White- Gene Expression 2 Flashcards
True or False: Alternative Splicing produces different forms of proteins from the same gene
True
Define a repressor molecule in relation to alternative splicing
prevents the splicing machinery from accessing the splice site
Define an activating molecule in relation to RNA splicing
it recruits and helps to direct the splicing machinery
What are the 3 ways in which the mRNA is able to travel through the cell? (spatial localization)
- cytoskeletal motors (anchor proteins and hold mRNA in place
- Random movement (diffusion and trapping)
- Random movement and degeneration (RNA that is not trapped is degraded)
What is the purpose of the poly A tail?
confers stability
Describe the poly A tail in relation to shortening? (how is it shortened? and what does it act as?)
shortened by an exonuclease
shortening acts as a timer
once it gets to 25 nucleotides, the two pathways converge and the mRNA is degraded
What are the two ways in which the mRNA can be degraded?
decapping (5’ cap protects the RNA from the degrading enzymes- removing= break down)
3’ end via poly A tail degradation
What are the two RNA’s that are involved in iron metabolism? And what do they do?
Ferritin mRNA- storage of iron
TfR mRNA- iron absorbance
Describe the iron cycle
- Iron is absorbed by the intestine
- plasma transferrin iron travels to the marrow erythroid precursors (TfR)
- goes into the blood stream via circulating erythrocytes
- macrophages
- recycled back as a plasma transferrin iron
(CAN also go to the liver where it is stored as ferritin)
Describe ferritin.
Intracellular protein that is found in most cells
granules=hemosiderin
Where is excess iron stored?
Liver, lungs, and pancreas
What happens in the cell during iron starvation?
- cells do not need to store iron
- decrease in ferritin mRNA
- cells must transport iron into the cell
- make more of the transferrin receptor (TfR) mRNA
What happens in the cell when there is excess iron?
- need to store the excess iron
- make more ferritin mRNA
- transport less iron into the cell
- make less TfR mRNA
Define IRE and IRP and describe what they do.
IRE-iron responsive elements; recognition sites for binding
IRP- aconitase
They bind together and regulate mRNA
What happens if the IRP binds to the IRE at the 5’ end of the ferritin mRNA?
translation is blocked
What happens if the IRP binds to the IRE At the 3’ end of the transferrin?
The transferrin receptor is made and the mRNA is stable
What happens if the IRP does NOT bind to the IRE at the 5’ ferritin mRNA?
mRNA is made and you get ferritin
What happens if the IRP does NOT bind to the IRE at the 3” transferrin receptor?
The RNA degrades and no transferrin receptor is made
Describe what happens with IRE/IRP in iron starvation
You need more iron obvs sooo
IRP binding to IRE or ferritin, no mRNA is made and you do not need to store iron (bc you want it in the cell)
NO FERRITIN IS MADE
IRP binds to IRE at 3’ transferrin receptor mRNA- transferrin receptor is made and you need to college more iron
What happens with the IRE/IRP when there is excess iron in the body
You need to store the iron because you do not need any more;
IRP binds to the iron to inactivate it; ferritin is made with no suppression
IRP does not bind to the TfR IRE and there is not any TfR made
What are microRNA’s and what do they do?
They are regulatory RNAs that regulate the messenger RNA’s
REPRESSORS
bind to the complementary sequence in the 3” end of the mRNA
degrade the RNA or block translation; cleaves RNA and shuts down expression
sorry Becky I know that is a lot of words LOL
Describe the maturation of the microRNA
Starts as a primary miRNA (pri-miRNA)
cuts down in size to a pre-miRNA
processed into mature miRNA
cropped in the nucleus and cleaved by the Dicer enzyme
Describe the RISC
The RNA induced silencing complex; microRNA joins with the Argonaute and other proteins to form the RISC
True or false: An miRNA can only regulate one mRNA
False
Describe miRNA’s in disease states
miRNA can change their expression profile in disease states; can be elevated in CVD or can be used to identify certain cancers
Describe how the microRNA’s are causative to the disease
The miRNA’s probably have mutations that cause the disease
Describe how the miRNA’s are responsive to disease
increased miRNA expression down regulates genes in response to disease to limit severity
Describe Tourette’s syndrome
It is an example of the microRNA’s being CAUSATIVE
neurological disorder manifested by motor and vocal tics
variant of SLITRK1 gene associated with Tourettes; change in recognition and increased miRNA binding
Describe the binding of the miRNA’s involved in tourette’s syndrome
miR-189 binds more efficiently to the target sequence of SLITRK1 and decreases its expression (since miRNAs are repressors) and leads to Tourettes
Describe the various post-translational modifications and steps required to get to a mature functional protein
- Nascent polypeptide chain needs to fold into its 3D conformation with the help of chaperones. Can bind to cofactors
- the polypeptide can be modified by protein kinases and glycosylated
- bind to other proteins
- modified enzymes act on the protein
Mature and functional
Describe heat shock proteins. Include what they do, when and why they are made
molecular chaperones that help with protein folding
They are made in dramatic amounts with increased temperature
WHY? Because when the temperatures rise, there is more of a chance that the proteins will misfold
What are the two families of heat shock proteins?
