DNA and protein synthesis

genome

• A genome is the complete set of genes present in a cell

• The full genome is present within every cell of an organism, but not every gene is expressed in every cell; the genes that are expressed depend on the cell type

proteome

• The proteome is the full range of proteins that a cell can produce

• The proteome is usually larger than the genome of an organism

  • This is due to the large amount of post-translational modification of proteins (often in the Golgi apparatus)

  • Each gene is also capable of producing multiple different proteins via alternative splicing

RNA nucleotides

• Like DNA, the nucleic acid RNA (ribonucleic acid) is a polynucleotide – it is made up of many nucleotides linked together in a long chain

• Both contain the nitrogenous bases adenine (A), guanine (G) and cytosine (C)

• RNA nucleotides never contain the nitrogenous base thymine (T); they contain the nitrogenous base uracil (U)

• RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose)

RNA molecules

• RNA molecules are only made up of one polynucleotide strand (they are single-stranded)

• Each RNA polynucleotide strand is made up of a sugar-phosphate backbone and exposed unpaired bases

  • Alternating ribose sugars and phosphate groups link together, with the nitrogenous bases of each nucleotide projecting out sideways from the single-stranded RNA molecule

examples of RNA molecules

• messenger RNA (mRNA)

• transfer RNA (tRNA)

• ribosomal RNA (rRNA)

mRNA

• mRNA is a transcript copy of a gene that encodes a specific polypeptide

  • It carries the genetic code from DNA in the nucleus to the ribosomes, where it is used to synthesise proteins during translation

tRNA

• tRNA has a folded shape, despite looking like it is double-stranded it is single-stranded

  • There are hydrogen bonds between some of the complementary bases holding the single strand together in certain regions

role of tRNA in protein synthesis

• The specific anticodon found on the tRNA molecule is complementary to a specific triplet of bases on an mRNA molecule

• This specificity allows amino acids to bind to a specific region of the tRNA molecule in their correct order

stages of protein synthesis

• Transcription – DNA is transcribed, and an mRNA molecule (messenger RNA) is produced

• Translation – mRNA is translated, and an amino acid sequence is produced

process of transcription

• Transcription occurs in the nucleus of the cell

• A section of the DNA molecule unwinds; this section contains the gene from which a particular polypeptide (protein) will be produced

• Unwinding occurs due to the breaking of hydrogen bonds between the complementary base pairs; the DNA is said to be 'unzipped'

  • This reaction is catalysed by the enzyme helicase, as in DNA replication

• The gene to be transcribed is now exposed

• A complementary copy of the code from the gene is made by creating a molecule of mRNA

  • Free activated RNA nucleotides pair up (via hydrogen bonds) with their complementary DNA bases on the ‘unzipped’ DNA molecule; this DNA strand is called the template strand

    • The strand of the DNA molecule that is not transcribed is called the non-template strand or the non-transcribed strand

    • The base sequence of the non-transcribed strand will be the same as the base sequence of the mRNA transcript, but with uracil replacing thymine

  • The sugar-phosphate groups of these RNA nucleotides are then bonded together by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule

• When the gene has been transcribed, the mRNA molecule is complete, the hydrogen bonds between the mRNA and DNA strands break, and the DNA molecule re-forms into its double helix strcuture

• The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope

the role of RNA polymerase

• RNA polymerase moves along the template strand in the 3' to 5' direction

  • This means that the mRNA molecule grows in the 5' to 3' direction

• Because the mRNA is formed by complementary pairing with the DNA template strand, the mRNA molecule contains the same sequence of nucleotides as the DNA coding strand (although the mRNA will contain uracil instead of thymine)

eukaryotic transcription

• The genome within eukaryotic cells contains many non-coding sections

• Non-coding DNA can be found:

  • between genes, as non-coding multiple repeats

  • within genes, as introns

• During transcription, eukaryotic cells transcribe the whole gene (all introns and exons) to produce pre-mRNA molecules

  • Pre-mRNA contains the introns and exons of a certain gene

splicing

• Before the pre-mRNA exits the nucleus, splicing occurs:

  • The non-coding sections are removed

  • The coding sections are joined together

  • The resulting mRNA molecule carries only the coding sequences (exons) of the gene

  • mRNA (after transcription) contains only exons and exits the nucleus before joining a ribosome for translation

    • This is called mature mRNA

alternative splicing

• The exons (coding regions) of genes can be spliced in many different ways to produce different mature mRNA molecules through alternative splicing

  • Different combinations of exons are joined together from the same pre-mRNA transcript

• This means that a single eukaryotic gene can code for more than one polypeptide chain

• This is part of the reason why the proteome is much bigger than the genome

prokaryotic transcription

• The transcription process is simpler and more direct in prokaryotic cells (such as bacteria) than in eukaryotic cells:

  • There is no pre-mRNA stage

    • In prokaryotes, transcription produces mRNA directly from the DNA template

    • This is because prokaryotic genes do not contain introns, so there is no need for splicing

  • Transcription and translation are coupled

    • In prokaryotes, translation can begin while transcription is still in progress, because both processes occur in the cytoplasm (prokaryotes do not have a nucleus)

    • This allows for rapid protein synthesis

stages of translation

• This stage of protein synthesis occurs in the cytoplasm of the cell

• After a transcribed mRNA molecule leaves the nucleus, it attaches to a ribosome

• Within the cytoplasm, there are free molecules of tRNA (transfer RNA)

• tRNA has an anticodon (a triplet of unpaired bases) at one end and a site for a specific amino acid at the other

  • There are at least 20 types, each with a unique anticodon and corresponding amino acid

• The tRNA molecules bind with their specific amino acids (found within the cytoplasm) and bring them to the mRNA molecule on the ribosome

• The anticodon on each tRNA molecule pairs with a complementary triplet (codon) on the mRNA molecule

• Two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid they are each carrying, side by side

• A peptide bond is then formed between the two amino acids

  • The formation of a peptide bond between amino acids requires energy, in the form of ATP

  • The ATP needed for translation is provided by the mitochondria within the cell

• This process continues until a ‘stop’ codon on the mRNA molecule is reached – this acts as a signal for translation to stop; the amino acid chain coded for by the mRNA molecule is complete

• This amino acid chain then forms the final polypeptide