pro euk

• size


  euk: larger

  pro: smaller
• nuclear envelope 


  euk: present

  pro: absent
• genetic material 


  euk: multiple linear dna associated with many proteins, found in membrane bound nucleus, no plasmids

  pro: singular circular dna associated with few histone-like proteins, found in nucleoid region, plasmids present
• ribosomes


  euk: 80s

  pro: 70s (no ER)
• organelles


  euk: many (many mbo)

  pro: few (no mbo)
• cell walls


  euk: composes of cellulose and chitin in fungi

  pro: composes of peptidoglycan
• pro and euk genome

  both have double helix dna

  both have extrachromosomal dna (mitochondrial dna and chloroplast circular dna for euk, plasmids for pro)
• level of dna coiling

  euk: high - negatively charged dna associated with positively charged histone via electrostatic attraction. dna wounded around 8 histone proteins twice to form nucleosome with linker dna joining adjacent nucleosomes, forming a 10nm fibre which coils around itself to form 30nm fibre, which forms looped domains when associated with scaffold proteins, forming 300nm fibres, which supercoils chromosomes at metaphase

  pro: relatively low. dna folded into looped domains by protein-dna associations, which undergo supercoiling with the help of dna gyrase and topoisomerase
• non-coding regions


  euk: common

  pro: not common
• • A short 3-nucleotide seg of RNA within telomerase binds to part of a DNA repeat in the 3’overhang by cbp
  • adjacent part of RNA within telomerase is used as T to syn short comple 6-nu
  • Telomerase cat fmtn of the pdeb btwn existing 3’OH group of DNA overhang and 5’ phos grp of incoming dntp, translocates 6 nu to the right in 5’ to 3’ and makes another repeat. process repeated, forming series of tandem repeats, elongating telomere.
  • telomerase primase makes an RNA primer near end of telomere. DNAp adds nu to the 3’OH end of primer, syn comple strand . nick sealed by ligase. RNA primer is removed.
• non-coding dna

  • introns
  • promoter
  • enhancer
  • silencer
  • telomeres
  • centromere
• promoter

  • located upstream TSS
  • has critical elements (TATA box determines precise location TSS - removal of it results in transc starting at variety locations forming a non functional protein)
  • func: recog & binding site for GTF which then recruit RNAp to form TIC to initiate transC
• enhancer

  recog & binding site for activators (STF)

  • increase freq of transC by promoting assembly of TIC (with help from dna bending protein that bend spacer dna)
• telomeres

  • ensure that genes are not eroded and vital genetic information is not lost with each round of DNA replication due to end replication problem. DNA molecule shortens with each round of replication as DNA polymerase requires a free 3’OH of a pre-existing strand to add nu, the last rna primer on the lagging strand with dna cannot be replaced with dna
• telomeres

  • protect and stabilise terminal ends of chromosome by forming a loop using the 3' overhang, preventing ss terminal end of chromosome from annealing to a complementary ss terminal end of another chromosome, prev fusion of 2 chromosomes. fmtn of loop also prevents cell's dna repair mech from detecting the chromosomes as damaged dna and triggering apoptosis
• telomeres


  allow their own extension as they have a 3' overhang, which provides an attachment point for the correct positioning of the enzyme telomerase, maintaining telomere length
• telomeres & centromeres


  non-coding dna made up of a series of tandem repeat sequences
• centromeres 


  non coding TRS at a location along the length of a chr that results in a specific 3d confo, allow kinetochore and subsequently spindle fibres to attach, allowing sep of sis chromatids to opp poles
• centromeres

  • allow sister chromatids to adhere to each other
  • allow kinetochore prot and subseq spindle fibres to attach, allow homo chromo to align along metaphase plate and be separated to opp poles
  • allow proper alignment and segregation of chromo
• purpose of regulating gene expression

  1. cellular differentiation
  2. adapt to changes
  3. conserve resources
• genomic lvl

  1. histone acetyl transferase/ deacetylase: addition of acetyl grps to lysine residues, removing + charge on histones, decrease EFOA btwn, tight binding of dna & histones loosened, promoter region more accessible to RNAp & GTF, allowing formation of TIC
  2. crc - temporarily alter structure of nucleosomes: cause dna to be more/less tightly coiled around histones
  3. dna methylation. addition of a methyl grp by dna methylases to selected cytosine residues, inhibits transcription by blocking binding of TF at P, recruiting dna-binding protein to methylated dna
  4. gene amplification
• transc lvl (STF) euk

  1. activators / repressors
• transc lvl prok

  • activated Catabolite Activator Protein (CAP) which binds to the CAP binding site at the promoter of the lac operon and increases the affinity of RNA polymerase to the promoter, transcription frequency increases, Positive gene regulation
  • binds to the operator, preventing RNA polymerase from binding to the promoter, transcription frequency decreases, Negative gene regulation
• Addition of a 7-methylguanosine nucleotide to the 5’ end of the pre-mRNA

