LECTURE 2 (DNA structure and stability) Flashcards
What is cancer?
A disease that involves alterations to gene structure and gene expression at the cellular level
What are the two mechanisms required to carry out protein synthesis?
- Transcription
[gene sequence is copied from DNA to an mRNA molecule] - Translation
[gene’s sequence encoded in mRNA directs the production of a protein]
What are nucleotides composed of?
- A sugar group
- A phosphate group
- A base
What are the four different bases?
- Adenine (Purine)
- Guanine (Purine)
- Cytosine (Pyrimidine)
- Thymine (Pyrimidine)
What does RNA Polymerase do?
- splits apart the two strands that form the double helix
- reads a strand and copies the sequence of nucleotides
What is a response element?
A short sequence of DNA within a promoter that is recognised by a specific protein and contributes to the regulation of the gene
What is the importance of the 5’ end of a gene?
- Contains nucleotide sequences that make up the PROMOTER REGION -> involved in regulating expression of the gene
- Nucleotide sequences interact with proteins that affect the activity of RNA polymerase + determine when and where a gene is expressed
What is found downstream of the promoter?
Nucleotides that will be transcribed into RNA and those coding for exons will be translated into protein (CODING REGION OF THE GENE)
What are the types of carcinogens?
- Chemicals
- Physical agents (Radiation)
- Biological agents (Viruses, bacteria, parasites)
What are mutations?
Random changes that occur within the sequence of bases in DNA. They can be large scale, altering the structure of the chromosomes, or small scale where they only alter a few or even a single base
What are the steps of cancer?
1) Normal cells undergo DNA repair in which a promoter causes the formation of Normal cells with DNA lesions (INITIATED CELLS)
2) CLONAL EXPANSION leads to proliferating cells acquiring mutations simultaneously with OVEREXPRESSION of ONCOGENES and DOWN-REGULATION of TUMOUR SUPPRESSOR GENES
3) Cell proliferation, apoptosis inhibition and neoplastic transformation leads to NEOPLASTIC CELLS
4) Angiogenesis, Migration, Invasion and Metastasis -> CANCER
What is the difference between germline mutations and somatic mutations?
GERMLINE MUTATIONS = occur in gametes + can be transmitted to offspring and every cell in the offspring will have the mutation + can increase cancer susceptibility
SOMATIC MUTATIONS = occur in other cells of the body + confined to just one cell and its daughter cells so cannot be passed onto offspring + can lead to cancer
What are chromosomal alterations?
Mutations that change chromosome structure or number. They occur when a section of a chromosome breaks off and rejoins incorrectly or does not rejoin at all
What are the different types of Chromosomal alterations?
- Amplifications
- Deletions
- Chromosomal rearrangements
What are Amplifications?
Where there is an increase in the amount of DNA present in a specific region of a chromosome
What are Deletions?
Deletions of large chromosomal regions leading to a loss of genes within those regions
What are examples of Chromosomal rearrangements?
- Translocations
- Insertions
- Inversions
Where are translocations often observed?
In liquid tumours
[particularly common in lymphoid tumours]
Describe Chronic Myelogenous Leukemia (CML)
Chronic Myelogenous Leukemia (CML) is caused by a chromosomal translocation between chromosomes 9 and 22 that generates the PHILADELPHIA CHROMOSOME -> Translocation creates a HYBRID KINASE that phosphorylates and activates many signal transduction proteins leading to cell proliferation
TREATMENT: The drug IMATINIB (GLEEVEC) inhibits the kinase and is effective in controlling CML
What is a point mutation?
Affects a single base and most commonly occurs when one base is substituted or replaced by another
Which mutations result in Frameshift mutations?
- Insertion
- Deletion
What is a carcinogen?
A substance, organism or agent capable of causing cancer. Carcinogens may occur naturally in the environment or be generated by humans
What is ionising radiation?
Any type of particle or electromagnetic wave that carries enough energy to ionise or remove electrons from an atom
What are the most frequently ionisation radiation-induced cancers?
- All forms of Leukemias (except CLL)
- Cancers of thyroid, skin, breast, ovary, uterus, lung, myeloma and salivary glands
How does Mechanism Radiation damage the DNA of the cell?
- It may directly alter the cellular DNA
- It may dislodge ions from water and other molecules of the cell and result in formation of highly reactive free radicals that may bring about the change
How is Ultraviolet radiation the most effective carcinogen?
The conjugated double bonds in the rings of the nitrogenous bases of DNA absorb UV radiation -> Directly and uniquely causes characteristic UV PHOTOPRODUCTS (cylocutane pyrimidine + photoproducts)
Excessive exposure to UV rays can cause various forms of which skin cancers?
- Squamous cell carcinoma
- Basal cell carcinoma
- Malignant melanoma
What is the common mechanism of action of chemical carcinogens?
An electrophilic (electron-deficient) form reacts with nucleophilic sites (sites that can donate electrons) in the PURINE and PYRIMIDINE rings of nucleic acids
Where is Aflatoxin B1 (AFB1) produced?
