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Genes and Genomics > Exam 1- Mutations and DNA > Flashcards

Exam 1- Mutations and DNA Flashcards

1
Q

What is Personal Genomics?

A

Looking at the sequence of individuals DNA in order to determine disease risk, personalize medicine, or plan pregnancy

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2
Q

What is Personalized Medicine?

A

Using individual genomics to specifically tailor treatment to the individual

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3
Q

What Was the 4 Criteria Scientists Needed for DNA?

A
  1. Must contain complex information
  2. Must replicate faithfully
  3. Must encode the phenotype
  4. Must be able to vary
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4
Q

What did the 1928 Griffith Experiment Determine?

A

There was some sort of genetic code that was passed down across generations that contained complex information… they just didn’t understand what it was

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5
Q

What did the 1944 Avery, MacLeod, and McCarty Experiment Determine?

A

Identified DNA as the hereditary molecule passed down over generations containing code

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6
Q

What did the 1952 Hershey-Chase Experiment Determine?

A

Proved that DNA was the hereditary molecule passes by the infecting phage into the host cell and inherited by the phylogeny base

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7
Q

What are Nucleotides?

A

The building blocks of DNA

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8
Q

What are Nucleotides Made of?

A

Phosphate, Sugar, and nitrogenous base

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9
Q

What is DNA?

A

A polymer of nucleic acids on a sugar-phosphate backbone

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10
Q

What are Purines?

A

Adenine and Guanine

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11
Q

What are Pyrimidines?

A

Cytosine and Thymine

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12
Q

What is the Base Pairing in DNA?

A

A-T and C-G

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13
Q

What did Chargaff Discover?

A

% A = % T and % G = % C in double stranded genomes. But A+T does not equal G+C

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14
Q

What are the Characteristics of the Genetic Code (4)

A
  1. Non Overlapping
  2. Triplet
  3. No gaps in the code (start-stop)
  4. 20 amino acids
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15
Q

How Many Nucleotides in a Codon?

A

3

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16
Q

What is a Genotype?

A

Genetic code for a gene

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17
Q

What is a Phenotype?

A

Physical traits coded by genes

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18
Q

What are the Components of a Gene?

A
  1. Introns
  2. Exons
  3. Promoter Region
  4. Enhancer & Silencer Regions
  5. Untranslated Regions
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19
Q

Where are Enhancer and Promoter Regions Located?

A

All throughout the DNA

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20
Q

What are Enhancer and Promoter Regions?

A

Regulatory Regions

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21
Q

What do Splice Sites do?

A

Split coding Exons and non-coding Introns

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22
Q

Where do Somatic Mutations Occur?

A

Non-reproductive Cells

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23
Q

Where do Gametic Mutations Occur?

A

Reproductive Cells (Germ-Line Mutations)

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24
Q

What are Spontaneous Mutations?

A

Natural mutations that occur randomly during transcription or proofreading. They are infrequent and inherited if in gametes.

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25
Q

What are Induced Mutations?

A

Mutations caused by high energy radiation or chemicals. They are higher frequency than spontaneous and have the same inheritance pattern as spontaneous mutations.

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26
Q

What are Base Substitution Mutations?

A

Transition vs Transversion mutations

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27
Q

What is a Transition Mutation?

A

Purine for Purine or Pyrimidine for Pyrimidine

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28
Q

What is a Transversion Mutation?

A

Purine for Pyrimidine or Pyrimidine for Purine

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29
Q

What are Insertion or Deletion Mutations?

A

Frameshift inducing mutations (groups of 1-2) or In-Frame mutations (groups of 3)

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30
Q

What are Expanding Nucleotide Repeats?

A

Inserts copies of set of nucleotides, this can disrupt protein function. (Example- Huntington’s Disease)

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31
Q

What are Forward Mutations?

A

Mutations that convert wild-type allele to mutant allele

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32
Q

What are Reverse Mutations?

A

Mutations that convert mutants to near wild-type

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33
Q

What is True Reversion?

A

The exact wild-type sequence restored, Mutation at the same base pair or same codon

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34
Q

What is Intragenic Reversion?

A

Mutation somewhere else in the gene, near wild-type allele (most common)

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35
Q

What is Second-Site Reversion?

