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Genetics PMY-3 > Gene Mutation, Repair And Transposition > Flashcards

Gene Mutation, Repair And Transposition Flashcards

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1
Q

What is the function of the DNA?

A

Stores information for cellular function

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2
Q

How can variations/changes in DNA affect someone or populations?

A
  1. Phenotypic variability
  2. Adaptation to environmental changes
  3. Evolution
  4. Genetic disease, cancer, cell death
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3
Q

How has phenotypic variation from mutation helped scientists?

A

Allows geneticists to identify and study the involved gene

-sometimes we only know the normal activity of a gene when we see what changes in a cell or organism after the mutation has occurred

Mutations can also act as markers for genes

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4
Q

What is DNA repair?

A

A cell has various mechanisms to correct base pair changes: DNA repair

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5
Q

What are the types of mutations?

A
  • Point or base substitutions
  • Missense mutation
  • Nonsense mutation
  • Silent mutation
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6
Q

What is a point/base substitution mutation?

A

A change from one base pair to another

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7
Q

What is a missense mutation?

A

A change in one nucleotide of a triplet within the protein coding portion of a gene resulting in a new triplet that codes for a different amino acid

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8
Q

What is a nonsense mutation?

A

A triplet is changed to a stop codon, resulting in the termination of translation of the protein (premature stop codon)
-defective protein product: extent of deficit depends on of the stop codon is at the beginning or later on in the sequence

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9
Q

What is a silent mutation?

A

There is an alteration of a codon but it doesn’t change the amino acid at that position

 -if the change affects a splice site, it could affect the protein product
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10
Q

Objective: in what scenario can a mutation be found?

A

-An alteration in DNA(not major alteration in chromosome)

-Can be found in coding or noncoding
regions of a gene

  • Mutations can occur in somatic cells during cell duplication
  • Mutations can occur with germ cells which are heritable
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11
Q

What is the effect of mutations in germ cells

A

These are heritable and increases genetic diversity and evolution or disease

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12
Q

What are the effects of mutations in somatic cells during cell duplication?

A

Not heritable but may lead to altered cellular function or tumors

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13
Q

What are coding regions of a gene?

A

Coding region of a gene- the regions which contain the information to be translated into protein

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14
Q

What are the noncoding regions of a gene?

A

Noncoding regions may include a gene regulatory region like the promoter or introns or splice signals

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15
Q

What are transitions?

A

Pyrimidine replaces pyrimidine or a purine replaces purine

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16
Q

What are transversions ?

A

Purine and pyrimidine are interchanged

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17
Q

What are frameshift mutations?

A
  • Results from the insertion of deletion of a base pair
  • This causes a shift in the reading frame
  • The codons for the amino acids are all changed and no longer make a proper protein
  • Almost always causes a premature stop codon soon after the frameshift
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18
Q

What do frameshift mutations usually lead to?

A
  • usually lead to a premature stop codon, resulting in shorter than normal protein
  • Worse if this change happens neat the start of the sequence
  • The RNA with a premature stop codon is often degraded by a special pathway called Nonsense Medicated Decay where the affected RNA is degraded
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19
Q

What are the types of loss of function mutations?

A
  • Null mutation
  • Recessive mutation
  • Dominant mutation
  • Dominant negative mutation
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20
Q

What is a loss of function mutation?

A

Reduces or eliminates the function of the gene product

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21
Q

What is a null mutation?

A

Complete loss of function

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22
Q

What is a recessive mutation?

A

Wild type phenotype is the other allele is wild type, 50% gene product (from the good allele) is enough to bring the wild type phenotype

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23
Q

What is a dominant mutation?

A

Mutant phenotype even when the other allele is wild type, 50% of gene product (from the good allele) is NOT ENOUGH and the defective phenotype is shown

   -Also known as haploinsufficiency
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24
Q

What is dominant negative mutation?

A

The one mutant allele is inactive and directly interferes with the function of the product from the good allele

-Example of dominant negative is when the nonfunctional gene product binds to the wild type product in a homodimer, inactivating or reducing the activity of the homodimer

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25
Q

What are gain of function mutations?

A

Mutation codes for an altered gene product with enhanced, negative or new functions
-amino acid change leads to new activity

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26
Q

What is a suppressor mutation?

