Molecular Pathology & Cancer Flashcards
Draw the structure of bases
Structures shown with sugar at the bottom for comparison. Green arrows indicate hydrogen donors for hydrogen bonding, and red arrows indicate the acceptors in hydrogen bonding (i.e. electron donors).
CG interaction involves 3 H-bonds whereas AT interaction involves 2 H-bonds.
Bases and (nucleoside) names are given, e.g. adenine and adenosine.
Draw the structures flipped over to show donors and acceptors aligned
Draw a nucleotide
Describe the strucure of RNA
Usually found in the cell as single strand, sometimes folded into a specific shape (e.g. clover leaf tRNA).
Describe the shape of DNA
Exists for most of the time in the cell in a double stranded form i.e. two polynucleotides strands held together by non-covalent bonds. This is the famous double helix model of Crick and Watson. This model has the following features.
Explain the sturcture of DNA
- The two polynucleotide strands run in opposite directions (anti-parallel strands),
i. e. one is 5’-3’, the other 3’-5’; - The sugar-phosphate-sugar backbone is on
the outside, and the bases on the inside;
- The two strands are held together by:
Hydrogen bonding between pairs of bases
(base-pairs) on opposite strands;
The two anti-parallel strands are twisted to
form a right-handed helix with about 10
base-pairs per turn.
Types of DNA damage: Strand breaks
Strand breaks – at the level of the polymer: they may occur by breaking bonds at sugar or phosphate (backbone)
- Single Strand Breaks (SSB)
- Double Strand Breaks (DSB)
Types of DNA damage: Nitrogen base damage
Causes changes in the base structure but may not break the polymer
- Oxidation of bases
- Alkylation of bases
- Hydroxylation of bases
- Cross-linking between bases
- Cross-linking between bases and proteins
State the types of agents that damage DNA
- Ionising radiation
- Ultraviolet radiation
- Chemical toxins
- Normal physiological agents
State different types of chemical toxins
- Alkylating agents e.g. methyl bromide – grain fumigant
- Cigarette smoke products (including radicals)
- Toxins from fungi e.g. aflatoxin (found on peanuts)
- Deaminating agents – e.g. intestinal dietary nitrates
- Intercalating agents – ethidium bromide
State normal physiological agens that damage DNA
- mitochondrial metabolism (reactive oxygen species - ROS)
- respiratory burst (ROS, RNS, free radicals)
Describe DNA Damage by Ionizing Radiation (IR)
- Ionizing radiation includes X rays, gamma rays, beta particles (high-speed electrons), alpha particles (the nucleus of the helium atom).
- These all have very high energy and can break covalent bonds in DNA or nearby molecules.
- The action can be direct on the DNA or indirect by 1st forming free radicals from water.
Explain different types of ionizing radiation
- X rays and gamma rays are electromagnetic waves like light, but their energy is much higher than that of light (their wavelengths are much shorter).
- Ultraviolet (UV) light is a radiation of intermediate energy that can damage cells (the well known sunburn), but UV light differs from the forms of electromagnetic radiation mentioned above in that it does not cause ionization (loss of an electron) in atoms or molecules, but rather excitation (change in energy level of an electron).
- The other forms of radiation–particles–are either negatively charged (electrons), positively charged (protons, alpha rays, and other heavy ions), or electrically neutral (neutrons).
Desrcibe DNA Damage by UV radiation
- UV radiation causes formation of cyclobutane pyrimidine dimers (CPDs) either T-T or C-T.
- Both of these lesions distort DNA’s structure, introducing bends or kinks and thereby impeding transcription and replication.
- Relatively flexible areas of the DNA double helix are most susceptible to damage.
- A commonly mutated oncogene, p53, contains a “hot spot” for UV-induced damage.
TRUE or FALSE: Alkylating agents transfer methyl or ethyl groups to nucleotides
TRUE
Alkylating agents transfer methyl or ethyl groups to nucleotides:
Adducts with DNA are formed
- Ethyl methanesulfonate (EMS) is commonly used in genetics to introduce point mutations (addition of a CH2, CH3 group to make ethylguanine), especially on guanidine. This disrupts normal G-C H-bonding . Causes guanine to bond better with thymine
- It can also alkylate thymidine to ethylthymine which bonds better to guanine.
- Nitrogen mustard (e.g. chlorethamine). This can also crosslink bases or strands.
Alkylation properties can be utilized in anticancer drugs
How do cigarette smoke cause DNA damage?
- It contains more than 3,500 different chemicals
- Cigarette smoke condensate contains polyphenols (catechol and hydroquinone)
- Catechol undergoes redox cycling, producing free radicals and reactive oxygen species (ROS)
- Strand breaks induced by cigarette smoke can be blocked by ROS scavengers
- It causes various biological effects including sister chromatid exchanges, micronuclei, tumour induction
Describe Tar radicals in cigarette smoke
- Tar radicals can bind to DNA to form adducts
- Tar fraction contains semiquinone species which
- Tar is a good metal chelator (many metal ions are free radicals)
- This leads to in-situ generation of reactive oxygen species in a process called redox cycling (semiquinolone can trasfer an electron to O2 to produce superoxide)
The resulting free radicals can damage DNA indirectly
What is one of the most common oxidation products of DNA?
8-oxo-G or 8-oxo-dG
Free radicals and oxidants are produced by which normal cellular process?
- Mitochondria: electron leakage to oxygen from complexes of the electron transport chain (produces superoxide→O2•-)
- Some metabolic processes involve redox cycling
- Peroxisomes and endoplasmic reticulum contain oxidases that produce hydrogen peroxide (H2O2)
- Phagocytic cells produce oxidants as antimicrobial agents (O2•-, H2O2, NO, HOCl) These free radicals and oxidants can also cause DNA oxidation
The production and effects of cellular FRs and ROS are normally limited by action of antioxidant enzymes, such as superoxide dismutase (SOD) and catalase or peroxidases which remove hydrogen peroxide.
Describe Oxidative damage to DNA
- It can directly cleave DNA backbone to yield SS breaks
- Induces oxidative base damage (over 20 different products)
- Typical reactions are:
–Hydroxylation (addition of –OH)
–Oxidation (addition of O / removal of H) (e.g forms 8-oxoadenine)
–Oxidative deamination (conversion of C-NH2 to C=O) converts an amine to an aldehyde/ketone
Examples of Common Oxidized Bases (A & G)
Example 1: instead of C=N →C=O
Example 2: Adition of oxygen then the ring is broken open
If an OH group was added instead of O→Forms 8-hydroxyguanine and 8-hydroxyadenine
Examples of Common Oxidized Bases (U, T & C)
- Uracil+OH→5-hydroxyuracil
- Uracil+2OH→Uracil glycol
(Same for thymine and cytosine)
Describe Spontaneous deamination of DNA
–cytosine to uracil (loss of amine group)
adenine to hypoxanthine (loss of amine group)
guanine to xanthine
~100/day/genome
Yields an abasic site (is a location in DNA that has neither a purine nor a pyrimidine base)