A

Mutation in a different gene can potentially restore wild-type phenotype (least common)

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36
Q

What is Mutation Rate Affected by?

A
  1. Size of the gene
  2. Rate that mismatched bases are incorporated into DNA
  3. Efficiency of repairing damage
  4. Organism life cycle
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37
Q

What Happens in Tautomerization?

A

When the common amine form or enol form transitions to a imine form or keto form. This would cause A to pair with C and T to pair with G

38
Q

What is Mispairing Due to Wobble?

A

Because there is flexibility in the DNA structure, opposite base pairing can happen as the structure flexes.

39
Q

What is Depurination?

A

Purines are randomly lost from DNA and an apurinic site where replication cannot continue. This can often be fixed, but if it is not, then an Adenine is put into the spot

40
Q

What is Deamination?

A

The amine group is lost. Typically this causes C to switch to U and Uracil would pair with Adenine

41
Q

What Happens During Replication Slippage?

A

Repeat expansion and single base pair insertions and deletions. We all have natural repeats in DNA, this becomes a problem when it passes a threshold and a phenotype occurs

42
Q

What Kind of Mutation do Base Analog Mutations Create?

A

Transition Mutations where A is ALSO able to pair with G and T ALSO pairs with C

43
Q

What do Alkylating Agents do?

A

Induce specific mispairing, adding bulky groups that distort the shape of DNA. G normally pairs with C, but when ethylated with a bulky group, it pairs with T

44
Q

What Kind of Mutations do Intercalating Agents Cause?

A

Insertions and Deletions (DNA needs to be nicked at the insertion point, leading to the loss of bases)

45
Q

Why Does UV Radiation Cause Mutations?

A

The higher the radiation, the smaller the particles, the easier to pierce through. This is why we need more protection when we deal with radiation (like sunscreen)

46
Q

What do thymine Dimers Cause?

A

Kinks in the DNA. This can be fixed, but if it doesn’t get fixed, replication cannot move past this point

47
Q

What Kind of Repair is DNA Polymerase Proofreading?

A

Direct repair where DNA polymerase 3 adds a mismatched base but notices it and corrects for it.

48
Q

What Repairs UV Mutations?

A

Photolyase direct repairs the UV damage. This recognizes thymine dimers and uses sun energy to activate and break bonds between the thymines.

49
Q

How does MutS Repair Mismatched DNA?

A

MutS identifies and binds to a mutated strand and calls in MutL, MutL then calls in MutH and breaks the phosphodiester bond. Once it is cut, exonuclease is recruited and DNA polymerase comes in and uses the template strand to re-synthesize DNA.

50
Q

What Happens During Base Excision Repair?

A

The base that is incorrect due to deamination or oxidation. DNA Glycosylase removes the incorrect base and generates an ATP site where AP endonuclease removes the rest of nucleotide so that DNA polymerase can come in and re-sythesize DNA

51
Q

What Happens During Nucleotide Excision Repair?

A

A bulky adduct distorts the DNA helix from alkylating agents or UV damage. Enzymes recognize and bind to the damaged regions and Excision Nuclease cuts the backbone and helicase removes the short chunk of DNA so that DNA polymerase can fill.

52
Q

What is the SOS Repair System?

A

When DNA polymerase cannot repair due to a mutation that was not caught, translesion polymerase 5 comes in and fixes the DNA by leaving replication errors so that DNA polymerase 3 can resume. This is an Emergency State

53
Q

What does Nucleotide Excision Repair Fix?

A

Alkylating agents, Intercalating agents, thymine dimers in humans

54
Q

What does Base Excision Repair Fix?

A

Deamination of C to U, Depurination

55
Q

What does Mismatch Repair Fix?

A

Tautomer Incorporation

56
Q

What does Direct UV Repair Fix?

A

Thymine dimers in prokaryotes

57
Q

What are Point Mutations?

A

Mutations in a single nucleotide

58
Q

What are Silent Mutations?

A

When the change of a single DNA nucleotide within a protein-coding portion of a gene does not affect the sequence of amino acids

59
Q

What are Missense Mutations?

