74 Cards in this Set
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coupled transcription and translation in
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prokaryotes
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features of RNA synthesis
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– The precursors are ribonucleoside triphosphates.
– Only one strand of DNA is used as a template.
– RNA chains can be initiated de novo (no primer required).
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What are the subunits of the E. coli RNA core polymerase
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Alpha2
beta
beta'
omega
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4 subunits of E. Coli RNA Polymerase holoenzyme
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α2, β, β', σ
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alpha in e. coli RNA polymerase
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assembly of the tetrameric core
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B in E. coli RNA polymerase
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ribonucleosidetrisphophate binding site
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B' in E. Coli RNA polymerase
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DNA template binding region
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sigma in E. coli RNA polymerase
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initiation of transcription
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+1 region
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transcript initiation site for prokaryotes
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upstream sequences
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(-) prefixes
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downstream sequences
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(+) prefixes
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prokaryotic promoter region
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-35 to -10 bp
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where does unwinding of DNA for transcription occur in prokaryotes?
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-10 region
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rho dependent terminators
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require protein factor rho, prokaryotes transcription
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rho independent terminators
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do not require rho, in prokaryotes for transcription
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Shine-Dalgarno sequence
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consensus sequence found in the bacterial 5' untranslated region of mRNA; contains the ribosome binding site
-binds 16s rRNA
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Ribozyme
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23s rRNA molecules, enzymatic activity, produces translation
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tRNAs
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adapters between amino acids and codons
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anticodon
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on tRNA
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codon
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mRNA
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role of aminoacyl-tRNA synthetase
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to specifically recognize tRNA molecules and attach the correct amino acids to them
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When tRNA is said to be charged, the tRNA is?
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bound to an a.a.
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Wobble Hypothesis
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tRNA can recognize more than one codon for specific amino acid
movement of FIRST nucleotide base in ANTICODON allows for nontraditional base pairing
5' side of anticodon
3' side of mRNA (third base in codon of mRNA)
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specificity of tRNAs
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tRNA molecules must have the correct anticodon sequence.
The third base is the wobble position.
tRNA molecules must be recognized by the correct aminoacyl- tRNA synthetase.
There may be more than one tRNA for each amino acid. For instance, you need at least two tRNAs for Ala.
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nonoverlapping code
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every three code for a codon; genetic code in which nucleotides do not overlap into other codons
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nucleotide triplets
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sets of 3 for codons
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genetic code is comma free
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the code is read consecutively, does not skip nucleotides
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genetic code is degenerate
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more then one codon corresponding to a single amino acid
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ordered genetic code
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redundant codons tend to differ only at the third position
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start codon
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AUG
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stop codons
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UAA, UAG, UGA
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Genetic code is nearly universal
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With a few minor exceptions, all codons specifiy the same amino acids in all organisms
exceptions-- mitochondrion and some protozoa
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Base Pair Insertion
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Insertion of 1 or more nucleotide pairs into a gene
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Suppressor Mutation
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A mutation that counteracts the the effects of the 1st mutation.
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What will the insertion of deletion of 3 base pairs cause?
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no frameshift will occur but there will be a loss or addition of amino acids
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reading frame
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Refers to the way in which codons are read during translation, in groups of three bases beginning with the start codon.
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Beadle and Tatum's Experiment
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Normal Strains: methionine was synthesized by cellular enzymes
Mutant Strains: Genetic defect in one gene prevented the synthesis of one protein required in one step of pathway to produce amino acid
Single gene controlled the synthesis of a single enzyme - one gene one enzyme hypothesis…
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Nonsense Mutation
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Stop codon is produced
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Missense mutation
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change one AA to another
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Silent Mutation
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no amino acid change
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pulse chase labeling
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RNA is synthesized in the nucleus and then transported to the cytoplasm.
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Alternative RNA Splicing
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Genes can create different polypeptides depending on which segments treated as exons. Can produce more protein products then # of genes. Different exons code different domains of protein (modular architecture with structural & functional regions)
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RNA splicing
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introns are excised (removed) and exons are spliced (connected together)
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TACTAAC box
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sequence recognized by enzymes in introns
Introns start with GT and end with AG
Eukaryotes
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types of intron excision
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The introns of tRNA precursors are excised by precise endonucleolytic cleavage and ligation reactions catalyzed by special splicing endonuclease and ligase activities.
The introns of some rRNA precursors are removed autocatalytically in a unique reaction mediated by the RNA molecule it…
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eukaryotes have how many RNA polymerases
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3
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RNA polymerase I eukaryotes
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location- nucleolus
products- rRNs excluding 5SrRNA,
sensitivity- no sensitivity
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RNA polymerase II, eukaryotes
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location- nucleus
products- nuclear pre-mRNA
sensitivity- complete
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RNA polymerase III
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location- nucleus
products- tRNAs, 5S rRNA, small nuclear RNA
sensitivity- intermediate
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modifications to eukaryotic pre-mRNAs
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A 7-Methyl guanosine cap is added to the 5’ end of the primary transcript by a 5’-5’ phosphate linkage.
A poly(A) tail (a 20-200 nucleotide polyadenosine tract) is added to the 3’ end of the transcript. The 3’ end is generated by cleavage rather than by termination.
When present, in…
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diagram of 3' end formation of mRNA and addition of poly A tail
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Prokaryotic Ribosome Subunits
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30S + 50S = 70S
protien synthesis
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eukaryotic ribosome subunit
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60S and 40S
80S ribosome
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5' UTR and 3'UTR
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regulate translation
localize mRNA in cell
don't code anything
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steps of eukaryotic gene expression
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transcription
2. RNA processing and splicing
3. transport to cytoplasm
4. translation
5. protein assembly
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PremRNA
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RNA transcript that is modified (INTRONS spliced in NUCLEUS) in ways that make it a functionally active mRNA
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what is added after transcription eukaryotes
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5' cap and poly A tail
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pulse chase labeling
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At first, labeled RNA is exclusively in the nucleus.
Later, the labeled RNA is found in the cytoplasm.
RNA is synthesized in the nucleus and then transported to the cytoplasm.
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tissue specific alternative RNA splicing
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different cells express different forms of mRNA from the same gene, increasing the capacity of genetic information
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DNA-RNA duplex
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Introns- loops
Exons- complementanry
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splicing
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• Removal of introns must be very precise.
• Conserved sequences for removal of the introns of nuclear mRNA genes are minimal.
– Dinucleotide sequences at the 5’ and 3’ ends of introns. (GT at 5' end, AG at 3' end)
– TACTAAC box about 30 nucleotides upstream from the 3’ splice si…
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TACTAAC
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sequence recognized by enzymes in introns
Introns start with GT and end with AG, 30 upstream from 3' splice site
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tRNA precursor excision
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endonucleolytic cleavage and ligation reactions catalyzed by special splicing endonuclease and ligase activities
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intron excision
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removed autocatalytically mediated by ribozyme
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nuclear premRNA (hnRNA) excision
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in 2 step reactions carried out by spliceosomes
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eukaryotic promoter region
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TATA- -30
CAAT -75
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E-site
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-exit
-release of tRNA
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P site of ribosome
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peptide bond formation, where first tRNA
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A site
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where tRNA enter ribosome
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prokaryote vs huma genome
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-human larger, more genes, less genome from protein encoding genes,
large noncoding regions
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difference between different cell types
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have the same genes, express different sets of genes, express genes at different times
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transcription factor for
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eukaryotic transcription
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partial degenerate
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last codon matters
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degenerancy
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also called redundancy
there is more than one codon for most amino acids
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BIOL 3303: TEST 2