Midterm #3 Flashcards
what are codons
nucleotide sequence triplets
what is the start codon/amino acid?
AUG - methionine
what are the stop codons
UAA, UAG, UGA - dont code for an amino acid
what are the untranslated regions (UTR) of mRNA?
the 5’ and 3’ end of the mRNA that are not translated into proteins (5’ UTR and 3’ UTR)
what is tRNA?
transfer RNA - carries amino acid to ribosome
what is an open reading frame?
the region of mRNA that codes for amino acids
what are aminoacyl tRNA synthestases?
enzymes that attach amino acids to tRNA - specific to amino acids
what is a charged tRNA?
a tRNA with an amino acid attached
what is the wobble hypothesis?
the idea that the base on the first position on the tRNA (5’ end) is usually an abnormal base like inosine, pseudouridine, tyrosine etc, which can pair with multiple nitrogenous bases
what is the function of the large subunit of the ribosome?
aids in the formation of peptide bonds
which genes code for the large subunit of the ribosome?
28s, 18s, 5.8s genes
what is the gene that codes for the small subunit of the ribosome?
5s genes
what is the function of the small subunit of the ribosome?
recognition of the translation start site
what are the differences between prokaryotic and eukaryotic mRNA in translation?
Prokaryotes:
- polycistronic = has multiple protein coding genes per mRNA transcript
- no mRNA transport out of nucleus
- has multiple translation start sites
Eukaryotes:
- monocistronic = has only one protein coding gene per mRNA transcript
- mRNA transport out of nucleus and into cytosol where translation occurs
- only has one translation start site
what is initiation in translation?
when the ribosome binds at the 5’ UTR and initiates polypeptide synthesis at the start site
how do prokaryotes signal for translation initiation?
uses shine dalgarno sequence to signal translation start site - small subunit has a complementary sequence
how to eukaryotes signal for translation initiation?
ribosome scanning = small subunit of scans mRNA until it finds an AUG to initiate translation - requires ATP
what are eukaryotic initiation factors (eIFs)?
proteins that help aid and initiate translation
what are the different eIFs?
eIF2, eIF4E, and Poly-A binding protein (PABP)
what is the function of eIF2?
recognizes the tRNA for methionine (AUG) and binds the initiator methionyl-tRNA (translation cant start w/o methionine)
what is the function of eIF4E?
recognizes and binds to the 5’ methyl cap
what is the function of the poly-A binding protein (PABP)?
binds to the poly-A tail
what are internal ribosome entry sites?
sites where translation can be initiated independent of the 5’ methyl cap - shortcut
what is elongation in translation?
the building of the polypeptide chain by the ribosome
what are eukaryotic elongation factors (eEFs)?
proteins that aid in elongation
what happens in the P(peptide) site of the ribosome?
where the amino aid chain is located and grows
what happens in the A (aminoacyl site) of the ribosome?
where the subsequent amino acids/tRNAs are brought in
what happens in the E (exit) site of the ribosome
where the tRNA exits the ribosome?
what are the different eEFs?
eEF1α and eEF2
what is the function of eEF1α?
brings in the new tRNA/amino acids into the A site of the ribosome
what is the function of eEF2?
moves the tRNA between the ribosome sites
what is termination of translation?
the end of translation
what happens during termination of translation?
release factors (proteins that release the polypeptide chain and mRNA from the ribosome) recognize the stop codon sequence and, releases the mRNA, and the ribosome dissociates
what are chaperone proteins?
proteins that facilitate the folding of the proteins by recognizing hydrophobic residues
what are chaperonins?
chaperone proteins that provide an isolated environment within which correct folding takes place
what is protein disulfide isomerase (PDI)?
an enzyme that recognizes cystine residues and adds disulfide bonds
what is peptidyl prolly isomerase?
an enzyme that recognizes proline residues and twists them into the trans conformation
what is proteolytic processing?
removing sections of polypeptides in order to activate the protein
what are glycoproteins?
