Cell Bio Exam 3 Flashcards
What are the five components of the nucleus?
1) Nuclear envelope 2)Nuclear lamina 3)Nucleoplasm 4)Nucleoli 5)Chromatin
What is the nuclear envelope?
The double membrane surrounding the nucleus. Consists of an outer and inner membrane and is perforated by large nuclear pores. The outer membrane is continuous with the RER and contains ribosomes.
What is the nuclear lamina?
The cytoskeleton of the nucleus, a fibrous meshwork of proteins on the inner surface of the inner nuclear membrane, made up of a network of intermediate filaments formed from nuclear lamins
What is the function of nucleoli?
Nucleoli synthesize ribosomes by producing the rRNA molecules and assembling them into ribosomes
What is chromatin?
The complex of DNA, histones, and nonhistone proteins found in the nucleus of eucaryotic cells. These chromatins make up chromosomes.
How is the nuclear envelope shape supported?
The nuclear lamina supports the nuclear membrane from the inside. Lamin protein filaments make up the cortical skeleton of the lamina.
Describe the role of the lamina in DNA replication.
Chromatin attaches to sites on the lamina during DNA replication. Lamina acts as a scaffold to regulate the replication.
What are SPECKLES?
Microdomains within the nucleus where mRNA is spliced. These are not evenly distributed throughout the nucleoplasm.
What are Cajal bodies?
These bodies bind to the nucleolus in actively transcribing cells, and may generate snRNPs
What are GEMs?
Geminis of the coiled bodie. These are associated with Cajal bodies and play a role in snRNP assembly for splicing. They contain SMN (survival of motor neuron) proteins, which are required for snRNP formation.
What are PML bodies?
Promycrocytic leukemia bodies. They play a role in transcription regulation and show increased expression in lymphoid cancers and other diseases.
Which direction do nuclear pores allow movement: IN or OUT?
Two of the above are true (LOL). Nuclear pores allow transport in AND out of the nucleus.
Describe the size of molecules able to travel through nuclear pores.
5kDa molecules can freely pass, 17 kDa molecules take time to pass, and 60 kDa don’t pass at all
What shape are nuclear pores seen on a freeze fracture scanning electron micrograph?
Nuclear pores are star shaped.
Describe the nuclear pore complexes.
They are octagons composed of >30 proteins called nucleoporins. They allow movement of small molecules by diffusion and large molecules can be transported by accessory proteins.
Describe the different paths of a small and large protein traveling through a nuclear pore.
Large molecules (>17kDa) will pass through the central transporter using a nuclear localization signal. Small molecules will diffuse through openings in the spoke-ring assembly
What amino acids are most common in central transporters of the nuclear pore?
Phenylalanine and glycine (F-G) repeats.
How is RNA able to pass out of the nuclear membrane even though it is hydrophillic?
RNA forms a ribonuclearprotein (RNP). The protein contains a nuclear export signal (NES) that has 5-6 hydrophobic residues that bind to exportin, this complex can then exit through the nuclear pores into the cytoplasm.
How is gene splicing related to the process of nuclear export?
Following splicing (Pre-mRNA to mRNA), exon junction complexes (EJCs) are bound to the splice junction. The EJC contains Aly, a protein that can bind to TAP. Once TAP is bound, the mRNA can be exported to the cytoplasm.
Describe the mechanism of TAP assisting in mRNA export.
TAP forms a heterodimer with p15. TAP/p15 then interacts with the FG repeats of the nucleoporins, guiding the mRNA for export.
How are EJCs useful for detecting mRNAs that have premature stop codons?
As the ribosomes slides along the mRNA during translation, the EJCs are displaced. If a premature stop codon is reached, then the resulting mRNA will still be partially associated with EJCs. The cell recognizes these mRNAs and destroys them to prevent further translation of the mutated mRNA.
What is a nuclear localization signal?
NLS: sequeence that targets cytoplasmic proteins to the nucleus. This sequence binds IMPORTIN α. These sequences are rich in Lysine (K) or other basic residues.
What protein does IMPORTIN α interact with once the NLS binds to it?
NLS-IMPORTINα interacts with cytoplasmic IMPORTIN β. This complex binds to one of the filaments of the nuclear pore and can then be transported into the nucleus.
Once the IMPORTIN-protein complex is in the nucleus, what protein does it bind to?
Ran-GTP. This association causes the IMPORTIN to release the protein.
How do the IMPORTINs leave the nucleus once the protein is released?
RanGTP-Importinβ leaves through the nuclear pore, and then binds to a cytoplasmic a GTPase (RanGAP1) causing the release of Importinβ. Importinα leaves by binding to Exportin and then leaving through the pore.
Where is [Ran-GTP] high? Where is [Ran-GDP] high?
