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Biology Test #1 > Cycle 4 > Flashcards

Cycle 4 Flashcards

1
Q

What are exogenous sources of DNA damage?

A
  • they come from the outside

- uv light, chemicals, ionizing radiation

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2
Q

What are endogenous sources of DNA damage?

A
  • they come from the inside
  • can occur from metabolism (in metabolism electrons move singly and are free radicals, these free radicals are very react and react with oxygen making ROS, if they then escape mitochondria, they can react and damage nuclear DNA)
  • DNA replication errors
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3
Q

DNA damage vs mutation

A

DNA damage:
- single stranded change (usually becomes mutation after the DNA replicates)

Mutation:

  • double stranded change.
  • happens because DNA does not remember correct base, it just adds the complementary base of the switched one
  • location of mutation determines it’s impact
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4
Q

What is the proofreading repair mechanism?

A

1) DNA polymerase adds the wrong pair and detects it
2) DNA polymerase fixes the mistake immediately
3) The enzyme reveres using it 3’ to 5’ exonuclease to remove the mispaired nucleotide from the strand
4) Then DNA polymerase resumes usual activity by extending it’s new chain in the 5’ to 3’ direction.
* * * very good mechanism, only one mispair survives every 1 million nucleotides polymerized

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5
Q

What is the role of the mismatch repair mechanism?

A

Correct 99% of the errors left after proofreading

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6
Q

How does the mismatch repair system work?

A

1) mismatch repair enzymes come and detect the error in the DNA backbone. It then goes and cleaves the DNA backbone of the newly synthesized area
2) the area is removed
3) DNA polymerase comes and fills in the gaps
4) DNA ligase then comes in and seals the nick left
5) Now the strand is correct!

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7
Q

What are thymine dimmers?

A
  • Thymine dimmers work by distorting the backbone of the DNA and halting polymerase.
  • NOT A MISMATCH, the error occurs because two thymines one beside the other have formed a covalent bond.
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8
Q

What are the causes of thymine dimmers?

A
  • exogenous source

- UV light

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9
Q

What are the repair mechanism of thymine dimmers?

A

1) Photolyase + white light
- if the double bond forms in the presence of UV
light
- the enzyme photolyase and white light will then
come split it up

2) Excision repair
- a thymine dimmer distorts the DNA molecule
- nuclease cuts the damaged DNA at the two
points and the damaged section is removed
- DNA polymerase comes and fills in the missing
nucleotides
- DNA ligase seals the nick

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10
Q

What are reactive oxygen species?

A
  • occurs when ionizing radiation (x rays, gamma rays, high energy) zap and split water molecules in cells
  • when the water molecules are split apart they are very unstable due to the unpaired electron in the outermost shell
  • very electronegative and unstable
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11
Q

How do ROS damage DNA?

A
  • They will damage the DNA to try and reach stability
  • They will do so by stealing electrons from the DNA
  • Damage leads to double stranded break
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12
Q

What is the oxygen paradox?

A
  • even though you need oxygen to survive it is ultimately oxygen that will kill you
  • having excess oxygen in a cell causes oxidative stress
  • oxidative stress is not good since it damages proteins
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13
Q

How do you get rid of ROS?

A
  • eating antioxidants
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14
Q

How are double strand breaks repaired?

A
  • Through non-homologous end joining. It works by piecing the DNA back together. But since the process does not involve DNA synthesis its likelihood for errors is higher.
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15
Q

What types of errors can non-homologous end joining cause?

A
  • Deletion
  • Insertion (since does not have memory of original can insert wrong bases)
  • Inversion
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16
Q

What are the causes of double stranded breaks?

A

radiation the breaks the double helix in both strands

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17
Q

What are the benefits of personalized medicine?

A

Take your base pairs, and DNA can make interpretations as to what drugs you best react to

18
Q

What are the components of the DNA sequence?

A
  • 25% unknown (prolly junk)
  • 10% essential (2% coding)
  • 10% intron (junk)
  • 55% transposons, viruses and dead genes
19
Q

What is a substitution mutation?

A
  • change in one base pairs
20
Q

What is a deletion mutation?

