Chapter 7- RNA and the Genetic Code Flashcards
monocistronic
eukaryotic mRNA is monocistronic, meaning that each mRNA molecule translates into only one protein product.
polycistronic
prokaryotic mRNA may be polycistronic, and starting translation at different locations in the mRNA can result in different proteins
aminoacyl-tRNA synthetase
different types activate different amino acids, requires 2 ATP
start codon
AUG (codes for methionine)
stop codon
UAA (U Are Annoying)
UGA (U Go Away)
UAG (U Are Gone)
only amino acids with one code
methionine and tryptophan
wobble position
third position for codon. usually the first two nucleotides are the same so the third is a variable one. mutations here are typically silent or degenerate mutations.
expressed mutations
- missense: one amino acid substitution
2. nonsense: mutation encodes for a premature stop codon (aka. truncation mutation)
TATA Box
promoter region for RNA polymerase II to bind during transcription. typically in -25 for gene location numbering system.
2 differences between DNA and RNA polymerases
RNA polymerases don’t require an RNA primer to start generating a transcript and they dont check their work, no editing done.
heterogeneous nuclear RNA (hnRNA)
primary transcript and after some modifications it becomes mRNA
steps between hmRNA and mRNA? (known as posttranscriptional processing)
- Intron/exon splicing
- 5’ cap
- 3’ poly-A tail
intron/exon splicing
spliceosome: made up of small nuclear RNA (snRNA) and small nuclear ribonucleoproteins (snRNPs). these recognize introns and cuts them out to form a lariat (lasso-shaped structure). they are then degraded.
introns- noncoding sequences are removed
exons- coding sequences are ligated
alternative splicing
primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene. many more proteins made from limited genes
RNA Polymerase I
Synthesizes rRNA
RNA Polymerase II
Synthesizes mRNA (and hnRNA)
RNA Polymerase III
Synthesizes tRNA and some rRNA
3 steps in translation
- initiation
- elongation (APE sites)
- termination
*Note: all steps require energy
what happens at the P site for translation (during elongation)
peptide bond forms using peptidyl transferase (enzyme part of the large subunit). GTP used for energy.
chaperones
assist in protein folding
carboxylation
usually serves as a Ca2+ binding site
phosphorylation
usually activates or deactivates a protein
operon
cluster of genes transcribed as a single mRNA. 2 types: inducible and repressible systems. offer a simple on-off switch for gene control in prokaryotes.
Jacob-Monod Model of an operon
- regulator gene- codes for repressor protein
- promoter site- RNA polymerase binding site
- operator site- nontranscribable and can bind a repressor protein
- structural gene- codes for protein
inducible system (prokaryotes)
repressor bound tightly to operator system so RNA polymerase cannot get to structural gene. inducer must remove the repressor. positive control mechanism b/c repressor is removed from operon by the inducer to promote transcription.
1 example of an inducible system (prokaryotes)
lac operon only induced in presence of high lactose and low glucose. assisted by binding of catabolite activator protein (CAP)-starts transcription.
negative control mechanism (prokaryotes)
repressible systems. repressor-corepressor complex binds to the operon to prevent transcription.
repressible systems (prokaryotes)
allow constant production of a protein. repressor is made by regulator gene in inactive until it binds to a corepressor. then this complex binds to the operator site preventing further transcription. negative control mechanism b/c typically protein being made is the corepressor.
1 example of a repressible system (prokaryotes)
trp operon controls manufacturing of tryptophan. when tryptophan is high in local environment it acts as a corepressor.
transcription factors
transcription-activating proteins that search DNA for specific DNA-binding motifs. 2 recognizable domains: DNA-binding domain and activation domain.
DNA-binding domain
part of transcription factor that binds to specific nucleotide sequence in the promoter region or to a DNA response element (sequence of DNA that binds only to specific transcription factors) to help recruiting transcriptional machinery.
activation domain
part of transcription factor that allows for binding of several transcription factors and other regulatory proteins, (ex: RNA polymerase and histone acetylase)
2 routes for gene amplification
- enhancers: several response elements, which allows for control of one gene’s expression by enhancing RNA polymerase at a single promoter site (signal moleule ex: cAMP).
- gene duplication: can duplicate in series and parallel
cis vs. trans regulators
cis: in same vicinity as gene they control
trans: produced and translocated back to the nucleus, travel through cell to their point of action
histone acetylation
coactivator that is recruited by transcription factors. involved in chromatin remodeling. acetylation of histone decreases + charge on lysine and open chromatin comformation allowing transcription machines to get to DNA.
histone deacetylases
gene silencing. proteins that remove acetyl groups from histones, resulting in closed chromatin formation and decrease in gene expression levels.
DNA methylation
DNA methylases add methyl groups to cytosine and adenine nucleotides. this typically silences gene expression.
enzymes involved in transcription
- helicase
- topoisomerases
* used to unwind DNA and prevent supercoils - RNA polymerase II (main player, binds to TATA box promoter region)
