BIO206 - Midterm #2

3 types of RNA polymerases (5 in plants), gazillions more proteins in transcription initiation, introns / exons in protein CDS, gazillion proteins for RNA processing

More things to coordinate especially if multicellular; larger genomes means more genes to recognize, control, & transcribe; compartmentalized cellular functions (organelles)

Enhancer elements in eukaryotic genes are upstream of promoters and control transcription efficiency

Exons & introns

Part of CDS that gets transcribed to RNA and encodes the protein

Part of CDS that gets transcribed but does not code for protein, found in between the exons of the CDS

Regions of a gene that are transcribed but not translated, found at the 5' and 3' ends of the protein CDS

Enhancers, upstream elements (GC box & CAAT box), core promoter (TATA box), 5' UTR, protein CDS (exons & introns), 3' UTR

Thousands of bp upstream of the upstream elements

Recognized by RNA polymerase II

Core promoter + upstream element

BREu, TATA (-25), BREd, Inr (+1), MTE (+17), DPE (+27)

Points RNA polymerase to the correct direction for transcription + minimum sequence of DNA required for accurate transcription

-100 to -80

GC box (-100) + CAAT box (-80)

TATAAA

GGGCGG

GCCCAATCT

RNA polymerases, general transcription factors (GTFs) for core promoter element, transcription factors for other elements in promoter, regulatory activator proteins that bind to distal enhancer elements, mediators which bridge the distal regulatory proteins & the core initiation complex

I, II, III

5.8S, 18S, 28S rRNA

All protein-coding genes (mRNA), snoRNA, miRNA, siRNA, IncRNA, most snRNA (functional RNAs)

tRNA, 5S rRNA, some snRNA, genes for other small RNAs

According to their "S" value, which refers to the rate of sedimentation in an ultracentrifuge where the larger the S value, the larger the rRNA

5 core subunits + 7 additional subunits

Help RNA polymerase II interact with the core promoter elements

GTFIIA, GTFIIB, GTFIID, GTFIIE, GTFIIF, GTFIIH

Bind to enhancer DNA elements thousands of bp upstream of core promoter

Bridges the interaction between activators/enhancers and the proteins bound to the core promoter elements (RNA polymerases, GTFs, etc.)

RNA polymerase, GTFs, mediator, chromatin remodelling complexes, histone-modifying enzymes

Multiple activators/enhancers can associate with the mediator to allow cells to control transcription more precisely

Sum of all protein-DNA & protein-protein interactions

Region of non-coding DNA between genes & between regulatory DNA sequences of enhancers

TFIID TBP subunit (TATA binding protein) + TFIID TAF subunits (TBP associated factors)

Binds to the TATA box of the core promoter

Binds to the Inr (initiator), MTE (motif ten element), DPE (downstream core promoter element) of the core promoter

Stabilizes TFIID promoter binding

Binds to BRE (B recognition element), a pair of sequences (BREu & BREd) flanking the TATA box of the core promoter

Stabilizes RNA polymerase interaction with TBP & TFIIB + helps attract TFIIE & TFIIH

Attracts & regulates TFIIH

Unwinds DNA at the transcription start site (helicase activity) + phosphorylates Ser5 of RNA polymerase CTD (C-terminal domain) to initiate elongation (kinase activity)

Protein-protein & protein-DNA interactions

TFIID TAF binds MTE, DPE, & Inr forming D complex; TFIIA displaces TAF1 of TFIID; TFIIA + TFIID TBP bind to TATA forming DA complex; TFIID undergoes major conformation change bending DNA by ~90°; TFIIB binds BREu & BREd stabilizing the DAB complex; TFIIF + RNA pol arrive to form the DABPolF complex; TFIIB hooks RNA pol into place; TFIIF binds DNA & stabilizes complex (helping RNA pol bind to region from -34 to +17); TFIIE arrives forming DABPolFE, TFIIH arrives forming DABPolFEH with TFIIH as helicase & kinase, mediator binds for additional contact points for regulation

DNA, TFIID, TFIIA, TFIIB, RNA polymerase II, TFIIF, TFIIE, TFIIH, mediator complex

Helicase + kinase

TFIIH unwinds DNA using XPB & XPD subunits while TFIIB holds the open DNA in place as RNA polymerase II clamps onto the DNA, keeping them from re-annealing

TFIIH phosphorylates the 5th serine of each RNA polymerase II C-terminal domain repeat, signalling RNA polymerase II to enter elongation phase

7 amino acids rich in alcohols, YSPTSPS

Most eukaryotic genes

Ribosome binding site (RBS) upstream of the start codon (AUG) of protein CDS in the 5' UTR

Transcription from eukaryotic genes produces immature pre-mRNA, which gets post-transcriptionally processed to produce mature mRNA that gets translated in the cytoplasm

5' capping, splicing out introns, 3' poly-adenylation tail

Immature pre-mRNA that has to go through post-transcriptional modification

5' cap, 5' UTR with RBS, protein CDS with exons adjacent, 3' UTR, poly-A tail

Signalling RNA polymerase II to enter elongation phase + coordinate post-transcriptional modifications during elongation