  • helps the cell to recognize mRNA so that subsequent steps such as splicing and polyadenylation can occur
  • signal to export mRNA out of nucleus
  • protects growing pre-mRNA chain from degradation by ribonucleases
  • promotes initiation of translation as it is recog by TIF
• • introns are excised and exons are joined together by spliceosomes which recognize the sequences at intron-exon boundaries so that functional proteins can be produced.
  • Alternative splicing, different exons of a single pre-mRNA can be joined together such that different mature mRNAs and different proteins can be produced
• 3’end of pre-mRNA cleaved by endonucleases and a poly-A polymerase recognises the polyadenylation signal (AAUAAA) and adds a long sequence of adenine nucleotides to 3’ end of the pre-mRNA, forming a poly(A) tail

  1. signal to export mature mRNA out of nucleus
  2. protects mature mRNA from degradation by ribonucleases
  3. required for initiation of translation
• 1. The longer the poly-A tail, the longer the mRNA can be used as a template to make proteins. poly-A tail is removed by ribonucleases in the 3’ to 5’ direction until critical length is reached, triggering removal of the 5’cap and degradation of the mRNA from the 5’end
  2. formation of TIC (phos/dephos TIF)
• 1. Covalent modification of polypeptides make functional proteins
  2. de/Phosphorylation of translation initiation factors can de/activate the protein and hence up / down regulate its activity.
  3. Proteins targetted for degradation are tagged with ubiqutin (by ubiquitin ligase) and then recognised and degraded by the proteasome.
• proto-oncogenes

  code for proteins that stimulate normal cell division
• oncogens (eg ras gene)

  (a) increase the amount of proto-oncogene’s protein product (b) increase the intrinsic activity of the proto-oncogene protein product
• oncogen formation (a)

  1. point mutation in base sequences of regulatory elements
  2. gene amplification, copies of a proto-oncogene in a cell is increased due to a mistake during DNA replication
  3. chromosomal translocation such that the proto-oncogene ends up under the control of a enhancer
  4. retroviral integration

  excessive production of proto-oncogene protein product, uncontrolled cell division
• oncogen formation (b)

  • point mutation within the proto-oncogenechanges the amino acid sequence, can then become hyperactive or more resistant to degradation -> uncontrolled cell divison
• Tumour suppressor genes: eg p53 gene

  codes for protein products that inhibit cell division or by activating cell cycle arrest to prevent uncontrolled cell division when mutated, they are inactivated.
• p53 gene: codes for an activator that can activate genes involved in

  1. cell cycle arrest - gives cell enough time to repair damaged DNA and prevent formation of mutant daughter cells
  2. DNA repair - prevents mutations that may lead to the formation of oncogenes or inactivated tumour suppressor genes
  3. initiating apoptosis when DNA damage is beyond repair, remove cells with damaged DNA with the potential to cause cancer
• Gain-in-function:

  mutation in just one copy of the allele results can result in uncontrolled cell division, due to the increased synthesis/activity of a functional product due to mutation.
• Loss-of-function mutation: mutations in both copies of the allele necessary for the loss-of-function phenotype to be observed, even when one copy is mutated, the non-mutant copy still produces a functional gene product.
• • dev of cancer requires accumulation of mutations in the genes which control regulatory checkpoints of the cell cycle in a single cell, disrupting normal cell cycle
  • a GIF mutation is a dominant mut where mut in just 1 allele of a proto-oncogene will result in overexpression, resulting in the production of excessive amounts or instrinsic activities of proto-oncogene protein product, leading to excessive cell proliferation. LIF mut is recessive where mut in both alleles of a TSG will result in the non-func protein, disrupting ability to inhibit cell cycle, enable DNA repair, promote apoptosis
• • Activation of the genes coding for telomerase lengthens telomeres allowing cell to dividing indefinitely as the chromosomes are prevented from shortening with each DNA replication cycle.
  • Loss of contact inhibition* will enable the cells to grow into a benign tumour
  • Angiogenesis occur within the tumour so that the blood vessels formed can transport oxygen and nutrients for its growth.The presence of blood vessels can result in the formation of a malignant tumour capable of metastasizing to other parts of the body via the bloodstream to form secondary tumours
• erp


  during dna rep, rna primer at 5' end of lagging strand is removed but gap cannot be replaced with comple dntps as rnap req 3'oh grp to add dntps, over repeated cycles of dna rep, gradual shortening of ends of chr
• spliceosome


  snrna in snrnp recog & bind to intron-exon boundaries via cbp, snrnp associate tgt to form spliceosomes that cleave pdeb btwn adj nu to excise introns & join exons