number of bacteria in the original sample.

15 x 10,000 = 150,000 microbes in sample

6. If you dilute the sample above by a factor of 10² you achieve a plate count of 213 colonies. What is the concentration of the original sample?

dilution sample 1:100 (213 colonies are formed)
The resulting number is used to estimate the number of bacteria in the original sample.

213 x 100 = 21,300 microbes in original sample

7. Why is it important to shake a suspended culture prior to removing a sample to dilute, plate, or count it?

Shaking a suspended culture prior to sampling is done to minimize error. Organism that has to be counted has to be alive which represent the number of colonies.

8. If you added 20 mµ (microliters) of sample to a hemocytometer and observe the number of cells indicated in each chamber, what is your total cell count per milliliters?

9. A technician performs the MPN on a water sample and obtains the following results: five turbid samples at 10ml (101 dilution), 4 turbid samples at 102 dilution, and one turbid sample at 103 dilution. What is the most probable concentration of microorganisms being tested for in the water sample? (Hint: use page 154 in your book)

10. What are seven physical factors that must be considered when culturing bacteria?

The seven factors that must be considered when culturing bacteria are pH, temperature, oxygen, moisture, hydrostatic pressure, osmotic pressure and radiation.

11. What are five nutritional factors that must be considered when culturing bacteria?

The five nutritional factors that must be considered when culturing bacteria are carbon sources, nitrogen sources, sulfur and phosphorus, trace elements and vitamins.

12. What is the difference between an obligate organism and a facultative one?

Obligate means that the organism must have the specified environmental condition and Facultative means that the organism can adjust to and tolerate the environmental condition but it can also live in other conditions.

13. What are exoenzymes?

Exoenzymes, also known as extracellular enzymes, are enzymes that are synthesized inside a cell but moves out by passing through the cell membrane to function in the periplasmic space or the environment next to the cell.

14. What is the purpose of sporulation?

Sporulation is a protective mechanism of bacteria so that it could withstand and survive the extreme environmental condition like high temperature, radiation and toxic wastes.

15. Describe each step of the sporulation cycle.

The Sporulation Cycle:

1) DNA replication – A long, compact, axial nucleoid is formed.

2) Spore septum begins. This is to isolate the newly replicated DNA and a small portion of cytoplasm

3) Plasma membrane starts to surround DNA, cytoplasm and membrane isolated in the previous stage.

4) Spore septum surrounds isolated portion forming forespore.

5) Peptidoglycan layer forms between membranes.

6) Spore coat forms.

7) Endospore is freed from cell.

16. When is it better to use the pour plate method than the streak plate method?

The pour plate method is better to use than the streak plate method during serial dilutions especially when growing microaerophiles that cannot tolerate exposure to oxygen in the air at the surface of the medium.

17. What is the difference between defined media and complex media? If you add blood serum to a medium what type would it be?

Defined media contain known specific kinds and amounts of chemical substances while complex media contain familiar materials but vary in chemical composition from batch to batch.

18. Compare and contrast selective media, differential media, and enrichment media.

Selective media allows growth of desired organisms but inhibits growth of unwanted organisms; differential media: contain a constituent that causes a change in color or pH in the medium when a particular biochemical reaction takes place making it easier to distinguish colonies of the desired organism; and enrichment media: contain special nutrients that allow growth of a particular organism which is used for preliminary isolation.

19. What are stock cultures, preserved cultures, and reference cultures?

Stock cultures are reserved cultures used to store an isolated organism in pure condition for use in the laboratory; preserved cultures are cultures in which organisms are maintained in a dormant state; and reference cultures are preserved cultures used to maintain an organism with its characteristics as originally defined.

20. What is lyophilization?

Lyophilization is a process more commonly known as freeze-drying. The word is derived from Greek, and means "made solvent-loving". Lyophilization is a way of drying something that minimizes damage to its internal structure. The form of drying is limited to those materials which are sensitive to heat and have delicate structures and substantial value. One of the only substances which cannot be preserved effectively by freeze-drying is mammalian cells, which are too fragile.

