Nucleotides

• • nucleic acids contain the elements C, H, O, N and P
  • they are large polymers formed from many monomers (nucleotides)
  • Nucleotides consist of: a pentose, a phosphate group, a nitrogenous base
  • nucleotides are linked together by condensation reactions forming a polynucleotide
  • the phosphate group at the 5th carbon of the pentose sugar (5') of one nucleotide forms a covalent bond with the hydroxyl (OH) group at the third carbon (3') of the pentose sugar of an adjacent nucleotide (DNA grows from the 5 to 3 direction) - phosphodiester bonds
• DNA:

  • Deoxyribonucleic acid
  • the sugar in DNA is a deoxyribose and has one fewer O2 atom than ribose
  • nucleotides in DNA have one of four bases - Adenine, Cytosine, Guanine and Thymine
• Pyrimidines:

  • smaller base
  • contain a single carbon ring structure
  • Thymine and Cytosine
• Purines:

  • larger base
  • contain a double carbon ring structure
  • Adenine and Guanine
• Complimentary base pairing:

  • Adenine forms two H bonds with Thymine
  • Cytosine forms three H bonds with Guanine
  • a pyrimidine always bonds with a purine to create a constant distance between the DNA 'backbones'
• • the order of the bases determines the genetic code of an organism
  • there is always an equal number of C&G, and A&T due to the complementary base pairing
• the double helix:

  • the DNA molecule can vary from a few nucleotides to millions
  • it is made of two strands of polynucleotides coiled into a helix
  • the two strands are held together by hydrogen bonds between the bases
  • the two strands run in opposite directions, so are said to be antiparallel
  • each strand has a phosphate group at one end (5') and a hydroxyl group at the other (3')
  • the pairing between the bases allows DNA to be copied and transcribed
• Ribonucleic acid:

  • DNA contains the information to code for proteins but cannot leave nucleus
  • short sections of DNA are copied (transcribed) forming mRNA. Then with the use of a ribosome and tRNA, proteins are synthesised
• RNA:

  • RNA exists as a single-stranded molecule
  • there are three forms of RNA, transfer RNA (tRNA), which adopts a clover leaf formation through hydrogen bonding between certain bases, ribsomal RNA (rRNA), and messenger RNA (mRNA), which is a straight chain molecule
  • RNA is shorter than DNA
  • the pentose sugar in RNA is ribose not deoxyribose
  • Thymine base is replaced with uracil:
  • Uracil is a pyrimidine that forms 2 hydrogen bonds with adenine
• RNA 2:

  • RNA polymers are also formed by phosphodiester bonds in condensation reactions
  • the mRNA that is formed moves out of the nucleus to a ribosome where a protein is synthesised
  • after protein synthesis the phosphodiester bonds in the mRNA are hydrolysed releasing the nucleotides that are released and reused.
• rRNA:

  • ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome , which is essential for protein synthesis in all living organisms
  • rRNA is the predominant rNA in most cells, composing of around 80% of cellular RNA
  • ribosomes are approximately 60% rRNA and 40% protein by weight
• Semi-conservative replication:

  • first the helix must unwind and the two strands must separate. this is carried out by the enzyme helicase
  • DNA binding proteins then attach to the separated polynucleotide strands to prevent them binding back together
  • free nucleotides come along and pair up with the newly exposed bases on the template strands
  • the nucleotides are phosphorylated and are activated. the phosphates provide energy for DNA replication to occur
  • hydrogen bonds form between the exposed bases on the nucleotide chain and the complimentary bases on the free nucleotides
• Semi-conservative replication 2:

  • DNA polymerase catalyses the formation of phosphodiester bonds between free nucleotides to form a polynucleotide chain
  • DNA polymerase can only join nucleotides together in the 5' to 3' direction
  • the particular strand running in this direction can thus be continuously produced and undergoes continuous replication - the leading strand
  • in the 3' to 5' direcyion, DNA polymerase produces short sections of joined nucleotides termed Okazaki fragments
• Semi-conservative replication 3:

  • the enzyme DNA ligase then joins together these fragments to form the lagging strand which undergoes discontinuous replication
  • the newly complete DNA molecules then wind up, forming helices once more
  • replication occurs at a rate of 50 bases per second
  • DNA polymerase also 'proof-reads' the polynucleotide strand as it produces it
  • the chances of incorrect nucleotides being added to the strand are once every 10 genes
  • DNA polymerase picks up 99.9% of these errors
  • these errors, if not corrected, can lead to mutations
• Meselson and Stahl:

