Information and Inheritance
- Created by: jessica
- Created on: 09-04-13 15:39
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- Information and Inheritance
- DNA
- bases have tautomerism, electrons are time shared against adjacent electrophilic atoms
- secondary structure is the helix, strands running antiparallel, seen in crystallography
- The sequence is always written and read in the 5' to 3' direction
- Visualize DNA by staining with ethidium bromide and capturing image on UV agarose gel.
- topoisomerases relieve the tension of the DNA coils by breaking transient DNA strands
- stacked bases are 0.34nm apart, complete turn every 3.4-3.6nm. forms a major and minor groove
- major and minor groove are where the DNA binding proteins read the base sequences
- Nuclear envelope protects the DNA from physical and chemical damage
- Nuclear pores are used to regulate the transfer of RNA and proteins in/out of the nucleus
- Chromosomes are formed from the formation of nucleosomes
- nucleosomes formed from histone core octamer, the DNA then wraps around the octomer
- histone octamer formed from H2A, H2B, H3, H4, with 2 copies of each,
- nucleosomes formed from histone core octamer, the DNA then wraps around the octomer
- Protein synthesis
- different pepties formed depending on where the transcription frame is started
- mRNA reading frames used to identify triplet codons
- tRNA have specific bases in amino acid acceptor stem and in the anticodon loop.
- correct amino acid fits well in the synthesis site
- tRNA can recognize various codons for the same amino acid via wobble base pairing
- imosine is only present in wobble base pairing
- ribosomes have three sites, A, P and R sites
- A site is the acceptor site, P site is the peptidyl tRNA site for peptide growing chain on mRNA, E is the exit site for releasing used empty tRNAs from the ribosome
- initiation complex formed on the small ribosome subunit
- the initiation factors are released on binding of the large subunit
- Cell differentiation
- stem cells are undifferentiated cells, totipotent stem cells can form any cell type
- progenitor cells give rise to a single type of differentiated cell
- Stem cells can divide symmetrically, producing identical daughter cells or asymmetrically generating an identical duaghter cell and another cell that has more restricted capabilities.
- Transcription
- RNA polymerase
- is a single beta barrel polypeptide, has a sigma subunit that is lost from the RNA polymerase on binding to DNA
- can back track and hydrolyse the previous base, the orientation determines the template strand
- RNA polymerase moves from left to right-using bottom strand as template, and vice versa
- one for each class of RNA in eukaryotes,
- pol 1 for rRNA, pol 2 for mRNA, snRNAs, miRNAs, Pol 3 for tRNA,
- promoter sites are on the DNA and direct the RNA polymerase to the start of transcription
- located upstream of the genes, with optimum frequency of 17 bases, called the TATAA box
- terminates when there are no phosphodiester bonds left, the melted DNA rewinds and the core enzyme is released
- the components that are needed to start are the template strand, activated precursors, Mg2+ ions, activators and RNA polymerase
- DNA footprinting carried out by DNAase degrading DNA with/without RNA
- is the first stage in gene expression
- in eukaryotes the introns are removed after transcription
- repressors
- proteins that bind to operator sequences that are overlapping or lying adjacent to promoters
- inhibit transcription initiation, modulated by small molecule ligands
- allows transcription regulation of specific genes in response to environmental changes
- TATA boxes are conserved sequences found 26-31bp upstream of the transcription start site
- initiator sequences are similar to the TATA box
- have a cytosine at the -1 position and an adenine residue at the transcription start site
- initiator sequences are similar to the TATA box
- promoter regions have a high number of CG bases where transcription factors bind to
- transcriptional controllers
- repressors and activators, co activators needed to help switch on genes and co repressors needed to help switch off genes
- RNA polymerase
- Nucleus
- contains a variety of subnuclear compartments e.g. sprekle, cajal body, nucleolus,
- nucleolus is the processing site of rRNA and ribosomal subunit assembly
- not bound by a membrane, is just an aggregate of rRNAs
- cajal body is where snRNP are recycled
- RNA structure and function
- tRNA is the information adaptor, has 4 stems and 3 loops
- translates codons in mRNA into amino acids
- anticodon on tRNA ensures that the right amino acid enters the chain at the right point as the anticodon is complementary to the mRNA codon
- forms an aminoacyl-tRNA bond before it can base pair with the codon on mRNA
- ribosomal RNA are part of the protein synthesis.
- have large and small subunits, join together for each translation cycle into a more compacted structure
- ribosomes have 3 or 4 different RNA molecules and up to 83 proteins.
- small subunit has one small rRNA and the large subunit has one large rRNA molecule, plus one molecule of 5S rRNA and in vertebrates a molecule of 5.8SrRNA.
- ribosomes have 3 or 4 different RNA molecules and up to 83 proteins.