[Ran-GTP] is high in the nucleus. [Ran-GDP] is high in the cytoplasm.
What is the difference between heterochromatin and euchromatin?
Heterochromatin is tightly packed chromatin in which genes are not expressed. Euchromatin is loosely packed and genes are actively transcribed.
Describe the structure of a nucleosome.
Nucleosomes are made of histone proteins that form octamers over which 146 base pairs of supercoiled DNA wind. The are rich in basic amino acids (lysine and arginine) because their positive charges can interact with the backbone of the DNA molecule.
What are the heterodimers that make up the histone octamer?
2 H2A-H2B dimers, and 2 H3-H4 dimers
Which histones are most highly conserved?
Those that make up the octamer: H2A, H2B, H3 and H4. H1 is less conserved
What type of bonds connect histones with DNA?
Ionic bonds between the positively charged amino acids and the negatively charged phosphates of the DNA backbone.
Where are regulatory sequences of histones found?
On the tails that extend out of the nucleosome. These amino acids are important for epigenetic effects.
What is the diameter of one nucleosome?
10nm
What is the diameter of the fiber that forms when the 10nm nucleosomes associate?
A 30nm fiber forms.
What is the larger fiber that forms from 30nm fibers?
80-100nm supercoiled loops form. These attach to a scaffold with multiple proteins.
What are the major methods of histone modification?
(1) Acetylation: causes looser winding, greater transcription (2) Methylation: tighter winding, transcriptional repression (3) Phosphorylation: may reduce affinity of histone for DNA , loosening the chromatin (4)Ubiquitination: promotes methylation (5)Sumoylation: negatively regulates gene transcription in yeast (6)Proline isomerization: allows for methylation
What enzyme activity is seen in many transcriptional coactivatiors?
Histone acetyl transferase (HAT)
What is CBP?
A coactivator, Creb-binding protein, that acetylates histones to loosen DNA
What molecule is recruited following acetylation of histones?
A chromatin remodeling complex called SWI/SNF that slides the histone proteins to expose naked DNA that contains the TATA box
Describe the overall process of gene activation.
1) A transcriptional activator binds to GRE and recruits a coactivator. 2)The coactivator acetylates and loosens the DNA from the histones 3)A chromatin remodeling complex is recruited, exposes TATA box 4)Transcription factor binds to TATA box 5)Further acetylation opens up DNA even more 6)Initiation complex assembled and RNA polymerase binds, transcription begins
What are the 4 models for the actions of histone remodeling proteins?
1)Nucleosome slides, exposing element 2)Histone octomer changes conformation 3)Histone subunits are exchanged (swi/snf-related) 4)Histone leaves the DNA (FACT complex)
What is the FACT complex?
A histone chaperone that both destabilizes and restores nucleosomal structure. Centromeric histone remodeling in yeast
What are HDACs?
Histone deacetylases. Important for transcriptional repression causing the DNA to be too tightly coiled to transcribe.
What is an example of a transcription repressor protein in higher organisms?
SMRT/N-CoR: Silencing mediator of retinoid and thyroid receptors/nuclear co-repressor.
How do repressor proteins function?
They recruit HDACs and Methyltransferases to silence the genes
Where does methylation occur on a cytosine?
On carbon #5 of cytosines that are usually next to guanines. This is referred to as a CpG island. In promoter regions, cytosines on both strands are methylated leading to gene silencing
How is dsRNA formed?
Repetitive non-coding DNA is transcribed in both directions leading to the formation of double-stranded RNA
What is the function of Dicer?
It cleaves dsRNA into smaller pieces that can be matched based on complementarity to euchromatin
What is the function of histone methyltransferase?
HMT is an enzyme that methylates K9 of H3 once the small RNA binds to euchromatin. The methylated K9 is then recognized by HP1, which begins the conversion to heterochromatin.
Describe telomeres.
A highly repetitive sequence at the ends of each chromosome that forms a “cap” by folding of a 3’ overhang that is left over from the DNA replication. These structures allow cells to determine their age because telomeres shorten with each cell division, eventually ceasing to divide when the telomeres are too short.
What enzyme elongates telomeres?
Telomerase, which is a reverse transcriptase. This enzyme has a piece of RNA that is complementary to the repetitive DNA of the telomere. It provides a place for DNA polymerase to begin replication.
What is epigenetics?
When the change in gene expression or phenotype is NOT the result of a change in DNA sequence, but rather changes in chromatin structure, histone modifications, DNA modifications, X-inactivation … etc.
What are centromeres?
Repetitve DNA called α-satellite DNA that has 171bp repeats. This structure recruits the kinetochore which binds to microtubules during cell division.
What epigenetic alterations occur after fertilzation of an egg?
The diploid genome is stripped of its methylation