Genetics

• Gene expression


  Transcription and subsequent translation of a gene or the information that is stored in the gene is made into a protein that will affect the phenotype of the organism
• Operon


  A unit of genetic function common in bacteria and phages; consists of coordinately-regulated clusters of genes with related functions
• Promoter


  A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA
• Operator


  A segment of DNA to which a transcription factor protein bind
• Regulatory genes

  A gene involved in controlling the expression of one or more other genes; may encode a protein, or it may work at the level of RNA. In prokaryotes, regulator genes often code for repressor proteins.
• Repressor


  Protein that physically obstructs the RNA polymerase from transcribing the genes
• Inhibitor


  A gene whose presence prevents the expression of some other gene at a different locus
• Inducer


  A molecule that starts gene expression; can bind to repressors or activators; function by disabling repressors (gene is thus expressed)
• Transcriptional Control Systems in Prokaryotes operate at the level of transcription (can make transcription proceed or not)
• Regulatory proteins can either shut down (negative control) or trigger transcription (positive control)
• Trp operon


  Codes for the components for production of tryptophan wherein the synthesis of tryptophan is only needed when it is absent
• Lac operon


  Operon required for the transport and metabolism of lactose in E. coli and some other enteric bacteria (structural genes: lacZ, lacY, and lacA)
• Lac operon (negative transcriptional control)

  1. When lactose is absent, the repressor is active and can bind to the operator so the operon is off

  2. In the presence of lactose, the operon is on, made possible by the binding of an allolactose, an isomer of lactose, to the repressor and inactivates it, thus transcription can proceed

  3. Resulting in the synthesis of the enzymes β-galactosidase, permease and transacetylase
• Lac operon (positive transcriptional control)


  1. When glucose is low: levels of cAMP (accumulates when glucose is low or absent) are high and readily binds with CAP (activator of transcription)

  2. CAP-cAMP complex binding leads to enhanced RNA polymerase binding, leading to the production of glucose from lactose
• Classes of Sequences in Eukaryotic genes

  • Producer genes or structural genes
  • Receptor site or operator gene
  • Integrator gene or regulator gene
  • Sensor site
• Producer and integrator genes


  Involved in RNA synthesis
• Receptor and sensor sites


  Help only in recognition without taking part in RNA synthesis
• Promoters


  DNA sequences that bind to the RNA polymerase II enzyme (binding sites of transcription factors)
• Enhancers


  DNA sequences that, when bound by transcription factors, enhance the transcription of an associated gene
• Transcriptional Control occurs during RNA synthesis which involves transcription factors which are proteins that control which genes are turned on or off in the genome
• Transcription regulators need not be located so close to the genes that they regulate
• The success and efficiency by which transcription regulators work is because they work in groups
• Transcription switches (regulators) allow cells to respond to changes in the environment
• Genes in tightly packed regions are off while those in loose regions are on
• Proper packaging of the chromatin material into chromosomes during the start of cell division is related to proper and efficient segregation
• How a cell can change the expression of its genes in response to external signals like hormones

  1. Hormone enters the cell and the nucleus and affects gene expression

  2. Hormone that cannot enter the cell starts a cascade of signal relay that ultimately affects gene expression
• Transcription produces immature RNA. All classes of RNA transcripts must be processed into mature species.
• In prokaryotes, mRNA stability seems to regulate. The terminator stem and loop stabilize mRNA against nucleolytic degradation, and in some cases, removal of this structure destabilizes mRNA so that it is transcribed less efficiently.
• In eukaryotes, for the mRNA to be translated into a useful protein, introns must be removed from the transcript and still preserve the coding sequence of the mature messenger RNA
• 5' capping


  Addition of 7-methyguanylate (or m7Gpp(pN)) shortly after the beginning of transcription. The 5' methylated cap is not encoded by the DNA sequence, but is an extension. The 5' cap binds through a phosphate bridge of 2 additional phosphates, into a 5' → 5' configuration, making the cap highly resistant to degradation by nucleases.
• 3' polyadenylation


  1. After transcription termination, cleavage and polyadenylation specificity factors (CPSF) bind to a poly(A) signal sequence (typically AAUAAA) and cleavage stimulation factor (CStF), interacts with a downstream G/U signal

  2. Binding complexes, CFI and CFII (cleavage factor I and II), help stabilize the assembly and form a loop in the RNA

  3. Poly(A) polymerase (PAP) binds and stimulates cleavage at the poly(A) site. CStF, CFI and CFII are released and PAP adds a string of 200 -250 adenine residues to the 3' end.
• The 5' cap and the 3' poly(A) tail is to protect the newly synthesized mRNA from degradation by exonucleases (They are extensions which are added)
• Splicing


  1. Removal of introns (non coding) and the exons (coding) are spliced together

  2. 95% of that sequence is introns and non-coding UTRs (untranslated regions)

  3. Pyrimidine rich region, where pyrimidines occur in these 10 - 15 bases, are important for the assembly of the splicing mechanism known as the spliceosome

  4. Spliceosome is made up of 5 snRNA (small nuclear RNAs) and approximately 170 associated proteins

  5. To remove the intron and splice the exons together, the snRNPs bind to the 5' end G - U sequence and the 3' end A - G sequence
• The cell spends so much energy producing introns that are only to be cut out and recycled because it lowers the probability that a mutation will occur in a region that may reduce or impair functionality, and it gives the cell options as to how to splice that mRNA back together (alternative splicing), allowing the cell to produce varied gene products with the same set of genes
• Categories of eukaryotic genes

  • Simple transcription units: encode a single protein
  • Complex transcription units: produce a primary transcript product that can be processed in alternate ways
• Alternative Splicing


  1. The cell can select different splice sites by producing splicing repressor proteins or splicing activator proteins that bind to alternate splicing sites

  2. This directs the spliceosomes to different splicing sites or blocks a site altogether
• Reactions involved in RNA processing

  • Nucleolytic cleavage: separation of mature rRNA from the primary transcript (generated by RNA pol I)
  • Chain extension: includes synthesis/regeneration of the CCA sequence at the 3' end of tRNA
  • Nucleotide modification: example: Synthesis of methylated nucleotides in tRNA or rRNA
• Translational Control


  Ways by which translation is regulated
• Translational Control (Untranslated regions of mRNAs)

  1. Where there is a translation repressor protein attached to the ribosome-binding site, no protein will be made

  2. When ribosome-binding site and AUG portions base pair with upstream untranslated region and thus translation initiation is not possible

  3. If the ribosome-binding site and AUG are included in the loop and the loop that they are part of is cross-linked to one of the other loops, it is not possible to even start protein synthesis

  4. An antisense RNA with the sequence complementary with the sequence of the ribosome-binding site and AUG binds to the mRNA at exactly the location of those 2 sequences, it is possible for protein synthesis to start
• microRNA (miRNA)


  Small regulatory RNAs that control the expression of thousands of animal and plant genes by base-pairing with specific mRNAs and controlling their stability and their translation