RNA Molecules

How are tRNA able to be so specific in binding to each of the 20 amino acids.

Aminoacyl-tRNA synthetase helps recognize the tRNA and its amino acid. - There are 20 different aminoacyl-tRNA synthetases (one for each amino acid) -recognizes the size, charge, and R groups of amino acids and nucleotide sequences of tRNA on acceptor stem and anticodon loop.

What different bases are present in tRNA that are not found anywhere else?

Modifications of the base uracil: . 1. Ribothymidine 2. Pseudoridine

How can aminoacyl-tRNA synthetases be so accurate? what do they recognize? How do they act as aa " double sieve".

Mischarging: addition of the wrong amino acids Some synthetases have relaxed specificity that can allow the addition of amino acids that are similarly structured to the correct one. AA double Sieve Activation site: 1st Sieve-the active site can only accept amino acids of the right size. Anything too big will not bind. Editing Site: 2nd Sieve-active site may mistakenly take in a similar amino acid that is incorrect related amino acids can be similar size, so then amino acids are sent to the editing site, correct amino acids will not fit in the editing site. and the one that bind will be taken off and degraded.

What is a tRNA?

RNA that helps bring in the correct amino acids while the mRNA is being read.

multiple 3' cleavage sites

Refers to the presence of more than one 3' cleavage site on a single pre-mRNA, which allows cleavage and polyadenylation to take place at different sites, producing mRNAs of different lengths

Wobble

a single anitcodon can pair with more than one codon

What is alternative splicing?

-Allows relatively small number of genes to produce a large number of products. 1. pre-mRNA is processed normally with the addition of the poly A tail and 5' cap. 2. When splicing occurs, there are multiple different ways that the introns and exons can be spliced. For example, in one path the only introns could be spliced out and in another way exon 1 could be spliced out.

There are 30-40 different tRNAs, where is there not 20-61 tRNAs?

1. 64 codons because of a three stop codons and 61 sense codons. Degenerate code- refer to the fact that the genetic code contains more codons than are needed to specify all 20 common amino acids. Isoaccepting tRNAs- different anticodons that specify the same amino acids. Wobble in base paring- base paring between codon and anitcodon in which there is nonstandard pairing, usually at the third position of the codon; allowing more than one codon to pair with the same anticodon.

What are the four different arm of tRNA?

1. Acceptor arm- 3' end of the structure contains CCA sequence (Where amino acids attaches to tRNA) 2. TYC arm- Named after the four bases that are found there: (Thymine (T), Pseudoridine (Y), and cytosine (C) ). 3. Anitcodon Arm- contains the anticodon arm hat pairs with the codon. This ensures that the amino acid links with the correct sequence.

How is pre-mRNA processed in Eukaryota organisms?

1. Addition of 5' cap ( methylated cap) - addition of a extra guanine nucleotide and methyl groups at the 2' position of the ribose sugar in one or more of the nucleotide. 2. Methylated RNA is released from RNA polymerase and specific consensus sequences on the mRNA are bound by cleavage factors near the 3' end of the mRNA. 3. The cleavage factors move the 3' end into position and poly A polymerase binds to the mRNA and cleaves the 3' end. 4. poly A polymerase starts to synthesize the Poly A tail through the addition of adenine residues to the cleavage site. 4. Additional proteins are added to the tail increasing the rate at which the poly A tail grows and Poly A polymerase is released from the pre-mRNA strand. Splicing: Introns are removed from the RNA and exons are joined together. Process of splicing: 1. Three different splice sites are present in the pre-mRNA ( 5' splice site, branch point, and 3' splice sites) 2. snRNAs, U1 attaches to the 5' splice sites and U2 attaches to the branch point. 2. Transesterification reaction. The 5' splice site is cut and attaches to the branch point to form a lariat (loop-like structure created in splicing of nuclear pre-mRNA) the U1 and U4 are released from the lariat and a complex of U4, U5, and U6 joins the spliceosome at the branch point. 4. Base pairing between the sequences in the mRNA and the snRNAs hold the splicesome together. 5. Exons are joined together and the intron is released as a lariat. The snRNAs are released from the lariat and the linear intron is degraded.

How are tRNA processed?

1. Large precursor tRNA is cleaved to produce an individual tRNA molecule. 2. An intron is removed by splicing 3. Bases are added to the 3' end 4. Modifications of several bases produces the mature tRNA

What is the structure of tRNA and how does the amino acid attach to the tRNA

1. The CCA arm is responsible for binding to the A of the CCA arm.

What is tRNA charging?

1. chemical reaction in which aminoacytl-tRNA synthetase attaches an amino acid to its corresponding tRNA. Attachment of an amino acid to a mature tRNA molecule that requires energy.

How is rRNA processed?

1. methyl groups are added to specific bases and to the 2'-carbon atoms of some ribose sugars 2. The RNA is cleaved into several intermediates in bacteria 3. Cleaved RNA is trimmed and mature rRNA is the result. * rRNA begins as from a larger precursor, it is cleaved and then processed into mature rRNA

What is recursive splicing?

A variation of splicing in which some long introns are removed in multiple steps.

How is the acceptor arm different from the other arms?

Doesn't contain a hairpin structure only a 5' and 3' end.

Editing Site 2nd seive

Editing Site: 2nd Sieve-active site may mistakenly take in a similar amino acid that is incorrect related amino acids can be similar size, so then amino acids are sent to the editing site, correct amino acids will not fit in the editing site. and the one that bind will be taken off and degraded.

What makes up the small and large rRNA subunit

Large rRNA subunit: joins amino acids to form peptide chain Small rRNA Subunit: read the mRNA

Can only one type of alternative processing happen on mRNA?

No, both 3' multiple cleavage sites can exist in the same pre-mRNA transcript. Examples of this is the production of calcitonin and calcitonin-gene -related peptide (CGRP)

How is the 3' end of the mRNA processed? What is the point of processing the very end of the mRNA?

Polyadenylation: 1. Pre-mRNA is cleaved at the position from 11 to 30 nucleotide downstream of the consensus sequence. in the 3' untranslated region. 2. The addition of adenine nucleotide (polyadenylation) takes place at the 3; end of the pre-mRNA, generating the poly (A) tail. The poly (A) tail consists of around 200 adenine nucleotide and does not require a template to be synthesized. Function: Protects the 3' end of the mRNA from enzymatic degradation and acts as a signal for transport of the mRNA from the nucleus to the cytoplasm. * Confers stability to the mRNA, because one way the eukaryotic cell can regulate gene expression is through RNA degradation. The he poly (A) tail is essential in protecting the mRNA fro degradation through increasing the time at during which the mRNA remains intact and available for translation before it degrades by these enzymes.

How does RNA editing affect the end product?

Process in which the protein-coding sequence of an mRNA is altered after transcription, so that the amino aids specified by the altered mRNA are different from those encoded by the genes.

What is trans splicing?

Process of splicing together exons from two or more pre-mRNAs.

Why is the addition of the poly A tail essential in transcription?

The addition of the poly-A tail protects the mRNA from degradation by exonucleases

What are the three primary regions of mRNA? Are all these regions Translated? What do they do?

Three regions of mRNA 1. 5' untranslated region (5' UTR or leader) - serves as a ribosome-binding site - contains the Shine-Dalgarno sequence in bacteria and 2. Protein-coding region - contains codons that specify the amino acids sequences of the protein. 3. 3' untranslated region (3' UTR or trailer) - sequence of nucleotide that do not code for anything, but help with stability of the molecule and regulation of translation . Only the protein coding region is translated into proteins.

Does Alternative Splicing occur in Humans?

yes, 95% of all human genes undergo alternative splicing.