Beyond Byssus

1. The marine mussel manufactures the ultimate underwater adhesive, a protein called byssus.



2. DNA is like a book of instructions in each cell.
   
   
   1. The instructions are written in the alphabet of A, T, G, and C. But merely knowing the letters does not tell us how the genes work.
   
   
   
   2. DNA consists of two strands of nucleotides twisted together in a double helix.
      
      
      1. All DNA is composed of nucleotide subunits utilizing the same four bases but the base sequence differs from species to species.
      
      
      
      2. In replication, the two strands unwind to serve as templates for assembly of new complementary strands.
   
   
   3. Each gene is a linear stretch of DNA nucleotides that codes for the assembly of amino acids into a polypeptide chain.
   
   
   
   4. The path from genes to proteins has two steps:
      
      
      1. In transcription, molecules of RNA are produced on the DNA templates in the nucleus.
      
      
      
      2. In translation, RNA molecules shipped from the nucleus to the cytoplasm are used as templates for polypeptide assembly.
   
   
   5. The overall plan is expressed thus:

   DNA-----^{transcription}-----> RNA-----^translation-----> proteins

14.1   How Is RNA Transcribed from DNA?

1. The Three Classes of RNA
   
   
   1. Messenger RNA (mRNA) carries the "blueprint" for protein assembly to the ribosome.
   
   
   
   2. Ribosomal RNA (rRNA) combines with proteins to form ribosomes upon which polypeptides are assembled.
   
   
   
   3. Transfer RNA (tRNA) brings the correct amino acid to the ribosome and pairs up with an mRNA code for that amino acid.


2. The Nature of Transcription
   
   
   1. RNA differs from DNA in two ways:
      
      
      1. RNA uses ribose sugar, not deoxyribose.
      
      
      
      2. RNA bases are A, G, C, and URACIL (U).
   
   
   2. Transcription differs from replication in three ways:
      
      
      1. Only one region of one DNA strand is used as a template.
      
      
      
      2. RNA polymerase is used instead of DNA polymerase.
      
      
      
      3. RNA is single stranded; DNA is double.
   
   
   3. Transcription begins when RNA polymerase binds to a promoter region (a base sequence at the start of a gene) and then moves along to the end of a gene; an RNA transcript is the result.


3. Finishing Touches on mRNA Transcripts
   
   
   1. Newly formed mRNA is an unfinished molecule, not yet ready for use.
   
   
   
   2. mRNA transcripts are modified before leaving the nucleus.
      
      
      1. The 5' end is capped with a special nucleotide that may serve as a "start" signal for translation.
      
      
      
      2. A "poly-A tail" of about 100-200 molecules of adenylic acid is added to the 3' end.
      
      
      
      3. Noncoding portions (introns) are snipped out, and actual coding regions (exons) are spliced together to produce the mature transcript.

14.2   Deciphering the mRNA Transcripts

1. What is the Genetic Code?
   
   
   1. Both DNA and its RNA transcript are linear sequences of nucleotides carrying the hereditary code.
   
   
   
   2. Every three bases (a triplet) specifies an amino acid to be included into a growing polypeptide chain; the complete set of triplets of is called the genetic code.
      
      
      1. Each base triplet in RNA is called a codon.
      
      
      
      2. The genetic code consists of sixty-one triplets that specify amino acids and three that serve to stop protein synthesis.
      
      
      
      3. AUG (specifies methionine) is the "start" codon.
      
      
      
      4. With few exceptions, the genetic code is universal for all forms of life.


2. Structure and Function of tRNA and rRNA
   
   
   1. Each kind of tRNA has an anticodon that is complementary to an mRNA codon; each tRNA also carries one specific amino acid.
   
   
   
   2. After the mRNA arrives in the cytoplasm, an anticodon on a tRNA bonds to the codon on the mRNA, and thus a correct amino acid is brought into place.
   
   
   
   3. The first two bases of the anticodon must pair up with the codon by the usual rules of base pairing (A with U and G with C), but there is some latitude in the pairing of the third base (called the "wobble effect").
   
   
   
   4. A ribosome has two subunits (each composed of rRNA and proteins) that perform together only during translation.

14.3   How Is mRNA Translated?

1. Stages of Translation
   
   
   1. In initiation, a complex forms in this sequence: initiator tRNA + small ribosomal subunit + mRNA + large ribosomal subunit.
   
   
   
   2. In elongation, a start codon on mRNA defines the reading frame; a series of tRNAs deliver amino acids in sequence by codon-anticodon matching; a peptide bond joins each amino acid to the next in sequence.
   
   
   
   3. In termination, a stop codon is reached and the polypeptide chain is released into the cytoplasm or enters the cytomembrane system for further processing.


2. What Happens to the New Polypeptides?
   
   
   1. The three steps just outlined can be repeated many times on the same mRNA because several ribosomes may be moving along the mRNA at the same time (polysome).
   
   
   
   2. Some polypeptides join the cytoplasm's pool of free proteins; others enter the rough ER of the cytomembrane system.

14.4   Do Mutations Affect Protein Synthesis?

1. A gene mutation is a change in one to several bases in the nucleotide sequence of DNA, which can result in a change in the protein synthesized.



2. Common Gene Mutations and Their Sources
   
   
   1. Mutations can result from base-pair substitutions, insertions ("frameshift mutation") deletions.
   
   
   
   2. They can also result when DNA regions (called transposable elements) move form one location to another in the same DNA molecule of a different one.


3. Causes of Gene Mutations
   
   
   1. Mutations are rare, chance events but each gene has a characteristic mutation rate.
   
   
   
   2. Mutations can be caused by mutagens such as ultraviolet radiation, ionizing radiation (gamma and X-rays) and chemicals such as alkylating agents, which act as carcinogens.


4. The Proof is in the Protein
   
   
   1. If a mutation arises in a somatic cell, it will affect only the owner of that cell and will not be passed on to offspring.
   
   
   
   2. If however, the mutation arises in a gamete, it may be passed on and thus enter the evolutionary arena.
   
   
   
   3. Either kind of mutation may prove to be harmful, beneficial, or neutral in its effects.

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