Chapter 7 Practice Questions

1. What is the difference between a chromosome and a plasmid?

A plasmid is a circular and double-stranded extra-chromosomal DNA separated from the chromosomal DNA that can replicate independently. A chromosome is a single piece of coiled and organized structure of DNA containing genes, regulatory elements, proteins and nucleotide sequences that is found in cells

The major general differences of plasmids against chromosomes include: plasmids have much less base pairs; are rarely organized by chaperone proteins; are easily transferred; contain non-essential genes; its function can be lost or gained without harming the organism; are usually found in "lower" organisms.

2. What is unique about the chromosomes of Vibrio cholerae and Deinoccocus radiodurans?

Both contain two chromosomes where steps for metabolic pathways can be controlled by one or the other chromosomes. Cells with only one large chromosome has a short life span and cannot reproduce.

3. Which microbe was the first to have its genome completely sequenced? When?

Haemophilus influenzae is the first microbe to have its genome completely sequenced which had been published in Science on July 28, 1995.

4. What is special about the genome of retroviruses? Why must they possess the gene for reverse transcriptase?

Normally, DNA makes RNA. A genome is the sum total of the genes of an organism. Genes are encoded in the sequence of chemical base pairs that make up the intertwining strands of DNA. In the genome for retrovirus, it contains viruses that contain RNA made from DNA. The uncorrected errors are in the mutations derived from this reverse process of transcription. This process cause permanent change in the genes of an organism and the enzyme reverse transcriptase is used to transcribe RNA to DNA.

5. Why is DNA synthesis said to be “semiconservative”?

Semiconservative replication describes the method by which DNA is replicated to produce two copies that contained one of the original strand and one new strand.

6. What role do DNA polymerase, DNA primase (a type of RNA polymerase), helicase, topoisomerase, RNase H, and ligase play in DNA replication?

DNA polymerase is a hand-shaped enzyme that strings nucleotides together to form a DNA strand. It synthesizes the DNA leading strand continuously in the 5’ to 3’ direction.

DNA primase is the enzyme that catalyzes the synthesis of the short RNA primers on single stranded DNA templates used by the DNA polymerase. This is to initiate the synthesis of Okazaki fragments on the lagging strand.

Helicase is made of six proteins arranged in a ring shape that unwinds the DNA double helix into two individual strands.

Topoisomerase is an enzyme that relaxes supercoiling of the replication fork. It cuts and puts it back again on one strand or both strands of a double stranded DNA. This enzymes is active on supercoiled DNA and circular shaped DNA strands.

RNase H is a nuclease that removes the RNA primer which previously began the DNA strand synthesis.

Ligase enzyme links short stretches of DNA together to create one long continuous DNA strand.

7. What is the difference between how the leading strand and lagging strand are copied during DNA replication? Why do they have to be synthesized differently in this fashion?

When the two single DNA strands separate, one can act as templates for the production of two new, complementary DNA strands. The double helix consists of two antiparallel DNA strands with complementary 5’ to 3’ strands running in opposite directions. The continuously synthesized strand is known as the leading strand, while the strand that is synthesized in short pieces and discontinuously is known as the lagging strand. The leading strand serve as a template for the synthesis of a continuous new strand going in the 5’ to 3’ direction.

They are synthesized in this fashion because DNA polymerase can only add new nucleotides to the 3’ end, so a short piece of RNA called an RNA primer, made by primase, starts synthesis. DNA polymerase can then add nucleotides to the 3’ end of the RNA.

8. What would happen if insufficient RNase H were produced by a cell? What if insufficient ligase were produced by a cell?

Insufficient RNase would mean insufficient or slow DNA synthesis because these enzymes are the ones that remove the RNA primer while insufficient ligase would create gaps between nucleotides in the DNA strand.

9. Where do transcription and translation occur in prokaryotes and eukaryotes?

In prokaryotes, transcription and translation both occur in the cytoplasm while for eukaryotes, transcription occurs in the cell nucleus and translation in the cytoplasm.