A

A single nucleotide change results in a codon that codes for a different amino acid

60
Q

What are Nonsense Mutations?

A

The altered DNA sequence prematurely signals the cell to stop building a protein

61
Q

What are Frameshift Mutations?

A

Mutations that alter the reading frame of codons. Translational Termination may happen early or late. This results in a nonfunctional protein.

62
Q

What are Neutral Mutations?

A

Missense mutations that alter amino acid sequence but does not significantly alter the function of the protein

63
Q

What are Gain-of-Function Mutations?

A

A protein is produced whose function is not normally present

64
Q

What are Loss-of-Function Mutations?

A

Complete or partial absence of normal protein function

65
Q

What Happens when a Silent Mutation is not Silent?

A
  1. the binding sites for transcription factors, if enhancer or promoter sequence is varied.
    a. a transcription factor may not bind as efficiently
    b. may bind more efficiently
    c. a completely different transcription factor now binds to a DNA region it didn’t before
  2. Point mutations cause incorrect splicing of introns and exons
66
Q

What Does it Mean to be Haplosufficient?

A

1 copy of functioning gene produces enough enzyme to catalyze reactions and give wild type phenotypes

67
Q

What Does it Mean to be Haploinsufficient?

A

1 copy of functioning gene does not produce enough enzyme to give wild type phenotype

68
Q

What is the Locus?

A

The point on the gene where the variability (mutation) occurs

69
Q

What is the Allele?

A

The form of the gene at the locus

70
Q

What Does it Mean to be Homozygous?

A

Same alleles

71
Q

What Does it Mean to be Heterozygous?

A

Different alleles

72
Q

What did Mendel Discover in 1865?

A

Discovered major fundamental principles of “heritable factors” using peas. Found that certain traits show up in offspring without any blending of parent characteristics. He bred pea plants to see how offspring were different from the parents.

73
Q

Why Did Mendel Choose Pea Plants?

A
  1. Easy to artificially fertilize
  2. Inexpensive
  3. Fast to grow and produce Seeds
  4. Controlled mating
  5. True Breeding plants
  6. Had observable binary forms of traits
74
Q

What is Mendel’s Law of Segregation?

A

Each inherited trait is defined by a gene pair. Parental genes are randomly separated to the gametes. Offspring inherit one genetic allele from each parent when sex cells unite in fertilization.

75
Q

What is Mendel’s Law of Independent Assortment?

A

Genes for different traits are sorted separately from one another so that the inheritance of one trait is not dependent on the inheritance of another

76
Q

What is Mendel’s Law of Dominance?

A

An organism with alternate forms of a gene will express the form that is dominant? (Aa)

77
Q

What are Most Cells in Your Body?

A

Diploid

78
Q

What are the Only Cells in Your Body That are Haploid?

A

Gametes

79
Q

How Many Chromosomes Does Each Person Have?

A

23 types and two copies of each (46 total)

80
Q

What is the Purpose of a Test Cross?

A

To determine the genotype that corresponds to a known phenotype, or to determine if two genes are linked or are on separate chromosomes.

81
Q

What do Recessive Traits Show on a Pedigree?

A

Usually skip a generation

82
Q

What do Dominant Traits Show on a Pedigree?

A

Traits show up often and do not skip a generation

83
Q

What do Autosomal Traits Show on a Pedigree?

A

Traits are seen in both Genders

84
Q

What do Sex-Linked Traits Show on a Pedigree?

A

Traits are only seen in one gender

85
Q

What does it Mean When There is a Line on a Pedigree?

A

The individual is deceased

86
Q

What do Squares Correspond to on a Pedigree?

A

Male

87
Q

What do Circles Show on a Pedigree?

A

Female

88
Q

What does a Double Line on a Pedigree Mean?

A

They are Related (1st cousins typically)

89
Q

What are Common Sex-Linked Traits?

A

Blood Clotting and Red-Green Colorblindness

90
Q

What Chromosomes do Parents Pass to Children?

A

Fathers pass X to daughters and Y to sons, mothers only pass on X to both

91
Q

How do you Calculate Mutation Rate?

A

Of Mutation Events (Colonies) / # Cells in Agar Spot

Genes and Genomics (7 decks)

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