A

A second mutation in the same gene that reverts or relieves the effects of the first mutation (first mutation is gain of function)

Example: one deletion soon followed by insertion which restores the reading frame

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27
Q

If a gain of function mutation is in a regulatory region of a gene, what may be the result?

A
  • higher expression of the gene
  • The gene turned on at the wrong time
  • The gene turned on in the wrong tissue or place
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28
Q

What are the types of lethal mutations?

A

Lethal mutations

Lethal condition mutations

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29
Q

What are lethal mutations?

A

-Interrupt an essential process and result in an early death

  • Typical of the mutations which lead to biochemical disorders
    • e.g., tay Sachs results in death in early childhood
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30
Q

What are lethal condition mutations?

A
  • Usually where the viability of the organism depends on the environment
  • E.g., the organism grows normally in total medium (with all nutrients) and not on minimal medium (with restricted nutrients)
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31
Q

What are neutral mutations?

A
  • Majority of these types occur in noncoding regions

- Neither beneficial or detrimental

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32
Q

What are somatic mutations?

A
  • Mutations restricted to the somatic cells and not transmitted to future generations
  • Mutation occurs in any cell of the bidy except germ cells
  • a Can occur on any chromosome
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33
Q

What are inherited mutations?

A
  • Autosomal mutations occur in the germ cells and are found on the autosomal chromosomes (1-22 in humans)
  • Sex-linked mutation can occur in the germ cells and are found on the X or Y chromosomes
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34
Q

What are inherited dominant mutations?

A

Phenotype seen in the first generation to inherit the mutation

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35
Q

What are inherited dominant mutations?

A

Phenotype not seen till the chance mating of two similarly affected persons brings two copies of the mutation into a single zygote which will now be homozygous for the mutation

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36
Q

Mutations occur…

A

Spontaneously and randomly

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37
Q

What are spontaneous mutations?

A

These are changes in nucleotide sequence that occurs naturally

Most arise from normal biological or chemical process in the organism that changes the structure of the nitrogenous bases

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38
Q

At what cellular function/genetic process dies spontaneous mutation occur?

A

Most often this occurs during DNA replication

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39
Q

What is the frequency of spontaneous mutations?

A

Rates vary among organisms, but in all extremely low

Some regions of DNA appear to be more prone to mutation that others FYI, nothing here to memorize

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40
Q

What are induced mutations?

A

Result from the influence exogenous factors, whether natural, or artificial

Radiation
UV light
Natural or synthetic chemicals(intrudes in processed foods)

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41
Q

What was the methodology of the Iceland Germ-line mutation rate study? What did they find out about mother’s?

A

In 2012, DNA sequencing of 78 parent/offspring sets -DNA sequences compared

  • Looking for single nucleotide changes called Single Nucleotide Polymorphisms(SNPs)
  • Newborn baby genome contains the average of 60 nucleotides changed (new mutations) compared to parents
  • Mothers contribute about 15 new mutations to baby at any age
42
Q

What did the Iceland Germ-line mutation rate study find out about fathers?

A

The number of new mutations from fathers depends significantly on the age of the father at the time of conception

Father 20 years old= about 25 new mutations

Father 40 years old about 65 new mutations

Both of these indicate about 2 mutations per year of life

May occur because make germ cells go through more cell divisions during a life time compared to females

43
Q

How do spontaneous changes occur?

A

DNA Replication errors

Tauromeric shifts

44
Q

Obj: What are the mechanisms of DNA replication errors?

A

Slippage; tautomeric shifts; depurination and deamination; oxidative damage; other mutagenic agents

45
Q

How are nucleotides miscorporated into new strand?

A

A form of DNA replication errors

-occasionally DNA polymerases insert incorrect nucleotides even after proof reading (3’ to 5’ exonuclease proof reading activity)

46
Q

What is replication slippage?

A

Small inserts or deletions can occur when DNA polymerase slips or stutters during replication

  • DNA template makes a loop during replication, a small deletion in the new strand occurs
  • DNA polymerase introduces nucleotides that are not present in the template strand and a small insertion in the new strand occurs
  • Replication slippage can occur anywhere but seen more commonly in regions containing tandemly repeated sequences
47
Q

Can purines and pyrimidines exist in tautomeric forms?explain this

A

Purines and pyrimidines can exist in tautomeric forms

  • An alternate chemical form that differs by a proton
  • Keto-enol forms of thymine and guanine
  • Amino-imino forms of cytosine and adenine
48
Q

What are the results and effects of tautomeric shifts?

