Friday January 22, 1999
Announcements: If you have just added the course then you can go to the web and listen to past lectures, but be sure to buy the note pack from the Student Book Store down town. If you are lefty, have long legs or have a disability be sure to sign the sheet in the front of class so that for the exam next Friday (Jan 29) you can be seated appropriately because there are assigned seats.

Lecture notes:

Every 3 nucleotides (base triplet) specifies an amino acid to be added to the growing polypeptide chain.

61 of the 64 triplets code for amino acids. 3 are stop signal. UAA is a stop signal

These triplets are called codons.

There are only 2 amino acids that have only one codon: methionine (AUG)
tryptophan (UGG)

• Methionine is also the START signal for protein synthesis. (AUG)

These same codes are used (with only a few minor exceptions) in bacteria, fungi, plants and animals.

There are 20 common amino acids that appear in proteins. These same amino acids appear in all proteins in all forms of life (and viruses).

• The differences in R groups and how amino acids are put together make possible the incredible diversity of proteins found on Earth.

Amino acids "condense" in the ribosome to form proteins (Fig. 2.25, p.31)

The bond between amino acids is called a peptide bond, so amino acids grouped together are called polypeptides.

Dietary: Essential and Non-Essential Amino Acids.
Or bodies can make or intercovert many amino acids. Those who cannot are called essential. We must get
these amino acids from the diet.

To make proteins you have to start with instructions.
The instructions start in the nucleus encoded in "genes" on the chromosomes.
The instructions on the genes are transferred to the factory (ribosomes) in the cytoplasm as mRNA strands.

Replication: making an exact copy of DNA during cell division.

Transcription: making a mRNA (messenger RNA) copy from a piece of DNA (a gene)

Translation: turning coded message on mRNA into a sequence of amino acids.

The mRNA: 1. Always has special messages at the beginning and end that signal start and stop.
2. A lot more information is transcribed that is needed for the protein sequence. There is some editing
done. (introns, exons)
3. The final piece of "mature" mRNA transcript the goes out the nucleus into the cytoplasm of the cell.

Now that we have the message, how do we make the protein? We need 1) a "gofer" and 2) a work station. TRNA is the "gofer" and rRNA in the form of ribosomes is the work station.

tRNA - (see Fig. 12.7 p.167)

1. A piece of RNA that is folded back on itself into loops and double stranded regions.
2. It has one open end with a tail where the amino acid is attached.
3. It has hairpin loops, one of which contains the anticodon.

The anticodon is the complementary triplet to the triplet codon which codes for the amino acid.

RRNA arranges itself with proteins to form a 2 piece protein factory called a ribosome.

1. A ribosome latches onto the mRNA. (Initiation)
2. A tRNA molecule arrives with the first amino acid needed attached to it.
3. The anticodon in the tRNA sticks to the codon on the mRNA.
4. The ribosome helps hold onto the first amino acid while the next tRNA molecule brings the next amino acid needed.
5. The first 2 amino acids are hooked together with a "peptide bond". (condensation result in peptide bond)
6. The ribosome shoves the 1^st tRNA molecule out and moves over one codon length.
7. The next tRNA/amino acid complex hooks up, is linked to the second amino acid, the shift occurs, the old tRNA is expelled, the new one arrives and so on… (chain elongation)
8. When a stop codon is reached, chain elongation ceases the ribosome subunits fall apart and protein is released. (termination)

DNA------------------>RNA----------------->PROTEINS
(transcription) (translation)

Primary structure: the sequence of amino acids.

Secondary structure: the pattern of bonding that results in helical coil or sheets.

Tertiary structure: folding and other arrangements brought about by the characteristics of the "R" groups of the amino
acids. This occurs within a single polypeptide chain.

Quaternary structure: interactions between separate polypeptide chains that make up a functioning protein.

Denaturation: is the disruption of the secondary, tertiary, and quaternary (if there is one) structures of protein. If severe enough, it can destroy functional ability of the protein.

Agents that cause denaturation: heat, acids/bases, alcohol, mechanical force.