Cell Biology Week 2 Flashcards
What is the D domain of the tRNA important for?
The D domain is important for ribosome recognition
DNA->protein in eukaryotes
DNA is transcribed to mRNA, which include introns and exons. The mRNA is processed: 5’capped, spliced, and 3’ Poly A tail added.
The processed mRNA is exported out of the nucleus and translated to protein via ribosomes
DNA->protein in prokaryotes
DNA is transcribed to mRNA which is directly translated to protein via ribosome
How is the genetic code translated?
The amino acid is added to tRNA via a tRNA synthases (there are 20) via ATP hydrolysis. The tRNA+amino acid then binds to the mRNA codon in ribosome and added to growing polypeptide chain
Prokaryotic Ribosomes
70S which are made of 50s and 30s subunits
Eukaryotic ribosome
80s which are made of 60s and 40s subunits
What is the final phase of protein synthesis?
The peptide is hydrolyzed when Release factor is bound to the A-site
Actinomycin D
drug that binds to DNA and blocks the movement of RNA polymerase (prevents RNA synthesis)
Drugs that only affect bacteria
Tetracycline, Streptomycin, Chloramphenicol, Erythromycin, Rifamycin
Drugs that affect both baccteria and eukaryotes
Puromycin, Actinomycin D
Drugs that only affect eukaryotes
Cyclohexamide, Anisomycin alpha-amanitin
alpha-amanitin
blocks mRNA synthesis by binding preferentially to RNA pol II
Upf proteins
Triggers mRNA degradation of mRNA that have been abnormally spliced
Post-translational modifications
chemical modifications of a protein by adding of biochemical functional groups, changing the chemical nature of the protein or making structural changes
molecular chaperones
help guide the folding of most proteins
Hsp60 family
a family of chaperones, uses GroES as cap and ATP hydrolysis to correctly fold protein
mono-ubiquitylation
protein targeted for histone regulation
multi-ubiquitylation
protein targeted for endocytosis
polyubiquitylation
protein targeted for proteasomal degradation or DNA repair
What do protein aggregation cause?
human disease
Sometimes proteins undergo rare conformational change and cannot undergo proteasomal degradation
Ex. prions
What types of proteins have what types of sorting signal?
Cytosol proteins do not have sorting signal
Nucleus proteins have nuclear localization signal
Mitochondrial proteins have sorting signal
Proteins cotranslated in ER have signal sequence
Lysosomal proteins are tagged w/ mannose-6-phosphate
Resident ER proteins have the KDEL sequence
When do ribosomes attach to ER membranes?
If they are synthesizing polypeptides destined for the endomembrane system or for export from the cell
Transported via cotranslational import
When do ribosomes remain free in cytosol?
If they are synthesizing polypeptide destined for cytosol or for import into the nucleus, mitochondria, chloroplasts or peroxisome
Transported via post-translational import
Function of miRNA
translational repression or mRNA degradation
Hypomethylation
leads to gene amplification
Hypermethylation
leads to gene deletion
miRNA based treatment
Two methods: miRNA that target native miRNA and miRNA that target mRNA
Miravirsen
inhibits the biogenesis of miR-122; treats hepatitis c infection
Why are euk cells organized into a complex set of organelles?
Because once the cells got bigger they ran into the surface to volume problem
signal sequence
specific sequence on a protein that is recognized by a specific receptor for delivery of that protein
Signal sequence can be placed at the end of the protein, or can be inside the protein at various regions that contribute to forming the signal patch
Nuclear envelope
double lipid bilayer and is continuous with the ER.
Proteins are transported through the nuclear pores, they do not cross through the membranes
How do proteins enter the nucleus?
Via gated transport through nuclear pores, need nuclear localization signal
Proteins 60kDa enter the nucleus by active transport
Nuclear localization signal (NLS)
signal that allows for the import of proteins into the nucleus
Most nuclear imports are signalled with a chain of positively charged amino acids
Describe active transport through nuclear pores?
Nuclear import receptors bind to the NLS on their cargo proteins and to the nucleoporins of the nuclear pore complex
GTP-Ran binding to the loaded nuclear import receptor occurs in the nucleus to release the protein into the nucleus
How is nuclear transport during T-cell activation controlled?
via phosphorylation/dephosphorylation
Calcineurin dephosphorylates the NF-AT therefore allowing for the import signal to be recognized thereby driving the protein into the nucleus
What does IL-2 do?
Clonal expansion of memory T-cells
cyclosporine
inhibits calcineurin -> inhibits T-cell activation
Collagen
secreted by smooth muscle cells via default (constitutive secretory) pathway
16 types - primarily types I, II, III
main component of connective tissue
co-translational translocation
as the peptide is being created, the peptide enters through the ER lumen
Pre-pro-peptide formation
once the final mRNA exits from the cell nucleus and enters into the cytoplasm, it links with the ribosomal subunits and the process of translation
signal recognition particle (SRP)
the SRP recognizes the signal sequence, and then directs the pre-pro-peptide into the ER
The new signal hypothesis
the binding of SRP to signal peptide causes a pause in translation -> SRP bound ribosome attaches to SRP receptor in ER membrane -> translation continues and translocation begins -> SRP and SRP receptor displaced and recycled
stop transfer sequence
used in single pass or multipass transmembrane proteins
Typically hydrophobic
How multipass transmembrane protein with internal ER signal sequence is inserted into the ER membrane
via many start and stop transfer sequences
Hydroxylation of prolines and lysines
is needed to aid crosslinking of alpha peptides; enzymatic step that required Vit. C as cofactor
In scurvy, lack of vit. C leads to lack to hydroxylation of prolines and lysines which cause looser triple helix of collagen
propeptide vs. procollagen
propetide is when the signal peptide on the n-terminal is dissolved in the ER
procollagen is composed of a twisted portion (center) and two loose ends on either end. Where the hydroxylated (both pro and lys) and glycosylated (only lys) propeptide twists towards the left tightly and then the 3 propeptides form a triple helix
How proteins exit the ER and enter Golgi
so from cytosol, ER is contranslational translocation thru the protein pore in the ER membrance. Once protein is in ER, all subsequent transport occurs via vesicle transport and lipid bilayer fusion
COPI
mediates transport forward through the Golgi in the default pathway for delivery to the plasma membrane or extracellular matrix and also back through the golgi to deliver ER proteins back to the ER where they belong.
KDEL signal sequence triggers this reverse transport back to ER
COPII
Only mediates the transport of vesicles forward from ER to golgi
clathrin
Clathrin coats regulate receptor mediated vesicle transport
In the transgolgi, clathrin coats sort lysosomal protein for transport to lysosomes, and also sort substances for storage in secretory vesicles
At the plasma membrane, clathrin coats are used for the uptake of extracellular material via receptor mediated endocytosis
unfolded protein response (UPR)
upregulate the expression and function of chaperones and foldases
activate ERAD
reduce the translation of mRNA to decrease the processing demand for newly synthesized proteins
ERAD
quality control system to rid the cell of misfolded and unfolded proteins that are toxic to cell