A
  • Tautomers increase the chance of mispairing during DNA replication
  • Can change the bonding structure allowing noncomplementary base Pairing
  • May lead to permanent base-pair changes

Results: A transient tautomeric shift in adenine during round 1 of replication

-Results in the formation of an A-T to C-G transition mutation in round 2 of replication

Daughter strand showing heritable mutation

49
Q

What is depurination?

A

The loss of one of the nitrogenous basis in intact DNA
-usually a purine (A or G)

  • The glycosidic linkage from the C1’ of the sugar to atom 9 of the purine ring is broken
    - Result: DNA polymerase May add a random nucleotide
50
Q

What is deamination ?

A

The amino group on cytosine or adenine is converted to a keto group

Cytosine —> uracil

Adenine —> hypoxanthine

51
Q

What causes oxidative damage to DNA?

A

Due to by-products of normal cellular processes: aerobic respiration

Also generated by exposure to high-energy radiation

  • Super oxide (O2- radical)
  • hydroxyl radicals (OH- radical)
  • Hydrogen peroxide
52
Q

What are the common types of modifications ?

A
  • Modification of bases
  • Loss of bases
  • Single stranded breaks
  • Many others less common
53
Q

What mutations are caused by UV radiation?

A

Mainly causes thymine dimers

-covalent crosslinks Shawn in red

54
Q

What are intercalating agents ?

A

These Chemicals have the tight shape to allow them to wedge between the base pairs
-Causes DNA to distort and unwind, leading to frame shift mutations

55
Q

What are base analogues?

A

5-bromouracil behaves like a thymine analogue but nature favors the tautomeric structure so causes A-T to C-G transition after one round of replication

56
Q

What do single gene mutations cause?

A

Mutations in one gene cause disease

Disease is monogenic disease

57
Q

Obj: What is allergic heterogeneity ?

A

Mutations in the same gene all lead to the same disease

Example here is the HBB gene that cause b-thalassemia - one disease, many mutation sites in the one gene

58
Q

Describe the transposable elements “jumping genes”

A

Barbara McClintock studded the genetics of maze, first to describe recombination and in 1950, developed the theory that mobile elements can move within and between chromosomes and regulate genes

  • Research was conceptually difficult, not immediately understood
  • in 1950’s Jacob and Monad discovered gene regulation of E. Coli and scientific community was ready to understand gene regulation
59
Q

In what organisms have transposable elements been found?

A

In all organisms found

60
Q

What are transposable elements?

A

DNA elements that move within or between genome

61
Q

Transposable elements can be from …….

Bp and can include…..

A

50-10,000 base pairs

Includes ORFs(open reading frames)

62
Q

How much of the human genome is derived from the transposable elements?

A

Almost 50% of human genome is derived from Transposabke elements

63
Q

What can be caused from transposable elements (negatively)?

A

Inversions, translocations, double stranded breaks

64
Q

What mechanism controls the functioning of transposable elements?

A

Mechanism thought to act as naturally occurring mutagens

65
Q

What can result by transposable elements insertions?

A

They may insert into a new location of the genome:

  • If they insert into the coding region of a gene, they can alter the reading frame
  • If they insert into the regulatory region of a gene, they can disrupt proper expression of the gene
66
Q

What are the steps involved in DNA transposon transposition : cut and paste?

A

Step 1: transposase cleaves DNA at ITRs

Step 2: Transposase makes staggered cuts at target site in chromosomal DNA

Step 3: transposase inserts transposing at target site

Step 4: gaps in target site are filled in by DNA polymerase and DNA ligase

Donor DNA is repaired with no trace of TE

67
Q

What are inverted terminal repeats (ITR)?

A

These are located on each end if the transposable elements (TE)and an open reading from codes for enzyme Transposase

-ITRs are between 9-40 bp long and are ifentical but inverted relative to each other

68
Q

Explain the functioning of the transposase enzyme

A
  • ITR is recognized, bound and cleaved by the transposase enzyme between ITR and DR, brings the two together
  • The transposing loop will be inserted into new target DNA which has a target site DNA site
  • Transposase will cut the target DNA at the target site leaving 5’ single stranded overhangs
  • Gaps are filled in by DNA pol and DNA ligase
69
Q

What are the types of transposable elements ?