Beginning of elongation = only Ser5 phosphorylated to recruit enzymes for 5' capping, middle of elongation = additional phosphorylation of Ser2 to recruit enzymes for splicing, end of elongation = Ser5 gets dephosphorylated while Ser2 remains phosphorylated to recruit enzymes to add poly-A-tail

γ phosphate of transcript is removed from the 5' end by RNA triphosphatase, β & γ phosphates removed from guanosine triphosphate by guanylyltransferase, 5'-5' phosphotriester links resulting guanosine monophosphate & transcript heads on to form 5'-to-5' triphosphate bridge and RNA methyltransferase adds methyl group to N7 position of purine ring of guanine (7-methylguanosine)

Nucleotide where the three phosphates are alpha, beta, gamma

Binds to the 5' cap, one of the signals that mRNA is mature

Allows 2' to 5' phosphodiester bond formation (as opposed to normal 3' to 5' phosphodiester bonds)

Extra branch in polynucleotide chain from 5' carbon of a nucleotide attaching to 2' carbon of ribonucleotide in chain

Introns get cut out of the exons at the 5' & 3' exon/intron junctions, 3' end of exon 1 joins to the 5' end of exon 2 to combine the 2 protein CDS together, 5' end of excised intron binds to 2' OH of the branch point adenine to make a looped structure resembling a Q

Phosphate at 5' exon/intron junction

2' to 5' phosphodiester bond forms between first nucleotide of the 5' intron end & branch point adenine

5' GU, adenine residue at branch point 15-45 bases upstream from 3' end, 3' AG

Pyrimidine rich region ~ 15b long, upstream of branch point adenine

G

Forms during transcription to identify exon/intron junctions & excise introns to splice exons

Protein + snRNA (small nuclear RNA) = snRNP (small nuclear ribonuclear-proteins)

Combination of many snRNPs

BBP branch point binding protein, snRNP U2, snRNP U1, snRNP U6, snRNP U4, snRNP U5

Branch point sequence (YNYURAY), 5' splice junction (GU), 3' splice junction (AG) where Y = pyrimidine (cytosine/thymine), N = any nucleotide, R = purine (guanine/adenine), U = uracil

U1 snRNP binds 5' splice junction & BBP + U2AF (U2 auxiliary factor) binds to branch point; U2 snRNP displaces BBP + U2AF & binds to branch point + 3' splice junction (U1 & U2 interaction vs. RNA is mediated by RNA-RNA hybridization); U4/U6 & U5 joins the complex followed by U4 dissociation to cause conformational change to open the catalytic site for first phosphoryl-transferase reaction of adenine attacking with free OH, second phosphoryl transferase reaction occurs joining two exons together

Exons can be joined in different patterns

Increases the number of proteins encoded by a single gene for genomic efficiency

AAUAAA signal located in 3' UTR of pre-mRNA

CstF (cleavage stimulating factor) & CPSF (cleavage & polyadenylation specificity factor)

250 adenine residues added by polyA polymerase (PAP), which does not need a template

CPSF binds AAUAAA sequence, recruitment of additional proteins such as CstF, pre-mRNA cleaved downstream of poly-A site & poly-A tail added by PAP

10-30 nucleotides downstream of AAUAAA signal at 3'CA that is upstream of GU-rich or U-rich region, where -OH is added and then replaced by poly-A tail

Degraded in the nucleus

Poly-A binding proteins bind to the poly-A tail

After pre-mRNA is cleaved for the addition of poly-A tail, RNA polymerase II runs on and eventually dissociates from the DNA

Lack of 5' cap on growing RNA molecule

Cap binding proteins (CBP, bound to 5' cap), poly-A binding proteins (bound to 3' poly-A tail), other proteins bound to correctly spliced exon

Forms the nuclear pore complex to exit the nucleus and enter the cytoplasm

Catalyze metabolic reactions as enzymes, build cellular structures, send/receive signals

Ribosome recognizes & binds to a sequence on mRNA upstream of protein CDS + ribosome synthesizes a polypeptide according to the nucleic acid sequence on mRNA

5' to 3' direction

N- to C-terminus by adding amino acids one-by-one

4 types of nucleotides need to code for 20 types of amino acids

4 to the power of n where 1 nucleotide (singlet, n) = 4 amino acids, 2 nucleotides (doublet, nn) = 16 amino acids, 3 nucleotides (triplet, nnn) = 64 amino acids, 4 nucleotides (quad, nnnn) = 256 amino acids

Smallest number of nucleotides that can have enough unique combinations for 20 amino acids

Amino acid specificity, comma-free, non-overlapping, unambiguous, polar, degenerate, nearly universal

Uses a nucleotide triplet to code for one amino acid

No nucleotides in between the triplet nucleotides used as punctuations

Neighbouring nucleotide triplets don't overlap

Meaning of the nucleotide triplet never changes

Written & read in the 5' to 3' direction

Multiple different nucleotide triplets may code for the same amino acid