FOB 7 - nucleotides

• nucleotide


  3 parts: phosphate group (attached to carbon 5 of ribose), ribose backbone (DNA minus second hydroxy group or RNA), a nitrogenous base (attached to carbon 1 of ribose, pyrimidines (C,T and U) and purines (G and A)) phosphate group link in phosphoester bond, base link by N-B-glycoside bond to C1 of ribose ring (N-1 pyrimidines and N-9 purines),
• pyrimidines and purines


  pyrimidines 6-membered structure, purines 9-membered double ring. pyrimidines link to ribose in nitrogen 1, and purines in nitrogen 9.
• purines


  adenine, two polar groups, an NH on the 4th carbon and a double-bonded N on the 3rd member. guanine
• pyrimidines


  cytosine, thymine and uracil. addition on methyl group instead of the double bond is the differences between thymine and uracil. polar group on the left side.
• base pairing


  T+A and C+G, purines and pyrimidines, are connected by hydrogen bonds. GC are stronger because held by 3 bonds versus AT 2 bonds
• nucleoside


  monomeric unit, contains nucleotide minus the phosphate group
• nucleic acid


  link nucleotides, three phosphate groups two of which are lost for energy to link them together. DNA no hydroxyl on C2 of ribose, T. RNA hydroxyl group, U. oligonucleotide: 2-50 nucleotides long, polynucleotide, greater than 50 long
• nucleotide other uses


  energy molecules ATP GDP, signalling cGMP/ cAMP, structural component of coenzyme and metabolic intermediates (acetyl-CoA).
• rna and dna structural components


  primary: polymer of nucleotides. secondary: double helix, tertiary: chromosomes.
• primary stucture


  (order of nucleic acids, determines what the DNA or RNA codes for, links in 5 prime to 3 prime direction adding onto 3 end in phosphodiester bondage in condensation reaction)
• secondary structure


  antiparallel right-handed double helix of two polynucleotide strands. held together by hydrogen bonding between base pairs that sit in the same plane and base-stacking interactions. each strand compliments the other, and the helical shape creates a major and minor groove. the vertically stacked bases are 3.4 angstroms 0.34nm apart with 10.5 bases per turn 36 A per turn.
• nucleic acids in the genome

  2 purines or pyrimidines will not base pair due to size. and C+G are bonded slightly closer together because they have stronger bonds. if 28% of the genome is cytosine 28% will be Guanine etc.
• rna vs dna


  nucleic acid, single stranded, uracil instead of thyamine, ribose instead of deoxyribose. 4 types mRNA (messenger RNA) transcribed from DNA carries genetic information from DNA to ribosomes where they are translated. tRNA: role in transition to protein. rRna (ribosomal RNA): form ribosomes. non-coding RNA: regulatory abilities (microRNA, siRNA and piRNA)
• RNA secondary structure examples

  microRNA. complimentary sections fold over each other and anneal together and form a ring on the end (hairpin) of non-complimentary base pairs. this makes it double-stranded and protects it from being degraded by the body
• genome


  entirety of the heredity genetic information of a cell
• chromosome


  un eukaryotes the genome is dividded into set of linear segments of DNA referred to as chromosomes (46 for humans, 23 pairs (somatic cells)).
• chromatin


  the complex of dna and proteins found together
• nucleosome


  the most basic unit of DNA packing involving DNA wound around histone protein complexes
• centromere


  the point that links sister chromatids and allows separation into daughter cells
• telomeres


  specialised dna sequences found at the end of the chromosome to allow complete replication and to protect against degradation of the chromosomal ends. consists of thousands of tandem 5'-TTAGGG-3' repeats up to 2500 repeats
• gene


  a second of DNA that can code for a specific biologically functional polypeptide or RNA molecule or set of closely related isoforms.
• somatic cells have


  46 chromosomes. 22 non-sex (autosomes) from each parent and allosomes X or Y. somatic cells are diploid containing double the usual DNA. stretched out we have 2m of dna
• dna packing


  supercoiled, the coiled coil. positive supercoil (extra helical twist) and negative supercoil (subtractive twisting). in nature, negatively supercoiled DNA is more common. in eukaryotes supercoils exist predominantly as plectonemic (supercoils) and solenoidal (in nucleosomes)
• how does supercoiling happen

  DNA is initially coiled at its correct torsional strain, the system is balanced. if the strands are pulled apart this creates supercoils as the torsional strain has increased due to the decreased lengths. topoisomerase unwinds the DNA for replication and transcription.
• nucleosomes


  made of histone proteins and DNA wrapped around it. histones in H1, H2A, H2B, H3 and H4 types. H3 and H4 are highly conserved, while H1, H2A and H2B are less conserved. they have high lysine and arginine content hence cationic, and interact with anionic DNA backbone. histone made of each of 2 of each histone protein except H1 (8 proteins total). a region of approx 146bp is wrap around each complex, with 3-8bp between (linker region). "beads on a string"
• nucleosomes 2


  the interface between DNA and histones in nucleosomes are extensive: aprox 142 hydrogen bonds (50% between the amino acid backbone of histones and phosphodiester backbone of DNA) hydrophobic interactions, +/- ionic interactions. a number of histones are highly conserved between species.
• histone modications


  increase the packing capacity of dna and constantly change their structure altering our ability to access it. each protein has a globular center and a long tail (n terminus) and the tail can be modified by acetylation, methylation or ubiquitination. example 27th amino acid (lysine) on H3 can be methylated 3 times which causes a tightening (H3K27me3).
• levels of packing in DNA

  DNA double helix, wrapped around histones "beads on a string", H1 sits out front of histone complex and links beads together forming a fibre which supercoils, extensive supercoiling forms rosettes, rosettes coil to form one coil, 10 coils form a chromatid, two of which make chromosomes.
• strands of DNA are

  reverse complement.
• coding for a protein

  DNA, one strand is template (the reverse complement of strand we copy), one is coding (final code of mRNA strand with T replaced by u). 3 nucleotides in a row (codon) codes for an amino acid.
• genes in dna


  separated by non-coding DNA. when transcribing, exons are translated and introns do not as only exons code. splicing removes introns and only keeps one exon.
• transcription


  converting DNA to RNA
• gene isoforms


  versions of genes that are slightly different and have more or less exons than another
• non-coding dna


  98% of genome, does not code for polypeptide products. contains numerous repeat sequences from transposable elements (regions of DNA that can move from one location in the genome to another, 45%). code for functional non-coding RNA molecules (tRNA, rRNA etc), contains many regulatory sequences involved in the regulation of transcription.