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Oncology > Chapter 2: Gene structure and mutations (Book §2.1-§2.2) > Flashcards

Chapter 2: Gene structure and mutations (Book §2.1-§2.2) Flashcards

1
Q

Where is genetic information coded in?

A

DNA

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2
Q

Fill in: Cancer is a disease that involves alterations to gene … (1) and gene … (2) at the cellular level

A

1: structure
2: expression

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3
Q

The role of accumulation of mutations gradually over time is well established for the process of carcinogenesis, but recent evidence from advances in sequencing technology stakes the conventional view. What two some examples?

A
  1. Small localized areas of hypermutation, called katagesis (Greek for ‘thunderstorm’), have been identified in cancer genomes
  2. One-off cell catastrophic events may also generate mutations that underlie carcinogenesis. A one-off cell crisis that shatters chromosomes and results in tens-thousands of genomic rearrangements is called chromothripsis
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4
Q

Cells have a defense mechanism against mutations, such as detection and repair of DNA damage. In which cell phase is this particularly crucial and why?

A

When a cell divides, as errors existing during replication will be passed on to daughter cells

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5
Q

When the cell cycle is paused, but the DNA cannot be repaired, what happens then?

A

Apoptosis

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6
Q

What is a nucleotide made up of?

A

A suger, phosphate and a nitrogenous base

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7
Q

What are possible DNA nitrogenous bases?

A

Adenine, guanine, cytosine and thymine

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8
Q

What does the central dogma (theory) state?

A

DNA is transcribed into RNA, which is then translated into protein

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9
Q

Where does gene expression refer to?

a. replication of a gene
b. transcription of a gene
c. translation of a gene

A

b. transcription of a gene

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10
Q

Does a gene start at the 5’ end, or the 3’ end?

A

5’

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11
Q

What does a gene look like / what regions does it have?

A

(super)Enhancer elements, a promoter region, TATA box, a start of site transcription, a coding sequence and a stop sign

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12
Q

What are enhancer elements?

A

Additional regulatory DNA sequences that are position- and orientation-independent relative to a promoter and are important for tissue-specific and stage-specific expression

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13
Q

What is the promoter region involved in?

A

Regulating the expression of the gene

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14
Q

Where can regulatory regions be located?

  1. Downstream
  2. Upstream
  3. Both
  4. Neither
A
  1. Both
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15
Q

What is one of the most important regulatory elements for most genes?

A

The TATA box

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16
Q

Where is the TATA box located

A

Just before the start site of transcription

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17
Q

How are proteins called that bind to the TATA box? And what do they do?

A

TATA box-binding protein (TBP), they are crucial for the initiation of transcription

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18
Q

A short sequence of DNA within a promoter that is recognized by a specific protein and contributes to the regulation of the gene is called …

A

A response element (RE)

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19
Q

Common response elements identify genes under a common type of regulation. What are two examples?

(this is just for illustration)

A
  1. Serum response element (SRE) in genes that are responsive to serum
  2. E2F in the promoters of cyclin E and cyclin A (essential for the regulation of the cell cycle)
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20
Q

How is the region called where nucleotides are transcribed into RNA that code for proteins?

A

Coding region

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21
Q

Most carcinogens are…

A

mutagens

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22
Q

How do mutagen agents cause carcinogenesis?

A

By modifying DNA (e.g. forming DNA adducts) or causing chromosomal damage (e.g. DNA strand breaks)

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23
Q

What type of mutations are shown from top to bottom in this figure? The first row is the original

A
  1. ( original )
  2. transition
  3. transversion
  4. insertion
  5. deletion
  6. chromosomal translocation
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24
Q

What is the difference between a transition and a transversion?

A

Transitions are interchanges of two-ring purines (A G) or of one-ring pyrimidines (C T): they therefore involve bases of similar shape. Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures

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25
Q

Is an insertion or deletion the same as a frameshift mutation?

A

Yes

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26
Q

Base substitutions during replication may occur for several reasons. What are they?

A
  1. DNA polymerase is not 100% accurate
  2. Modifications of bases owing to oxidation or covalent additions or alterations of chromatin structure can cause misreading
27
Q

What is a chromosomal translocation?

