Exam 4: Microbial Genetics II Mutation Types and Causes Flashcards

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1
Q

What is a mutation? Why do mutations occur? Are mutations good or bad? Explain.

A

Random haritable charitable change in the nucleotide sequence of DNA. Mistakes, relatively rare, typically occur during DNA replication. Most have insignificant effect to or no effect on phenotype. If they do have an effect far more mutations have deleterious effects than have a beneficial effect upon the individual.

Alterations can be passed to daughter cells in unicellular organisms. In multicellular organisms mutations in reproductive cells can be passed to offspring.

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2
Q

Describe the relationship between mutation, natural selection, and evolution?

A

Mutations are the ultimate source of genetic variation and natural selection acts upon this genetic variant. Without mutations there’s no genetic variation and thus no evolution.

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3
Q

Under what conditions or during what times are mutations more likely to occur?

A

Most likely to occur during DNA replication. If a population is small and isolated then inbreeding will increase the incidence of existing mutations.

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4
Q

What effect do most mutations have on the fitness of an organism?

A

Most are deleterious and are likely to decrease the fitness of an organism.

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5
Q

What effect do most mutations have on the function of a gene?

A

Most mutations will inhibit the function of the gene. That can be turning it on when it’s not supposed to be or keeping it off when it should be off.

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6
Q

If a mutation does affect gene function, is it more likely to impair function or to improve function? Explain.

A

Most likely will impair the function causing the function to deviate from its normal status.

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7
Q

Give at least one specific example of a deleterious mutation.

A

Antennapedia- drosophila (fruit flies) have legs instead of antennae.

Sickle cell, cystic fibrosis, tay sachs disease.

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8
Q

Give at least one specific example of a beneficial mutation.

A

Lactose tolerance- historically humans were lactose intolerant, they drink milk from their mother then milk consumption ends and the lactose processing gene is turned off. However mutation occurred where individuals continued to possess the lactose gene into adulthood, giving them the ability to drink milk throughout life. With the advancements of farming and access to milk products they had another food source they could use. This was an advantage giving them an edge to stay alive and ultimately reproduce, giving the gene to future generations.

Globally outside the US most people still contain the wild type gene and cannot produce lactose. Lactose production is still the minority on a global scale.

Antibiotic resistance- advantageous to bacteria.

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9
Q

What is mutation rate?

A

Likelihood a gene will be altered by a new mutation. Expressed as the number of new mutations in a given gene per cell generation.

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10
Q

What factors affect mutation rate?

A

Type of mutation in question- varies mutation to mutation.
Size of gene- bigger gene more likely for mutations.
Chromosomal location of gene- some areas are more likely to have mutations then others.
Species studied
Strain of species studied
Efficiency of the DNA repair systems
Presence of mutagens- like radiation

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11
Q

What is mutation frequency?

A

Refers to the prevalence of a particular mutant allele in a population. Frequency of a particular mutation is initially very low because the mutation rate is very low.

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12
Q

What factors affect mutation frequency?

A

Will vary depending on location for example the rate of blue eye mutation might be the same everywhere but the frequency will change depending on the population you evaluate. Natural selection can significantly alter the frequency of the mutation allele. Deleterious alleles commonly decrease in frequency while beneficial alleles commonly increase in frequency.

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13
Q

All mutations are initially rare. Do they all remain rare? Explain.

A

Yes, initially all mutations are rare. But there are factors that can increase their frequency. Radiation, antibiotic usage, and mutagens can increase the frequency of mutations.

Antibiotic bacteria resistance rate might be very low but if you look at samples from individuals you might find that these bacteria are resistant to penicillin. The initial rate of the mutation was very low but with more prevalent use of penicillin an environment was created that selected for individuals that were resistant. Frequency went up but the mutation rate stays low.

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14
Q

What is a chromosomal mutation?

A

Changes in chromosome structure. X-rays are great at causing breaks in chromosomes then errors occur when the body tries to fix it. e.g Deletions, insertions, and translocations.

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15
Q

What is a genome mutation?

A

Changes in chromosome number. E.g. Trisomy 21 “down syndrome”. In most cases 3 copies of chromosomes produce nonviable embryos so are rarely seen except for with chromosome 21.

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16
Q

What is a single-gene mutation?

A

Relatively small changes in DNA structure, occur within a single gene.

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17
Q

What is a point mutation?

A

Point mutations affect a single base pair. Two main classes are substitutions and insertions/deletions.

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18
Q

What is a base substitution mutation?

A

One nucleotide substituted for another. Two types transitions and transversions.

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19
Q

What is an insertion mutation?

A

One more nucleotides added.

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20
Q

What is a deletion mutation?

A

One or more nucleotides removed.

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21
Q

What is a transition mutation?

A

Type of base substitution. Pyrimidine changed to another pyrimidine, C-> T. Purine changed to another purine, A->G. More likely to occur than transversions as it is easier to mix them up.

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22
Q

What is a transversion mutation? How hard is it to make?

A

Type of base substitution. Purine and pyrimidines are interchanged, A->C or G and C-> A or G. Harder mistakes to make so are less common than transitions.

