Genetic Code is Unequivocal
each codon corresponds to only one amino acid.
Genetic Code is degenerate
for a given amino acid, there may be more than one codon.
First 2 amino acids of a codon
play a determining role in which amino acid the codon codes for.
often correspond to amino acids with similar properties or chemical structures.
Codon Usage Bias
Not all codons coding for a given amino acid are used with the same frequency in the genes of an organism.
varies between 75 and 90 nucleotides
tRNA secondary structure
the shape of a clover leaf: internal base pairings between complementary bases make the stems and single stranded sequences make the loops.
"a double-stand stem that ends in a single
strand sequence, in which a OH group in position 2' or 3' of the terminal
nucleotide can bind the amino acid. "
"contains this triplet of bases. Ψ symbolizes
pseudo-uridine, a modified base."
Anti Codon Arm
contains the anti-codon triplet at the center of a loop. This part of the tRNA recognizes the complementary codon on the mRNA.
named because it contains another modified base : dihydrouridine.
length varies between 2 and 21 nucleotides.
takes the shape of the letter « L ».
produces an aminoacyl-AMP complex, and then reatcs the aminoacyl-AMP with the tRNA to form an aminoacyl-tRNA.
when the tRNA is bound to the synthesase, it drags the a.a. to this, which cannot accept the correct a.a. If an incorrect a.a. enters, it is removed.
the identity of the 3rd nucleotide in a codon is variable to a certain degree.
the tRNA that encorporates the first methionine from the AUG start codon.
ribosome binding site, located 10nt upstream of the AUG, sequence is AGGAGGU.
recognizes the 30s ribosomal subunit and prevents it from binding the 50s unit
binds a GTP molecule and a tRNAfmet, once all factors come together, GTP is hydrolysed and the 70s subunit is complete.
binds to 30s subunits and reinforces interactions with IF2 and IF3
GCCa/gCC *AUG* G
an RNA molecule which catalyzes a chemical reaction.
binds to tRNA as it enters A site, temporarily preventing peptide bonding. If the codon, anticodon pair is correct GTP is hydrolysed and peptide bond is formed.
binds to the A site and accelerates movement of the last two tRNAs to the hybrid sites A/P and P/E, by GTP hydrolysis, it recreates the A and P site.
bind to the A site of a ribosome when a stop codon is reached in the mRNA, and encorporates a H2O, instead of an amino acid, triggers release of chain.
When a stem and loop signal that binds a specific tranlation factor and allows selenocysteine to be incorporated.
blocks binding of aminoacyl-tRNA to the ribosome
inhibits peptidyl-transferase activity of the ribosome
blocks the movement of the ribosome
binds the A site and prevents translation
Negative translational control (Shine-Dalgarno)
proteins bind shine-dalgarno sequence, when ribosomal proteins are in excell they bind to their shine sequence.
Negative translational control (Eukaryotes)
repressors bind to the 5' end or the 3' UTR and interfere with communication of the cap complex
Extracellular singal translation control
extracellular signal molecules can alter translation of proteins, for example aconitase and iron metabolism.
Recognition of DNA template
RNA pol binds promoter and dissociates the two strands, forming a transcription bubble.
once RNApol binds DNA it begins to synthesize 2-9 nt long RNAs
RNApol goes beyond 9nt and sysnthesizes the entire mRNA.
formation of phosphodiester bonds stops and transctiptional apparatus dissociates.
RNA Synthesis PhysChem
Reaction is energetically favourable, -deltaG and is irreversible
enzyme assembly, recognizes promoters and binds to activators. 2 are needed to make RNApol.
Catalytic centre along with beta prime
beta prime factor
Catalytic centre along with beta
reduces the affinity of the core enzyme for sequences that are not promoters and increases the affinity of the core enzyme for sequences that are promoters.
"-10" consensus sequence for RNApol.
"-35" consensus seuqnece for RNApol.
form a GC rich hairpin and a stretch of 6 Us at the end of the transcript, both interact with RNApol and terminate transcription.
Rho dependent termination
Rho protein binds to a C-rich/G-poor RNA sequence and indunce termination.
A region of DNA that normally enduces termination is not always read as such 100% of the time, thus some times a longer mRNA is produced.
proteins that increase transcription by enhancing the ability of the RNA polymerase to bind to a promoter and/or enhance the ability of the RNA polymerase to unwind the DNA.
DNA binding proteins that decrease transcription by inhibiting the ability of RNA polymerase to bind to a promoter region.
cleaves lactose into glucose and galactose
B-galactoside permease (LacY)
membrane protein that pumps lactose into the cell
B-galactoside transacetylase (LacA)
enzyme involved in lactose metabolism
negatively correlated to glucose levels.
only works once cAMP is present binds to its DNA binding region and promotes lac operon expression.
Binds to an operator sequence and loops DNA preventing Lac expresison, is inactivated by lactose.
the sugar in RNA
causes the OH of carbon 2 of ribose to react with a phosphorus, cleaving the diester bond
the ds form adopted by RNA, different from the DNA helix, it has a narrower major groove, and a shallow minor groove.
Makes peptide bonds during translation
grp II self splicing
introns are removed in the same way as normal splicing, but does not need any proteins, still needs the important A.
grp I self splicing
introns are removed without proteins, but requires a free G-nucleotide in any phosphorylated state.
RNA sequences that can cleave other RNA by first pairing, then cleaving and then unpairing.
responsible for rRNA synthesis
methylation and isomerization of uridine into pseudo-uridine
position themselves through base pairings and attract enzymes responsible for rRNA modification