proteins with carbs attached to them
what is the function of glycoproteins?
protein folding in the ER, targeting proteins for transport, and cell-cell recognition
what are GTPase activating proteins (GAP)?
activates the activity of GTPase - makes hydrolysis happen faster
what are guanine exchange factors (GEF)?
protein that transforms GTP to GDP
what are kinases?
enzymes that add a phosphate group
what are phosphatases?
enzymes that remove phosphate groups
what is the proteasome?
trash compactor that breaks down misfiled proteins
what is the nuclear lamina?
a cytoskeletal structural complex composed of lamin proteins (intermediate filaments)
what is the nuclear pore complex?
channels for all transport in and out of nucleus
what are the two modes of passage in and out of the nuclear pore complex?
- Passive diffusion = fiddusion with no energy involved (goes down concentration gradient)
- energy dependent transport - mode of transport for most proteins and RNA
what is a nuclear localization signal (NLS)?
signals that specific protein needs to be brought into the nucleus
what are importins?
a family of receptors that bind to the NLS and transport proteins into the nucleus
what is Ran?
GTP binding protein
what are the steps of importing transport with Ran?
- importin binds to the NLS and transports the cargo protein through the nuclear pore complex
- Ran/GTP (activated Ran) binds to the importin and dislodges the cargo protein
- Ran/GTP transports importin out of the nucleus
- Conversion of Ran/GTP to Ran/GDP by RanGAP releases importin
what is an exportin?
a family of receptors that binds to the NES (nuclear export signal) and transports proteins out of the nucleus
what are the steps exporting proteins with Ran?
- NES of proteins bound for export is recognized by Ran/GTP
- binding of Ran/GTP stabilizes the complex and transports it out of the nucleus
- conversion of Ran/GTP to Ran/GDP by RanGAP releases cargo protein
what are peroxisomes?
small membrane bound organelles present in nearly all eukaryotic cells
what is a plasmalogen?
a specialized phospholipid
what are the functions of plasmalogens?
- contribute to structual integrity of cell membranes
- acts as antioxidants protecting cells from oxidative stress
what is the process of assembly of peroxisomes?
V1 and V2 vesicles fuse together
*these vesicles have distinct membrane proteins
what is the process of importing peroxisomal matrix proteins?
- protein that contains PTS1 targeting signal is recognized by Pex5
- this complex binds to the docking complex on the peroxisomal membrane
- Pex5 and Pex14 form a membrane pore
- cargo protein is translocated into the peroxisome
- Pex5 is recycled back to cytosol after translocation
what are the two ways a peroxisome can be formed?
- de novo formation - fusing of vesicles from ER
- alternative formation - growth and divison of already existing peroxisomes
what is the signficance of globular actin?
have binding sites that that mediate head to tail interaction
what is the significance of filamentous actin?
can grow at both ends and has polarity
actin is _ when bound to ATP and _ when bound to ADP
more stable; less stable and more likely to fall apart
what is treadmilling?
when ATP actin is added at the barbed end while ADP-actin dissociates from the pointed end
what is the function of formin in actin filament formation?
formin dimers bind to ATP-actin initiating the polymerization of long unbranched actin filaments
what is the function of profilin in actin filament formation?
binds to actin monomers and stimulates the exchange of bound ADP for ATP, increasing the local concentration of ATP actin
what is the function of Arp2/3 in actin formation?
makes the actin branches
what is the function of tropomyosin?
stabilizes the actin filaments by binding lengthwise along the growth of the filament
what is the function of capping proteins?
stabilize actin by binding to the barbed or pointed ends
actin bundles are supported by _
crosslinking proteins
actin networks are connected by _
large, flexible proteins that crosslink orthogonally (90°)
actin bundles give rigidity and shape to cell protrusions for _ versus actin networks offer mechanical support and are involved in cellular activities such as _
interactions w/ the environment; mobility and shape changes
