Nucleic Acids

• The structure of DNA

  • 2 polynucleotide chains/strands hydrigen bond together to make DNA double helix molecule: deoxyribose (pentose sugar) and phosphate group make up the outside backbone
  • bases hydrogen bond in the centre: A only pairs with T using 2 H bonds, G only pairs with C using 3 H bonds
  • these bases H bond together because they are complementary to each other. Purines must pair with pyrimidine so the width of the helix is constant
  • the 2 DNA strands are antiparallel: they run in opposite directions ie 5'->3' and 3'->5'
  • the 2 polynucleotide strands twist to form a double helix
• Nucleic Acids = DNA and RNA

  • replication -> DNA -> transcription --> RNA --> translation --> protein
  • the repeating unit of nucleic acids is a nucleotide
  • the monomer of nucleic acids = (mono) nucleotide
  • in DNA = deoxyribonucleotide
  • in RNA: ribonucleotide
  • a condensation reaction forms a phosphodiester bond between the nucleotides to form a polynucleotide
• the structure of a generalsied nucleotide

  made of three parts:

  • phosphate group: phosphate attached to organic molecule, negatively charged
  • pentose sugar: there are two types: deoxyribose in DNA, Ribose in RNA
  • nitrogenous base: of which there are 2 types: purines (double helix) (Adenine and Guanine) and pyrimidines (single helix) (cytosine and thymine and uracil)
• specific examples of nucleotides in the cell

  • the energy currency of all cells is a molecule called ATP
  • this is an abbreviation for adenosine triphosphate
  • cellular respiration is the conversion of consumed/stored energy into ATP
  • there are many steps involved in the respiration pathway
  • the ultimate step in respiration is the addition of a phosphate to a molecule of ADP (adenosine diphosphate) to form ATP

  
• the formation and utilisation of ATP in the cell:

  • hydrophilic: reactions requiring energy occur in aqueous environments
  • small: moves easily into, out of and within cells
  • easily regenerated: is reformed from ADP and Pi in one reaction
  • intermediate energy in bond: provides the required quantity of energy without excess being wasted as heat

  
• nucleotide components, number of phosphates, name of pentose sugar, possible nitrogenous bases, presence of phosphodiester bonds in polymer:

  • as a monomer within DNA: 1, deoxyribose, A,T,G,C, phosphodiester bond present in polymer
  • as a monomer within RNA: 1, ribose, A, G, C, U, presence of phosphodiester bond in polymer
  • as ATP: 3, ribose, adenine, no phosphodiester bond in polymer
  • as ADP: 2, ribose, adenine, no phosphodiester bond in polymer
• other examples of nucleotides:

  • hydrogen acceptors/coenzymes in respiration: NAD and FAD
  • hydrogen acceptor in p/s: NADP
  • second messenger in hormone signalling: cyclic AMP/cAMP
• the structure of chromosomes and chromatin:

  • the DNA of eukaryotic cells is in the nucleus (there is also DNA in mitochondria and chloroplasts)
  • in the cell cycle, DNA remains in the form of chromatin in interphase, chromatin = nuclear DNA wrapped around histones
  • during mitosis/meiosis and before cell division, the DNA in the nucleus condenses/coils and chromosomes appear
  • chromosome = one molecule of DNA
  • 2 identical chromatids formed on a chromsome after DNA replication
• • histones - positively charged proteins which Eukaryotic DNA is wrapped around
  • chromosome - appearance of chromosomes after DNA replication
  • chromosome duplication = DNA replication
• DNA replication (P1)

  • both parent strands act as a template for the addition of complementary nucleotides (not the case for transcription)

  1. Unwinding of DNA (Helix Unzipping)

  • Enzyme involved: DNA helicase
  • Process:
  • DNA helicase breaks the hydrogen bonds between complementary base pairs.
  • The double helix unwinds, forming two template strands.

