L01-4
What shape is genomic DNA in eukaryotes? What about prokaryotes?
Prokaryotes: circular
Condensins, cohesins, and scaffold proteins are associated with
Higher order packaging
Explain the position effect
1. expression of a gene can be altered by moving it to another location in the genome
2. gene moving towards heterochromatin gets inactivated while going away from heterochromatin activates the gene
3. barrier sequences which separate the regions are called insulators, and many insulator proteins bind to this sequence regulating position effect
What do unique combinations of histone code and histone code reader mean
Unique biological properties; different histone codes are read by different code readers
A chromosome is a DNA segment of 168bp attached with histone core octamer and H1 only. Since it protects additional 20-22bp of linker DNA, H1 is also called linker histone.
Linker DNA gets shorter, about 32bp
3 letter DNA code ->3 letter ____ code -> 20 ___
RNA; amino acid
What is observed at "beads on a string"
10nM Chromatin fiber in first order packaging
What two enzyme classes regulate nucleosome arrangement of DNA?
Chromatin remodeling complex (slide nucleosome to new location , eject it from DNA or replace it with different histone)
Histone modifying enzymes (covalent modification of N-terminal tails)
What does chromatin remodeling and covalent modifications work together to regulate?
Chromosome structure/ Gene regulation
If you have decreased H1, what are you at risk of
Increased expression of oncogenes leading to cancer
DNA + Protein=
chromatin
What molecules create physical contact between segments of DNA?
Condensins and cohesins which belong to SMC family
Histone variants alter DNA binding affinity. True or false?
BONUS: Name the clinical correlate associated
True. Floating Harbor Syndrome occurs as a result of a single amino acid change. Serine changes to threonine in H2AZ; resulting in reduced expression of H2AZ. It causes craniofacial abnormalities
How can repositioning of nucleosomes affect transcription?
A. Moving nucleosomes could expose a promoter resulting in repression of transcription.
B. Moving nucleosomes could cover a promoter resulting in repression of transcription.
C. Moving nucleosomes could expose a promoter resulting in activation of transcription.
D. Answers A and B
E. Answers B and C
E
What stabilizes the second level of DNA packaging?
N-terminal tails stabilize the 30nM fiber
Name the copies in the nucleosome
H2A, H2B, H3, H4
Which histone binds linker DNA and binds DNA wrapped around the histone octamer?
H1; it has two DNA binding sites to carry out each role described
What does histone acetyltransferase do?
An enzyme that covalently modify specific amino acid residues in N-terminal tails of histones. They acetylate specific lysine residues
If you have less than 50 nucleotides, you have a _____. If you have more than 50 nucleotides, you have a _____
oligonucleotide; polynucleotide
What is ideal about less packaging of DNA?
Allows transcription factors and RNA polymerase to gain access to the gene to allow for transcription
How are histones able to interact with DNA?
They have positive charges from Lys and Arg which reacts with negatively charged DNA from phosphate groups
Compare and contrast heterochromatin and euchromatin
Heterochromatin is highly condensed chromatin that is not transcriptionally active (gene turned off), euchromatin is less condensed and is transcriptionally active (gene turned on)
Name the 4 covalent modifications of histone residues
acetylation, methylation, phosphorylation, ubiquitination
What happens to tightly packaged DNA in terms of gene expression?
it is prevented
Name a disease where transcriptionally dynamic active regions are altered.
brachydactyly( deletions) , F-syndrome(inversion and duplication), polydactyly (duplication and deletion)