A

Autonomous transposons

Nonautonomous transposons

70
Q

What are autonomous transposons?

A
  • TE contains transposase ORF (encoding for transposase enzyme) plus/minus another ORF that encodes for a gene
  • Intact ITR to the left and right of the ORFs (flanking the ORF)
71
Q

What are nonautonomous transposons?

A
  • contains DNA but NOT transposase gene

- To function there has to be transposase enzyme available

72
Q

What are the types of retrotransposons?

A
  • Long terminal repeat (LTR) retrotransposons

- Non-LTR Retrotransposons

73
Q

What are long-terminal repeat(LRT) transposons?

A
  • Long term repeats flank the retrotransposon
  • Contains transcription promoters in the 5’ untranslated region and polyadenylation sites in the 3’ untranslated region
  • Can be autonomous or non-autonomous (+/- integrate and reverse transcriptase)
74
Q

What are Non-LTR Retrotransposons?

A
  • Lacks the LTR region
  • Contains transcription promoters in the 5’ untranslated region and polyadenylation sites in the 3’ untranslaated region
  • Can be autonomous or nom-autonomous (+/- integrate and reverse transcriptase
75
Q

What are the functions of Retrotransposons?

A
  • RNA is made
  • integrate and reverse transcriptase enzymes produced
  • The RNA is converted back to dsDNA by reverse transcriptase
  • Integrase inserts dsDNA into chromosomal DNA
76
Q

What are the steps of Retrotransposon functioning?

A

Step 1 and 2: Retrotransposon is transcribed and translated by cellular enzymes

Step 3: reverse transcriptase creates double-stranded DNA copies of each Retrotransposon RNA

Step 4: integrase inserts double-strandedDNA-copies into chromosomal DNA

77
Q

What are the functions of DNA Repair?

A
  • counteract spontaneous and induced DNA damage
  • Maintain the integrity of genetic material
  • Counteract genetic damage that would result in genetic diseases and cancer
78
Q

How often dies DNA pol. 3 male a mistake in bacteria?

A

Once every 100,000 base pairs (10^-5)

79
Q

How does DNA pol. 3 prevent mistakes? How useful is this?

A
  1. DNA pol. 3 proofreads each step and can “reverse its direction, cut out the bad nucleotide (3’-5’ exonuclease activity) and replace with the proper nuccleotide
  2. This improved the efficiency of replication 100 fold, to a mistake every 10,000,000 (10^-7)
80
Q

What polymerase proofreads DNA in eukaryotes?

A

DNA polymerase delta and epsilon deal with elongation have proofreading ability (3’-5’ exonuclease)

81
Q

What is mismatch repair?

A

After proofreading, there may be base-base mismatching, small insertions or deletions

-repair based on DNA methylation

82
Q

What enzyme in bacteria can be used for mismatch repair?

A

In bacteria, the enzyme DNA adenine methylase will recognize the DNA sequence and methylated the adenine nuccleotide

83
Q

How is DNA mismatch fixed?

A
  • Endonuclease will nick the phosphate backbone of the new un-methylated strand of DNA
  • Exonuclease will unwind and degrade the nicked DNA till the mismatch is removed
  • DNA polymerase will fill in the gap using the correct DNA strand as a template
  • DNA ligase will seal the nicked backbone
84
Q

Contrast endonuclease and exponuckease

A

Endonuclease -internal cuts in DNA

Exonuclease-Nucleotides moved from the ends

85
Q

What bacterial proteins are involved in the DNA repair?

A
  • MutH recognizes the mismatch and has endonuclease activity
  • MutL helps form a stable complex of DNA binding proteins
  • MutS assists in the recognition of the mutation. Mutation in these proteins and the bacteria is deficient in MMR
86
Q

What proteins in humans are involved in DNA repair?

A
  • hMSH2 recognizes the mismatch and recruits other repair proteins
  • hMLH1 helps form a stable complex of DNA binding proteins

Mutations in these genes are associated with hereditary nonpolyposis colorectal cancer

87
Q

Mutations in bacterial and human proteins involved in DNA repair ….