  2. Formation of New Strands (Complementary Base Pairing)

  • Enzyme involved: DNA polymerase
  • Process:
  • Free activated nucleotides (with extra phosphate groups) bind to their complementary bases on the exposed template strands.
• DNA replication (p2)

  3. Joining of Nucleotides (Sugar-Phosphate Backbone Formation)

  • Enzyme involved: DNA polymerase
  • Process:
  • DNA polymerase catalyzes formation of phosphodiester bonds between nucleotides via condensation reactions.
  • creates a sugar-phosphate backbone, forming a new complementary strand.

  4. Leading and Lagging Strand Synthesis

  • DNA strands are antiparallel - replication occurs differently on each strand:
  • Leading strand: Replicated continuously in the 5’ to 3’ direction.
  • Lagging strand: Replicated discontinuously in small Okazaki fragments, later joined by DNA ligase.
• DNA replication (P3)

  5. Completion and Proofreading

  • Enzyme involved: DNA polymerase
  • Process:
  • DNA polymerase checks for errors and corrects mismatched bases to ensure high accuracy (fidelity).
  • two new identical DNA molecules rewind into a double helix.

  Enzyme and Function

  DNA helicase

  • Unwinds the DNA and breaks hydrogen bonds

  DNA polymerase

  • Joins free nucleotides to complementary bases and forms phosphodiester bonds

  DNA ligase

  • Joins Okazaki fragments on the lagging strand
• Meselson and Stahl experiment

  1. Growing Bacteria in Heavy Nitrogen (¹⁵N)

  • grew E. coli bacteria in a medium containing heavy nitrogen isotope (¹⁵N).
  • bacteria incorporated ¹⁵N into their DNA bases, making DNA denser than normal.

  2. Transferring Bacteria to Light Nitrogen (¹⁴N)

  • bacteria then transferred to a medium containing light nitrogen (¹⁴N) and allowed to replicate once.

  3. Centrifugation After Each DNA Replication Cycle

  After each round of DNA replication, the scientists extracted and centrifuged the bacterial DNA in a density gradient solution to observe band positions.
• Meselson Stahl experiment (P2)

  After One Round of Replication (Generation 1)

  • DNA formed a single band at intermediate density.
  • ruled out conservative replication (which would have produced one heavy and one light band).
  • It was consistent with semi-conservative or dispersive replication.

  After Two Rounds of Replication (Generation 2)

  • The DNA formed two bands:

  1. One intermediate band (mixture of ¹⁵N and ¹⁴N, hybrid DNA).
  2. One light band (DNA fully containing ¹⁴N).

  • ruled out dispersive replication (which would have only shown one blended band).
  • It confirmed semi-conservative replication.
• Meselson Stahl experiment

  
• The genetic code:

  = the base or nucleotide sequence of the DNA which codes for the aa sequence of proteins

  • the base nucleotide sequence of DNA/gene determines -> aa sequence of protein (1 structure) determines -> final folding of pp chain (3 structure) determines -> function of proteins (e.g. shape of active site)

  there are only 4 dif bases in DNA but there are 20 dif amino acid proteins -> 3 bases in a row code for 1 amino acid, this is called a codon, there are G4 possible codons. the genetic code is a triplet code
• • codons are found within genes
  • a gene is a section of DNA (made of hundreds of base pairs) which codes for a protein
  • genes make up a small proportion of the genome (1.5%)
  • the rest is knwon as non-coding, intergenic or satellite DNA
• definitions:

  • codon = 3 adjacent bases/ nucleotides that code for an amino acid
  • gene = a sequence of DNA, organised into codons, that codes for (a) protein
  • genome = all the DNA that is present in an organism (=> all the genes)
• the properties of the genetic code:

  1. genetic code is a triplet code
  2. genetic code is degenerate: there are 64 codons but only 20 aas, so most aas have more than 1 codon coding for them , so genetic code is degenerate code because for most aas there is more than one possible codon - a muttaion within a gene may not change the aas sequence/ 1 structure of protein if changed triplet code still codes for the same aas
  3. genetic code is non-overlapping: each codon is read seperately from the codon before it and the codon after it - no base is shared between adjacent codons - they're direct units
• the properties of the genetic code:

  • genetic code is non-overlaapping - important because it does not limit the aa sequence of a protein

  4. the genetic code is universal: teh same specific codons code for same aas in all living organisms
• mutations:

  = a change in base sequence of DNA

  • occur randomly, either during DNA replication or from environmental caused e.g. UV radiation, mutagens in pollution
  • most are harmless as they occur in non-coding DNA. also the degenerate nature of genetic code means that a change in base sequence of a codon may still code for the same aa. these mutations are known as silent mutations
• mutations (P2):

  • some are deleterious as they occur in a codon of a gene so that the base sequence is changed and wrong aa is coded for in codon. therefore 1 structure of protein si changed and so final folding (3 structure) and its function is lost
  • in the case of an enzyme, the shape of the active site is lost
  • occasionally, mutations are advantageous and bring about evolution by natural selection
• KEY TERMS (P1):

  • amino acid: organic compound consisting of a carboxyl, an amine and an R group (where R may be one of 20 dif. atomic groupings). Polymerise by peptide bodns to form proteins
  • antiparallel: a term used to describe double stranded DNA that runs in opposite directions
  • base-pairing rule: rule governing the pairing of complementary in DNA
  • Codon: sequence of three adjacent nucleotides constituting the genetic code
  • DNA: macromolecule comprising many millions o funits containing a phosphate group, sugar and a base, stores genetic information of cell
• KEY TERMS (P2):

  • DNA Ligase: enzyme that links together two DNA strands that have double-strand break
  • DNA polymerase: enzyme that catalyses the incorporation fo deoxyribonucleotides into a DNA strand
  • DNA replication: semi conservative process by which two identical DNA molecules are produced from a single double-stranded DNA molecule
  • gene expression: the process by which information from a gene is used to produce a functional gene product
  • genetic code: set of rules by which information encoded in DNA or mRNA is translated into proteins
• KEY TERMS (P3):

  • genome: entire haploid complement of genetic material of a cell or organism
  • helicase: enzyme that seperates two annealed DNA strands using energy from ATP hydrolysis
  • histone: protein found in the nuclei of eukaryotic cells, which package and order the DNA into structural units called nucleosomes
  • hydrogen bonds: intermolecular bond that forms between h and either oxygen, nitrogen or fluorine
  • lagging strand: strand of DNA double helix that is orientated in a 3' to 5' manner and which is replicated in fragments
• KEY TERMS (P4):

  • leading strand: strand of DNA double helix that is oritented in a 5' to 3' manner and is repliacted in one continuous piece
  • nucleic acids: polynucleotide molecule that occurs in two forms, DNA and RNA
  • nucleotides: structural units of DNA
  • Okazaki fragments: relatively short piece of DNA created on the lagging strand during DNA replication
  • protein: organic polymer formed from the assambly of aas joined by peptide bonds
  • purine: two ringed base in a nucleotide
  • pyrimidine: single ringed base in a nucleotide
• KEY TERMS (P5):

  • replication fork: a structure, created by DNA helicase, that forms within the nucleus during DNA replication
  • RNA: ribonucleic acid. single stranded nucleic acid that consists of nucleotides that contain ribose sugar
  • semi-conservative replication: process of DNA replicated in which the DNA helic is unwound and each original strand serves a sa template for synthesis of a new complementary strand
• differences between DNA and RNA (P1)

  • DNA: bases present are: A, T, G, C
  • RNA: bases present are A, U, G, C
  • DNA: permanent it is the blue-print of the cell
  • RNA: may be temporary existing for short periods only
  • DNA: double polynucleotide chain made of deoxyribonucleotides
  • RNA: single polynucleotide chain made of ribonucleotides
  • DNA: chemically v. stable bec of H bonding
  • RNA: chemically less stable
  • DNA: always a double helix
  • RNA: may have a single or double helix - can fold in on itself
• dif between DNA and RNA (P2)

