Genetic Code and Protein Synthesis

• DNA, chromosomes and the genetic code:

  DNA is the molecule that carries the genetic code;

  • in eukaryotes, DNA is found within a nucleus, surrounded by the nuclear envelope
  • The DNA double helix is wrapped around histone proteins to form nucleosomes
  • nucleosomes are then coiled up to form chromatin which is organised into chromosomes
  • the DNA is compact so large amounts can be stored in a small space and organised
• Differences in prokaryotic and eukaryotic DNA:

  • prokaryotic DNA isn't in a nucleus - it is free-floating in the cytoplasm, whereas eukaryotes have a nucleus containing DNA
  • prokaryotic DNA is shorter, circular and not wrapped around histone proteins, whereas eukaryotic DNA is longer, linear and is wrapped around histone proteins
  • prokaryotic DNA is condensed by supercoiling and eukaryotic DNA is condensed by the formation of nucleosomes and supercoiling
  • prokaryotic DNA is found in a main chromosome and smaller structures called plasmids, whereas eukaryotic DNA forms several chromosomes but no plasmids
• DNA of organelles:

  • the mitochondria and chloroplasts on eukaryotic cells also contain DNA which, like the DNA of prokaryotes, is short, circular and not associated with protein
• Genes:

  • a gene is a section of DNA that codes for one polypeptide, and polypeptides in turn determine the nature and development of organisms
  • a gene can also code for a functional RNA (including ribosomal ENA and tRNAs). A gene occupies a fixed position, called a locus, on a particular chromosome
• Homologous chromosomes:

  • individuals have two copies of each gene. Each gene is found at the same position (locus) on a pair of homologous chromosomes
  • homologous chromosomes are of the same length and contain the same genes
• Alleles:

  • alleles are two or more alternative forms of a gene that arise by mutation
• Genome:

  • the genome is the complete set of genes in a cell, including those in mitochondria and/or chloroplasts
• Proteome:

  • the proteome is the full range of proteins produced by the genome
• The genetic code:

  • DNA carries the genetic code to allow the cell to make proteins
  • as enzymes are proteins, and enzymes control all the chemical processes going on inside cells, proteins are vital to a cell's functions
  • the only difference between DNA strands is their length and sequence of bases
• Features of the genetic code:

  the code in DNA is a triplet code, meaning that 3 bases code for one amino acid. The genetic code has 3 important features;

  • the code is universal. A given triplet specifies the same amino acid in all organisms
  • the code in non-overlapping. The bases in the DNA code are only read once (in 1 direction) and the triplets do not share bases
  • the code is degenerate. This means that more than one triplet can code for the same amino acid
• Protein structure:

  • the specified sequence of bases of a gene controls the sequence of amino acids in proteins (primary structure)
  • the specified tertiary structure and function of that protein is formed as bonds form between the R-groups of the different amino acids
  • so, differences in the base sequence of alleles of a single gene (e.g due to mutation), may result in non-functional proteins such as non-functional enzymes
• Non-coding DNA:

  • in eukaryotic cells, much of the DNA in the nucleus does not code for the synthesis of proteins
  • there is some non-coding DNA between genes. This contains multiple repeats of base sequences. These are called variable number tandem repeats (VNTR), and for every individual the number and length of core sequences is unique
• Exons and introns:

  • eukaryotic DNA also contains non-coding sections called introns within genes. All the sections within the gene that do code for polypeptides are called exons
  • exons are sections of DNA that are expressed to produce proteins and introns are intervening sequences of junk DNA, the function of which is not fully understood
  • prokaryotes have no introns in their DNA
• Comparison of DNA and RNA:

  • DNA is double-stranded whereas RNA is single-stranded
  • DNA contains thymine whereas RNA contains uracil
  • DNA contains deoxyribose sugar whereas RNA contains ribose sugar
  • DNA is found in the nucleus whereas RNA is found in the nucleus and cytoplasm
  • both DNA and RNA are made of nucleotides
  • both DNA and RNA contain adenine, guanine and cytosine
• The role of RNA:

  there are 3 different types of RNA involved in synthesis of proteins;

  • messenger RNA (mRNA)
  • ribosomal RNA (rRNA)
  • transfer RNA (tRNA)
• Messenger RNA (mRNA):

  • messenger RNA molecules may consist of thousands of nucleotides in a single linear strand
  • mRNA is formed by transcription of a gene in DNA in the nucleus. It is complementary to the DNA in its base sequence
  • mRNA is variable in length, depending on the length of the gene from which it has been copied. As it is only a copy of one gene, it will be much shorter than DNA
  • an amino acid is coded for by a triplet of bases on mRNA called a codon. mRNA is single stranded and therefore has unpaired bases and so is easily broken down in the cytoplasm; it only needs to exist temporarily until the protein is manufactured
• Ribosomal RNA (rRNA):