A

Mutations in any of these result in any of the genes that code for MMR can be associated with many other cancers as well

88
Q

Explain post-replication repair

A

If DNA repair has skipped over a lesion (damage or abnormal change) such as a thymine dimer

  • Replication skips over the lesion and continues
  • The correct complimentary sequence is taken from the other parental strand
  • New gap is filled in by DNA polymerase and backbone is sealed by DNA linkage
89
Q

Explain the SOS Repair system in E. Coli

A
  • Last resort to minimize DNA damage
  • DNA synthesis becomes error-prone; inserts random/incorrect nucleotides in places that normally would stall replication
  • Bacteria induce expression of 20 genes; their products allow replication to move forth
  • SOS repair cam itself become mutagenic; allows cells to survive with DNA damage (cell would otherwise kill itself)
90
Q

What organisms use photoreactivation DNA repair?

A
  • Bacteria, fungi and plants

- Not in humans

91
Q

Explain how photoreactivation repair functions?

A
  • UV light induces the formation of pyrimidine dimers
  • Following this radiation, if the DNA is exposed to visible light, particularly in the blue range, the pyrimidine dimers can be reversed
  • The blue light activates the activity of the Photoreactivation Enzyme also called PRE or photo lyase
92
Q

What organisms use Base excision repair(BRE)?

A

Repair mechanism found in prokaryotes and eukaryotes

93
Q

Give an example of Base excision Repair (BER) repairing U-G mismatch

A
  • Repairs the most common mutation is the deamination of cytosine to uracil
  • Here, uracil DNA glycolase recognizes and excises the incorrect base and created an apurinic/apyrimidinic.
  • The sugar with the missing base is recognized by an enzyme called AP endonuclease makes a cut in the backbone
  • DNA polymerase fills and DNA ligase repairs the gap
94
Q

What is the function Nucleotide Excision Repair(NER)?

A

Repairs the bulky lesions in DNA that alter or distort the double helix such as UV induced pyrimidine dimers

95
Q

Give the history of nucleotide excision repair(NER)

A

UV sensitive E. Coli mutants

  • A group of genes were identified, ultraviolet repair (uvr)
  • uvrA, uvrB and uvrC were found mutated in these UV sensitive E. Coli
  • the activity of the uvr genes have been worked out and the pathway shown to the right
  • uvrA, uvrB recognize and bind to the lesion and the recruit uvrC and then uvrA dissociates
  • uvrB cleaves the phosphodiester bond 4 nucleotides downstream and uvrC cleaves the phosphodiester bond 8 nucleotides upstream of the DNA damage

The gap is filled by DNA polymerase and backbone lighted by DNA ligase

96
Q

What organisms use a Nucleotide Excision Repair (NER)?

A

Prokaryotes but similar system is found in eukaryotes

97
Q

What causes Xeroderma pigmentosa in humans ?

A
  • NER in eukaryotes involves about 30 genes

- If any of these genes are mutated, it can lead to xeroderma pigmentisa (XP)

98
Q

What is Xeroderma Pigmentosa?

A
  • XP is an autosomal recessive disorder that predisposes individuals to severe skin abnormalities and skin cancers as well as developmental and neurological defects
  • by age 2, freaking of the skin in sun-exposed regions
  • Skin coloring changes
  • 2000-fold higher rate of cancer
  • Persons with XP are very sensitive to UV light, can get a sunburn after just a few minutes in the sun
99
Q

How can Xeroderma Pigmentosa be arrested?

A

Early detection and protection from sunlight can arrest it

100
Q

What 3 diseases are caused by defects in NER?

A
  • Cockayne syndrome (CS)
  • Xeroderma Pigmentosa (XP)
  • Trichothiodystrophy (TTD)
101
Q

What causes Cockayne syndrome (CS)?

A
  • Autosomal recessive inheritance
  • Developmental and neurological defects
  • Sunlight sensitivity but no increase in cancers
  • Premature aging, with death by age 20
102
Q

What causes Trichothiodystrophy ? What are the effects?

A
  • Mainly autosomal recessive inheritance
    • rare X linked case found
  • Sulfur-deficient brittle hair, brittle skin and nails
  • Hair has tiger banding under polarized microscopy
  • Dwarfism, retardation
  • Facial deformities and sensitivity to sunlight
  • No increase in cancers- six year life span

Genetics PMY-3 (27 decks)

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