Topic 3: RNA structure, transcription, and translation

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Tetracycline

antibiotic that inhibits initiation by binding the 30s and blocks the A site

Streptomycin

antibiotic that inhibits initiation by binding to the smaller 30s ribosomal subunit of bacteria Can cause loss of hearing

Rifampin

antibiotic that inhibits the transcription in prokaryotes known to interfere with contraceptives

What is an amino-acyl tRNA or charged tRNA?

it is a tRNA that has the appropriate amino acid attached to it

degenerate

the reason why there are 61 codons for 20 amino acids means any nucleotide can occupy the 3rd position of an mRNA codon

What are the modifications for primary transcript to be converted into mRNA?

1. A 5' cap and 3' PolyA tail will be added to the primary transcript. The 5' end is capped with a methyl group. Folic acid (vit. B12 is required for this) At 3' end PolyA adds ~150-250 adenines The purpose of these 2 things is to protect the transcript from degradation in the cytoplasm. Act as a signal for ribosomal binding and initiation of translation 2. Introns will be removed by a process called RNA splicing

During RNA splicing how are non-coding segments of the primary transcript, introns, removed?

1. A large ribonuclear complex called a spliceosome recognizes the ends of the introns and removes it. 2. The spliceosome then joins the exons back together. • RNA polymerase and σ factor are required. • mRNA is produced by RNA polymerase II and transcription factors. 3. This modified RNA strand is now mRNA. mRNA can now leave the nucleus and enter the cytoplasm for translation

How is RNA different from DNA?

1. RNA uses ribose as its sugar (2'C has -OH) 2. RNA uses uracil instead of thymine. Base pair is A=U 3. RNA is often single stranded

Explain the process of transcription in eukaryotes?

1. The promoter region contains an A/T rich area called the TATA box which is recognized by transcription factors 2. RNA pol II recognizes the transcription factors and binds to the DNA 3. RNA polymerase II unwinds the DNA and begins to add nucleotides complementary to the template DNA 4. the new strand of RNA separates from the template DNA and exits RNA polymerase II 5. as the polymerase reads the DNA, the DNA is rewound into a helix 6. when the termination sequence is reached on the DNA, transcription is terminated and the primary transcript is released Before the primary transcript is ready to leave the nucleus it must be processed or modified to produce mRNA

What are the major types of RNA that participate directly in protein synthesis?

1. primary RNA (not a major type but a precursor to mRNA 2. messenger RNA (mRNA) 3. transfer RNA (tRNA) 4. ribosomal RNA (rRNA) 5. small interfering RNA (siRNA) or micro RNA (miRNA)

What is required for transcription in a eukaryote?

3 RNA polymerases in eukaryotes -RNA pol I=rRNA -RNA pol II=mRNA* -RNA pol III=mRNA these polymerases use a variety of proteins called transcription factors (TF) to identify promoter regions

What are the subunits for the 70S prokaryotic ribosome?

50S and 30S

What are the subunits for the 80S eukaryotic ribosome?

60s and 40s

Why is RNA polymerase in prokaryotes a primary target for antibiotics?

Because RNA polymerase is responsible for generating all types of RNA transcripts (primary transcript, mRNA, rRNA, and tRNA)

Explain initiation?

a small ribosomal subunit attaches to the 5' methyl cap The ribosome then slides to the translation initiation site called the start codon, AUG

To produce mRNA in a eukaryote what has to happen to the primary transcript?

addition of 5' cap addition of a 3' polyadenylated tail (PolyA tail) removal of introns and rejoining of the exons (splicing) When this is done the primary transcript is said to have undergone post transcriptional modification and is now mRNA

erythromycin

antibiotic that inhibits elongation by binding the 50s ribosomal subunit and inhibiting translocation

Cloramphenicol

antibiotic that inhibits elongation by binding the 50s ribosome and blocking transfer of the amino acid to growing peptide chain

Why is the difference in eukaryotic ribosomes based by species important?

because some antibiotics specifically target prokaryotic ribosomes

Why are transcription and translation not physically separate in a prokaryote

because they lack a nucleus

chloramphenicol

binds the 50S ribosome and blocks transfer of the amino acid to growing peptide chain

How is RNA polymerase similar to DNA polymerase?

can catalyze the formation of phosphodiester bonds. The bonds form between newly synthesized RNA, and the incoming nucleotides that base pair with the DNA template reads the DNA template in the 3' to 5' direction synthesizes the new RNA strand in the 5' to 3' direction

What is mRNA?

contains the nucleotide sequence specifying the amino acid sequence of a protein has been process introns have been removed and 5' cap and poly A tail have been added

What is the difference between degenerate code and wobble pairing?

degenerate: refers to the sequence on the mRNA encoding for an amino acid, even when following strict base pairing rules wobble pairing: is the type of pairing between the tRNA with the mRNA

What is the primary transcript? What does it contain? What will it do?

directly produced by transcription contains introns will undergo further processing to become mRNA

Explain termination

elongation continues until a stop codon is encountered in the A site A protein called the release factor binds the stop codon in the A site and causes the completed polypeptide to be released from the tRNA Once the polypeptide is released all the subunits dissociate and translation is terminated

How many phases are in translation and how does it differ in prokaryotes and eukaryotes?

initiation, elongation, termination differ in the ribosomal subunits used to translate

What is rRNA?

part of the ribosome that aligns the mRNA with the tRNA for translation

How is RNA similar to DNA?

phosphate, sugar, nitrogenous base

What makes up a ribosome?

rRNA and proteins

How is RNA polymerase different from DNA polymerase?

recognizes promoters at the beginning of genes (not origins) can initiate RNA synthesis without a primer uses ribonucleotides contain 2' OH groups uses UTP in place of TTP lacks 3' to 5' exonuclease activity (proofreading) must copy the correct strand of the DNA to yield the right transcript for translation

What is tRNA responsible for? is the structure of tRNA?

responsible for recognizing the mRNA and carrying the appropriate amino acid necessary for protein synthesis has a cloverleaf shape carries amino acids bound to its 3' end to the ribosomes for protein synthesis has an anticodon which base-pairs with the codons (three nucleotides) on the mRNA

codons

sequence of 3 nucleotide bases, triplets, found in mRNA that code for specific amino acids 4 different ribonucleotides (A,C,G, and U) that could be arranged into triplets 64 codon sequences that can be generated 3 stop codons: UAA, UAG, UGA

What is siRNA and miRNA?

siRNA: small interfering which were originally derived from viral genomes miRNA micro RNA originate from the host cell genome they function in a very similar manner 17-21 nucleotides responsible for binding to mRNA and interfering with translation=RNA interference

What is the single transcription factor like protein in prokaryotes?

sigma

transcription

synthesis of RNA from a DNA template (gene) first step of protein production

Wobble hypothesis

the 5' end of the tRNA anti-codon doesn't have to follow strict base pairing rules with the 3' position codon on the mRNA So the 3rd position doesn't have to follow Watson-Crick pairing G can go with C and U

translation

the conversion of genetic information from RNA to amino acids to form polypeptides (proteins)

reading frame

the start of a reading from is where the ribosome begins to read the mRNA

Why is RNA important?

transcription, translation, translational regulation

Where does transcription and translation take place in a eukaryotic cell?

transcription: nucleus (specifically nucleolus) translation: cytoplasm only 1 protein product is produced from each transcript (most commonly)


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