Unit 13- Transcription Flashcards
Ribozymes
catalytic RNA
structure levels of RNA
- primary structure: seq of bases
- secondary structure: folding due to hydrogen bonding between complements of same strand
Characteristics of DNA
- composed of nucleotides
- sugar: deoxyribose
- H group
- nucleotides joined by phosphodiester bonds
- usually double stranded
- secondary structure: double helix
- stable
Characteristics of RNA
- composed of nucleotides
- sugar: ribose
- OH group (highly reactive)
- nucleotides joined by phosphodiester bonds
- usually single stranded
- many types of secondary structures
*easily degradable
ribosomal RNA (rRNA)
- prokaryotic and eukaryotic
- location (eukaryotic): cytoplasm
- function: structural and functional components of the ribosomes
Messenger RNA (mRNA)
- prokaryotic and eukaryotic
- location (eukaryotic): nucleus and cytoplasm
- function: carries genetic info for proteins (from DNA to ribosomes)
Transfer RNA (tRNA)
- prokaryotic and eukaryotic
- location (eukaryotic): cytoplasm
- function: helps incorporate amino acids into polypeptide chain
small nuclear RNA (snRNA)
- eukaryotic
- location: nucleus
- function: processing of pre-mRNA (alt splicing)
small nucleolar RNA (snoRNA)
- eukaryotic
- location: nucleus
- function: processing and assembly of rRNA
microRNA (miRNA)
- eukaryotic
- location: nucleus and cytoplasm
- function: inhibits translation of mRNA
small interfering RNA (siRNA)
- eukaryotic
- location: nucleus and cytoplams
- function: triggers degradation of other RNA molecs
piwi-interacting RNA (piRNA)
- eukaryotic
- location: nucleus and cytoplasm
- function: suppresses the transcription of transposable ele in reproductive cells
CRISPER RNA (crRNA)
- PROKARYOTIC
- function: assists destruction of foreign DNA
Long noncoding RNA (lncRNA)
- eukaryotic
- location: nucleus and cytoplasm
- function: variety
transcription components
- DNA template
- Raw materials (ribonucleotide triphosphates) needed to build a new RNA molecule
- proteins
transcribed strand
template strand
transcription unit
- A promoter (region that transcription factors,TFs,bind
- RNA-coding sequence
- Terminator
RNA transcription strand
- goes 5’ to 3’ and added to 3’-OH
- uses EITHER top or bottom strand of DNA
bacteria initiation
- ribonucleoside triphosphates (rNTPS) added to the 3’OH group end
- transcription apparatus
- bacterial promoters
- Initial RNA synthesis: no primer required
- Location of consensus sequence determines position of start site
transcription apparatus
bacterial RNA polymerase: five subunits make up core enzyme
- 2 copies of a
- single copy of B
- single copy of B+
- stabilizing enzyme: w
Sigma (o) factor: recognizes and binds to the promoter (after binding RNA pol. Enzyme —> creats holoenzymes)
RNA polymerase 1
- all eukaryotes
- Transcribes: large rRNAs
RNA polymerase 2
- all eukaryotes
- Transcribes: pre-mRNA, some snRNAs, snoRNAs, some miRNAs
RNA polymerase 3
- all eukaryotes
- Transcribes: tRNAs, small rRNAs, some snRNAs, some miRNAs
RNA polymerase 4
- plants
- Transcribes: some siRNAs
- methylation and chromatin structure
RNA polymerase 5
- plants
- Transcribes: RNA molec taking place in heterochromatin formation
- methylation and chromatin structure
bacterial promoters
Consensus sequences: most commonly encountered nucleotides at each site
–-10 consensus: 10 bp upstream of the start site
Pribnow box
5’ TATAAT 3’
3’ ATATTA 5’
–35 consensus sequence: TTGACA
reading consensus seq
- Y = pyrimidines
- R = purines
- N = no patticular base is more common
- base/ base = both are equally common
bacteria Elongation
RNA elongation carried out by the action of RNA polymerase
bacteria Termination
- Rho-dependent termination: uses rho factor
- Rho-independent termination: hairpin structure formed by inverted repeats, followed by a string of uracils
before eukaryotic transcription
- chromatin modification
- Acetyltransferases add acetyl groups to amino acids at the ends of the histone proteins, which
destabilizes nucleosome structure and makes the DNA more accessible. - chromatin-remodeling proteins may bind to the chromatin and displace nucleosomes from promoters and other regions
eukaryotic promoters
- basal transcription apparatus
- transcriptional activator proteins
- RNA polymerase II –> mRNA synthesis
- core promoter TATA box (TATAAAA), -25 to -30 bp, bound by transcription factors
- regulatory promoter: located immediately upstream of the core promoter. bounded to.
- enhancers
eukaryotic initiation
- binding of the TFID transcription factor to the TATA box
- TATA binding protein (TBP)
Binding of a preassembled holoenzyme containing general transcription factors, RNA polymerase II, and the mediator
eukaryotic elongation
- DNA helix enters RNA polymerase II through a cleft in the enzyme and unwinds
- DNA-RNA duplex is bent at 90 degrees, which positions 3’ end of the RNA end of the RNA at the active site of the enzyme.
- At the active site, new nucleotides are added to the 3’ end of the growing RNA molecule
eukaryotic termination
- 3 RNA polymerases found in all eukaryotes use diff mechanisms of termination
- transcription RNa polymerase II is terminated when an exonuclease (ase = cutting) enzyme Rat1: attatvhes to the cleaved 5’ end of RNA, move down the RNA, reaches the polymerase enzyme
Archaea transcription
- closer relationship between archaea and eukaryotes
- RNA polymerase more similar
- Archaea promoters similar to TATA box
- Archaea possess a TATA-binding protein
