nucleus!!!

nucleus

This organelle determines whether the cell type is a prokaryote or eukaryote

rough ER

The outer membrane of the nucleus is continuous with the _ _

perinuclear space

The space between the inner and outer membranes are the:

lamin

The __ are the polypeptides that form dimers and form the long filaments that supports the shape of the nucleus

collapse

If the lamin network is mutated, it can cause the nucleus to __

Progeria

Mutations in the Lamin A can lead to the __ disorder, where reverse aging can be seen

scaffold

a term to describe supporting framework — something that gives shape and strength to a structure

LBR and emerin

_ and - are proteins that connect the filamentaneous network to the inner nuclear membrane

tetramer

When 2 dimers come together, this forms a __

nucleus

organelle where DNA replication and transcribed to RNA, and processing of RNA takes place

cytoplasm

The enzymes and proteins needed for DNA replication and RNA synthesis (like helicase, SSBPs, DNA polymerase, RNA polymerase, etc.) are made in the ___

facilitated, simple

___ diffusion is a type of passive transport, like __ diffusion — but it’s not the same thing.

It still moves down the gradient, just with help from proteins instead of slipping through on its own.

FG-nucleoporins

_-_ is apart of the nuclear pore complexes that interacts with the importins to bring the cargo through

RanGAP

the gatekeeper in the cytoplasm where the RanGTP, bound to the importin, is converted to the RanGDP, releasing the importin from Ran

NTF2

RanGDP must go back into the nucleus, which is carried by __

Ran-GEF

This converts Ran-GDP to Ran-GTP

GTP, GDP

Only Ran-__exists inside the nucleus.

Only Ran-__exists in the cytoplasm.

NES

a specific sequence on proteins or RNA, which tag molecules for export

NES, cargo, Ran-GTP

What components make up the exportin complex?

mRNP

RNA-binding proteins form a __ around the mRNA

expor

Nuclear __ proteins help to bring the mRNA + mRNP through the nuclear pore complex

RNA helicase

The mRNP (mRNA + RBP), after passing through the NPC, encounter the _ _

ATP

What is the energy molecule that helps to unwind the mRNA and remove the RNA binding proteins and export proteins?

NXF1/TAP

What is one of the main export proteins that help to move the mRNP?

both

Does phosphorylation activate or inactive protien fucntion?

snRNAs

U1, U2, U4, U5, U6 are examples of ___

Crm1

Which exportin protein helps to transfer the snRNA to the cytoplasm?

snRNPs

SnRNA’s are joined with proteins in the cytoplasm to form:

Snurportin

What recognizes snRNP's in the cytoplasm and transport it back into the nucleus?

Cajal bodies

When snRNP’s are transported into the nucleus, chemical modifications like pseudorydylation and methyl groups take place within the _ _

spliceosomes

What are complexes within the nucleus that modified snRNP’s join to become?

UPR

If there are too many proteins accumulated or misfolded proteins in the cytoplasm, the __ can be activated

kinases

In the UPR, sensors in the cytoplasm/ER can detect protein build-up, leading to the activation of __

inhibits

When kinases phosphorylate transcription factors, it inhibits/activates transcription of mRNA

H2A, H2B, H4, H4

Can you list the histone proteins that make up the octamer?

2

How many of each histone protein, besides H1, are there?

nucleosomes

DNA that wraps around octamers to form:

H1

The _ acts like a linker protein between 2 nucleosomes

Chromatosome

a nucleosome but with H1 binding

FISH

a test where fluorescent DNA probes attach to specific chromosome regions, and you can see the number of chromosomes, where chromosomes are found, or any abnormalities

territories

Using FISH, we can see that chromosomes form distinct ___inside the nucleus rather than mixing together.

heterochromatin, euchromatin

___(telochromatin & NADs) sit near the nuclear periphery or nucleolus, mostly inactive, whereas __ stays toward the center, more open and actively transcribed.

NAD’s

heterochromatin regions that sit around the nucleolus instead of the nuclear envelope

Topologically Associated Domains

The genome is divided into TADs — 3D regions of chromatin that interact more within themselves than with other regions.

Each TAD acts like a small “neighborhood” where enhancers and promoters interact only with each other — not with other neighborhoods

Cohesin

Forms ring-shaped structures that loop the DNA into a confined domain (like tying a section of rope into a loop), This loop brings distant parts of DNA closer — for example, an enhancer and its promoter, so a gene can be turned on

CTCF

sits at the edges of loops, marking the boundaries of a region (called a TAD, or topologically associated domain), tells cohesin where to stop looping

LAD’s, NAD’s

Inactive heterochromatin loops associate with the __ (on the periphery), or the _ (near the nucleolus)

replication, transcription

__ factories make new DNA in the S phase, and _factories make RNA

periphery

After DNA is transcribed or replicated, DNA folds up and moves towards the __ of the nucleus/nucleolus

LADs

repressed chromatin regions anchored to the nuclear lamina (when histones, DNA, lamina are bound)

polycomb bodies

where polycomb proteins gather, and are repressive via epigenetic modifications

No

Are the nuclear bodies within the nucleus membrane-bound?

nuclear bodies

The nucleolus, polycomb bodies, speckles, and cajal bodies within the nucleus are all examples of?

• all comparments

speckles

non-membrane toolboxes inside the nucleus that store and release splicing factors when nearby genes are being transcribed.

• storage of pre-mRNA splicing

U1, U2, U4, U5, U6

What are the main snrp’s that make up a spliceosome?

cajal bodies

non-membrane compartments within the nucleus that do chemical modifications on snrp’s and assemble the spliceosome

polycomb body

clusters of gene-silencing proteins that help keep DNA tightly packed and inactive.

PCR2

the first complex that trimethylates the H3 position 27 lysine mark

PCR1

the second complex that comes and binds to the H3K27me3 mark in order to cause chromatin to tightly condense

FC

The rDNA becomes the pre-RNA in which region of the nucleolus?

45s

What is the long pre-rna in eukaryotes?

18s, 5.8s, 28s

This 45S pre-rRNA contains the sequences for: *list the number rRNA’s

snoRNA

In the dense fibrillar component (DFC), the _ _ _ and associated proteins guide the chemical modifications and cleaving of this long 45S pre-rRNA.

40s, 60s

After modification done by snoRNA, the

18S rRNA → will go into the _ subunit

5.8S rRNA + 28S rRNA → will go into the _ subunit

RNA polymerase 1

The 5.8s, 18s, and 28s rRNA’s are transcribed together within the nucleolus by _ _ _, generating a 45s ribosomal precursor

nucleosomes

Methylation of H3 lysine 27 spreads to adjacent __, creating repressed chromatin domains

crispr-cas9

_-_ is a gene editing tool, which lets scientists cut DNA at a very specific spot to change or remove a gene

gRNA

the RNA that acts as a map or GPS to tell Cas9 where to cut in the DNA

Cas9

the pair of tiny molecular scissors that cut DNA; endonuclease that can cut DNA at a specific location

double

DNA cleavage: Cas9 induces a _-stranded break, repaired by the cell’s DNA repair machinery, often leading to gene disruption or modification

bacterial

CRISPR-Cas9 are apart of a _ defense mechanism, which helps to get rid of defected genes