7 - Nucleus, Nucleosome, and Nucleolus (FOR FINAL)

cells need to have inheritable info - Genome

• essential info inhertied from mother to daughter cells

• the inheritable info is needed to be replicated for further cell division

• protect the heritable info

nucleoid downsidses

• direct access to DNA

• efficient for transcription, but dangerous

• ex: exposure to reactive oxygen species (ROS) can damage DNA

• less control over what gets transcribed

organelle: nucleus

membrane bound

contains and protects DNA

• allows specific proteins to pass and assist transcription

• can duplicate genome during cell cycle - can disintegrate and reform

• interacts with ER and ribosomes

where is translation taken place

cytosol/cytoplasm

separate from where euk transcripts made in nucleus

where is most of rRNA transcription taken place

most of rRNA transcription is taken place in NUCLEOLUS

how is the nucleus similar to DNA

the nucleus is more complex and inefficient in exchange for stability

chromatin

chromatin exponentially condenses DNA to allow it to fit within the cell’s nucleus

• composed of histone protein octamers bound to DNA

• helps control gene expression through key histone markers

bigger picture of histones: they are a major protein component of chromosomes

DNA wrap around the histone octamer

formation of nucleosome

where does the DNA sit in the histone and nucleosome complex

regular DNA sits between histone wrapped DNA (first step)

what is the length of the DNA wrap around the histone core

DNA wrapped around the histone core is almost two tines in one nucleosome

what is the last fully open state called

the last fully open state is called beads on a string form of chromatin

most decondensed and accessible state of DNA packaging in a eukaryotic cell

higher order structure of the beads versions

the higher order structures can cause inaccesibility and are

• euchromatin

• heterochromatin

what is euchromatin

euchromatin is loosely packed, accessible DNA

what is heterochromatin

heterochromatin is tightly packed, inaccessible DNA

what is constitutive heterochromatin

always inaccessible, like pericentromeric and peritelomeric

what is facultative heterochromatin

can unpack into euchromatin and be accessed

can vary by cell type

what is histone H1

histone H1 is a non core histone that interacts linked DNA between nucleosomes

what does the binding of H1 stabilize

the binding of H1 stabilizes the histone beads and allows them to pack further

what does clamp proteins do

clamp proteins pull groups of condensed beads into ribbons

• specific DNA sequences promote more or less loops

• there are matching specific DNA sequences

• there is a looped domain

• then there is a chromosome loop forming clamp proteins

coding areas of a chromosome

they are all in service of gene expression

• genes

• exons

• euchromatin (active genes turned on or off)

what are structural areas for

attachment point for spindle fibers for during cell division

• telomeres

• chromatin

• histones

• heterochromatin (usually inactive)

what are individual sections of our chromosomes

individual sections of our chromosomes are constantly open at the DNA level to allow access

what do chromosomes ahve to navgiate through

they have to navigate through duplication and cell division

cell cycle, mitosis, etc

what does the formation of mitotic chromosome allow

the formation of mitotic chromosome allows separating genome in limited space in cell

what are the three essential components for faithful transmission of the chromosome

the three essential components are

• telomere

• replication origin

• centromere

are chromosomes sitting in the cell randomly

genome is highly organized in interphase nucleus at the chromosome level

NOT random

is DNA wrapped onto histones accessible for transcription?

sometimes - accessibility depends on chromatin remodeling and histone modifications

where and what do epigenetics affect

epigenetics act on the DNA double helix from the DNA to RNA section of central dogma

(transcription - replication)

affects the ability of genes to become transcribed

modification on histone tail: methylation

heterochromatin formation, gene silencing

modification on histone tail:

methylation + acetylation

acetylation + phosphorylation

gene expression

what are the three marks on histones that are the major ones

three major ones

• promoting heterochromation

• charge

• steric hindrance

what does promoting heterochromation mean

some marks promote nucleusomes binding to each other by recruiting other proteins

what does the charge mark mean

lysines are postiive, normally can bind to negative phosphate backbone of DNA

acetylation removed pos charge and loosens the DNA

what does steric hindrance as a mark mean

trimethyl lysin can act as landing pad to bring in proteins that physically block transcription

DNA could be open/euchromatin

as membranes evolved around DNA, why is it important to keep rRNA separate

it is important to keep rRNA separate because

• rRNA is more precious by percentage

• rRNA is also transcribed much more than any DNA

what place contains the rRNA and where is the rRNA transcribed

rRNA is IN the nucleus

rRNA is TRANSCRIBED in the nucleolus

what is the nucleolus

it is the site of rRNA and ribosome biogenesis

• secret base of RNA and the ribosome within the nucleus

• nucleolus must interact with rDNA sequences on chromosomes

• like the nucleus, nucleolus disintegrate in mitotsis and must reform

what do the nucleolar organizer regions (NORs) on five chromosomes encode for rRNA

NORs contain multiple repeats of rRNA (200+)

redundancy and simultaneous transcription

where do ribosomes act on the central dogma

in the RNA to protein section, the translation section

what percent of RNA production is rRNA based

80-90% of ALL RNA production is rRNA based

• rRNA dominated prod of RNAs in cell

• tRNAs is 10-12%, mRNAs are 2-5%

• RNA and ribosomes are still the major backbone of the cell

what are the nucleus and nucleolus surrounded by

the nucleus and nucleolus are surrounded by the nucelar envelope

how does transcropt across nuclear membranes happen

transport across nuclear membranes is because of nuclear pores that create a gate for molecules

• nuclear membrane is shared with the ER

• globular proteins smaller than 60kDa can diffuse in and out through nuclear pores

steps of nuclear membrane dissolving by retracting into the ER

interphase: the nucleus is intact

prophase: nucleus begins dissolving

metaphase: ER ends up partially surrounding mitotic duplication, nucleus totally dissolved

anaphase: nucleus is totally dissolved

telophase: nucleus begins reforming

what is the nuclear pore complex (NPC)

NPC are made of ~30 different proteins

500-100 protein molecules/NPC

what is the nuclear localization signal (NLS)

proteins can contain a NLS that targets them into the nucleus

NLS signal allows for specificity in what gets in/out

scientists can also attach NLS signals to proteins to localize proteins into nucleus