Additional information

1. Telomeres and telomerase: Telomeres are DNA-protein structures located at both ends of each chromosome. They consist of tandem repeats of TTAGGG. With each cell division, a small portion of telomeric DNA is lost. When telomere length reaches a critical limit, the cell undergoes senescence and/or apoptosis.

   Telomere length is maintained by the enzyme telomerase, which adds TTAGGG repeats to chromosome ends. Telomeres are essential for the telophase stage of mitosis. When telomeres become too short, mitosis and cell division cannot occur.

2. Rb and p53 tumor suppressor proteins*

• Rb or retinoblastoma protein: Rb prevents the cell from entering S phase from G1 phase. Phosphorylated Rb is inactive. Rb normally binds to the transcription factor E2F and inhibits it. In the presence of growth factors, cyclin D-CDK4/6 and cyclin E-CDK2 phosphorylate and inactivate Rb. As a result, E2F is released; it binds DNA and increases transcription of S phase genes (for example, DNA polymerase). The Rb gene is mutated in hereditary retinoblastoma.
• p53 protein: p53 prevents cell transition from G1 to S. It is activated in the presence of DNA damage. As a transcription activator, p53 turns on the expression of genes like P21 and P27, which inhibit the cell cycle. It also induces apoptosis in cells with severe DNA damage. In normal cells, Mdm 2 keeps p53 levels low. DNA damage activates a set of kinases that phosphorylate Mdm2, causing it to dissociate from p53. Mutations in p53 lead to unregulated cell division and cancers.

* HPV 16 and 18 viral proteins E6 and E7 bind to and inhibit p53 and Rb respectively, leading to malignancies like cervical cancers.

3. ATM and ATR

ATM and ATR are tumor suppressor proteins that inactivate cdc25C phosphatase and prevent the cell from proceeding to M phase.

ATM mediates the cell response to double stranded DNA breaks induced by ionizing radiation. Mutations in ATM gene are seen in ataxia telangiectasia.

ATR mediates the cell response to UV induced DNA damage and double stranded DNA breaks.

4. Extracellular vesicles (EVs)** are small membrane vesicles secreted by most cell types. Their role is to provide intercellular communication both locally and systemically. Cells may use EVs to transfer nucleic acids, proteins, and lipids. EVs play a role in tumor progression and metastases.

   Transfer of EV content between cells confers the means for these interactions and induces significant cellular behaviour changes in the receiving cell. EVs are implicated in the regulation of numerous physiological and pathological processes, including development and neurological and cardiovascular diseases. Importantly, EV signalling is essential in almost all the steps necessary for the progress of carcinomas, from primary tumours to metastasis. EVs help tumors in angiogenesis, invasion, metastasis, and conversion of local fibroblasts into cancer associated fibroblasts. In Ca breast metastasis to the brain, EVs are taken up by the BBB by transcytosis.

5. DNA is read from upstream to downstream, i.e. from 3’ to 5’ ends.

6. t RNA (transfer RNA): tRNA transfers amino acids to the growing peptide chain. It has a folded structure with three hairpin loops that resemble a three-leaf clover. It contains an anticodon that is complementary to the mRNA codon. The 3’ end of tRNA is called the acceptor arm and binds to the amino acid.

   The enzyme aminoacyl-tRNA synthetase adds an amino acid to its specific tRNA, which “charges” the tRNA. This enzyme also has proofreading activity, ensuring that the correct amino acid binds to its specific tRNA.

7. How to write complementary DNA sequences? Because of complementary base pairing, if you know the sequence of one DNA strand, you can predict the sequence of the strand that will pair with it (the complementary strand). When writing complementary DNA sequences, write the final answer in the 5’ to 3’ direction. This usually requires reversing the complementary sequence.

   e.g. what will be the complementary DNA sequence to ATTGCGA? By convention, assume the given sequence is written 5’ to 3’: 5’ ATTGCGA 3’. Using complementary base pairing, the paired strand is 3’ TAACGCT 5’. Now reverse it to write it 5’ to 3’, so the answer is 5’ TCGCAAT 3’, also written simply as TCGCAAT. When writing an RNA sequence, replace T with U (for uracil).

8. Protooncogenes and tumor suppressor genes

9. Common tumor markers