Thinking Classroom by Tara Drakes, Ph.D.

Bacteria can repair double-stranded DNA breaks through non-homologous end joining or homologous recombination.

taracjdrakes — 2024-09-30 00:33:05 UTC

(a) Why might double-stranded breaks have more detrimental consequences than single-stranded breaks?

(b) Which of these two aforementioned processes is more accurate (less error-prone), and why?

(c) Consider the requirements of homologous recombination. How would you design an experiment to drive homologous repair at the malT gene?

Throughout most of an organism’s life, several genes may remain inactive.

taracjdrakes — 2024-09-30 00:33:20 UTC

(a) What staining pattern would you expect to observe at these loci in G-banding procedures?

(b) To activate these genes, what process(es) (that we have discussed in class) are required to take place?

DNA Methylation/MMR

taracjdrakes — 2024-09-30 00:33:43 UTC

(a) Why is DNA methylation key to the success of mismatch repair?

(b) In humans, defects in the mismatch repair system are associated with some types of leukaemias. What steps do you think scientists may have taken to prove that mismatch repair defects may cause leukemia?

Imagine that you are a computational biologist developing software to identify transposition events in the human genome.

taracjdrakes — 2024-09-30 00:33:55 UTC

What types of sequences would your computational program look for to determine sites of previous transposition events?

What types of sequences would your computational program look for to determine sites of future transposition events?

DNA Methylation/MMR

2024-09-30 15:44:37 UTC

(a)DNA methylation helps distinguish between the original DNA and the newly synthesized strand. This enzyme helps recognize which strand contains the mismatch errors in order for the repair to accurately identify the correct DNA strand for the repair process to occur.

(b)For scientists to prove that MMR defects may cause leukemia, I would anticipate that they have done studies that analyze the genetic makeup of individuals with leukemia to look for mutations. These DNA strands would then be compared with that of healthy individuals. Additionally, I would believe that scientific researchers would look at other individuals with previously known diseases induced by MMR deficiencies, to see the correlation of and similarities with such MMR mutations. This could help link MMR defects to leukemia.

DNA Methylation/MMR

2024-09-30 15:46:01 UTC

(a) It is key to the success of mismatch repair because methylation occurs on the template strand. This helps distinguish the newly synthesized DNA strand from the older template DNA strand during DNA replication specifically in bacteria.

(b) Scientists may have shown that mismatch repair (MMR) defects can cause leukemia by studying cells with known MMR deficiencies and analyzing patient samples for mutations in MMR genes, linking these defects to the development of the disease.

a- inactive Genes are typically found in regions of the chromosome known as heterochromatin

jamelia20001031 — 2024-09-30 15:49:35 UTC

Therefore you would expect to observe a staining pattern that reflects the heterochromatin state hence presenting darkly stained areas in G-Banding

Question 2

2024-09-30 15:49:54 UTC

a) With Giemsa dye, darker bands would be expecting in G-banding as it composed of heterochromatin containing inactive genes which are tightly packed and more resistant to trypsin.

Question 2

2024-09-30 15:51:12 UTC

b) histone modifications to cause a more relaxed chromatin structure like eurochromatin

b)

2024-09-30 15:52:45 UTC

in order for G-banding to occur, the miotic chromosomes need to be digested with trypsin; a proteolytic enzyme. Afterwards, Gemisia staining is used. Trypsin resistant regions on the chromosome are more protein rich and will take up take up Giemsa dye easily

Throughout most of an organism’s life, several genes remain inactive.

2024-09-30 15:52:54 UTC

A. Inactive genes are usually tightly coiled therefore, making them heterochromatin. Hence, they are more resistant to the enzyme trypsin and will be more aggressively taken up by the Giemsa stain, making those stains darker than the other regions.

B. Tightly coiled heterochromatin are genetically inactive therefore, to make them active we can uncoil them.

2024-09-30 15:53:48 UTC

b) homologous repair

jamelia20001031 — 2024-09-30 15:53:56 UTC

To activate inactive genes in heterochromatin, chromatin remodeling, histone modification, and the binding of transcription factors are necessary. Chromatin remodeling alters the structure of chromatin to make DNA more accessible for transcription. Histone modification, such as acetylation or methylation, can lead to a more euchromatic state, allowing for gene expression. Transcription factors bind to the promoter regions of genes to initiate transcription. Other regulatory elements may also play a role in enhancing gene activation.

jamelia20001031 — 2024-09-30 15:54:59 UTC

2 (b) To activate inactive genes in heterochromatin, chromatin remodeling, histone modification, and the binding of transcription factors are necessary. Chromatin remodeling alters the structure of chromatin to make DNA more accessible for transcription. Histone modification, such as acetylation or methylation, can lead to a more euchromatic state, allowing for gene expression. Transcription factors bind to the promoter regions of genes to initiate transcription. Other regulatory elements may also play a role in enhancing gene activation.

DNA Methylation/ MMR

2024-09-30 15:55:21 UTC

(a) DNA methylation is the key to mismatch repair because the methyl tag allows for differentiation between the old and new strand. This allows the repair complex to then bring the mismatched bases close to the methylated sequence so that the new strand is identified. The nucleotides on the new strand between the tagged sequence and mismatch are removed and then they are replaced with the propwr sequence by DNA polymerase and ligase

(b) Scientists likely tagged certain sequences so that they could observe whether there was a change in the sequence in cells that did not give rise to leukemia and those that did. There were likely also untagged sequences with mismatch repair that were observed to see if leukemia was caused by the mismatch repair.