Lecture 3/5 Flashcards
what is basal level of transcription?
whatever occurs at a rest-like state (usually really low or not at all)
what does the RNA pol complex bind to to get the basal level of transcription?
TATA box (also in proks) – usually the most important, ~25-30nt upstream to the start of transcription
CAAT box ~70-80nt upstream
GC box ~110 nt upstream
what process is affected by mutations in core promoter sequences? Why?
transcription, as it can cause bad binding of the RNA pol complex
what are enhancers/repressors?
sequences within the DNA to which a transcription factor can bind to activate or repress transcription
where on the chromosome are enhancer/repressor sequences?
they can be anywhere along the chromosome, near or far to the +1 region
can you find enhancer/repressor sequences in an intron?
yes
can you find enhancer/repressor sequences in an exon?
no
does the orientation of enhancer/repressor need to be in one direction
no, it can be reversed
are enhancer sequences gene-specific?
no, they might be used by multiple genes
are promoters gene-specific?
yes
what needs to bind to the enhance sequence in order to get transcription above basal rates?
transcription factors (which are proteins)
is basal transcription the same for every gene?
no
what does the binding of a repressor cause?
it can block the binding of RNA pol complex to promoter region
What is one thing the RNA pol complex looks for to know where to bind?
TATA box (and TATA binding protein)
How might enhancers that are really far from each other be connected to the transcription complex?
it loops the DNA
what happens to transcription if cohesin comes in to loop the DNA and it blocks access to the activating protein?
the expression of the gene is different, lowered
what is one thing that changes gene expression in different tissues?
presence or lack thereof of different transcription factors
what is acetylcholine used for?
it’s used at neuromuscular junctions for muscle contractions
what are nestled genes?
genes transcribed in the same direction using the same promoter sequences, one is often in the intron of another gene
what are nestled genes in euks similar to in proks?
operons
what is the order of how acetylcholine gets to the muscles?
synthesized in the cytoplasm, packaged into synaptic vesicles, released at the synapse
what is an example of nestled genes?
unc-17 gene is located in an intron of cha-1 gene
do genes grouped together usually have anything in common?
yes, they often have common functions and are regulated by common elements
can nestled genes share an exon
yes, but likely not translating to a protein
which RNAs get translated?
mRNAs
how are polypeptides created?
ribosomes translate the mRNA sequence to synthesize the polypeptide
are polypeptides modified at all after they’re synthesized?
yes, substantially
what are the two crucial elements for translation and what do they do?
tRNAs (transfer RNAs) mediate translation of mRNA codons to amino acids
ribosomes coordinate movement of tRNAs and have enzymatic activity for peptide bonds
when do ribosomes/ribosomal complex come in to start translation in proks?
as the transcripts are being made, since transcription and translation are coupled
are tRNAs long or short
short, 74-95 nt long
what are the components of tRNA
has an anticodon that is complementary to an mRNA codon
a specific tRNA is covalently coupled (charged) to a specific amino acid –> ready to become a protein
base pairing bt an mRNA codon and an anticodon of a charged tRNA directs amino acid incorporation into a growing polypeptide
how many amino acids are there
~20
what is the difference between tRNA and charged tRNA?
charged tRNA has an amino acid
how many tRNAs are there?
~20
what is the primary structure of tRNA?
nucleotide sequence
what is the secondary structure of tRNA and how is it formed?
the cloverleaf shape, and it’s formed bc of short complementary sequences within the tRNA transcript
what is the tertiary structure of tRNA and how is it formed?
L shape, it’s formed by 3D folding
what’s at the end of the L’s stem on tRNA?
anticodon
there is always a staggered end on tRNA, why and which end?
there’s a 3’ overhand bc we need the OH group to attach the amino acid
what is the polarity of a codon?
5’ to 3’
what is the polarity of an anticodon?
3’ to 5’
what is an anticodon?
region of 3 nucleotides that attaches to the mRNA
what happens at the two different ends of the tRNA
at 3’ overhang, amino acids are attached. at anticodon, mRNAs (transcript) binds
what do aminoacyl-tRNA synthetases do?
recognize a specific amino acid and the structural features of its corresponding tRNA, attaches phosphate from ATP to amino acid and uses that energy to attach the amino acid to the tRNA which makes it charged
how many aminoacyl-tRNA synthetases are there?
there’s a different one for every amino acid
what are the pockets in aminoacyl-tRNA synthetases for?
there’s a pocket for ATP and a pocket for the amino acid