- have large and small subunits, join together for each translation cycle into a more compacted structure
- microRNA inhibits protein synthesis by degrading specific mRNAs
- various RNA types, mRNA, tRNA, rRNA, microRNA
- miRNAs control expression of more than 1/3rd of all human genes
- they target specific mRNAs for degredation by argonaute/dicer silencing complexes
- siRNAs interfere with translation by mopping out specific sense mRNAs
- miRNAs control expression of more than 1/3rd of all human genes
- primary structure similar to DNA, but has uracil not thymine
- the ribose sugar makes it more labile than DNA, can be cleaved into mononucleotides by alkaline solution
- RNA can be single or double stranded
- tRNA is the information adaptor, has 4 stems and 3 loops
- Genotype
- the particular set of alleles for all the genes carried by an individual
- wild type genotype is the term for standard genotype for breeding experiments
- Control of gene operon
- e.g. lac operon degrades lactose
- needs induction-the inactivation of the lac repressor and the activation by catabolite activator protein and cAMP
- are conordinated gene expression of bacterial gene clusters
- adjacent genes are simultaneously switched on/off, behave as single transcription units, makes a polycistronic mRNA
- polycistronic mRNA is read by ribosomes, producing a single polypeptide
- adjacent genes are simultaneously switched on/off, behave as single transcription units, makes a polycistronic mRNA
- undergoes proteolysis to give separate proteins
- allows rapid production of all proteins needed in a process
- e.g. lac operon degrades lactose
- Control of gene expression in eukaryotes
- Pre-transcriptional regulation
- modulation of access of genes in transcription by modification of the histones and DNA methylation
- gene rearrangements changes the area from active to inactive and vice versa-heterochromatin and euchromatin
- histones can be used as chromatin remodeling tools, bending the DNA
- increase amount of protein by increasing gene copy number
- decoders recognise/bind to modified histone tails
- transcriptional control
- transcription switches are specific DNA sequences or chromatin modifications recognized by transcription regulators
- silencers are localised nucleosome modifications that keep a chromatin region transcriptionally inactive
- limit the enhancer activity to specific genes
- insulators are DNA sequences that stop the action of an enhancer on the trancription of a downstream gene
- limit the enhancer activity to specific genes
- insulators are DNA sequences that stop the action of an enhancer on the trancription of a downstream gene
- enhancer between 2 genes can be used by activators activating both genes at the same time
- Post transcriptional control
- Alternative splicing can retain or discrad introns/exons depending on the mutations affecting the splicing
- 2 main deamination based editing mechanisms
- Cytosine to Uracil-edited sites in introns and exons
- Adenosine to Inosine-the ADR enzymes bind to exon sites to be edited
- Alternative polyadenylation in B lymphocytes
- on first infection the full length of IgM mRNA is transcribed.
- when the antigens bind, sub-optimal cleavage and polyadenylation of the site produces a shorter antigen specific IgM mRNA
- on first infection the full length of IgM mRNA is transcribed.
- Translational control
- Post translational control of protein activity, targeting and protein degradation
- Controlled via mRNA 5'UNT and 3'UNT regions and smalll non coding RNAs
- the mRNA 5'UNT is important to bind the small ribosomal subunit for initiation
- repressors bind here to interefere with initiation
- the mRNA 3'UNT is important for mRNA stability, containing localisation sequences
- repressors bind here and interefere with mRNA circularisation
- 3 main degradation paythways
- removal of 3' polyA tail
- decapping and exonucleoltic decay of both endsor decapping and endonucleases breaking down the mRNA
- deadenylation and initiation complex formation for 5' cap and 3' polyA binding
- Pre-transcriptional regulation
- DNA replication
- is a semi conservative process
- requires DNA polymerases, dNTPs, dATP, dCTP, dGTP, dTTP, physiological pH and ionic conditions
- primer is a strand of DNA/RNA with a free 3' hydroxyl and hybridised to the template strand
- grows in the 5' to 3' direction
- RNA primers are extended by DNA polymerase III
- DNA polymerases have a sliding clamp to hold the enzyme to the DNA and to allow it to move down the template
- initiated when the initiator protein recognizes the replication origin
- helicases bind to initiator protein on OriC and uses ATP to melt hydrogen bonds, unwinding DNA
- single stranded binding protein prevetns strands from reannealing by cooperative binding to opened strands, keeping bases exposed
- Replication fork is the asymmetric extension of the RNA primer by DNA polymerase
- continuous synthesis on the leading strand and discontinuous synthesis on the laggin strand
- Okazaki fragments that are made in the lagging strand are joined together by DNA ligase
- continuous synthesis on the leading strand and discontinuous synthesis on the laggin strand
- DNA polymerases prrof read DNA during synthesis
- Mutation and Repair
- silent mutations, missense mutations, nonsense mutations and frame shift mutations
- spontaneous, DNA replicatiion errors and environmentally induced errors are all types of mutations
- transitions are when a purine is replaced for a purine
- Transversions are when purine is replaced with pyrimidine base or vice versa
- deletions occur when the template strand loops
- insertions caused when newly synthesized strand loops
- 5000 purine bases are lost through depurination each day
- deamination of amino groups gives different bases with different pairings
- mismatch repair proteins recruit endonuclease to make a nick and then the helicase can unwind the DNA. Exonuclease degrades the DNA removing the error
- glycosidase for the mutated base flips it out of the helix then cuts it away
- Mitosis and Meiosis
- mitosis used for somatic cell division
- prophase, metaphase, anaphase, telophase, cytokinesis
- meiosis for germ line sex cell production
- 3 chromosomal elements essential for chromosome duplication and segregation
- replication origin, telomeres, centromeres
- cohesions keep the chromatids together
- cohesions and condensins are part of the scaffold
- mitosis used for somatic cell division
- DNA
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