DNA RNA proteins

DNA template - directed duplication of the genome prior to cell division

DNA replication

DNA template-directed biosynthesis of RNA

Transcription

RNA template-directed biosynthesis of RNA

Reverse Transcription

mRNA template-directed biosynthesis of protein

Translation

RNA in living cells

• ____ RNA : encode amino acid sequences of all polypeptide in cell

• _____ RNA : match anticodon to MRNA while carrying a specific amino acid used for protein

  synthesis

• _____ RNA: makes up large+small ribosomal units

messenger, transfer, ribosomal

RNA in Eukaryotic Cells

• _____: regulate gene sequence via binding to specific nucleotide sequences

• _____ : enzymes/catalytic RNA molecules

MicroRNA, ribozymes

RNA in virus acts as _____

genomic material

• ribosome structure : single stranded → can be folded into compact structures with specific function

• ribosome function : can act as ____ (ribosomes); uses metal ions as cofactors

catalyst

List the three elements in mRNA processing

splicing, polyadenylation of 3’ end, capping 5’ end

Define splicing.

eliminate introns, join exons

enzyme that using 2Mg2+ ions for catalysis, adds rNTPs (ribonucleoside triphosphate) to 3' end of growing mRNA strands (is complementary to template DNA Strand)

• unwinds ~17 bp of DNA & covers ~35 bp of DNA

RNA polymerase

RNA pol binds to ______RNA pol generates supercuil that is later relieved by topoisomerases sequence to begin transcription (primer not required)

• growing end temporary base pair with DNA template for ~8bp inserts 50-90 nt/sec

• bubble of ~17 bp formed when DNA unwinds

promoter

RNA pol generates supercuil that is later relieved by ______

topoisomerases

directionality

• DNA nontemplate (coding) strand: ___

• DNA template strand: ____

• RNA transcript: ____

5’ → 3’, 3’ → 5’, 5’ → 3’

RNA Polymerase lacks 3’ → 5' exonuclease (= high error rate) meaning no ______ ability

proofreading

Explain the role of the beta sub-unit of RNA polymerase

main catalytic subunit

Explain the role of the sigma sub-unit of RNA polymerase.

responsible for DNA binding

another name for consensus Sequences at -10 (TATAAT) and- 35 (TTGACA) for subunit binding

• AT rich upstream promoter element between -40 and -60 binds subunit

• T rich sequence promotes strand separation

TATA Sequences

List the two types of termination of transcription seen in E. coli.

• ____ is characterized by UUU near 3' end of transcript

• ____ has commun CA rich Sequence (RUT Site)→ protein process until termination

p independent, p dependent

Describe the elements involved in the regulation of the affinity of RNA polymerase for a promoter.

• _____ Sequence : deviating from consensus sequence

• ______ sequence : cAMP receptor protein (CRP)

• _____ protein: block necessary binding sites

promotor, activator, repressor

serves as binding site on mRNA & protects it from degradation

— RNA pol II synthesize RNA beyond cleavage signal sequence

• cleavage signal: bound by endonuclease + polyadenylate polymerase bound to CTD

polyA tail

enzymes in polyadenylation

• cleaves RNA 10-30 nt downstream to highly conserve AAUAA

endonuclease

enzymes in polyadenylation

• Synthesize 80-250nt of A

polyadenylate polymerase an unprocessed , newly synthesized RNA molecule

an unprocessed , newly synthesized RNA molecule

primary transcript

protects RNA from nucleases ; forms binding site for ribosome

5’-cap

What is the nucleotide involved in making the 5’-cap?

7-methylguanosine

coding regions < 1000 bp in length

exons

Non-coding regions 50-700,000 bp in length

introns

most common intron that splices spliceosomal introns

- frequent in protein-coding regions of eukaryotic genomes

splicesome

are spliced by protein based enzymes

tRNA introns

primary transcript is cleared by ______

endonucleases

exons are joined by _____

ATP-dependent ligase

short noncoding RNAs of ~22 nucleotides

• role : binds to specific region of mRNA to alter translation

• assist in clearing mRNAs or block mRNA from translation

microRNA

name the two endoribonucleases (large recursors that synthesize miRNAs)

Drosha and Dicer

enzyme that catalyze the degradation of cellular mRNAs

Ribonucleases

enzyme used by virus which uses RNA to make DNA

• it then degrades the RNA from DNA-RNA hybrid and replaces it with DNA

• then DNA is incorporated into host cell

reverse transcriptase

the genetic code is written in ____ direction

5’ → 3’

Identify start codon sequence. What AA does it code for?

AUG, Methionine (MET, M)

Identify stop codon sequence.

UAA, UAG, UGA

third base is in “wobble” position → less important in binding to tRNA

• some RNA contains Inosinate which forms weak H bonds to ______

U, C, A

HIV Drugs ending in dine/sine are

reverse transcriptase inhibitor

HIV drugs ending in avir are

protease inhibitor