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23
Q

What types of mutations listed above are likely to constitute frameshift mutations?

A

More likely to occur with insertions or deletions compared to transitions or transversions.

24
Q

How are silent mutations and neutral mutations alike, and how do they differ?

A

They are similar in that they generally do not affect the phenotype. However they differ in that for silent mutations the resulting amino acid is the same but for neutral mutations the amino acid sequence is altered.

25
Q

Silent mutations

A

Amino acid sequence is not altered. e.g. TTT->TTC(phe->phe). Genetic codes are degenerate, alterations of the third based on a codon often does not alter the encoded amino acid. Phenotype not affected.

26
Q

Neutral mutation

A

type of missense mutation. Amino acid sequence is altered. No detectable effect on protein function.

27
Q

How are missense mutations and nonsense mutations alike, and how do they differ?

A

Same in that the amino acid sequence is altered however missense its one amino acid for another and for nonsense its one amino acid for a stop. Both are likely to affect the phenotype.

28
Q

Missense mutations

A

Amino acid sequence is altered. One amino acid substituted for another. e.g. GAA-> GTA (glu->val). Phenotype may be affected. This is the cause of sickle-cell disease.

29
Q

Nonsense mutations

A

Normal codon is changed into a stop codon. e.g. AAA->AAG lys->Stop.Translation is prematurely terminated, truncated polypeptide formed. Protein function is generally adversely affected.

30
Q

What is the relationship between a missense mutation and a neutral mutation?

A

Neutral mutation is a type of missense mutation however no detectable effect on protein function is observed.

31
Q

What is a frameshift mutation? Compared to a missense mutation, is it more likely or less likely to disrupt gene function? Explain.

A

Frameshift mutation: Caused by the insertion or deletion of one or more nucleotides. e.g GAA TAG-> GAA ATA G. Alter the frame in which codons are read, shifted codons downstream of the mutation encode inappropriate amino acids. Termination codon appears early. Very likely that protein function is adversely affected.

32
Q

Compare and contrast spontaneous mutations and induced mutations.

A

Spontaneous mutations arise from abnormalities in biological processes, the underlying cause lies within the cell. Induced mutations are caused by environmental agents, cause originates outside the cell.

33
Q

What are the key causes of spontaneous mutations?

A
  • abnormalities in crossing voer
  • aberrant segregation of chromosomes during meiosis (change in number of chromosome)
  • alteration of DNA by chemical products of normal metabolic process
  • Mistakes by DNA polymerase during replication.
  • Spontaneous changes in nucleotide structure
  • integration of transposable elements.
34
Q

How does depurination occur? How common are depurination events? What needs to occur for it to give rise to a mutation? Can it cause transition mutations, transversion mutations, or both? Explain.

A

Reaction with water (hydrolysis) removes a prine (A or G) from the DNA and occurs very slowly as it is not catalyzed by an enzyme. It’s a naturally occurring process and is a potential when water is present. Results in apurinic site.

Most common type of naturally occurring chemical change. ~10,000 purines are lost every 20 hours. Generally recognized by DNA repair enzymes but mutations arise if the system fails. Both transition and transversion mutations can arise.

35
Q

How does the removal of an amino group from cytosine alter its hydrogen-bonding characteristics? What is the name for this modified base? Is this change likely to be corrected?

A

Hydrolysis (chemical reaction with water) can result in the removal of the amino group from the cytosine base to form uracil. NH2 replaced with O. The DNA system generally removes this base, uracil is recognized as an inappropriate base in DNA. . If it happens immediately before replication it will not get repaired. Mutation may arise if the repair system fails, uracil hydrogen bonds with A not G

36
Q

How does the removal of an amino group from 5-methyl cytosine alter its hydrogen-bonding characteristics? What is the name for this modified base? How likely is this change to be corrected as compared to the deamination of (non-methylated) cytosine?

A

Methylation of cytosine occurs in many eukaryotic species and sometimes prokaryotes. Removal of an amino group from the 5-melty cysteine produces thymine. Thymine is a normal base so DNA repair cannot determine which is the incorrect base. GT pair instead of the correct GC pair. Methylated sites are hot spots for mutations. 50/50 split in if the repair corrects the right one it guesses if the G is correct or the T is correct.

37
Q

What is a tautomeric shift? How might a tautomeric shift give rise to a mutation?

A

All 4 of DNA bases constantly shift between two different chemical structures involving the movement of a H atom and a double bond; these are tautomeric shifts.

Tautomeric shifts immediately prior to DNA replication can cause mutations. Resulting mismatch could be repaired how if its not then a mutation results.
38
Q

Stable form of T, G, C, and A?

A

Common, stable form of T and G is the keto form, interconverted to the enol form at a lower rate. Hydrogen released and grabbed by oxygen so the double bond moves. Keto vs. Enol form, enol has a OH because it’s an alcohol.

Common stable form of C and A is the amino form, interconverted to an imino from at a low rate. Nitrogen has two H bonds in the amino form but moves in the imino form, the double bond moves with the hydrogen off the nitrogen.