10. How does transcription in prokaryotes differ from eukaryotes?

In prokaryotes, transcription occurs in the cytoplasm while eukaryotes, in the cell’s nucleus. The proceeding process of translation where mRNA is the end product of transcription, in prokaryotes, mRNA’s translation into proteins also occurs in the cytoplasm while in eukaryotes, mRNA moves to the cytoplasm from the nucleus.

11. What are four key differences between DNA polymerase and RNA polymerase? (“they are different molecules” doesn’t count as one!)

The key differences between DNA polymerase and RNA polymerase:
1) RNA polymerases can initiate a new strand but DNA polymerases cannot.
2) RNA polymerase synthesizes RNA while DNA polymerasesynthesizes DNA.
3) RNA polymerase does not need a primer to initiate synthesis while DNA polymerase needs a primer.

12. Compare and contrast codons and anticodons?

Codon is a sequence of three nucleotides in mRNA that specifies the insertion of an amino acid into a polypeptide. An anticodon is also three nucleotides by which a tRNA recognizes an mRNA codon.

13. What is alternative splicing? Why is it necessary in eukaryotes?

Alternative splicing is a process in which exons of the RNA produced during transcription of a gene are reconnected.

14. What is an operon? In what ways is it similar to alternative splicing?

An operon is a sequence of closely associated genes that regulate enzyme production.

15. During translation, what amino acid sequence would the following mRNA segment be converted into: AUGGACAUUGAACCG? UACCUGUAACUUGGC

16. How come there are only 20 amino acids when there are 64 different codons?

The language that codes for each amino acid is represented by a sequence of three bases called a codon, a 3 base sequence in mRNA which codes for a specific amino acid or a start or stop translation signal. There are 64 possible combinations of the 4 bases taken by threes that can be presented by 4 by 3. This is more than enough combinations to represent the 20 different amino acids. Each codon is specific for only one amino acid.

17. How come prokaryotes can both transcribe and translate a gene at the same time, but eukaryotes cannot?

The location of genetic transcription and translation occurs in the cytoplasm for prokaryotes while for eukaryotes, transcription occurs in its cell nucleus and moves out to the cytoplasm for the process of translation.

18. Which regulatory mechanisms occur at the DNA-level, which occur at the protein-level?

Regulatory mechanisms control to keep the internal environment stable and maintained within narrow limits even if there are environmental changes. Feedback inhibition occurs at protein-level while genetic regulation process (enzyme induction and enzyme repression) occurs at the DNA-level.

19. What is feedback inhibition?

Feedback inhibition is inhibiting enzyme activity by shutting down the first enzyme in the biosynthetic pathway.

20. What are the two types of DNA modifications that block transcription of a gene?

DNA modificatin that block transcription of genes:
1) DNA is condensed too tightly - enzymes cannot get close to the bases.
2) DNA is methylated.

21. What is the difference between a repressor and an activator and how can each be affected by an inducer?

A repressor is a protein that binds to the regulatory sites and prevents transcription factors or RNA polymerase from attachment. The site where RNA polymerase binds with DNA is called the promoter which happens when general transcription factors bind with it and genes are turned on. But when specific transcription factors bind to the regulatory site associated with a gene, genes are unblocked by an activator. Therefore, genes are blocked by repressors while activators turn genes on.
The process that turns on the transciption gene is induction and the substance that acts to induce transcription is called an inducer. So, when an inducer steps in, it removes the transcription factors from the regulatory sites. Both repressors and activators are controlled by inducers.

22. What is an enhancer and how does it help control how much of a particular protein is made?

Regulatory sites far from promoter are called enhancers. It binds with activator protein to increase transcription process even if it is not close to the genes.

23. How does the presence of lactose control the production of lactase?

The presence of lactose will allow RNA polymerase to function in the mRNA. The repressor had binding sites where lactose can attach. Once lactose links with the repressor proteins, its conformation changes and can no longer attach to the promoter site of the operon. This will allow the RNA polymerase to repeatedly transcribe structural genes and translation of the abandoned mRNA makes the enzymes which includes beta galactosidase, permease, transacetylase and lactase for processing lactose.

24. What is the difference between spontaneous mutations and induced mutations? What type are caused by ultraviolet radiation?

