Bio 2: Exam 2 Flashcards
(25 cards)
how many different types of RNA polymerases in eukaryotes? What are they?
3 Types:
- RNA Polymerase 1: transcribes all rRNA except for the smallest sub unit, 5S. Located in nucleolus.
- RNA Polymerase 2: transcribes mRNA.
- RNA Polymerase 3: transcribes small RNA including tRNA and 5S.
What is the difference between a ‘patch’ and ‘LS’?
Locating Sequence: a continuous sequence in the peptide chain that signals where the protein should go
Patch: if the signal is in a contiguous section of the folded protein, but the AAs are not next to each other in the unfolded peptide.
What are Transcription Factors?
RNA polymerase cannot bind to DNA without TFs. TFs unravel tightly coiled chromatin and displace histones. They can also selectively activate or repress gene expression by binding to specific sites on the coding region of DNA.
How do “stops” and “starts” work with relationship to the translocon?
Both “stops” and “starts” are hydrophobic regions. A “start” (re)opens the translocon and (re)initiates synthesis of the protein into the lumen. A “stop” closes the translocon to the lumen, and opens a lateral door where the hydrophobic area is released into the bilayer. If synthesis after a “stop” continues, then it will create a domain in the cytoplasm.
What happens in the Golgi?
- finish N-glycosylation (which was started in ER)
- do O-glycosylation
- make GAGs for proteoglycans
- sort proteins for distribution (on the trans side)
what does LS stand for?
Locating signal. Generic term for the signal that tells proteins where to go.
What is the transit peptide (TP)?
Transit peptide is the LS used to send proteins to the mitochondria.
What is the scavenger pathway?
Sometimes receptors are misdirected to the PM. Once there, they can catch enzymes from outside the cell and then bring them to the appropriate place. The best example is the receptor for M6P in the lysosome. This allows us to treat some diseases lysosomal storage diseases. (and other diseases which affect EMS?)
Can heterochromatin be transcribed? Can it be degraded by DNase?
Heterochromatin cannot be transcribed and is not affected by DNase. It is too tightly coiled. Generally speaking, heterochromatin is the form that DNA takes during Mitosis/Meiosis when the cell is dividing… the X’s and Y’s.
What form of DNA is being transcribed (Hetero, Euchromatin, Looser, Loosest?)
Euchromatin, looser is being transcribed.
what is the primary means for controlling gene expression in eukaryotes?
Transcriptional control.
what are the 7 types of control for eukaryotic gene expression and protein activity?
- Genomic Control (DNA amplification [rare], DNA methylation, histone modification (loose/looser/loosest… opens to be transcribed)
- Transcription Control: rate at which RNA polymerase binds and transcribes, controlled by TFs
- RNA Processing Control: splicing, capping, polyadenylation
- RNA Transport Control: control rate and which RNA leave nucleus and goes to cytosol
- Translational Control: control rate of initiation translation by using and initiation factors and repressors
- mRNA Degradation Control: half-life of mRNA
- Protein Activity Control: phosphorylation can inhibit/induce some protein activity
What can increase the rate of transcription… what two elements must bind, and what happens to the DNA?
When the activator binds to the enhancer, the rate of DNA transcription increases. The activator binds to the enhancer (which is on the DNA) and folds the protein into different conformations. The activator also binds to the TF/polymerase complex.
Name a protein found in the following locations:
- cytoplasm
- endosome
- peroxisome
.
What is the core promoter? Where is it on the DNA, upstream or downstream of the transcription start place?
The core promoter is necessary to begin transcription. It is located just upstream (approx. 40bp) of +1 (beginning of transcription). It contains the TATA region which is where some of the TF bind. Also called basal promoter.
What is the difference between cis and trans acting elements? Which are part of the DNA?
cis: part of the DNA, regulatory regions, -ie silencer, enhancer
trans: proteins that attach to DNA, -ie TFs
Do genes have introns and exons?
yes, the introns and exons are located in the genes (on DNA) and are spliced out in the pre-mRNA. So, beads on a string have both introns and exons included.
What determines which genes are transcribed in each cell?
the transcription factors.
What and where is the translocon? What is it’s function?
The translocon is a transport protein located in the ER membrane. The SRP attaches to the 5’ end of the peptide, the ER signaling sequence, the ribosome is taken to the SRP receptor where it docks, and continues to transcribe it’s RNA into the lumen of the ER.
At what point in the cell cycle is the nucleus disassembled? When is it re-assembled?
It is disassembled at the beginning of mitosis, and reassembled at the end of mitosis.
What shape is the DNA in when H1 is not attached?
H1 is not attached for beads on a string (11nm/looser). It is attached for “loose” (30nm) and everything larger.
What do kinases and phosphatases do?
Kinases add phosphate groups, and phosphatases remove them.
Can RNA polymerase bind directly to DNA? What does it bind to?
RNA polymerase cannot bind to the core promoter. Basal TFs must bind to the core promoter and then RNA polymerase binds to them.
What is the function of the 5’ cap put on RNA? What is it made of?
The 5’ cap is made from GTP and protects the RNA from nucleases. It also positions RNA on ribosome for translation.
