BSC 300 Final - Nuclear Structure & Chromatin Organization

what percent of human DNA encodes proteins & functional RNAs?

~1.5 (the rest is regulatory sequences & introns)

gene

dna sequence encoding a functional gene product (protein or rna) including the protein coding, enhancer, and promoter regions

solitary genes

25-50% of prot-coding genes in multicellular orgs represented only once in haploid genome

gene families

diff proteins w/ specific but similar phys fns; heavily used products that must be transcribed @ high rates

simple transcription unit (~10% in humans)

from gene, get one mRNA to be used in translation

effect of mutation within a transcription-control region

may reduce or prevent transcription, thus reducing or eliminating synthesis of the encoded protein

effect of mutation within an exon

may result in abnormal protein w/ diminished activity

effect of mutation within an intron

if it introduces a new splice site, it results in an abnormally spliced mRNA encoding a mutated protein

complex transcription unit

primary transcript contains alternative splice sites - can be processed into mRNAs w/ same 5’ & 3’ exons but diff internal exons (alt splicing)

mobile DNA elements

include transposons & retrotransposons; promote generation of gene families by gene duplication; exon shuffling creates new versions of genes & complex regulatory regions; SELECTED AGAINST

recombination / unequal crossing over

can cause gene duplication or unequal distribution of exons

possible outcomes of gene duplication

redundancy, neofunctionalization, subfunctionalization, gene loss or pseudogene

redundancy (gene duplication)

duplicate gene retains its fn & increases basal transcript levels

neofunctionalization (gene duplication)

duplicated genes tend to accumulate mutations faster and these mutations may result in new and different functions

subfunctionalization (gene duplication)

mutation in both copies of the gene lead to functionality of the original gene being distributed among the two copies

gene loss or pseudogene (gene duplication)

the extra copy of the gene may be lost over time due to not being needed, or it may become a pseudogene (copy retained but mutations lead to nonfunctionality)

deduced mechanism for evolution of tubulin genes

ancestral cell had only one tubulin; duplication event occurred before speciation.

a- & b-tubulin are

homologous, orthologous, paralogous

homologous genes

evolved from common ancestor

orthologous genes

same fn but differ bc of speciation

paralogous genes

differ bc of gene duplication

nucleosome

dna wrapped around histone octamer (both considered part of nucleosome)- can be stacked to form 30 nm fibers

10 nm nucleosome filament

“beads on a string” - nucleosomes linked together by DNA strand

chromosomes

consist of chromatin fibers (composed of DNA & assoc proteins)

lowest level of chromosome organization

nucleosomes

linker DNA

used to join nucleosomes together; btwn octamers?

histone octamer

2 mcs each of histone H2A, H2B, H3, H4 that adopt disc shape around which 147bp coil forms in a left handed turn; neg dna binds tightly to + lysine in histones

what nucleosome structures plays a role in regulating higher order of packing

n-terminal AA tail; fifth histone protein (H1)

how does H1 (histone protein) regulate higher level chromatin structure

binds linker DNA & DNA wrapped around the octamer; pulls nucleosomes together into regular repeated array (lg supercoiled loops) to establish 30nm chromatin fiber

how is dna compacted to a nucleosome?

DNA wrapped around octamer, H1 binds linker & nucleosomes to form 30 nm fiber, which forms anchored loops, which form chromosomes

chromatin-remodeling complexes

hlyze ATP to slide DNA along nucleosome and make it more accessible - may make chromatin more or less compact

what controls chromatin condensation & fn?

modifications of histone tails (usually contain several modifications)h

istone code

specific post-TL modification combinations in diff chromatin regions which specifically influence chromatin fn by creating or removing chromatin-assoc protein binding sites

reversible histone modifications

acetylation, phosphorylation, methylation, ubiquitination

acetylation of lysines (histone mod.)

neutralize + charge of lys, weakening histone/DNA assoc & making DNA more accessible

methylation (histone mod.)

prevents acetylation, resulting in more compact DNA not as accessible for TS

heterochromatin

highly condensed interphase chromatin - essentially inactive and without transcription

where is heterochromatin located?

concentrated around the center (centromere) & termini (telomeres) of chromosomes

euchromatin (eu=good)

more relaxed & therefore more accessible; variable state of decondensed chromatin; TRANSCRIPTIONALLY ACTIVE

heterochromatin regulation

H3K9me (enzyme) promotes heterochromatin spreading by recruiting specific methyltransferases that modify adjacent nucleosomes; will continue to spread until a barrier DNA sequence is encountered

epigenetic regulation

depends on factors other than DNA seq; can be transmitted from parent to progeny cells & regulate gene expression w/o altering nucleotide sequence; usually reversible

example of epigenetic regulation

x-chromosome inactivation - two ch can have identical DNA seq, but one is inactivated and the other is not

homologous chromosomes

most human cells are diploid: contain one maternal & one paternal copy of each chromosome

non-homologous chromosomes in men

X and Y (sex chromosomes)

nuclear organization - chromatin in interphase

chromatin fibers from each chromosome are concentrated into distinct territories - genes physically moved to nuclear sites called “transcription factories” where ts machinery is located

centromere

located at center/waist of chromosome; contain constitutive heterochromatin; site of microtubule attachment during mitosis

telomeres

do not encode genetic information; encode repetitive sequences; at ends of each chromosome & prevents degradation

telomeres & tumors

in somatic cells, telomere lengths are reduced each cell division. when it gets short enough, cells stop dividing. cells that are able to resume telomerase expression continue to proliferate (instead of dying) and do not show normal signs of aging. Approximately 90% of human tumors have cells w/ active telomerase

Approximately ___% of human tumors have cells w/ active telomerase

90