A
  • when you lose a base pairs

- most common mutation

21
Q

What is an insertion mutation?

A
  • when you insert an extra base pair into the sequence
22
Q

What is an inversion mutation?

A
  • when the sequence of the top is inverted with the bottom
23
Q

What is the silent point mutation?

A
  • when the effect is not seen since they code for the same amino acid
    (ex. TTC becomes TTT, however mRNA AAG and AAA code for the same protein Lys)
24
Q

What is a nonsense mutation?

A
  • creates a stop codon making a premature termination in translation
25
Q

What is a missense mutation?

A
  • changes the protein

- varies in effect depending on the location and function of the amino acid

26
Q

What is a SNP?

A
  • a single nucleotide difference in DNA sequence
    (ie ONE base pair change)
  • con commonly occur in genome between genes
  • most SNPS have no effect on health and development
27
Q

What can SNPs predict?

A
  • response to drugs
  • susceptibility to environmental factors like toxins
  • risk of developing particular disease
28
Q

what types of mutation does DNA polymerase slippage cause?

A
  • insertion and deletion
29
Q

Explain DNA polymerase insertion slippage mutation

A

1) It affects the synthesized strand
2) When it slips backward a loop with extra base pairs is formed. It now has extra bases since it doesn’t realize that the particular CAG has already been made
3) Now an extra 3 bases introduced
4) In the following replication bth strands will become the parent strand, and the loop with the 3 extra bases

30
Q

Explain DNA polymerase deletion slippage mutation

A

1) occurs on the template strand
2) If DNA slips forward this results in a deletion mutation, since it missed to add the 3 bases from the template strand
3) Thus the newly synthesized strand will be missing three base pairs
4) after replication on strand of the DNA synthesized will be three bases short

31
Q

What is a tautomeric shift?

A
  • This occurs when the structure of the base changes os that now it’s preferred partner changes
  • ex. after tautomeric shift thymine (enol) wants to pair with guanine(keto) instead of adenine
  • note that after bases undergo spontaneous tautomerization, it will preferentially pair with this different base, thus the tautomer is not considered a mismatch
32
Q

What are the two types of tautomeric shifts?

A
  • transition (purine-purine, prymidine-prymidine)

- transversion (purine-prymidine)

33
Q

which bases are the purine?

A

adenine and guanine

34
Q

which bases are the pyrmidines?

A

cytosine and thymine

35
Q

What are base analogues?

A

it is something that can substitute a base. Ex. 5BU is so similar to thymine that it is incorporated into DNA by polyermases as if it were thymine

36
Q

What are the issues with base analogues?

A

They are usually very tautomerically unstable. so the issue is that base analogue like 5BU swicth between the alternative forms, resulting in mutation

37
Q

What are transposable elements?

A

They are small regions of the genome that can be referred to as jumping genes since they can jump from one location to another. This process is called transposition. For example, in corn a TE gene involved in pigment synthesies can be inserted in the middle of the gene. In this case it no longer produces pigment and the color is light. When the TE element is excised it can produce the dark colour.

38
Q

What accounts for the increase in genome size?

A

Transpoable elements occur between genes. Thus we can see that the difference in gense comes from TE. Ex. barley has many TE, thus explaining why it has a high C value even though it is not a complex organism.

39
Q

What is the distribution of transposable elements in the human genome?

A
  • 50% of genome have TE
  • 70-80% of TEs have negligible effects
  • most TE are “dead” due to inactivating mutations (cannot undergo transposition)
  • active TEs have evolved to insert into “safe havens” in the genome.
    - host will usually inactivate most active TEs
    - some mutations however can activate the TEs
40
Q

What do transposable elements do when they land in different regions?

A
  • if they land in non-coding
    (usually silent and inactivated)
  • land in protein-coding gene
    - insertions can lead to disease causing mutations, or
    gene shuffling (ex. now expressed different
    promoters)
41
Q

What does multifactorial mean?

A

means it is no singularly caused by one mutation, associated with SNPs
ex. heart disease multifactorial, cystic fibrosis is not

Biology Test #1 (5 decks)

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