lecture 36 chapter 39 the genetic code

Proofreading by the aminoacyl tRNA synthetase

increases the fidelity of protein synthesis

Characteristics of the genetic code are:

1. Three nucleotides, called a codon, encode an amino acid. 2. The code is non-overlapping. 3. The code has no internal punctuation. 4. The code is directional - it is read in the 5' to 3' direction. 5. The code is degenerate: some amino acids are encoded by more than one codon. There are 64 codons. 61 specify the 20 different amino acids. 3 are termination signals referred to as Stop Codons: (UAA, UAG, UGA) 6. The genetic code is nearly universal

General characteristics of tRNA molecules include:1. Each is a single strand of RNA between _____ nucleotides in length. 2. Transfer RNA molecules contain unusual modified bases (methylation, deamination, pseudo-uridylation) such as inosine, methy-Cytidine, Dihydrouridine. 3. The three-dimensional structure of the molecule is ____ 4. In a two-dimensional representation, all tRNA molecules appear as a cloverleaf pattern. The amino acid-accepting region is____ bonds that form stems and loops. 5. The 5' end is ___ 6. The amino acid is attached to _____ 7. The anticodon is in a _____

1.73 and 93 3.The three-dimensional structure of the molecule is L shaped 4. the acceptor stem, which contains the 3' CCA terminal region. Many of the nucleotides are involved in hydrogen 5. phosphorylated and the 5' terminal residue is usually pG 6.a hydroxyl group of adenosine in the CCA region of the acceptor stem.. loop near the center of the sequence.

In E. coli, the ribosome sediments at

70S and is composed of two subunits, a large 50S subunit and a smaller 30S subunit. • The 50S subunit is composed of 34 proteins and a 23S RNA as well as a 5S RNA. • The 30S subunit contains 21 proteins and a molecule of 16S RNA. • 20,000 ribosome are present in a bacterial cell, a fourth of its mass.

Generalizations of the codon-anticodon interactions are:

Codons that differ in either of the first two nucleotides must be recognized by different tRNA. • The first base of the anticodon determines the degree of wobble. If the first base is inosine, the anticodon can recognize three codons.

Degeneracy in the genetic code

Degeneracy reduces the deleterious effects of mutation • (a silent mutation changes the mRNA but not the encoded protein) • 4 codons specify Glycine • Wild type GGG mutated to GGC specifies the same amino acid: Glycine

Ataxia

Mutations editing activity of alanine tRNA synthetase leads to misincorporation of serine and glycine and causes a form of ataxia - lack of voluntary muscle movements.

Charcot-Marie-Tooth Disease:

Peripheral nerve disorder including degeneration of motor and sensory nerve function that is caused by mutations in genes for Glycine or Tryrosine tRNA synthetases.

Two-thirds of the mass of ribosomes is

RNA, which is critical for the structure and function of the ribosome.

Mutations and Human Disease

Ras mutations in cancer, especially lung, pancreatic and colon cancers • Missense mutations change the normal codon to one that encodes a different amino acid. • Results in a constitutively active Ras GTPase which promotes cancer cell proliferation

Anticodon-Codon Base-pairing

The anticodon forms base pairs with the codon: • By convention, sequences are written in the 5' to 3' direction. • Thus the anticodon that pairs with AUG is written CAU. • Some tRNA molecules can recognize more than one codon.

wobble

The recognition of the third base in the codon by the anticodon

stop codons

UAA UGA UAG

The synthesis of long proteins requires

a low error frequency • Error frequencies of 10-4 allow for the accurate synthesis of even large proteins at a very rapid rate.

Serine

although smaller than threonine, is occasionally linked to tRNAThr because of the presence of the hydroxyl group.

amino acid activation The first step is the formation of _____ The aminoacyl group is then transferred to a specific tRNA recognized by the synthetase. The aminoacyl-AMP never leaves ____

aminoacyl adenylate or aminoacyl-AMP. 2.the active site of the synthetase.

Synthetases

are the true "translators" of the genetic code in that they assign a particular amino acid to a specific tRNA. • Many aspects of the tRNA molecule, in addition to the anticodon, are used as recognition sites by the synthetases to achieve this specificity.

The CCA arm of tRNAthr

can swing into the editing site where the serine is removed. Because threonine is larger than serine, it cannot fit into the editing site. • The double sieve of an acylation site and an editing site increases the fidelity of many synthetases.

Aminoacyl tRNA synthetases

catalyze the activation of amino acids.

Threonyl-tRNA synthetase

contains a zinc ion at the active site that interacts with the hydroxyl group of threonine.

The ribosomal RNA

fold into complex structures with many short duplex regions. • Ribosomal RNA is the actual catalyst for protein synthesis, with the ribosomal proteins making only a minor contribution.

Amino acids are activated by

formation of an ester linkage between the carboxyl group of the amino acid and either the 2' or 3' hydroxyl group of the terminal adenosine of the tRNA, forming an aminoacyl tRNA or charged tRNA.

Threonyl-tRNA synthetase has an editing site

in addition to an active site, to remove a serine inappropriately joined to tRNAThr.

Valine

is similar in overall structure to threonine but lacks the hydroxyl group and thus is not joined to the tRNAThr.

the site of protein synthesis.

ribesome

Each aminoacyl-tRNA synthetase is

specific for a particular amino acid.

Because transcription and translation both occur in the 5'-to-3' direction, bacterial protein synthesis begins before

transcription is complete. • Several ribosomes can translate an mRNA molecule at the same time, forming polyribosomes or polysomes

The Genetic Code

transmits information from nucleic acids to protein molecules • Protein synthesis is a process of translation. • Nucleic acid sequence information is translated into amino acid sequence information. • The genetic code links these two types of information.

Wobble: Inosine base-pairing

• Inosine in the anticoding is formed by deamination of adenosine • Inosine can form wobble base-pairs with C, U, and A.