26. Gene Function

  1. Define: gene, codon, reading frame
  2. List the major pieces of evidence that led to the hypothesis that DNA influences the production of proteins.
  3. Define and describe the process of transcription.
  4. Define introns and exons. Discuss their occurrence and possible roles.
  5. Summarize the sequence of events that occur in translation.
  6. Describe the functions of mRNA, tRNA, and rRNA.
  7. Distinguish between the processes of initiation, elongation, and termination in protein synthesis.

Genes

Central Dogma of Molecular Biology

Central Dogma of Molecular Biochemistry with Enzymes

Flow of information in cells. DNA serves as a template for copying itself (replication). DNA can also serve as a template for RNA (transcription). RNA is decoded into amino acids to generate proteins (translation). Credit Daniel Horspool (CC-BY-SA 3.0)

DNA was described as a molecule consisting of 2 anti-parallel strands in a double helix by Francis Crick and James Watson. The elegant model illustrated the intrinsic redundancy that made DNA a suitable data storage vessel for genetic information. Francis Crick later posited a notion of how this information went from storage to an actual program that runs cells. Crick first posited it as a “sequence hypothesis”. This idea of information flow is called the Central Dogma of Molecular Biology. DNA stores the information that is expressed as an intermediate message of RNA. This RNA is then translated in amino acids to yield proteins.

Transcription

DNA is simply a storage vessel of genetic information. It sits in the nucleus and must be called upon through a process of transcription where an enzyme called RNA Polymerase“reads aloud” the stored information into a molecule called messenger RNA (mRNA). Since DNA is double-stranded in an anti-parallel fashion, we automatically know the sequence of the second strand by knowing the first. The mRNA is made through complimentary base-pairing to the template strand, which is the reverse complement of the coding strand. The coding strand is the strand that reads identical in sequence to the mRNA with the exceptions of T’s being replaced by U’s.
Simple transcription initiation1
Simple transcription elongation1

Translation

RNA-codonThis coding strand is later decoded by the ribosomes with the help of transfer RNA’s tRNA‘s) that act as a decoder of the information and protein assembler in a process called translation. The ribosome scans along the mRNA and recognizes nucleotides in batches of 3 . These batches of 3 can be translated into an amino acid and is known as a codon. Since there are 4 types of bases and they are read as groups of 3, there are 43 (or 64) combinations of these codons. However, there are only 20 amino acids used to build proteins. This indicates that there is room for redundancy. Three of these codons tell the ribosome to stop, like a period in a sentence. These are called stop codons. There is one special codon that performs double duty: ATG. The codon (ATG) that encodes the amino acid Methionine also acts as a start codon that tells the ribosome where to start reading from. Like nucleic acids, proteins have a polarity and are synthesized in an amino to carboxyl direction. We abbreviate this by terming the beginning of the protein sequence, N-terminal, and the ending of the sequence as the C-terminal.

Ribosome mRNA translation en

Ribosomes are large complexes of enzymes that coordinate the decoding of mRNA into amino acids to generate proteins.


RNA-codons-aminoacids

Aminoacids table

The standard genetic code.

Complementation

George Beadle and Edward Tatum first described the concept that each gene corresponded to an enzyme in a metabolic pathway by exposing the yeast Neurospora crassa to mutagenic conditions (Beadle & Tatum, 1941). Following these procedures Joshua Lederberg continued these studies with Tatum where they generated two mutants strains in Escherichia coli . These bacteria were auxotrophs, unable to generate some basic nutrients necessary to sustain their growth.  The two strains were described as met bio Thr+ Leu+ Thi+ (Strain A) and Met+ Bio+ thr leu thi (Strain B). Strain A can sufficiently synthesize the amino acids threonine, leucine and the cofactor thiamine while deficient in producing the cofactor biotin and the amino acid methionine while the converse was true of Strain B. When either of these two strains were plated onto minimal media, no growth occurred. Supplementing minimal media with methionine and biotin permitted Strain A to grow as normal. When the two strains were mixed together and plated on minimal media, there was growth of bacteria. The two strains were capable of complementing each other in some way as if a sexual exchange of genetic material had occurred (Lederberg & Tatum, 1946).

Bacteria are equipped with all the necessary capacities to replicate DNA. Common bacterial species have bee adapted for use in the lab to carry DNA and propagate it for uses in biotechnology. In addition to chromosomal DNA of the bacterial genome, bacteria also have extrachromosomal DNA called plasmids. These plasmids replicate independently of the bacterial chromosome and can occur in high copy. These circular pieces of DNA are modified in labs to carry specific pieces of DNA so they can be studied or used for expression into proteins. Plasmids can naturally carry important traits, including antibiotic resistance. Plasmids are relatively small, ranging in size from 1000 bases to 1,000,000 bases long (1kb-1000kb).

Plasmid (english)

Bacterial DNA usually exists as a large circular chromosome (red). Plasmids are extrachromosomal and autonomously replicating pieces of DNA (blue).

Through a process called conjugation, bacteria can “sexually” transfer genetic material to another by passing plasmids through a structure called a conjugation pilus.

Conjugation

Conjugation process between a plasmid bearing donor and a plasmid-less recipient. The donor creates a conjugation pilus to create a cytosolic bridge with the donor where the plasmid is replicated into the recipient through the rolling circle method of replication. The recipient then becomes competent to act as a donor.