Module 2 - Genetic information in cells

• Initiation, Elongation and Termination in Translation

  1. Termination:

  2. Stop codon is recognised

  3. No tRNA for stop, instead, a release factor comes and binds in it's place with a stop codon

  4. This promotes hydrolysis to separate tRNA and polypeptide

  5. tRNA is recycled, polypeptide free

  6. All components break apart, energy is required and all components including mRNA are recycled
• Polyribosomes in Eukaryotic and Prokaryotic cells

  • Many ribosomes translate to a mRNA molecule simultaneously
  • Each ribosome makes one copy of the same polypeptide
• Asexual Reproduction in Bacteria happens quickly as long as they have enough food and are in a non-toxic environment, they will grow exponentially
• Amino acid sequence


  MET SER PHE VAL SER ASN
• Nucleotide substitution


  Involves replacing one nucleotide with a different nucleotide. This does not change the reading from of a gene, ie the codons that are used to specify the order of amino acids in a polypeptide. Only one codon, and therefore only on amino acid is affected. Due to the redundancy of the genetic code the amino acid will sometimes be unchanged, this is an example of a silent mutation
• Nucleotide insertion


  Involves adding one more nucleotides. Unless a multiple of 3 nucleotides are added, an insertion does change the reading frame so that all codons after that point are changed. All of the Amino Acids added to the polypeptide after that insertion point are likely to be different to the 'correct' ones and hence the protein is unlikely to function as it should. By chance a codon can be changed to a stop codon, causing pre mature termination of translation
• Completing a functional protein, gene structure and how it relates to proteins


  • Putting the amino acids together is the primary structure
  • Post translational modifications:
  • Addition of phosphate groups
  • Addition of Oligosacaccharides (carbohydrates) added on in glycosylation
  • Removal of signal peptide
  • Removal of internal sections
  • In eukaryotes there is also information on intro splicing in the DNA
• Initiation, Elongation and Termination in Translation

  1. Elongation:

  2. Codon recognition - tRNA with 4 amino acid in P site, with new tRNA with anti codon binds with the mRNA that is currently in the P site. tRNA will be established in a site (1 amino acid) GTP is required

  3. Bond formation - Formation of covalent bond between growing peptide and the amino acid. The bond between tRNA and the growing peptide is broken, and the peptide bond is formed with the new amino acid bonded to the new tRNA. All of the polypeptide transfers over. P site and tRNA empty bonds between the tRNA and the amino acid, are high energy because they were made by the aminoacyl tRNA synthetase enzyme. This energy is used to form the new peptide bond catalyst to form the bond making rRNA

  4. Translocation - tRNA is shuffled to the left and recycled, GTP is required for this
• Initiation, Elongation and Termination in Translation


  1. Initiation:

  2. Small ribosomal subunit finds start codon

  3. Regular tRNA is needed to start translation

  4. All proteins start the polypeptide chain with MET sometimes deleted

  5. GTP energy is closely related to ATP

  6. Initiated tRNA has one amino acid, delivered to the P site on a large subunit leaving a site empty for the next tRNA with an amino acid to come
• Sister Chromatids


  Are duplicated (identical) copies of a chromosome, made by DNA replication. They are joined at the centromere and separate to form two distinct chromosomes during anaphase of cell division.
• Replication


  of DNA (to replicate)
• Transcription


  (to transcribe) same language (nucleotides)
• Translation


  (to translate) different language (amino acids)
• DNA synthesis


  Monomers can only attctahc to the 3' end, one by one by DNA polymerase. Nucleotides have three phosphate groups attached, the other 2 phosphates that don't get attached are severed off. The other 2 phosphate groups for an activated monomer that will drive the synthesis of the covalent bonds
• Eukaryotic pre-mRNA transcripts


  1. mRNA produced by transcription = pre-mRNA

  2. It needs more processing before it can be used for translation

  3. mRNA processing in the nucleus:

  4. Spliceosome nucleotides : 5' cap, polyA tail

  5. Functions:

  6. Protects mRNA

  7. Assists in the exit from the nucleus

  8. Assists in ribosome attatchment

  9. 5' cap: Modified GTP, 3x Phosphates

  10. Poly A tail: Continued synthesis with A's only

  11. Introns: Spliceosome DNA, copied to pre-mRNA, NOT NEEDED, So they are cut out/ discarded, Exons get spliced together, DNA and mRNA that was transcribed from DNA and hybridised them together - base pair matching, Loops of dna - introns get transcribed then cut (like ripping the pages out of a book), Spliceosome accurately cuts out intrinsic which are the same size as a ribosome, they contain RNA, and so they recognise the sequence.
• Eukaryotic mRNA transcript modifications during RNA processing

  • a 5' cap (Of modified GTP) is attached to the 5' end. This occurs as soon as the first 20-40 nucleotides of the new mRNA molecule have been made.
  • A poly-A tail is added to the 3' end of the mRNA as soon as its synthesis is completed
  • Introns are spliced out by spliceosomes
• Transcription of a gene and the roles of RNA polymerase, promotors and proteins transcription factors

  Catalysed by RNA polymerase, No helicase or primer needed
• Microtubules shorten at the Centrosome end
• Packing DNA in eukaryotic chromosomes


