BIOL 300 - Chapter 8

what are the 3 levels of chromatin organization?

10nm chain of nucleosomes > 30 nm fiber > 250nm fiber > chromatid

what is a nucleosome?

structural unit of chromatin thats in all eukaryotes

what are the components of a nucleosome?

made up of 200bp of DNA, and made by a histone octamer with DNA wrapped around it

what is a dimer?

pair of histones

what are the features of a nucleasome?

core DNA is 145-147bp long and resistent to nuclease digestion but has no sequence specificity, made up of 4 histone dimers,

what core histone proteins make up a histone octamer?

H2A, H2B, H3, H4 - 2 of each kind

why does the core DNA in a nucleosome have no sequence specificity?

because the core DNA is the same in ALL DNA in all eukaryotic organisms, so chromosome have to be packed in a general yet certain way

what is linker DNA?

DNA that’s accessible to nuclease enzymes, held in place by H1

what are the characteristics of histone octamers?

4 core histone types, small basic proteins that are rich in basic amino acids so they can neutralize negative DNA backbone charges

what are characteristics of histone tails?

have flexible amino or carboxyl terminal regions of core histones, sites of extensive posttranslational modification

what is posttranslational modification?

changes to proteins after synthesis in translation

where did histones originate from?

archaea - they’re highly conserved orthologs, so they descended from one common ancestor

how many histone variants are there?

5 H2A variants, 3 H3 variants, 2 H2B variants, 0 H4 variants

what histone protein is the only one to not have any variant types?

H4

how are the core histones and their variants paralogs?

core proteins are homologous within the same species that arose from a single ancestor through gene duplication

is sequence homology present between core histone proteins?

no, they’re all independent of each other, but share the same 3D structural mold: histone fold

what is an HFD?

histone folding domain

what makes up the two subcomplexes in an octamer?

1 H3-H4 tetramer, and 2 H2A-H2B dimmers

what can the H3-H4 tetramer specifically do in DNA?

can organize DNA in vitro into particles that display core particle properties

What characteristics does the H1 histone have?

serves as linker between nucleosomes, highly conserved, not required for nucleosome formation

what are chromatosomes?

nucleosomes with the H1 linker

what are the characteristics of histone tail posttranslational modification?

through covalent bonding, can occur on both N and C termini, can be maintained through cell division, and are removable

what are the three main modification types?

methylation, acetylation, and phosphorylation

what is methylation?

adds a -CH3 group, occurs on NH3+ groups on Lysine and Arginine and doesn’t affect positive charge

what is acetylation?

adds a -CO-CH3 group, happens on the NH3+ group of Lysine, and neutralizes the positive charge

what is phosphorylation?

adds a -PO4 group, occurs on the hydroxyl group of Serine and Threonine, and introduces a negative charge

how does histone modification alter genetic processes?

can change gene expression and condensation, happen on different histones and activate/repress gene expressions

what is the histone code?

hypothesis that states multiple modifications to histones regulate gene expression

how do most histone modifications function?

they provide binding sites for non histone proteins, changing chromatin structure

how is the histone code interpreted by non histone proteins?

takes action based on certain markings - could change chromatin accessibility based on histone codes

what are the two nucleosome assembly methods?

replication, and transcription/DNA repair

what is needed for replication as a nucleosome assembly method?

requires newly synthesized histones from all four canonical histone genes

how do you efficiently make a large group of canonical histone genes?

arrange genes into clusters to allow for translation and transcription at the same time

what is needed for transcription/DNA repair as a nucleosome assembly method?

doesn’t require newly synthesized histones, and looks at the replication independent pathway

what is the replication independent pathway?

disassembly and reasembly can occur when DNA is not being synthesized - retains most of nucleosome structure even if not fully condensed, and allows for variation in nucleosome assembly mechanisms (histone composition can change)

what does the clustering of canonical histones ensure?

there are similar amounts of each histone for quick transcription/translation, and they’re all triggered by DNA synthesis

what happens as replication occurs on the replication-coupled pathway for nucleosome assembly?

nucleosomes are disassembled from template DNA and template fork, but replication is immediately followed by new nucleosome formation on daughter duplexes with no discrimination between new and old tetramers/dimmers, or between variants except in centromere

what is nucleosome positioning?

determining which sequence is in the core and which sequence is in the linker

how is nucleosome positioning sequence independent?

transcription can occur after nucleosome positioning and change overtime, and either suppress or support gene expression

what are repressed genes?

genes not actively transcribed; nucleosomes are present at promoters so transcription can’t occur, and are in phase throughout the gene

what are actively expressed genes?

genes that are actively transcribed; nucleosomes are absent from promoters and out of phase