Transcription And mRNA Processing

Question 0

Not all RNA encodes proteins

Answer 0

mRNA codes for proteins but there are:
rRNA-form core of ribosome, catalyze protein synthesis
miRNA-regulate gene expression
tRNA-adaptor between mRNA and amino acids

Question 1

Genes are transcribed into RNA according to the needs of the cell

Answer 1

All DNA is replicated but not all DNA is transcribed

Each gene can be transcribed and translated with a different efficiency

Question 2

RNA vs DNA

Answer 2

RNA:
ribose not deoxyribose
Uracil not thymine
RNA can base pair with RNA or DNA strands (RNA-RNA hybrids have catalytic activity in ribozymes or serve a regulatory function in miRNAs)

Question 3

RNA synthesis basics

Answer 3

5'->3'
rNTPs serve as substrates
RNA polymerase 
RNA sequence same as non template strand except with U instead of T
No primer needed 
No exonuclease activities
Initiation, elongation, termination

Question 4

Promoter and terminator

Answer 4

Promoters are not transcribed but terminators are (still non coding)
Cis-acting sequences in promoter (-35 box, TATA box) and terminator

Question 5

Transcription start/stop sites are not the same as the start/end of the coding region of a gene

Answer 5

Gene includes promoter and terminator
RNA transcript includes 5’ untranslated region (sequence before first AUG initiation codon) and 3’ untranslated region (sequence after termination codon)
Terminator transcribed into RNA but trimmed later
Promoter orientation dictated which strand will be transcribed, different genes

Question 6

RNA polymerases

Answer 6

Bacteria only have one RNA polymerase that transcribed all types of DNA (targeted by rifampicin) but eukaryotes have 3.
RNA polymerase II transcribed protein coding genes (where most disease mutations are)
Alpha-amanitin is a toxin that inhibits RNA polymerase II

Question 7

Steps for RNA polymerase II transcription

Answer 7

TATA Binding protein binds TATA box
Other transcription factors are recruited along with RNA polymerase to form pre-initiation complex
Polymerase must be phosphorylated to leave promoter and start transcribing mRNA

Question 8

mRNA processing

Answer 8

Occurs co-transcriptionally
RNA polymerase recruits RNA processing enzymes
In bacteria, mRNA is translated co-transcriptionally
In eukaryotes, mRNAs are covalently modified at 5’ and 3’ ends and undergo RNA splicing then transported out of nucleus for translation

Question 9

5’ and 3’ modifications

Answer 9

7-methyl G at 5’
Polyadenylation at 3’ ~200 A’s
for stability, transport to cytoplasm, translational efficiency

Question 10

Splicing

Answer 10

Introns removed from primary transcript to produce mature RNA for translation
Done in nucleus co-transcriptionally
Expands repertoire of gene products (different isoforms) via alternative splicing, expand size for increasing rate of crossing over by homologous combination, exon shuffling, regulating splicing

Question 11

Mechanisms of mRNA splicing

Answer 11

Assembly of snRNPs (small nuclear ribonucleoprotein particles) brings two ends of intron together
Specific adenine nucleotide with 2’ -OH in intron attacks 5’ splice site and cuts sugar-phosphate backbone
Cut 5’ end covalently linked to adenine forming a lariat
Free 3’-OH end of first exon reacts with second exon, cutting intron at 3’ and joining 2 exons

Question 12

Hutchinson-Gilford progeria syndrome

Answer 12

Errors in RNA splicing
Single base change results in abnormal splice that deletes 150 bases
Abnormal lamin A is called progerin