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BIOL 207 (Principles of Genetics) > Topic B: Mutation and Repair > Flashcards

Topic B: Mutation and Repair Flashcards

1
Q

What is the main driving force behind evolution? Why?

A
  • Variation in genetic material (such as mutation)
  • variation in genetic material allows organisms to have phenotypic variation in their species, which allows for adaptation to an ever changing environment
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2
Q

What is a mutation?

A

A heritable alteration/change in the nucleotide/DNA sequence of cellular DNA.

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3
Q

What is a mutant?

A

An organism or cell bearing a mutation that typically expresses itself in the phenotype of the organism or cell.

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4
Q

What is a phenotype?

A
  • The observable traits of an organism/cell
  • a little bit misleading, phenotype is not ALWAYS directly observable with the naked eye. (Ex. Shape of the liver is a phenotype, we do not see this regularly)
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5
Q

Genetic variation is the result of 2 things:

A
  • Mutation
  • Recombination
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6
Q

What is recombination in terms of genetic variation?

A
  • new combinations of genetic material through crossing over in meiosis.
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7
Q

Mutation is the ______ _______ of evolutionary change.

A

Mutation is the ultimate source of evolutionary change.

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8
Q

What are the two classifications of mutations, based on what cells the mutations effect?

A
  • Somatic mutations
  • Germline mutations
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9
Q

What is a somatic mutation?

A
  • mutations that occur after an embryo has been formed
  • somatic cells (body cells) are effected by the mutation, which in then only effects descendants of the somatic cells effected.
  • only effects specific portions of the body
  • NOT transmitted to the next generation (no gametes by the effected person carry the mutation)
  • ex. Lung cancer
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10
Q

What are germline mutations?

A
  • Mutations that effect the germline cells (cells that form gametes)
  • mutation that effects the sperm or ovary before fertilization occurs
  • mutation is found throughout the entire body
  • because germline cells are effected, mutation can be transmitted to the next generation (half of the gametes by the original generation carry the mutation)
  • ex. sickle cell disease
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11
Q

What are the two ways mutations may arise?

A
  • may arise spontaneously (without outside influences)
  • may be induced by agents called mutagens (with outside influence)
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12
Q

What are spontaneous mutations?

A
  • Mutations that arise spontaneously, without any outside influences
  • due to natural DNA replication errors, from normal cellular processes.
    ex. if DNA polymerase III (proofreading enzyme) misses a mistake made in the DNA code
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13
Q

What are induced mutations?

A
  • mutations that are caused by outside influencers called mutagens
  • a mutagen is anything that can cause mutations in an organism/cell
  • typically there is a linear response to the level of mutation. With higher mutagen exposure, there will be higher increases in mutant frequency
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14
Q

What are the 3 broad classes of mutagens?

A
  • Chemical
  • physical (radiation, like X-rays and UV)
  • biological (viruses or bacteria)
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15
Q

Mutagens may effect:

A
  • single base pairs, or a small number of adjacent base pairs
    OR
  • large segments of DNA, whole chromosomes or chromosome sets
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16
Q

What is a point mutation?

A
  • where a single base pair or a small number of base pairs are effected by mutation
  • can be called single base substitution
  • ex. when a single pyrimidine mutates to another pyrimidine (ex.T to C) OR when a pyrimidine mutates to a purine (ex.T to G)
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17
Q

What is a wildtype phenotype?

A

the most common phenotype found in a species

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18
Q

What is an indel mutation?

A
  • small mutation where either a nucleotide base is removed from a sequence, (ex. “T” is removed from the DNA code) or an additional nucleotide base is added to a sequence. (ex. new “T” is added to a code)
  • indel mutation is a insertion or deletion mutation.
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19
Q

what is a genome?

A
  • the sum total of all DNA of an organism
  • multiple chromosomes
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20
Q

What are chromosomes made up of?

A
  • supercoiled DNA and histone proteins
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21
Q

What is DNA made of?

A
  • genes interspaced by intergenic regions
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22
Q

What is a gene?

A
  • A unit of heredity that may influence the outcome of an organism’s trait
  • can be passed from parent to offspring
  • contains the information to make a functional product - either an RNA or a protein (Not always DNA)
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23
Q

Where do genes reside?

A
  • genes reside at fixed locations on a chromosome called a locus/loci
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24
Q

What is the central dogma

A
  • information flows in one direction, from DNA to RNA to protein
  • DNA makes RNA, RNA makes protein
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25
Q

What is replication? What is the product of replication?

A
  • when DNA makes copies that are transmitted from cell to cell and from parent to offspring
  • DNA polymerase uses previous DNA to make new DNA, which is the product.
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26
Q

What is transcription? What is the product?

A
  • transcription produces an RNA copy of a gene
  • RNA polymerase uses the DNA produced from replication to produce mRNA
  • mRNA (messenger RNA) is the product of transcription)
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27
Q

Where does transcription take place?

A
  • occurs in the nucleus
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28
Q

What is mRNA used for in transcription?

A
  • mRNA is a temporary copy of a gene that contains information to make a polypeptide
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29
Q

What is the transcription start site? What are the locations before and after the TSS called?

