Lecture 9: DNA to protein Flashcards
Elongation factors
Drive translation forwards and improve its accuracy. Speed up synthesis by hydrolyzing GTP
RNA related exosomes
Protein complex that cleans up damaged RNAs before they leave the nucleus
Contain RNAses to chop up RNA
Other type of exosome
Cell derived vesicles present in most eukaryotic fluids
Contain molecular constituents of their cell of origin
Most contain an evolutionarily conserved common set of protein molecules
miRNAs regulate expression of over ___% of all protein coding genes
Regulate expression of over 70% of all protein coding genes
What causes termination of translation
Binding of release factor to the A site (stop codon)
What protein helps mRNA out of nucleus
Nuclear export receptor protein
Step four of translation
Small subunit moves 3 nucleotides along the mRNA and ejects the tRNA in the E site
Fungi and antibiotics
Fungi produce many antibacterial compounds that exploit differences in ribosomal subunits. New abx have been created that target bacteria via their ribosomal structure
How do alternative starting points arise in translation
Consensus sequences flank the start codon (AUG) and tell the ribosome to begin translation on that certain AUG
Editing pocket
Second AA binding site in aminoacyl-tRNA synthetase that excludes correct AA but allows closely related AAs in. If it is occupied, the editing pocket with inactivate the tRNA
Step one of translation
New tRNA binds to A site pairing with codon
Why are tRNA introns not spliced by spliceosome
Splicing requires the tRNA to be folded properly and will not proceed if it is not. Therefore, this represents a quality control step in tRNA generation
Wobble pase pairing
Nucleotides in the third “wobble” position can bind with multiple different nucleotides in anticodon
Nucleolus
Ribosome producing factory. Site where rRNA is processed and assembled into ribosome subunits.
Significance of nucleolus size
Size of the nucleolus reflects to cells need to generate proteins
tRNA modifications
10% of nucleotides in tRNA are modified
rRNA is responsible for (3)
Overall structure, the ability to position tRNAs and its catalytic activity
Primary role of proteins in ribosome
Stabilize the RNA core
MicroRNA definition, function
Small non-coding RNA molecule
Functions in RNA silencing and post-transcriptional regulation of gene expression via RNA degradation
TATA box
Promotor region on DNA 25 nucleotides from the transcription initiation site
Cajal bodies
Area where most snoRNAs are assembled into snRNP
5’ Cap does what
Allows mRNA to be distinguished from non coding RNAs and is also important for establishing translation
Step two of translation
Carboxyl end of growing peptide is released from tRNA in P-site. Peptide bond formation between previous AA added and the new one. tRNAs are in P site and A site
Ribozyme
RNA capable of enzymatic function
snoRNA - what are they and what do they do
Small nucleolar RNAs
Help implement biochemical modifications of noncoding RNAs with help of other proteins
Nonsense mediated decay
Eliminates mRNAs that have premature stop codon as they try to exit the nuclear pore
Protein folding begins
Before translation even finishes
aminoacyl-tRNA synthetase
Helps ensure that the correct amino acid is coupled to the tRNA
snRNP
snoRNA + specific proteins= snRNP
Causes for concern for use of miRNA for therapeutic intervention
Precise delivery to tissue of significance
Off target interactions
miRNA therapeutic potential
Can be used as knock-down tool to knockout gene and see what happens. Can target genes specifically. Tremendous potential for disease intervention in any case where stopping gene activity would be valuable
Chaperone proteins
Ensure that peptides fold into the correct functional conformation or refold them if they get damaged
Proteasome
Searches for misfolded proteins in nucleus and cytoplasm, ingests them and degrades them. Ubuiqulylation (at lysine 48) is the sign that the proteasome needs to degrade it.
What are the steps involved in RNA processing before leaving the nucleus
5’ capping
Poly A tail
RNA splicing
hsp60 family of heat shock proteins
This is a barrel shaped protein that fixes misfolded proteins. Captures proteins using hydrophobic interactions
Step three of translation
Large subunit moves along mRNA held by small subunit, shifting tRNAs to P and E sites on small subunit
What occurs in all living cells
The flow of information from DNA to RNA to protein
Transcription and translation
What usually indicates protein is misfolded
Exposed section of hydrophobic amino acids
miRNA processing
Transcription into Pri-miRNA
Processed by Drosha into Pre-miRNA
Exported from nucleus as DS-RNA
Processed by Dicer- loop is cut off, miRNA binds complementary strand of mRNA
Most common modification of noncoding RNAs
Pseudouridylation and 2’O methylation
