1. Proteins that bind to DNA often have common structural features. (Common structural features shared between proteins are called domains) Many of them have a feature known as a 'zinc finger,' A zinc finger arises from zinc interacting with cysteine and histidine, causing a portion of the polypeptide chain to extend, much like a finger. Another common structural feature is a leucine zipper, which involves placement of leucines every seven residues in a protein. The leucines interact with similarly spaced leucines (hydrophobic interactions) in another protein. A third common structural feature of DNA binding proteins is called Helix-turn-Helix.

2. Splicing is a process that occurs in eukaryotic cells only in which RNAs have sections removed (introns) and the remaining sections joined (spliced) together. The remaining sections after splicing are called exons. Splicing allows eukaryotic cells to mix and match exons and create different proteins in different tissues from the same DNA.

3. tRNAs are modified chemically in both prokaryotes and eukaryotes. mRNAs are not modified in prokaryotes, but in eukaryotes, they are capped at the 5' end and have a poly-A "tail" at the 3' end.

End of material for exam 2 HERE

Highlights Translation

1. Translation is the process whereby proteins are synthesized from the information contained in mRNAs. We can think of protein synthesis (translation) as occurring in 4 steps - 1) activation of amino acids; 2) chain initiation (start of translation); 3) chain elongation; and 4) chain termination.

2. The information in mRNA is encoded as the Genetic Code. The genetic code specifies how nucleic acid information is converted to make a protein. Information in mRNA is encoded in groups of three nucleotides (called a codon or a triplet). There are 64 possible codons. 61 of them code for amino acids. Three of them (UAA, UGA, UAG) tell the ribosome to STOP translating. A start codon (AUG) is among the 61 above.

3. The genetic code is universal (all cells use the same code - only very rare exception have very slightly altered codes)

4. Codons you should know include the codon that always starts translation (AUG - specifies methionine) and three codons that STOP translation - UAA, UAG, UGA.

5. The third base of many (but not all) codons is unnecessary for identifying an amino acid. For example, glycine can be coded by GGG, GGA, GGC, and GGU. This could be written as GGX, where X stood for any base. The third base of a codon is therefore called the 'wobble' position of a codon, as it is not very specific. Note that in translation, the anticodon of the tRNA is base paired to the codon on the mRNA in an antiparallel fashion. Thus, the wobble base of the anticodon is the one at the 5' end of the anticodon.

6. tRNAs function to carry amino acids to the ribosomes for incorporation into proteins during the process of translation.

7. Amino acid activation can be thought of as the first step in the process of translation. Amino acids are activated by covalently linking them to the 3' end of specific tRNAs. Enzymes called aminoacyl-tRNA-synthetases catalyze the covalent linkage of amino acids to tRNAs. There is one aminoacyl-tRNA synthetase for each amino acid.

8. Amino acids are not linked randomly to tRNAs. Rather, aminacyl-tRNA-synthetases "look" at the anti-codon of a tRNA to decide which amino acid to put on the 3' end of each tRNA. In this way, each tRNA with a particular anti-codon always has the same amino acid on the end of it. Therefore when a tRNA base pairs with a messenger RNA in translation, it is always bringing the right amino acid to be incorporated into the growing protein chain.

9. The first amino acid put into proteins is methionine, since that is the amino acid specified in the genetic code for the first codon of a protein - AUG. Prokaryotes use a modified form of methionine for the first amino acid. It is known as fmet (formyl-methionine). fmet is used ONLY as the first amino acid of a protein. When AUG appears in the middle of a coding region of an mRNA, methionine (not fmet) is put into the protein. The formyl group is put onto methionine after the methionine is attached to the tRNA.

10. Translation initiation requires 1) an mRNA; 2) a start codon in the mRNA - AUG; 3) the 30S ribosomal subunit; 4) the 50S ribosomal subunit; 5) proteins called initiation factors; and 6) GTP.

11. During initiation of translation, the first tRNA (linked to fmet) forms base pairing between its anti-codon and the codon of the mRNA. A sequence known as the Shine-Dalgarno sequence in the mRNA (in prokaryotes only) helps the ribosome to properly align the mRNA in the ribosome. The Shine-Dalgarno sequence forms a base paired region with the 16S rRNA of the 30S subunit of the ribosome.