  • grew bacteria on a medium containing N15, a heavy isotope of nitrogen, for a number of generations
  • the DNA was heavier than N14 DNA
  • the bacteria were then placed on a medium of N14 for 1 generation
  • the DNA produced had a mass half-way between the N14 and N15 DNA
  • the second generation on N14 produced DNA between N14/15 and only N14
• Genetic code:

  • a molecule of DNA codes for many proteins
  • each chromosome can be thought of as consisting of many genes
  • most of an organism's DNA does not code for protein
  • the total set of genes in a cell is termed the genome
  • it is the sequence of nitrogenous bases that codes for the production of a polypeptide
  • a sequence of 3 bases code for the production of one amino acid, so the genetic code is termed the triplet code
  • on an mRNA molecule, the sequences are termed codons
  • the genetic code is universal
• Degenerate code:

  • there are 64 possible codons, but only 20 amino acids that occur regularly
  • therefore many amino acids are coded for by more than one codon
  • there is a start codon - ATG - which signals the start of the sequence that codes for a protein
  • the stop codons are TAA, TAG and TGA
• Gene - a section of DNA that contains the complete sequence of codons to code for a polypeptide
• • DNA is contained inside the nucleus. This has a double membrane around it called the nuclear envelope. This protects the DNA from being damaged in the cytoplasm
  • protein synthesis occurs in the cytoplasm on ribosomes. to allow this to occur, the DNA that codes for the protein has to be copied in a process called transcription - this produces mRNA
• Transcription:

  • DNA helicase unwinds and unzips the part of the DNA that contains the gene - this starts at the promoter region
  • only one of the two DNA strands codes for the protein - the sense strand, runs from 5' to 3'
  • the other strand is a complimentary copy of the sense strand and is called the antisense strand
  • it acts as the template for mRNA so the mRNA formed will carry the same base sequence as the sense strand
• Promoter region:

  • determines where transcription begins and which strand of DNA is used as the template
  • in prokaryotes, the DNA polymerase recognises the promoter and binds to it
  • in eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase
• Transcription 2:

  • as the DNA unzips, free RNA nucleotides will pair with the exposed complimentary bases on the antisense strand
  • the free nucleotides are activated as they have two additional phosphate groups that provide energy for mRNA synthesis
  • RNA polymerase will then move along the RNA and catalyse the reactions that form phosphodiester bonds in the RNA
  • transcription will stop when it reaches a stop codon. This process forms a short strand of RNA called messenger RNA. it has the same base sequence as the sense strand, with uracil in place of thymine
  • the mRNA leaves the nucleus
• Transcription: Ribosome

  • free-floating amino acids are attached to tRNA molecules by the enzyme animoacyl-tRNA synthetase
  • tRNA carries the amino acids to the ribosomes
  • the tRNA has an anticodon which will bind with the complementary codon on mRNA
  • amino acids are added one at a time, growing the polypeptide chain
  • peptidyl transferase is responsible for catalysing this process
  • when a stop codon is reached, production ceases and the polypeptide chain is released
  • mRNA is short-lived so excessive proteins are not produced
• ATP - adenosine triphosphate:

  • phosphorylated nucleotide
  • used for the transfer of energy in all cells
  • unstable, meaning the hydrolysis of ATP releases energy
  • phosphate groups are all negatively charged so repel each other
• • the energy released from energy-yielding (exergonic) reactions such as respiration is transferred to ATP
  • the energy is stored as the chemical potential energy of ATP
  • this energy can be released to supply the needs of energy-requiring (endergonic) reactions
  • ATP acts as the intermediary between these reactions
  • ATP cannot be transported between cells, so every cell must produce its own ATP
  • when a phosphate group is lost, ATP becomes ADP
  • ATP allows the release of small quantities of energy
• energy is released from ATP because:

  • the hydrolysis of ATP to ADP is exergonic (the system has changed to favour stability)
  • the release of energy comes from the shift to stability
  • when ATP is hydrolysed, the phosphate is transferred to another molecule
  • this molecule is said to be phosphorylated
  • the molecule becomes less stable so work is done
• • ATP cannot be stored due to its instability
  • ATP is created by the breakdown of fats and carbs in respiration
  • ATP is small and water soluble for movement and aqueous reactions and is easily regenerated