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40 Cards in this Set

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Define chromatin
Chromatin is the material that collectively composes a chromosome that has DNA + Protein associated with it
Name four reasons of why chromosomes are important
Compact form to fit into cell, protect DNA/stable, efficient transmission to daughter cell, and confer organization: key in gene regulation
Define histones
Histones are proteins that are major players in packaging DNA
Define nucleosome
Also involved in packaging DNA, a nucleosome is an octamer of histones
Describe what nonhistone proteins do
Nonhistone proteins are associated with DNA as they regulate transcription, replication, repair and recombination
True or False: Histones are found in prokaryotes as well as eukaryotes
False. In prokaryotes they use other basic +charged proteins
What is the majority of DNA in eukaryotic cells packaged into?
Nucleosomes
True or False: DNA is always bound by histones and never free to float around
True
What is the nucleosome core made up of?
8 histones with DNA wrapped around
Describe core DNA
Very tightly associated, wrapped 1.65 times around histone core and has an invariant # of base pairs (~147)
Where is the linker DNA located?
Between two cores; length varies depending on species
How many times is DNA compacted into nucleosomes?
6 times compaction
What does the enzyme Micrococcal nuclease (Mnase) do?
Cleaves DNA that are not associated with proteins. Can undergo "light digestion", which cleaves once between some linkers
True or False: Histones are positively charged while DNA is negatively charged
True
How long is DNA in a diploid set of chromosomes?
~2m (6'6"=Lebron James' height!)
Describe what "light digestion" is by Mnase
Cleaves once between some linkers, usually during a short period of time or low concentration of enzyme
True or False: DNA is always in the 10-30nm range. Even during replication
False. DNA is always in the 10-30nm range, except during replication when it compacts further (>30nm)
Describe what "extensive digestion" is
Digests all DNA up to core
True or False: Histones have been conserved through evolution
True
What support shows that histones are conserved?
Eukaryotes have very similar histones in very different types of species
What are the names of the five most abundant types of histones?
H1, H2A, H2B, H3, H4
Which histone is labeled the "linker histone"? How is it different from the other histones?
H1. Binds outside of core region and is a little larger than core histones (~21 kD)
What histones make up the "core histones"? How many of each are wrapped by DNA?
H2A, H2B, H3, H4 are the core histones and 2 of each are used to make an octamer (11-15 kD)
How many linker histones are required per nucleosome?
One (H1) linker histone
What percent do two basic amino acids provide histone with to make it positively charged? What are the two aa?
~20% The two aa are lysine (K) and arginine (R)
Which blots are used to detect protein, RNA and DNA respectively?
Western, Northern and Southern
Why is sodium dodecyl sulfate (SDS) used in gel electrophoresis?
Because it's a detergent that disrupts all non-covalent/ hydrophobic interactions and adds a negative charge- causes protein to separate based on size
True or False: Histones still can form the core even without DNA present
False. Histones assemble in an ordered manner ONLY in the presence of DNA
What happens when DNA is NOT present?
Histones will still bind to each other but not as an octamer. As a result, H2A and H2B form a dimer and H3 and H4 form a tetramer
Describe what a histone-fold domain is
It is a domain that has 3 alpha helices, separated by loops which mediates dimerization
What other kinds of proteins are required to assist with the assembly of nucleosomes?
Accessory proteins
Name the steps taken to assemble the nucleosome
1) H3-H4 tetramer binds DNA and wraps it to a certain extent
2) Two H2A and H2B dimers join soon after
After the nucleosome is assembled, what is left sticking out? Why is this important?
Amino terminal ends called tails are left sticking out of the nucleosome. They are important because they become extensively modified and have biological functions
What type of treatment are N terminal tails sensitive to? What does it do to them?
Protease treatment. Cleaves proteins + charged residues (i.e. trypsin)
survenir
to occur, to happen
What aa residue(s) can undergo acetylation the best?
Lysine (K)
What aa residue(s) can undergo methylation the best?
Lysine (K) and Arginine (R)
Why are N terminal tail modifications important?
They are important in nucleosome function by altering chromatin accessibility
Why is the core histone protected from protease treatment?
Because it is folded upon itself
Besides being modified, what else do the N terminal tails do?
They help stabilize DNA wrapping around the octamer in a left-handed manner, resulting in negative supercoils