A
  • starts at “+1” on a DNA sequence
  • location where transcription for mRNA starts (where it starts getting made)
  • location before TSS is called “upstream”, location after is called “Downstream”
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30
Q

in transcription, RNA polymerase bonds to what site on the DNA strand?

A

Promoter site, which is located before transcription start site

31
Q

mRNA gets made in the same direction that DNA does, from __________________. Because of this, the mRNA uses the opposite strand, _________, to ‘copy’ from, complimenting it.

A

mRNA gets made in the same direction that DNA does, from 5’ ——-3’. Because of this, the mRNA uses the opposite strand, 3’ —— 5’, to ‘copy’ from, complimenting it’s bases.

32
Q

5’ —– 3’ DNA strand mRNA ‘copies’ is called the:

A

non-template or coding strand

33
Q

3’—–5’ DNA strand mRNA ‘compliments’, and actually uses in its formation is called the:

A

template or non-coding strand.

34
Q

What is translation? How does it work?

A
  • the producing of a polypeptide using the information in mRNA, which occurs in the cytoplasm.
  • ribosomes bind to mRNA at the “start” codon of the coding region on the mRNA strand, and works with tRNA to make proteins
  • polypeptide is the product of translation, which becomes part of a functional protein that contributes to an organisms traits.
35
Q

How many copies of each chromosome do diploids have? How many copies of each gene?

A
  • Diploids carry 2 copies of each chromosomes
  • diploids carry 2 copies of each gene
36
Q

How many alleles can a diploids carry of a single gene?

A
  • diploids can carry a maximum of 2 alleles of a single gene
37
Q

How many copies of a chromosome do monoploids have?

A
  • one copy
38
Q

What is expression? What controls expression in transcription?

A

Expression: How many copies of that gene is expressed or produced

The promoter sequence controls expression in transcription

39
Q

If a mutation occurs at the promoter sequence in transcription, and RNA polymerase binding is PREVENTED, what is the impact on:
- transcription levels
- polypeptide production
- total gene product activity

A
  • no transcription will occur
  • no polypeptide will be produced
  • there will be no gene production activity
40
Q

What is the mutation called if a mutation occurs at the promoter sequence in transcription, and RNA polymerase binding is PREVENTED

A

Knockout or Null mutation

41
Q

If a mutation occurs at the promoter sequence in transcription, and there is a DECREASE in efficiency on RNA polymerase binding, what is the impact on:
- transcription levels
- polypeptide production
- total gene product activity

A
  • reduced transcription levels
  • reduced production of polypeptides
  • reduced overall activity
42
Q

What is the mutation called If a mutation occurs at the promoter sequence in transcription, and there is a DECREASE in efficiency on RNA polymerase binding

A

Knockdown (when expression is reduced)

43
Q

If a mutation occurs at the promoter sequence in transcription, and there is an INCREASE in efficiency on RNA polymerase binding, what is the impact on:
- transcription levels
- polypeptide production
- total gene product activity

A
  • increased transcription levels
  • increased production of polypeptides
  • overall increased activity
44
Q

What is the mutation called If a mutation occurs at the promoter sequence in transcription, and there is an INCREASE in efficiency on RNA polymerase binding

A

Overexpression

45
Q

What is the mutation called If a mutation occurs at the promoter sequence in transcription, and there is no effect on RNA polymerase binding

A

Silent mutation

46
Q

If a mutation occurs after the promoter sequence, in the coding region, what can potentially happen?

A
  • a point mutation in the coding region can have a number of potential impact on the activity of the polypeptide encoded by that gene
  • in general, expression will be normal, but the FUNCTION OR ACTIVITY will be altered!
47
Q

If a mutation has NO impact on a polypeptides function/activity, what is it called?

A

Silent mutation

48
Q

If a mutation has abolished impact on a polypeptides function/activity, causing the polypeptide to not work at all, what is it called?

A

Loss of function/Knockout/Null mutation

49
Q

If a mutation causes reduced function of a polypeptide, what is the mutation called?

A

knockdown mutation

50
Q

If a mutation causes increased or new function of a polypeptide, what is the mutation called?

A

gain of function mutation

51
Q

Ribosomes read codons in ______

A

triplets

52
Q

each codon set in mRNA is associated with an

A

Amino acid

53
Q

What is the start of the polypeptide chain being created called? the end?

A

Start: N-Terminus
End: C-Terminus

54
Q

Genetic code is degenerate, meaning ….

A
  • Many amino acids are encoded by more than one codon.
  • If point mutation occurs, since multiple codons will be associated with the same amino acid, even if there is a change in the code of the DNA, the amino acid will not be changed and the polypeptide sequence will stay the same
  • Ex. If AUC was changed to AUU due to point mutation, no change occurs because both codons are associated with the amino acid Isoleucine (ILE)
  • So mutation occurs, but code doesn’t change (called a silent mutation)
55
Q

Amino acid properties are based and grouped on the nature of…

A
  • their side chains (“R-group”)
56
Q

The four groups of amino acids are ….

