Unit 6 Gene Expression and Regulation

• DNA and sometimes RNA are the primary sources of hereditary material
• DNA


  Wrapped around proteins known as histone proteins
• Chromatin condensation


  1. Nucleosomes

  2. Chromatin

  3. Chromosomes

  
• Deoxyribose sugar


  One less oxygen than ribose sugar
• DNA directionality


  From the 5 prime end to the 3 prime end with the hydroxyl, but new nucleotides aren't added from the 5' they are added from the 3'

  
• The base pair rule is universal for DNA no matter the organism
• Base pairing rules come from conserved evolution of Purines and Pyrimidines

  
• Prokaryote DNA (bacteria)


  • Free-floating in the cytoplasm (cytosol) and specifically in the nucleoid region
  • Circular chromosomes, cannot clearly distinguish the start and end points
  • Smaller genomes
  • Contains plasmids located in the cytoplasm (some eukaryotes contain plasmids located in the nucleus)

  
• Cloning DNA using bacteria

  1. Obtain a plasmid

  2. Insert foreign DNA, creating a recombinant DNA molecule plasmid

  3. Dividing bacteria pass the recombinant DNA plasmid onto its descendents
• Nucleosome


  DNA wrapped around 8 histone proteins
• Gene


  A sequence of nucleotides coding for specific proteins

  
• Purines


  Have larger double-ring bases (Guanine and Adenine)

  
• Pyrimidines


  Have smaller single ring base (Cytosine, Thymine, and Uracil)

  
• Genome


  All genetic material
• Plasmids


  Small, circular, double stranded DNA molecules, existing independently of the bacterial chromosomes and are occasionally transferred between cells. They are used to confer resistance against environmental conditions
• Enzymes used in DNA replication

  • Helicase
  • Ligase
  • DNA polymerase
  • Topoisomerase
• New molecules are synthesized from 5' to the 3' → added onto the 3' hydroxyl group
• All characteristics come from inheritance
• DNA is a polynucleotide
• DNA polymerase is adding bases antiparallel
• Primer lays down to allow nucleotides to be added
• Leading strand


  Needs 1 RNA primer
• Lagging strand


  Needs many RNA primers (because of the many fragments)
• DNA polymerase cannot start without primers
• Purpose of RNA primer

  To act as a binding site where DNA polymerase can add the nucleotide bases
• Okazaki fragments


  Fragments of the lagging strand
• Semiconservative


  Replicated DNA will have one new strand and one old strand
• Primer


  Short segment of RNA

  
• Each codon codes for an amino acid
• Not all sections of DNA code for proteins, only around 1% do but these sections are still important

  
• Template Strand/Antisense strand/Non Coding strand, (minus) - strand

  All are the same
• Sense strand/Coding Strand/(plus) + strand

  All are the same
• Transcription


  1. RNA Polymerase adds nucleotides on the template strand

  2. Section of DNA opens forming a transcription bubble

  3. Adds uracil not thymine

  4. Transcription factors will bind on to the promoter region to help RNA polymerase bind onto the gene and form transcription initiation factor

  
• Bacteria do not have nuclei so mRNA in prokaryotes is immediately translated without additional processing. In eukaryotes, the original RNA called pre-mRNA is processed before leaving the nucleus
• Pre-mRNA processing


  1. Adds a modifying guanine nucleotide on the 5' end/cap

  2. Adds a polyA tail

  3. Introns are removed and exons are spliced

  
• 5' cap


  Determines where the ribosomal area attaches and increases stability

  
• PolyA tail


  Increases the lifespan of the mRNA
• The 5' end cap and the poly-A-tail both help in the attachment of the nucleotide bases
• Mature transcript destination


  • If it goes to a ribosomes in the cytoplasm then it will code for proteins only inside the cell
  • If it goes to a ribosome in the rough endoplasmic reticulum then it will code for a protein used in the cell membrane or outside the cell

  
• Alternative splicing


  • The process that clips different exons together to make new sequences
  • Gives different exon sequences making multiple proteins from one mature mRNA
  • Many genes can form two or more different polypeptides depending on which segments are treated as exons