39
Q

Compare the two tautomers of guanine, both in terms of their structures and in terms of their abilities to hydrogen-bond with other bases.

A

Keto form of G binds to C, normal. However enol G binds to T. Double bond moves from the O to the adjacent N.

40
Q

Compare the two tautomers of adenine, both in terms of their structures and in terms of their abilities to hydrogen-bond with other bases.

A

Amino form A binds to T, normal. However imino form A binds to C.

41
Q

Compare the two tautomers of thymine, both in terms of their structures and in terms of their abilities to hydrogen-bond with other bases.

A

Keto form of T binds to A, normal. However Enol form T binds to G.

42
Q

Compare the two tautomers of cytosine, both in terms of their structures and in terms of their abilities to hydrogen-bond with other bases.

A

Amino form C binds to G, normal. However, the imino form of C binds to A.

43
Q

What is formed when guanine is oxidized by reactive oxygen compounds? What are the hydrogen-bonding characteristics of this modified guanine as compared to those of guanine? If this change is not corrected, is it more likely to give rise to transition mutations or transversion mutations? Explain.

A

All aerobic organisms produce reactive oxygen species (ROS) as products of oxygen metabolism, toxic forms of oxygen. ROS can accumulate and damage cellular molecules, including DNA. Various molecules can act as protective antioxidants, e.g vitamin C.

Guanine bases are particularly vulnerable to oxidation, will get converted to 8-oxoguanine. Pairs with base A instead of C. Transversion mutation of C-G -> T-A results

44
Q

What is a mutagen? List three different examples of mutagens.

A

Chemical substance or physical agent originating outside of the cell. Alter DNA structure after entering the cell. X-rays, UV light, nitrous acid, nitrogen mustard.

45
Q

What feature defines ionizing radiation? How can ionizing radiation cause mutations? What are two different forms of ionizing radiation?

A

X-rays and gamma rays. Energizes electrons causing some to escape from their atoms. Free electrons strike other atoms and produce ions that can react with DNA. These reactions can cause mutations. Can cause physical breaks in chromosomes. These breaks can lead to larger-scale chromosomal mutations such as deletions, inversions, and trans locations.

46
Q

Describe two distinctly different situations in which the use of ionizing radiation for the purpose of causing mutations is beneficial to humans. (Think about the Controlling Microbes unit and the What is a Gene? unit.)

A

That experiment with neurospora crassa, radiation used to increase mutation prevalence for studying.

47
Q

What is an example of non-ionizing radiation? In what specific way does it damage DNA?

A

Ultraviolet radiation. Has more energy than visible light but less than ionizing radiation. Causes the formation of new covalent bonds between pyrimidine bases (T and C). Prevents bonding with bases in complementary DNA strands , distorts sugar phosphate backbone, and prevents proper replication and transcription. Cells have multiple methods of repairing these dimers, and almost all the time it is fixed successfully.

48
Q

What is a nucleotide analog? How can such a molecule cause a mutation?

A

Molecules that are structurally similar to normal nucleotides. Incorporated into DNA in a palace of normal nucleotides. Two possible outcomes, inhibit nucleic acid polymerase or result in mismatched base pairs.

49
Q

In what way can nitrous acid (HNO2) alter a nitrogenous base, and how might this alteration result in a mutation? What type of mutation is such a mutagen likely to cause – a transition or a transversion?

A

Replaces adenine’s amine group with keto group. Adenine is converted into hypoxanthine, a guanine analog. Replication converts A-T base pairs into a G-C base pair.

With cytosine it can replace amino groups into keto groups. Cytosine is converted to uracil. Replication converts a C-G base pair into a T-A base pair.

50
Q

Describe the general structure of a frameshift mutagen. Describe the mechanism by which such a mutagen can cause a mutation. What type of mutation is such a mutagen likely to cause?

A

Ethidium bromide and acridine are intercalating agents. These two dimensional molecules can slip between base pairs. DNA structure is distorted. DNA polymerase can insert or delete on or more bases in daughter strands.

51
Q

Oxidative stress

A

refers to an imbalance between production of ROS and the ability to break them down.

52
Q

5’-bromouracil

A
  • Nucleotide analog
  • modified form of thymine
  • An electron-withdrawing bromine replaces a non-polar methyl group
  • Stable is keto less-stable is enol.
  • Adenine binds to keto while guanine binds to enol.
  • Transition mutation results.
53
Q

Acylovir

A
  • Nucleotide analog of guanosine.
  • effective aginst herpies viruses.
  • interferes with DNA synthesis. Chain termination due to lack of 3’ OH group.
54
Q

Azidothymidine (AZT)

A
  • adenosine nucleotide analog.
  • effective aginst HIV and other retroviruses.
  • Interferes with viral DNA synthesis. Causes chain terminator.
55
Q

Ethyl methanesulfonate (EMS)

A
  • Nucleotide-altering chemcial.
  • Adds an ethyl group to guanine keto group.
  • Guanine is converted into 6-ehtylganine which can H bond with thymine instead of normal cystoine.
  • Can also add ethyl group to thymines keto group.
  • Thymine converted into 4-ethylthmin, which can H bond with guanne instead of normal adenine.