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