By the molds ASPERGILLUS FLAVUS and ASPERGILLUS PARASITICUS which are able to contaminate food commodities
Describe the mechanism of Aflatoxin
1) AFLATOXIN reaches the liver and is metabolised into a more active and toxic metabolite via metabolic activator CYP450 (in Liver Hepatocyte)
2) EPOXIDE binds to Guanine base in DNA which causes mutation in P53 (Tumour suppressor gene)
3) Hepatocytes turn into tumour cell (HEPATOCELLULAR CARCINOMA)
What are the different types of DNA repair systems?
- One-step repair
- Nucleotide excision repair
- Base excision repair
- Mismatch repair
- Recombinational repair
Describe One-step repair
When an enzyme or protein directly removes atoms that shouldn’t be on the base, restoring the original structure
What does Direct Reversal (DR) deal with?
Small chemical additions (adducts) on nucleotide bases
What is Nucleotide excision repair specific for?
Helix-distorting lesions such as pyrimidine dimers and bulky DNA adducts induced by environmental agents
[happens in the G1 page]
Describe the process of Nucleotide excision repair of UV damaged DNA
1) UV exposure creates thymine dimers which are recognised by an ENDONUCLEASE COMPLEX causing single strand cleavage on both sides of segment
2) Damaged DNA is discarded
3) DNA POLYMERASE fills the gap with the correct nucleotides and DNA LIGASE seals the gap
What is Base excision repair?
Base excision repair corrects small DNA lesions and happens throughout the cell cycle
What does each glycosylase in Base excision repair do?
Detect and remove a specific kind of damaged base
What is DNA mismatch repair (MMR)?
The cellular post replication process that preserves DNA homeostasis and guarantees genomic stability. It corrects spontaneous base-base mispairs and small insertions-deletion loops that are generates during DNA replication and happens in the S phase.
Describe the process of DNA mismatch repair (MMR)
1) Recognition of the mismatch is carried out by proteins MSH2/6 and MSH2/3
2) MLH1/PMS2 and MLH1/PMS1 are recruited and the newly synthesised strand is identified
3) Endonuclease and exonuclease remove the nucleotide around including the mismatch
4) DNA polymerases resynthesise a newly replicated strand
What is Lynch syndrome?
- The most common of the inherited colon cancer susceptibility syndromes
- Autosomal dominant
- Inherit a germline mutation in one of several DNA mismatch repair genes (errors in DNA cannot be fixed -> abnormal cells build up and cause cancer)
Approximately ____% of Colorectal cancers are hereditary
5%
What can cause Double-stranded breaks in DNA and why is it dangerous?
High-energy radiation can cause double-stranded breaks in DNA (splitting a chromosome in two)
Dangerous because large segments of chromosomes, and hundreds of genes they contain, may be lost if break is not repaired
Which pathways are involved in the repair of double-stranded DNA breaks?
- Non-homologous end joining
- Homologous recombination pathways
Describe homologous recombination
1) A double stranded break activates the ATAXIA TELANGIECTASIA MUTATED (ATM) KINASE and the RAD50/MRE11/NBS1 complex (a substrate of ATM) uses its 5’-3’ exonuclease activity to create single x0002 stranded 3’ ends
2) BRCA1/2 aids in the nuclear transport of RAD51and RAD52 facilitates RAD51 binding to these exposed ends to form a nucleoprotein filament
3) RAD51 can exchange a homologous sequence from a single strand within a double-stranded molecule with a single-stranded sequence. The sequences from the double-stranded molecule are used as a template sequence for repair.
4) RESOLVASES restore the junctions formed as a result of homologous recombination called HOLLIDAY JUNCTIONS -> Two copies of intact DNA molecules are produced with rarely any errors
What is Ataxia Telangiectasia?
A rare inherited childhood neurological disorder that affects the part of the brain that controls motor movement and speech. Both cellular and humoral immunity are affected.
MODE OF INHERITANCE:
- Autosomal recessive
- ATM gene
- Due to chromosome instability
SYMPTOMS:
- Cerebellar ataxia
- Oculocutaneous telangiectasia (Bulbar conjuctivae, Ears, Neck, Cubital fossae)
- Recurrent infection
- Increase risk of malignancy
LABAROTORY FINDINGS:
- High serum alpha-fetoprotein (AFP
[the most consistent lab abnormality]
- High carcinoembryonic antigen (CEA)
- Low IgA, IgG and IgE
It is also associated with increase sensitivity to ionising radiation
What is a BRCA mutation?
A mutation in either of the BRCA1 and BRCA2 genes (tumour suppressor genes). Harmful mutations in these genes may produce a hereditary breast-ovarian cancer syndrome in affected people.
When is Non-homologous end-joining (NHEJ) used?
At other points of the cell cycle when sister chromatids are not available for use as a template
[can occur throughout the cell cycle]
Describe Non-homologous end-joining (NHEJ)
Direct joining of the broken ends which requires proteins that recognise and bind to the exposed ends and bring them together for ligating. A protein called “KU” is used.
Which cancer does faulty DNA mismatch repair cause?
Hereditary nonpolyposis colon cancer
Which condition is Non-homologous end joining linked to?
Ataxia-telangiectasia
Which conditions is Homologous recombination repair linked to?
- Breast/ovarian cancer
- Fanconi anaemia
