Lecture 12 molecular structure of chromosomes and transposition PDF

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Professor Sarah Hall...

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LECTURE 12: molecular structure of chromosomes and transposition Chromosomes and genomes ● Chromosomes contain genetic material, whereas the genome contains ALL the genetic material of an organism ● Type of DNA sequences on genome facilitates its function for all criteria of the genetic material such as: ○ Sequence for creating RNA and proteins ○ Sequence for replicating chromosomes ○ Sequence for segregating chromosomes → must be able to be inherited ○

Sequence for allowing chromosomes to become compact → fit inside the nucleus

Bacterial chromosomes: ● Circular (few million bps long) ● DNA replication starts at an origin of replication ● Intergenic regions: “in between the genes” ○ Same nucleotides are copied over and over Operons in bacteria ● Each gene sequences encodes an mRNA that codes a protein ● Promoter: polymerases bind to it to start transcribing ● Operons have multiple sequences of different genes that encode different proteins ○ Regulated by a single promoter

Bacterial genome compaction ● DNA is in direct contact with the cytoplasm ● Microdomains: a loop of DNA that comes back to the core ○ 400-500 microdomains in bacteria ● Nucleoid-associated proteins (NAPs) ○ Form the micro and macrodomain

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Bend or connect DNA regions together → bind the DNA tightly together

DNA supercoiling ● Twisted to change the shape of DNA ● Different directions of supercoiling are called topoisomers of each other ● Underwinding or overwinding of DNA can cause supercoiling ● Underwinding: ○ Negative supercoiling (less than 10 bp per turn) ○ Unstable DNA structure ○ Pops out bases to release the tension ● Overwinding ○ Positive supercoiling (more than 10 bp per turn) ○ Unstable → pops out bases to release tension ●

In bacteria: ○ 1 negative supercoil per 40 turns of the double helix ○ Help make the chromosome compact

Controlling supercoiling ● DNA gyrase (topoisomerase II) ○ Uses ATP energy to create negative supercoils ○ Relaxes positive supercoils to a neutral position ○ Critical for bacteria to survive → required for negative supercoils needed for replication ○

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Blocking DNA gyrase with quinolones or coumarins stops bacteria from doing this ■ Quinine: the high concentration of quinine in tonic water kills malaria bacteria DNA topoisomerase I ○ Relaxes the negative supercoils ○ Breaks one strand to rotate the DNA to create positive supercoil

Eukaryotic chromosomes ● Parts of the gene: ○ Introns: the noncoding part of the gene ○ 3’ UTR (untranslated region): stabilizes the RNA but does not incorporate into the protein sequence ○ Exons: coding part of the gene ● Transcription ○ Makes the primary RNA ○ Has introns, exons, and 3’ UTR ● Splicing ○ Makes the mRNA ○ Cuts the RNA at borders of exons and intron sequences ○ Takes out all the introns, only keeping coding exons ● Repetitive DNA ○ More in eukaryotes than prokaryotes

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Telomeres ■ Structures at the end of the chromosome to prevent degradation ■ Made of DNA sequences that are repeated ■ Protects enzymes called exonucleases from binding to ends of DNA and chewing them up ■ Regulate cell division → important for cellular aging ● ● ●

Shorten when the cell divides Helps the cell keep track of how many times it has divided based on the length of the telomere Too much telomere (from high telomerase, the enzyme that generates telomeres) can make the cells think they are always young → can result in tumor formation from unregulated cell division

Nucleosomes: ● Has 8 histone proteins (octamer) ○ H2A, H2B, H3, H4 (two of each) ● 146-147 base pairs wrap around the octamer to form the nucleosome ● Linker region: ○ Unprotected piece of DNA ○ H1 protein is the linker protein ● Regulates gene expression and chromatin structure ● The charge of the modification determines DNA compaction/regulation ○ DNA is negatively charged ○ Methylated histone is + so DNA wraps tightly around it → protein can’t access DNA ○ ● ●

Acetylated histone is - so DNA repels and wraps loosely → protein can access DNA

Heterochromatin: tightly wound Euchromatin: 30nm fiber in radial loops → looser for proteins to reach it

Nuclear matrix ● Ensures that the chromosomes turn back from the fuzzy unraveled state to neat and orderly for segregation during cell division ● Nuclear lamina: ○ Filaments that coat the inside of the membrane ○ Serve as anchors ■ Bind to DNA and lamina to anchor the DNA to the nucleus ● Internal nuclear matrix: ○ Filaments that create the structure ○ Proteins bind to the matrix but also associate with the DNA to organize DNA in certain regions of the nucleus ○ Radial loop domains: ■ Matrix-attachment regions (MARs) or

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Scaffold-attachment regions (SARs) Bind to the filaments

Transposition ● If it has (1) transposase and (2) indirect repeats, then it is a transposition ○ If it can do it all by itself, it is an autonomous TE ○ If it can’t, its non-autonomous ■ They jump ● Transposase: ○ Binds to inverted repeats on either side ○ Comes together so transposase enzymes can meet each other ○ Form a donut loop, transposases cuts the DNA to release the donut ○ Donut finds a new place, cuts the DNA, and inserts itself ○ Damage: ■ Breaks in DNA can cause translocations, inventions, etc ■ Reinserting can cause harm too ● TEs (transposable elements) of DNA are incorporated into the chromosome ● Transposons cut and insert themselves into another area ● Insertion elements ○ Most basic TE ○ Inverted repeats (IR): same DNA sequence flips over on opposite sides ○ Direct repeats (DR): does not repeat, goes from 5’ to 3’ ○ Between the two flipped sequences is a transposase gene ● Simple transposon ○ Inverted repeats, direct repeats, transposase gene are all there again ○ Antibiotic-resistance gene: beneficial to bacterial cells...