Hsp 60 and Hsp70
Describe the proteasome in as much detail as possible
Also called the garbage disposal
controls protein activity by deciding which proteins are around
removes misfolded proteins
has a hollow chamber where proteins are degraded; binds to proteins selected for destruction. The hollow chamber acts as a gate for a proteasome- activated upon demand.
What is the purpose of ubiquitin?
removes unfolded or abnormal proteins via a recognition tag
Describe the process of the formation of the ubiquitin ligase that aids in protein destruction.
- The ubiquitin activating enzyme E1 binds to ubiquitin via a cysteine side chain
- ubiquitin is transferred to E2 and E3
- complex is primed and marks proteins for destruction
Describe the process of adding a protein to the ubiquitin ligase
The ubiquitin is added to a lysine side chain on the protein
E1 enzymes continues to add ubiquitin
targeted ubiquitin chain is recognized by the proteasome
How can proteosomes be used as therapy?
Can treat multiple myelomas- cancer of the plasma cells, abnormal cells accumulate in the bone marrow and interfere with RBC production- specificity of the proteasome inhibits the myeloma cells
proteasome inhibition can prevent the degradation of pro-apoptotic factors for cell suicide; leads to cell apoptosis
Describe the activation of the ubiquitin ligase
- ATP is used to phosphorylate the E2 E3 complex via protein kinase
- allosteric transition caused by ligand binding
- allosteric transition caused by protein subunit addition
Describe the activation of the degradation signal
- ATP is used to phosphorylate the protein via protein kinase
- unmasking via protein dissociation
- creation of destabilizing N terminus
What are the 4 types of gene expression?
- coordinated expression of genes; genes do not exist in a vacuum
- Decision for specialization; what kind of cell do I want to become?
- methylation and genomic imprinting: what genes get expressed from mom and dad
- X-chromosome inactivation; evens things out
Describe coordinated gene expression
- expression of critical regulatory protein can trigger battery of downstream genes
- responds to need
ex: response to stress- increase in blood sugar
Describe the decision for specialization
The cell is able to make a decision at each step of cell division
(1 or none, 2 or 3, 4 or 5)
different cell types result
Describe the various “specializations” that can happen from an HSC (hematopoietic stem cell)
HPC: hematopoietic pluripotent stem cell
myeloid lineage and lymphatic lineage
What are the cells that come from the myeloid lineage?
Erythrocyte, megakaryocyte-> platelets, neutrophil, eosinophil, basophil, and macrophages
What are the cells that come from the lymphoid lineage?
B cells, T cells, and NK-cells
Describe the inheritance of DNA methylation
The methylation of cytosine occurs at CG sequences
methylation is inherited
cytosine is methylated by “maintenance methyltransferase”
DNA methylation of the parent strand serves as a template for the daughter strand
Define genomic imprinting
the expression of some genes based on inheritance from the mother or the father
differential expression of genetic material depending on the parent of origin
Define epigenetics
The regulation of expression of gene activity without altering gene structure
Describe Prader Willi Syndrome
caused by a paternal deletion of Chromosome 15; paternal genes are not expressed and maternal genes are not expressed either even though they are present
hypogonadism,
short stature and small hands and feet; behavioral problems,
What are the stages of prader will syndrome?
1- infantile hypotonia, poor suck, feeding difficulties
2- hyperphagia (uncontrollable eating)
Describe X-inactivation
Occurs in females; one of the X chromosomes is inactivated via high condensation (heterochromatin)
inactivation is random- can be mom or dads chromosome that is expressed
maintained post cell divisions
Where does X inactivation start and spread?
At the X inactivation center
XIC makes XIST RNA that coats the entire X chromosome
