Transcription Flashcards
Central dogma
Normal flow of information in the cell- DNA holds information, transmits it between generations of cells, RNA is copied from DNA, proteins are made from RNA
RNA
Singled-stranded nucleic acid, transcribed from DNA, has uracil instead of thymine, ribose instead of deoxyribose
Similarities between RNA and DNA
Composed of nucleotides, synthesized in 5’-3’ direction, sequence is complementary to DNA template, 5’ phosphate, 3’ OH, internal phosphodiester bonds
RNA polymerase
Synthesized RNA from DNA template, adds new base at 3’ end, uses NTPs as source, needs 3’ OH to add another base
Function of RNA polymerase
Synthesis in 5’-3’ direction, reads DNA template in 3’-5’ direction, polymerase can correct errors
Prokaryotic RNA polymerase
4 subunits, sigma factors scan DNA for promotors, polymerase binds to sigma, sigma separates, scans again, apoenzyme produces RNA, transcription in cytoplasm, allows simultaneous translation
Holoenzyme
RNA polymerase bound to sigma factor
Apoenzyme
RNA polymerase without sigma factor
Eukaryotic RNA polymerase
Transcription in nucleus, different polymerases produce various types of RNA- RNA polymerase I, II, and III
RNA polymerase I
Produces rRNA except 5S- structural and functional part of ribosomes
RNA polymerase II
Produces mRNA- carries protein coding sequence
RNA polymerase III
Produces tRNA, small RNAs (5S rRNA)- protein synthesis, splicing, gene regulation
Action of polymerase
Reads template strand in 3’-5’ direction, adds ribonucleotides in 5’-3’ direction, RNA strand is displaced from 5’ end before synthesis is complete
Template strand
DNA strand used by RNA polymerase
Coding strand
DNA strand resembling the RNA produced, but it is not a substrate for RNA polymerase
Polycistronic genes
Some prokaryotic genes, one RNA codes for more than one protein, all proteins part of the same metabolic pathway, can regulate whole pathway at once (ex- lac operon)
Eukaryotic genes
Genes have several regions that are not important, promotor is at the 5’ end, not transcribed into RNA
Prokaryotic promoter elements
Pribnow box at -10 TATAAT, recognized by sigma70 factor, TTGACA sequence at -35, recognized by sigma factors
Eukaryotic promoter elements
Hogness or TATA box at -25, recognized by TFIID, CAAT boxes and GC rich regions between -40 and -100, specific transcription factor binding regions
Eukaryotic transcription complex
In addition to RNA polymerase, TATA binding protein (TBP) and other transcription factors (TFII) are necessary for initiation, co-activators are promoter specific
Cis element
DNA sequence that can potentially bind to a protein factor
Trans factor
Protein that can potentially bind to a DNA sequence
Enhancer element
Cis element that binds transcriptional activators and increases transcription rate
Repressor
Proteins that bind to silencer elements and lower transcription rate
Silencer element
Cis element that binds to repressors and lowers transcription rate
Eukaryotic mRNA processing
Transcribed as hnRNA, 5’ cap added early during synthesis, poly A tail added, introns spliced out, transported out of the nucleus to the cytoplasm and ribosomes
5’ cap structure
Cap is methylated GTP, triphosphate linkage, not cleaved by RNase, reverse insertion 5’ to 5’ linkage
Polyadenylation
Poly A tail is not added at the end of the primary transcript, specific site indicates where to add poly A, RNA is cleaved and many A’s added by specific enzyme, not encoded in DNA, binding site for proteins that stabilize mRNA
Splicing of mRNA
Introns must be removed before mRNA is mature, bases at each end of intron are signals, series of snRNPs perform splicing, forms a lariat structure and rejoins exons
Thalassemias
A mutation found in patients with beta+-thalassemia is a point mutation near the 3’ end of the beta-globin gene (AATAAA to AACAAA) changes the sequence in hnRNA at the polyadenylation site
Prokaryotic rRNA precursor
Large precursor to ribosomal RNA, also includes some tRNA, after folding into secondary structure, excess material is lost by cleavage of the backbone
Maturation of rRNA
Transcribed as 45S precursor, several cleavage steps, 5.8S RNA pairs with 28S
RIbosome assembly
Ribosomes are built in the nucleus (nucleolus), rRNA precursor cleaved in nucleolus, 5S is from separate gene, proteins are added to rRNAs, each subunit exported separately to the cytoplasm
Structure of tRNA
Cloverleaf pattern, several bases altered after synthesis, includes thymine and pseudouracil
Processing of tRNA
Introns and exons are present in prescursor, cleavage and splicing are necessary, bases altered, 3’ CCA added enzymatically
Inhibitors of RNA synthesis
Drugs that bind to DNA and sterically hinder replication and transcription- actinomycin D
Drugs that inhibit bacterial RNA synthesis
Drugs that bind to bacterial RNA polymerase- rifampicin/rifamycin- prevents transcription initiation, streptolydigin- prevents message elongation
Rifampicin/Rifamycin
Prevents transcription initiation, not elongation, used to treat tuberculosis, meningitis, inhibits prokaryotic transcription initiation, binds to beta-subunit of bacterial RNA polymerase interferes with formation of initial phosphodiester bond in mRNA
Streptolydigin
Prevents message elongation