  • DNA: always found in nucleus (mitochondria and chloroplasts have their own too)
  • RNA: made in the nucleus but found in the cytoplasm
  • DNA: the sugar is deoxyribose C5H10O4
  • RNA: sugar is ribose C5H10O5
  • DNA: only one basic form but with a variety as wide as there are dif organisms on planet
  • RNA: three types: mRNA - messenger RNA, tRNA - transfer RNA, rRNA - ribosomal RNA
  • DNA: ratio of A;T is 1 and G:C is 1 because A always pairs with T and G always pairs with C
  • RNA: ration of bases varies since no pairing involved
• dif. between DNA and RNA (P3)

  • DNA: amount is constant for all cells of one species
  • RNA: amount of varies from cell to cell + at dif. times according to how much is needed
• protein synthesis:

  1st stage: Transcription:

  • the synthesis of RNA from DNA
  • DNA never leaves nucleus - too large
  • proetins are synthesised on ribosomes in cytoplasm. a copy of the gene must be made which can leave the nucleus (via the nuclear pores in the nuclear envelope)
  • this copy is called messenger RNA (mRNA)
  • codons on the DNA are transcribed ot the mRNA

  2nd stage: translation:

  • code carried by mRNA is translated to aa sequence of protein
• 1 transcription:

  • the DNA helix is unwound at the start of the gene
  • and the H bonds between the two strands are broken by helicase
  • free complementary ribonucleotides form H bonds with the template (non-coding) strand
  • a condenstation reactino is carried out by RNA polymerase
  • and phosphodiester bonds form the sugar phosphate backbone of the growing RNA chain
  • the coding strand is not transcribed
  • unlike DNA replication, transcription involves only one template strand
  • when transcription of the gene is finished, mRNA leaves the nucleus through nuclear pores
• transcription

  A) antisense strand

  B) helicase

  C) coding

  D) template

  
• 2 translation

  = the translation of the codons on the mRNA to the aa sequence of the protein

  carried out with help of 2 other types of RNA:

  ribosomal RNA (rRNA):

  • together with ribosomal protein makes up ribosome. it has a structural and enzymatic role. ribosome is the site for the 2 stage of protein synthesis: ribosomes 'house' and catalyse process of translation
  • the mRNA attaches to the ribosome between large and small subunits
  • in eukaryotic cells, the ribosome is present on surface membrane of the RER. the pp chain forms into the lumen of the RER
• translation carried out with help of 2 other types of RNA:

  2 transfer RNA (tRNA)

  • deliver correct aas to ribosome
  • a small clover leaf shaped molecule of RNA => double helical in places, around 80 nucleotides long, contains:
  • attatchment point for a specific aas at one end
  • an anti codon (3 bases in a row) at other end, stop codons dont have complementary antocodon/ tRNA

  
• translation process (P1):

  • the start codon (always A, U,G) and the subsequent codon on the mRNA are positioned inside ribosome
  • the first tRNA (tRNA 1) that corresponds to the start codon with its aa attached (aa1) , moves into the ribosome
  • the anticodon on the first tRNA base pairs/ h bonds to its complementary codon on the mRNA
  • the second tRNA enters ribosome (carrying aa2) and its anticodon base pairs (forms H bonds) with second codon on mRNA
  • a peptide bond is formed between aa1 and aa2 by a condensation reaction
• translation process (p2):

  • once this bond has been formed, ribosome moves along mRNA to reach the next codon
  • the first tRNA detaches from its aa and moved out to teh cytoplasm
  • a tRNA corresponding to the thrid codon brings aa 3 to ribosome and it's anticodon h bonds with codon 3 in the mRNA
  • this process is repeated until ribosome has moved along the coding length of the mRNA and a stop codon is reached
  • translation is terminated and ribosome seperates from mRNA: the primary structure of the pp has been made
  • pp chain formation finishes inside lumen of RER and is transported to golgi