DNA to protein Flashcards
structural genes
encode the amino acid sequence of a polypeptide
bacterial promoter
provides the site to begin transcription; site for RNA polymerase binding
transcription factors
recognizes base sequences in the DNA and controls transcription
ribosomal binding site
provides a location for the ribosome to bind and begin translation
transcription initiation
transcription factors binding to promoter site and enables RNA polymerase to bind and an open complex is formed
transcription synthesis/elongation
RNA polymerase moves along DNA in open complex to synthesize RNA
transcription termination
terminator is reached that causes RNA polymerase and RNA transcript to dissociate from DNA
transcriptional start site
first base used as a template for RNA transcription and is denoted +1
Pribnow box
the -10 region in the bacterial promoter region with 5’-TATAAT-3’ as DNA sequence
bacteria sequence elements
two portions essential for promoter region is -35 and -10
RNA polymerase core enzyme
five subunits associate to form RNA polymerase and catalyze the synthesis of RNA
RNA polymerase holoenzyme
Association of the RNA polymerase core enzymes and sigma factor (recognizes the promoter)
sigma factor release
after the unwinding occurs at the -10 region, sigma factor is released and then transitions to the elongation phase of transcription
RNA synthesis
nucleoside triphosphates are used as precursors and pyrophosphate is released
rho dependent termination
a rho protein produces a stem loop structure and RNA dissociates
intrinsic termination
rho independent termination; two sequences begin the stem loop and NusA causes stopping of transcription and RNA is removed
RNA polymerase I
transcribes all of the genes that encode ribosomal RNA except for 5S RNA
RNA polymerase II
major role in cellular transcription because it transcribes all the structural genes
RNA polymerase III
transcribes all tRNA genes and the 5S rRNA gene
core promoter
eukaryotic promoter region with TATA box at -25 and transcriptional start site
basal transcription
core promoter produces a low level of transcription
eukaryotic regulatory elements
affect the ability of RNA polymerase to recognize the core promoter and begin the process of transcription
cis-acting elements
DNA sequences such as TATA box, enhancers, and silencers exert their effects over a particular gene; always on the same chromosome
trans-acting elements
regulatory transcription factors that bind to the cis-acting elements
general transcription factors
there are 5 different proteins always needed for RNA polymerase II to initiate transcription of structural genes
chromatin remodeling
either histone acetyltransferases or ATP dependent chromatin remodeling opens DNA from its winding of histones
nucleolus
ribosomal subunits are assembled 45S rRNA is processed
pre-mRNA
heterogeneous nuclear RNA (hnRNA); transcription of structural genes produces a long transcript that must undergo splicing of introns before exiting the nucleus
spliceosome
large complex of snRNPs that splices the introns in pre-mRNA in the nucleus of eukaryotes
snRNPs
small nuclear ribonucleoproteins; composed of small nuclear RNA and a set of proteins
alternative splicing
two or more different proteins can be derived from a single gene with different exons being chosen
5’ cap
a 7-mylguanosine is covalently attached for the proper exit of most mRNA from nucleus and translation
polyA tail
a string of adenine nucleotides are added enzymatically to the 3’ end in a process called polyadenylation
sense codons
sequence of 3 bases in most codons specifies a particular amino acid
start codon
AUG specifies methionine as usually first codon of polypeptide
anticodons
3 nucleotide sequences of tRNA that are complementary to mRNA codons
polypeptide-amino acid
polypeptides are composed of 20 different kinds of amino acids, so at least 20 codons are needed for each amino acid
codon system
there is a 3 base codon system that produced 64 potential different codons
degenerate genetic code
since only 20 different codons are needed, but there are 64 different potentials, more than one codon can specify same amino acid
peptide formation
condensation reaction forms bond; the beginning of the polypeptide has amino group exposed and the ending has carboxyl group exposed
primary structure
the polypeptide sequence
secondary structure
alpha helix and beta sheets with hydrogen bonds
tertiary structure
folding with hydrophobic, ionic, hydrogen, van der waals, and disulfide bonding
quaternary structure
two or more polypeptides
adaptor hypothesis
the anticodon in a tRNA specifies the type of amino acid it carries
aminoacyl-tRNA synthetase
20 different aminoacyl-tRNA synthetases that catalyze the covalent bonding of the amino acid to tRNA
aminoacyl tRNA
charged tRNA that has the amino acid attached to the 3’ end
isoacceptor tRNA
two or more tRNA that differ at the wobble base are able to recognize the same codon
translation: initiation
ribosomal subunits, mRNA, and first tRNA assemble into a complex
translation: elongation
ribosome slides in 5’-3’ direction and tRNA molecules bind to the mRNA; amino acids are linked together
translation: termination
stop codon is reached and disassembly occurs
Shine-Dalgarno sequence
the ribosomal binding site for bacteria where mRNA and ribosomes bind together
translation-initiator tRNA
in archaea and eukaryotes carries a methionine; in bacteria methionine has been covalently modified to N-formylmethionine
translation-initiation site
tRNA fmet enters at the p site
translation-elongation stage
tRNA enters at the A site
peptidyl transfer
polypeptide is transferred from the P site to the A site by peptidyltransferase; ribosome then moves one codon to the right
translation-termination
stop codons are recognized by released factors and not by tRNA
bacterial coupling
a ribosome attaches to the 5’ end of mRNA and starts translation before transcription ends
polyribosome
an mRNA transcript that has many bound ribosomes in the act of translation
