• Formation of peptide bonds
• RNA and ribosomes
• Genetic Code
• DNA Repair
• Elementary science (some principles)

Formation of peptide bonds

There are plenty of Web sites that introduce messnger RNA, ribosomes and other components of the protein biosynthetic apparatus but they sometimes skate over the basic chemistry.

Peptide bonds are formed by an enzyme calatalysed reaction between aminoacyl-tRNA and polypeptidyl-tRNA. Each of the 21 amino amino acids incorporated into nascent polyppeptid chains has its own transfer RNA ("tRNA") molecules (typically a small family of these). tRNAs are typically of 70-80 nucleotides in length and contain several modified nucleosides.
First we need to attach an amino acid to an appropripate (cognate) tRNA. As an example, threonine is attached by an ester link to the 3'-end of a its tRNA by a reaction that in summary is:

Thr + ATP + tRNA^Thr → Thr-tRNA^Thr + AMP + PP_i The reaction takes place in two stages, both catalysed by the same enzyme, aminoacyl-tRNA synthetase (threonyl tRNA synthetase in this case). The two stages (picture below) are ① formation of an aminoadenylate intermediate and ② the formation of aminoacyl-tRNA.
So now we can imagine a population of aminoacyl-tRNA molecules and a growing peptide chain with the "most recent tRNA to have been added". The fundamemtal reaction is one we have

ester + amine → amide + alcohol

polypeptidyl-tRNA + aminoacyl-tRNA → polypeptide+1-tRNA + tRNA

• 2ndary structure
• Pseudoknots
• tRNA
• rRNA
• ribozymes
• ribosomes
• peptide bond formation
• ribosome structure/function including animations

Secondary structure elements

        				   A A
(1)  5'....A C A A G A C A C G A C A C G A     G
     3'....U G U U C U G U G U U G U G C U     A
        				   G A

                                           A A
(2)  5'....A C A A G A C A C G A C A C G A     G
     3'....U G U U C U G U G U U G U G C U     A
                 A A                       G A
                C   C
                  A

                   G A                         A A
(3)  5'....A C A A     G A C A C G A C A C G A     G
     3'....U G U U     C U G U G U U G U G C U     A
                  A   A                        G A
                  C   C
                    A

(1) is a stable helix even though it contains a G:U base pair: G:C and A:U stabilise the helix; G:U has no stabilising or destabilising effect.
(2) and (3) are both less stable but (2) is better than (3) because in (2) the "upper strand" still has base stacking interactions (between an A and a G).

Pseudoknots

Transfer RNA

                                A 3'(OH)
                                C
                                C
                                73
                      (P)5' 1 . 72  acceptor
                            2 . 71  stem
                            3 . 70
                            4 . 69
                            5 . 68  T--stem-----loop
                            6 . 67
      D--loop---stem        7 . 66                C 59  
                           U      65 64 63 62 61       A
         15 A             9        .  .  .  .  .       
       16     13 12 11 10                               57
      17       .  .  .  .         49 40 51 52 53      C
       G                                          T Ψ
       G      22 23 24 25          48
         20 A            26           47
                           27 . 43 44    46
                           28 . 42    45   variable loop
            anticodon      29 . 41
               stem        30 . 40
                           31 . 39
                          32     38
            anticodon      U     37
               loop         34  36
                              37

Ribosomes

More-or-less a complete issue of Science2000 289: 878... is devoted to recent developments. Here is the text of the summary by T R Cech:
The amino acids we obtain by digestion of steak, salmon, or a lettuce salad are loaded onto transfer RNAs (tRNAs) and rebuilt into proteins in the ribosome, the cell's macromolecular protein-synthesis factory. The bacterial ribosome is composed of three RNA molecules and more than 50 proteins. Its key components are so highly conserved among all of Earth's species that a similar entity must have fueled protein synthesis in the common ancestor of all extant life. Although the chemical reaction catalyzed by the ribosome is simple--the joining of amino acids through amide (peptide) linkages--it performs the remarkable task of choosing the amino acids to be added to the growing polypeptide chain by reading successive messenger RNA (mRNA) codons. On page 905 of this issue, Steitz, Moore, and colleagues now provide the first atomic-resolution view of the larger of the two subunits of the ribosome. From this structure they deduce on page 920 that RNA components of the large subunit accomplish the key peptidyl transferase reaction. Thus, ribosomal RNA (rRNA) does not exist as a framework to organize catalytic proteins. Instead, the proteins are the structural units and they help to organize key ribozyme (catalytic RNA) elements, an idea long championed by Harry Noller, Carl Woese, and others.
These landmark publications are but the latest chapter in a progression of ribosome structural studies that have spanned four decades. Early electron micrographs of ribosomes in action led to immunoelectron microscopy and ultimately to cryo-electron microscopy images of about 20 Å resolution . Proteins were also located within the ribosome by neutron scattering. However, to achieve atomic resolution, x-ray crystallography is required, a daunting task given the huge size (2.6 x 106 daltons) and asymmetry of the ribosome. The pioneering crystallization of ribosomes from the bacterium Haloarcula marismortui in the 1980s by Ada Yonath and H. G. Wittmann provided the first rays of hope, but it is only in the past few years that crystal structures have been determined for the large subunit (5 Å resolution) (3e small subunit (5.5 Å resolution) , and the whole ribosome complexed with tRNAs (7.8 Å resolution)
Now, at 2.4 Å, almost the entire chain of the 23S rRNA and its tiny 5S rRNA partner, totaling 3043 nucleotides, have been fitted into the electron density map of the H. marismortui large ribosomal subunit. The RNA secondary structure (intramolecular base-pairing pattern) of the large-subunit rRNA had been determined previously , and is present as predicted in the x-ray structure. In addition, a large number of unpredicted RNA tertiary structure interactions are now seen. Overall, the RNA forms a huge single mass of tightly packed helices, not six discrete domains connected by floppy linkers as a naïve observer might predict from looking at the secondary structure diagram.
Where, then, are all of the proteins, and what is their function? The globular domains of 26 proteins are found largely on the exterior of the subunit (see the figure). Twelve of these proteins have unusual snake-like extensions, devoid of tertiary structure and in some cases even secondary structure, and an additional protein is entirely extended; their shapes are molded by their interactions with the RNA. From these pictures, and from what is known about protein cofactors that facilitate the action of some other ribozymes, it is likely that these ribosomal proteins buttress, stabilize, and orient the otherwise floppy RNA into a specific, active structure.
The original contains references and links removed here. Here is the picture from Cech's article:

.... and the original text.....
A ribosome's true colors. (Top) The large subunit of the ribosome seen from the viewpoint of the small subunit, with proteins in purple, 23S rRNA in orange and white, 5S rRNA (at the top) in burgundy and white, and A-site tRNA (green) and P-site tRNA (red) docked according to. (Bottom) The peptidyl transfer mechanism catalyzed by RNA. The general base (adenine 2451 in Escherichia coli 23S rRNA) is rendered unusually basic by its environment within the folded structure; it could abstract the proton at any of several steps, one of which is shown here.

Compararable detail for the smaller 30S subunit can be found in the 21^st September 2000 issue of Nature The editorial reads:
The ribosome is the protein factory of the cell, translating the genetic information encoded in messenger RNA into proteins. In bacteria, the ribosome is made up of a large and a small subunit known as the 50S and 30S subunits respectively.
The structure of the small, 30S, ribosomal subunit of the bacteria Thermus thermophilus is revealed at a resolution of 3 Å in the journal Nature. In a second article, functional insights gained from this structure are described, and the structure of the 30S subunit interacting with antibiotics, which can interfere with ribosomal decoding and translocation, is presented.
The ribosome has been intensively studied for the last 40 years and, as James Williamson says in an accompanying News and Views article, the structure, "finally provides a face to players that have long been known by their functions."

One set of views of the 30S subunit and its legend are below.

Figure 2. Overview of the 30S structure.
a, Secondary structure diagram of 16S RNA (modified with permission from http://www.rna.icmb.utexas.edu/CSl/2STR/Schematics/e.coli16s.27.5.5.schem.ps; see also ref. 21), showing the definition of the various helical elements used throughout the text. The numbering and diagram correspond to the E. coli sequence. Red, 5' domain; green, central domain; orange, 3' major domain; cyan, 3' minor domain.
b, Stereo view of the tertiary structure of 16S RNA from our refined model, showing the 50S or 'front' view, with the same colouring for the domains. H, head; Be, beak; N, neck; P, platform; Sh, shoulder; Sp, spur; Bo, body.
c, d, Front (50S) and back sides of the 30S. Grey, RNA; blue, proteins.

Structure and function animation from MRC Cambridge including excellent animations of the phases of protein biosynthesis.

TOP (of this section).

The phrase "genetic code" has been misused to mean a genome (for example). Rather it is the relationship of the sequence of mRNA (or the + or non-transcribing strand) of DNA. The code is a non-overlapping triplet (like a language with only 3-letter words). After the general features of the code were established, the code itself was established in the 1960s by groups led by H.G. Khorans and Marshall Nirenberg. They shared a Nobel prize with Robert Holley who was the first to sequence a tRNA molecule and identify an anticodon. The general nature of the Genetic code is that it is a 3D array which cannot easily be represented on a flat sheet of paper (or computer screen) but is easily represented as such in computer software (this speeds up the process of "looking up the code"):

  

	U	C	A	G
U	F F L L	S S S S	Y Y ✳ Q in some ciliates ✳ Q in some ciliates	C C ✳ U W (mycoplasmas, mitos...) W	U C A G
C	L T in yeast mitos. L  ditto L ditto (below also) L  S in C. cyl.	P P P P	H H Q Q	R R R R	U C A G
A	I I I M in several mitos. M	T T T T	N N K K	S S R ✳,G,S in mitos. R ✳,G,S in mitos.	U C A G
G	V V V V	A A A A	D D E E	G G G G	U C A G