  • rRNA together with protein forms ribosomes, which are the sit of mRNA translation and protein synthesis
  • rRNA is coded for by numerous genes in many different chromosomes
• Transfer RNA (tRNA):

  • tRNA is a relatively small molecule that is made up of around 80 nucleotides. It is a single strand which folds back on itself
  • the tRNA molecule forms hydrogen bonds within complementary sections of the molecule. These help to stabilise the molecule. One end of the chain attaches to an amino acid
  • there are several types of tRNA, each able to carry a single specific amino acid. At the base of the tRNA molecule is a sequence of 3 bases, known as an anticodon
  • for each amino acid carried there is a different sequence of bases on the anticodon of tRNA
• Protein synthesis:

  • proteins are made up of a polypeptide chain. The DNA in the nucleus contains the instructions to make all the organism's proteins
  • which proteins are manufactured depends on the activities of the particular cell
• Transcription overview:

  • transcription takes place in the nucleus of the cell and involves the formation of pre-mRNA, that is a complementary sequence of bases to the DNA
  • this will carry the genetic code out of the nucleus to the ribosome, therefore DNA never has to leave the nucleus so there is less chance it will be damaged
• RNA processing overview:

  • RNA processing takes place in the nucleus so that non-functioning sequences of bases are spliced from the pre-mRNA to form mRNA
  • the mRNA then leaves the nucleus and attaches to a ribosome
• Translation overview:

  • translation which occurs on ribosomes, involves the translation of the mRNA message into a specific sequence of amino acids to form a polypeptide
• Transcription:

  • transcription in eukaryotes is the process of making pre-mRNA using part of the DNA as a template
  • a portion of the gene to be transcribed is represented here as the separated strands of DNA with their bases exposed
• Transcription:

  • the two DNA strands are separated by DNA helicase which breaks the hydrogen bonds
  • one strand of the DNA acts as a template upon which pre-mRNA is built - this template strand is sometimes referred to as the DNA sense strand
  • free RNA nucleotides line up against the DNA template by complementary base pairing
  • the adjacent RNA nucleotides bond together to form a pre-mRNA molecule carrying a sequence of bases that is complementary to that on the sense strand of the DNA molecule
  • RNA polymerase catalyses the formation of phosphodiester bonds between the RNA nucleotides, forming the sugar-phosphate backbone of the mRNA molecule
• Splicing:

  • in the pre-mRNA in eukaryotic cells the introns are removed by enzymes and other molecules before the mRNA moves into the cytoplasm
  • the remaining exons are joined together in a number of different combinations. This is known as splicing
  • following splicing, mRNA molecules leave the nucleus through the nuclear pores
  • introns stay in the nucleus and exons exit the nucleus (they are expressed)
• Transcription in prokaryotes:

  transcription is different in prokaryotes;

  • prokaryotic genes do not contain non-coding sections (introns), therefore they do not produce pre-mRNA that requires splicing
  • transcription in prokaryotes does not occur in a nucleus
• Translating the mRNA code - using a codon chart:

  • the codon chart shows the amino acid coded for by each mRNA codon
  • often it is only the first 2 bases of the triplet that are specific for a particular amino acid, and any third base will do. This also reduces the chance that a change in the bases will alter the function of the polypeptide
  • there are 3 stop codons. These indicate the end of a section of mRNA, after which point translation stops
  • the codon for methionine, AUG, is used as a start codon. This means that the polypeptide normally start with a methionine group when they are freshly translated. It is often removed in the processing stage that converts the polypeptide into a functional protein
• Translation: and the two amino acids

  • a ribosome binds to mRNA
  • a specific tRNA molecule with a complementary anticodon to the first codon on the mRNA arrives at the ribosome. The tRNA is carrying a specific amino acid
  • a second tRNA molecule joins in the same way and the 2 amino acids being carried bind in a condensation reaction, forming a peptide bond. This process requires energy from ATP
  • a ribosome can only hold 2 tRNA molecules at one time. The first tRNA molecules leaves the ribosome, leaving its amino acid behind
  • the ribosome moves down the mRNA and the cycle and the cycle repeats until a stop codon on on mRNA is reached
  • a polypeptide chain is produced which detaches from the ribosome
• Polypeptide chains:

  the polypeptide chain (primary structure) can be then;

  • folded into further secondary and tertiary structures in the rough endoplasmic reticulum
  • modified/packaged into vesicles by the Golgi apparatus