Spontaneous mutation occurs in the absence of any agent known to cause changes in the DNA. Induced mutation are produced by mutagens. Ultraviolet rays are mutagens and so, it falls under the category type - induced mutation.

25. How accurate is DNA replication? (That is, how many errors typically result per nucleotide? Per gene?)

DNA replication is extremely accurate. It has a proofreading activity that corrects errors of 1 to 100 nucleotides. Overall, only a single error can occur in 10,000,000 nucleotides.

26. What type of mutation is shown here? AGTGCCGTCAC
TCACGGCCAGTG

frameshift mutation

27. Why are addition and deletion mutations typically more harmful than substitution mutations?

Addition and deletion mutations are harmful because they alter sequences in the nitrogenous bases.

28. Compare and contrast the four types of chromosomal mutations.

Four types of chromosomal mutations:
1) deletion - A region of the chromosome containing one or more nucleotides from the DNA is removed and deficiency will occur where genetic materials is lost.
2) duplication - An extra copy of a region of the chromosome exists. Multiple copies of genes in a chromosome is produced.
3) inversion - This occurs when a chromosome is broken, the region disengages and binds back but in inverted position. This does not change the amount of genetic materials but might have altered its quality. It may cause upgrade or downgrade of a gene.
4) translocation - Like inversion, this may cause upgrade or downgrade of gene where a region breaks off from a chromosome will attach with another promoter region of another chromosome.

29. Compare and contrast the four types of chemical mutagens listed in table 7.4.

Four types of chemical mutagens:
1) base analog - is a molecule similar in structure to one of the nitrogenous bases normally found in DNA.
2) alkylating agent - is a substance that add alkyl group to another molecule
3) deaminating agent - is a substance where an amino group is removed from a nitrogenous base.
4) acridine agent - contains one pyrimidine ring and two benzene rings.

30. What is the difference between a mutagen and a carcinogen?

A mutagen is an agent in the environment that brings about mutation either directly or indirectly such as chemicals and radiation. A carcinogen is an agent that can cause cancer.

31. Compare and contrast the ways high-energy radiation and lower-energy radiation affect DNA.

The most harmful effect of radiation on DNA is the formation of harmful covalent bonds between certain bases.

32. How would the results of a fluctuation test differ if the mutation you are looking at is induced rather than spontaneous?

Results in a fluctuation test will show that in spontaneous mutation, there will be varied results in the colonies produce while in induced mutations, rate consistency will be shown in the presence of a mutagen.

33. What is the purpose of the Ames test? How is it performed?

The Ames Test is used to screen chemicals for mutagenic properties which indicate potential carcinogens.

How it is performed:

1) Two cultures are prepared of Salmonella bacteria that have lost the ability to synthesize histidine

2) The suspected mutagen is placed in a well. (The substance diffuses outward, creating a concentration gradient).

3) Each sample is poured onto a plate of medium lacking histidine.

4) The plates are incubated at 37^oC for two days.

5) Mutagenic substance will cause some organisms to mutate and grow into colonies on medium.

6) The number of colonies on the experimental and control plates are compared.

34. What is the purpose of PCR? How is it performed?

Polymerase chain reaction (PCR) is a technique by which small samples of DNA can be quickly amplified or increased to quantities that are large enough for analysis.

How it is performed:

1) Target DNA will serve as a template for DNA synthesis.

2) Incubate target DNA at 94^oC for 1 minute to separate the strands.

3) Add primers to help start the reaction, nucleotides for assembly into new DNA, and DNA polymerase, the enzyme for catalyzing the synthesis.

4) Primers attach to single-stranded DNA during incubation at 60^oC for 1 minute.

5) Incubate at 72^oC for 1 minute; during this time, two copies of target DNA are formed. The polymerase synthesizes new complementary strands.

6) Repeat the cycle of heating and cooling to make two or more copies of target DNA.

7) After each cycle of synthesis, the DNA is heated to convert the new DNA into single strands. Process is repeated (thermal cycling). Each newly synthesized DNA strand serves in turn as a template for more new DNA until desired number of strands is obtained.