A

The exchange of one part of one chromosome for another part of a different chromosome (leads to changes in base sequence of DNA)

28
Q

What is gene amplification?

A

The copy number of a gene increases from the two copies present in the normal diploid genome to sometimes hundreds of copies (may also occur in cancer cells)

29
Q

There are two different types of mutations: driver and passenger mutations. What are they/what is the difference?

A
  • Driver mutations are located in cancer genes by definition and confer a growth advantage on cells
  • Passenger mutations do not confer a growth advantage and ‘are there for the ride’
30
Q

Some mutations may give rise to a cell that has an increased rate of mutation as a result of, for example, defective DNA repair. What is this called?

A

Mutator phenotype

31
Q

Mutations occurring in the promoter region may alter the regulation of the gene and effect the levels or temporal/spatial expression of the gene product. Explain the consequences of this. (for illustration)

A

Over- or under expression of the protein product or the appearance of the protein product at the wrong time/place (respectively)

32
Q

What is chromothripsis?

A

Chromothripsis is a mutational process by which up to thousands of clustered chromosomal rearrangements occur in a single event in localised and confined genomic regions in one or a few chromosomes, and is known to be involved in both cancer and congenital diseases

33
Q

The cause of chromothripsis is still unknown, but some suggestions have been proposed. What are some? (I really dunno if you’re supposed to know this)

A

Ionizing radiation that leads to chromosome breaks; telomere dysfunction which may lead to end-end chromosome fusions; or aborted apoptosis such that cells which have initiated DNA fragments survive. Defective or delayed DNA replication and defective DNA damage responses hav also been considered.

34
Q

What are several classes of carcinogens?

A

Radiation, chemicals, infections pathogens and particular endogenous reactions (these will be discussed step-by-step)

35
Q

Radiation is energy. What are the two forms of radiation?

A

traveling in waves (gamma rays) or as a stream of atomic particles (alpha and beta particles by radioactive atoms)

36
Q

The amount of energy released by a particular radiation source affects the …

A

mechanism and extent of damage to the DNA.

37
Q

How is the amount of energy that is released by a particular radiation source and absorbed by the body tissue measured? Explain the unit

A

in grays (Gy) One gray is the release to the body tissue of 1 joule (J) of energy per 1 kg of tissue

38
Q

What is Linear Energy Transfer (LET)

A

LET is used to help describe the rate at which energy is released. Specifically, it describes the amount of energy released by radiation source as it travels a fixed distance.

39
Q

What is an example of high-LET radiation and low-LET radiation?

A

high: alpha particles low: X-rays

40
Q

What emits more energy, high-LET radiation or low-LET radiation?

A

High-LET radiation

41
Q

What causes more biological damage; high- or low-LET radiation?

A

High-LET radiation

42
Q

True/false: Double-stranded DNA breaks are more commonly caused by low-LET radiation and lead to chromosomal translocations and deletions

A

False! high-LET radiation often causes double-stranded breaks that leads to chromosomal translocations and deletions

43
Q

In what measurement/unit is the amount of biological damage caused by a particular source of radiation measured?

A

Sieverts (Sv) (the numerical value of these units is determined by multiplying the gray units by a factor relating to the LET value of a particular type of radiation)

44
Q

Earlier we described two forms of radiation (waves and particles), but radiation can also be divided into two classes. What are they?

A

Ionizing- and UV-radation

45
Q

Ionizing radiation included alpha- and beta particles, and gamma rays. What is the order of highest to lowest energy radiation?

A

(high) gamma -> beta -> alpha (low)

46
Q

A gamma ray can strike a molecule so that electrons may be displaced from atoms within the molecule, creating an electrical change (because one/more electrons are lost). How is this changed molecule called?

A

An ion (thus the term ‘ionizing radiation’)

47
Q

Ionizing radiation can damage DNA directly and indirectly. Explain the two phenomena.