  The packing is very organised. DNA double helix has negative charges along its length, due to the phosphate group in each nucleotide. DNA associates with positively charged histone proteins to reduce the repulsion of like charges, stabilising the nucleosome with weak interactions. The basic level of packing is for loops of DNA to wind around eight histone proteins, forming a nucleosome. The packing is also very dynamic, During cell division, all the DNA is very tightly packed (loops of DNA containing nucleosomes packed into bigger loops) so that the chromosomes can be easily completely separated into each of the daughter cells. During interphase, some chromatin remains tightly packed (Heterochromatin), while some chromatin remains loosely packed (Euchromatin) allowing enzymes and other proteins to access and transcribe the genes
• Meselson-Stahl experiment


  The Meselson-Stahl experiment tested the three models of DNA replication. Bacteria is grown in 'heavy' nitrogen (15N) then lighter 14N, The DNA becomes 'labelled' with 14N or 15N, DNA samples were put through a centrifuge, Different isotopes of nitrogen allow you to be able to distinguish between the new DNA and the old. The hybrid is made out of 1 strand of 15N and one strand of 14N
• Redundancy and Nearly Universal features of the genetic code


  Redundancy/Degeneracy: Many scenarios where different condos specify the same amino acid eg. UUU and UUC both code for The, More than one codon, means that mutations are less likely to cause harm. Nearly universal: All organisms use the same genetic code, Gene transfer between species eg. Jellyfish and glowing pig
• How translation starts in Eukaryotes and Prokaryotes


  Eukaryotes: The first AUG in the mRNA sequence reading from the 5' end is the start codon. Prokaryotes: The ribosome recognises a particular sequence of bases (the 'Shine-Dalgarno' sequence, or the ribosome-binding sequence) in the mRNA that precedes the AUG start codon. This is often not the first AUG codon in the mRNA
• Initiation of transcription in eukaryotes


  Several proteins called transcription factors need to bind at the promotor site before RNA polymerase can bind
• Enzymes and molecules involved in replicating each strand of DNA

  • DNA pol iii - polymerase 5' to 3' builds DNA polymer, proofreading endonuclease 3' to 5', to check and correct it's work
  • DNA pol I - same as pol iii and exonuclease 5' to 3', removes RNA primer, and its directions are based on the new strand
  • Primer to start off leading strand, DNA polymerase iii continues to make it
  • DNA polymerase I (prokaryotes) can still make DNA, but removes RNA, and at the same time builds up DNA
  • DNA ligase covalently joins DNA bases together, DNA ligase will fix the gap in DNA phosphate, caused by multiple Okazaki fragments
• Proteins involved in unwinding the DNA helix


  • DNA Helicase Enzyme, uses ATP to separate DNA strands
  • Topoisomerases (gyrases) releases torsional stress from unzipping the DNA helicases, prevents reassociation
  • Topoisomerases (gyrases) releases torsional stress from unzipping the DNA helicases
• The template strand is always the bottom strand
• Ribosomes in translation


  Platform/ scaffhold, holds the RNA in place, Catalysis, Made up of ribosomal RNA and a whole bunch of different types of proteins
• Differences between RNA polymerase and DNA polymerase

  RNA polymerase separates the two strands of DNA at the site of transcription (it does not need the help of a helicase enzyme) and it can start the synthesis of RNA with out a primer (it does not proofread), Makes RNA instead of DNA, it makes a copy of only one strand rather than of two strands
• Codons GGG and GGC both code for the amino acid Ala

  The term used to describe this feature of the genetic code is redundancy or degeneracy
• GGCTGATGT 3'


  DNA sequence
• 5' GGCUGAUGU 3'


  DNA sequence
• it has the longest polypeptide so it must have started translating first
• it has the longest mRNA molecule so it must have started transcribing first
• Ribosomes in translation


  • Platform/ scaffold, holds the RNA in place
  • Catalysis
  • Made up of ribosomal RNA and a whole bunch of different types of proteins
• RNA polymerase

  • Separates the two strands of DNA at the site of transcription (it does not need the help of a helicase enzyme)
  • Can start the synthesis of RNA with out a primer (it does not proofread)
  • Makes RNA instead of DNA, it makes a copy of only one strand rather than of two strands
• Redundancy / Degeneracy


  The term used to describe this feature of the genetic code
• 5' AUG CCU AGA AGU AAC CGC 3'


  Base sequence of the corresponding coding strand on the DNA that this mRNA was transcribed from
• 5' AUG CCU AGA AGU AAC CGC 3'

  Base sequence of the corresponding template strand on the DNA that this mRNA was transcribed from
• Mutations


  • Occur in DNA, which is then used as a template for transcription, which is then translated into amino acids
  • If a mutation occurred in mRNA it won't matter, as there are many of them
• Introns


  • Spliceosome DNA, copied to pre-mRNA, NOT NEEDED
  • So they are cut out/ discarded
  • Exons get spliced together
  • DNA and mRNA that was transcribed from DNA and hybridised them together - base pair matching
  • Loops of dna - introns get transcribed then cut (like ripping the pages out of a book)
  • Spliceosome accurately cuts out intrinsic which are the same size as a ribosome, they contain RNA, and so they recognise the sequence
  • Interruptions (non-coding)
  • Expressed (coding)