A
  • nonpolar
  • polar, uncharged
  • polar, negatively charged (Acidic)
  • polar, positively charged (basic)
57
Q

Describe the standard amino acid structure (The “building block”)

A
  • Central Carbon linked to:
  • Carboxyl group (COOH)
  • Hydrogen (H)
  • Amino group (NH3+)
  • R-Group (where the individual amino acid will have different compounds here)
58
Q

What are the 9 Nonpolar amino acids?

A
  • Glycine (Gly)
  • Alanine (Ala)
  • Valine (Val)
  • Leucine (Leu)
  • Isoleucine (Ile)
  • Methionine (Met)
  • Phenylalanine (Phe)
  • Tryptophan (Trp)
  • Proline (Pro)
59
Q

What are the 6 polar (uncharged) amino acids?

A
  • Serine (Ser)
  • Threonine (T)
  • Cycteine (Cys)
  • Tyrosine (Tyr)
  • Asparagine (Asn)
  • Glutamine (Gln)
60
Q

What are the 2 acidic (polar negatively charged) amino acids?

A
  • Aspartate (Asp)
  • Glutamate (Glu)
61
Q

What are the 3 basic (polar positively charged) amino acids?

A
  • Lysine (Lys)
  • Arginine (Arg)
  • histidine (His)
62
Q

What is the most likely effect with a nonsense mutation?

A
  • No protein is made, Codon is altered to a “stop” codon
63
Q

What is the most likely effect for a missense conservative mutation?

A

changes the codon so a different amino acid is produced, but produces an amino acid in the same group, causing minor changes in general.

64
Q

What is the most likely effect for a missense non-conservative mutation?

A

changes the codon so a different amino acid is made, from a different amino acid group, causing major changes (change of function of protein)
ex. if the original amino acid was supposed to be a polar AA, but the mutation causes a nonpolar AA to form instead.

65
Q

What are the most likely consequences of an indel mutation in the coding region?

A
  • Nucleotide-pair deletion: frameshift causing extensive missense.
  • The indel mutation results in “frameshift” and the effects are normally harm-causing
  • By taking out or adding a new nucleotide base, it “shifts” the entire structure of the mRNA strand (because ribosome reads in triplets), so none of the nucleotide bases after the mutation will be the same codon, resulting in them all potentially having different amino acids.
  • this can result in a protein that is completely different from the original DNA coding strand
66
Q

What are mutations the result of?

A

Mutations are the result of failure in repair of damage occurred to DNA

67
Q

Why does DNA damage not automatically mean mutations?

A
  • Not all DNA damage results in mutation, because the majority of DNA damage is repaired, due to repair mechanisms
  • mutations only occur when DNA damage is NOT fixed (AKA mutations are the result of failed repair)
68
Q

What are the two “paths” that could potentially occur when DNA damage takes place?

A

1: DNA damage –> DNA repair –> genetic stability

  1. DNA damage –> defective/incomplete DNA repair
    –> Genetic instability –> mutation
69
Q

What are the 6 broad commonalities between different repair pathways when repairing DNA?

A
  1. recognition of change (Surveillance proteins find damaged DNA)
  2. Damage is marked (Surveillance proteins mark the damage)
  3. DNA is cleaved around the damaged area
  4. Damaged region is excised (AKA it is removed from the strand)
  5. repair is carried out thru DNA synthesis (the correct/non-damaged strand is made)
  6. new and preexisting DNA are joined by ligase
70
Q

What are deleterious mutations?

A
  • Most mutations that arise are deleterious
  • Deleterious mutations are mutations that are not advantageous, or harmful
  • Decreased the overall fitness (impedes the organisms ability to transmit its genes) of individuals
  • Change the end-product of a gene to a less efficient or non-functional form
  • The effect can range from being only slightly negative to being lethal
71
Q

What are beneficial mutations?

A
  • Beneficial mutations are those that have a positive effect on an individual
  • Increases the fitness of individuals
  • Change the end-product of a gene to a more efficient form or create a new function altogether
  • Beneficial mutations are those that make individuals stronger, or more resistant to a particular disease, or more tolerant to a particular environmental stress
  • If the mutated individuals fitness is increased, or it lives longer, it can mate more, and the mutation may eventually become the wildtype gene.
72
Q

What are neutral mutations?

A
  • Neutral mutations have no effect on the fitness (do not alter the organisms ability to transmit its genes) of individuals
  • Includes: mutations in non-coding regions of DNA, mutations that occur in a gene but do not affect the product of that genes, mutations that result in a new phenotype that has neither positive or negative effect on an individual in their current environment
73
Q

Explain how mutations can be selected for or against in a population

A
  • If a mutation is beneficial, it increases the fitness of the individual. There will be a higher frequency of the mutation in future generations due to higher fitness. After many generations, the mutation may become the wildtype gene. This causes a mutation to be “selected” for in a population.
  • If a mutation is harmful, it decreases the fitness of the individual. The next few generations will have less frequency of the mutation due to the lowered fitness, and after many generations it will not be present at all. This causes a mutation to be “selected” against in a population.

BIOL 207 (Principles of Genetics) (8 decks)

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