A

Directly: by causing ionization of the atoms comprising DNA Indirectly: by the interaction with water molecules (= radiolysis) to generate reactive oxygen species (ROS) that may interact with DNA/biomolecules

48
Q

What does the electrical spectrum look like? (this is for your own understanding)

A
49
Q

In what way can people be exposed to ionizing radiation?

A

Such as on high-altitude flights, a required X-ray or atomic bombing

50
Q

The Life Span Study by Preston showed some incredible insights in 2007 regarding the 80,000 atomic bomb survivors. What are they? (I added this because it’s interesting, you do not have to know this)

A
  1. leukemia is the most frequent ionizing radiation-induced cancer (think about Marie Curie who died of leukemia after working her adult life with radioactivity)
  2. age is an important risk factor, whereby those exposed as children are most affected
  3. the risks of solid cancer increase with dose in a linear fashion
51
Q

UV radiation from the sun is also carcinogenic. Why is UV so carcinogenic? (1)

Which cancer is especially related to UV-radiation? (2)

A

1) The conducted double bonds in the rings of nitrogenous bases of DNA absorb UV radiation
2) Skin cancer

52
Q

What are the three types of UV light?

A

UVA (wavelength 320-280) UVB (wavelength 290-320) UVC (wavelength 200-290) (you don’t have to know the wavelengths)

53
Q

Which UV-type is the most effective carcinogen (UVA, UVB or UVC)? Why?

A

UVB, it directly and uniquely causes characteristic UV photoproducts: cyclobutane pyrimidine dimers and pyrimidine-pyrimidone photoproducts.

54
Q

Which UV photoproduct is more common, cyclobutane pyrimidine dimers or pyrimidine-pyrimidine photoproducts?

A

Cyclobutane pyrimidine dimers by 20-40x more than pyrimidine-pyrimidine photoproducts

55
Q

What does the pyrimidine photoproduct mimic? And why is this less common than a cyclobutane pyrimidine dimer?

A

An abasic site (so a nucleotide minus a base). This abasic site is more efficiently repaired than the dimers

56
Q

What does the cyclobutane pyrimidine dimer cause? How is it repaired?

A

The formation of a pyrimidine dimer causes a bend in the DNA helix, and, as a result, DNA polymerase cannot read the template and preferentially incorporates an “A” residue. Consequently , TT dimers are often restored but TC and CC dimers result in transitions (TC -> TT and CC -> TT)

57
Q

Cyclobutane pyrimidine dimers are responsible for at least …% of UVB-induced mutations and is a unique molecular signature for … cancer

A

80%, skin

58
Q

UVA indirectly damages DNA via free radical-mediated damage. Explain this process.

A

Water is fragmented by UVA, generating electron-seeking ROS (e.g. hydroxyl radical) that cause DNA damage (e.g. oxidation of bases). G -> T transversions are characteristic of UVA damage

59
Q

The depth of transmission for each type of UV light is dependent on the wavelength. Explain to layer of the skin each UV light reaches

A

UVC radiation is almost completly absorbed by the ozone layer and rarely reaches the skin, but human may be exposed from commercial sources such as germicidal lamps UVC penetrates into the basal level of the epidermis UVA penetrates into the more acellular dermis level

60
Q

True/false: Melanin formation (=tanning) is a natural defense mechanism against UV absorption

A

True

61
Q

Why is there peeling of the skin after a sunburn?

A

This is the cellular mechanism for the elimination of UV-damaged skin cells to innate apoptosis (p53 plays a big role here)

62
Q

True/false: tumor suppressor p53 plays an important role in squamous cell carcinoma (SCC), basal cell carcinoma (BCC) and melanoma

A

(partly) False, it does play a role in SCC and BCC, but not in melanoma

63
Q

Mutations in the p53 gene may induce formation of tumor cells (specific CC -> TT transitions were identified). The pattern of mutation is not random but rather tends to be localized to nine places. How are these places called?

A

Hotspots (they are not repaired efficiently, resulting in loss of p53 function)

64
Q

Fill in: UV radiation not only induces p53 mutations, but also selects for the clonal expression of the p53 mutated cells, by inducing … in normal cells with wild-type p53

A

apoptosis

Oncology (18 decks)

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