Transcription 5

• Gene


  The basic physical and functional unit of heredity
• Genome


  All genetic material of an organism (coding, non-coding, mitochondrial and chloroplast DNA)
• Genomics


  The branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes
• Locus


  Gene position on chromosome
• Allele


  Variant form of a gene or versions of the same gene at the same place on a chromosome
• Genotype


  Organism's complete set of genetic material/genes
• Phenotype


  The set of observable characteristics or traits of an organism
• Heterozygote


  An individual having two different alleles at a genetic locus
• Homozygote


  An individual having two copies of the same allele at a locus
• Gene


  • A sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein
  • Genes are arranged along chromosomes
  • The gene is located at a site on a chromosome called the gene locus
  • Genes can be coding (mRNA) and non-coding (rRNA and tRNA)

  
• DNA replication is the way of transmitting genetic information to the next generation/cell

  
• DNA replication is the main condition for cell division

  
• DNA has to be copied before a cell divides
• DNA replication takes place during the S or synthesis phase of interphase

  
• New cells will need identical DNA strands
• DNA replication


  • Begins at Origins of Replication
  • Two strands open forming Replication Forks (Y-shaped region)
  • New strands grow at the forks

  
• Replication Bubbles


  • Form as the 2 DNA strands open at the origin
  • Prokaryotes (bacteria) have a single bubble
  • Eukaryotic chromosomes have MANY bubbles
• DNA replication


  1. Enzyme Helicase unwinds and separates the 2 DNA strands

  2. Single-Strand Binding Proteins attach and keep the 2 DNA strands separated and untwisted

  3. Enzyme Topoisomerase attaches to the 2 forks of the bubble to relieve stress on the DNA molecule as it separates

  
• DNA polymerases


  • Eukaryotic cells contain five DNA polymerases: α, β, γ, δ, and ε
  • γ is located in mitochondria and is responsible for replication of mitochondrial DNA
  • The other four enzymes are located in the nucleus
  • α (RNA primer), δ, and ε are most active in dividing cells, suggesting that they function in replication
  • β is active in nondividing and dividing cells, suggesting that it may function primarily in the repair of DNA damage

  
• DNA polymerase can only add nucleotides to the 3' end of the DNA
• This causes the NEW strand to be built in a 5' to 3' direction
• DNA polymerase cannot synthesize de novo chain
• Leading strand


  • Synthesized continuously in the direction of replication fork movement

  
• Lagging strand


  • Synthesized in small pieces (Okazaki fragments) backward from the overall direction of replication
  • The Okazaki fragments are then joined by the action of DNA ligase

  
• Synthesis of the new DNA strands

  1. The Leading Strand is synthesized as a single strand from the point of origin toward the opening replication fork

  2. The Lagging Strand is synthesized discontinuously against overall direction of replication

  
• Okazaki Fragments


  Series of short segments on the lagging strand that must be joined together by an enzyme ligase

  
• Proofreading of new DNA

  • DNA polymerase initially makes about 1 in 10,000 base pairing errors
  • Enzymes proofread and correct these mistakes
  • The new error rate for DNA that has been proofread is 1 in 1 billion base pairing errors

  
• DNA repair


  1. Chemicals & ultraviolet radiation damage the DNA in our body cells

  2. Cells must continuously repair DAMAGED DNA

  3. Excision repair occurs when any of over 50 repair enzymes remove damaged parts of DNA

  4. DNA polymerase and DNA ligase replace and bond the new nucleotides together

  
• Transcription


  Transcription of genetic material from DNA to RNA

  
• RNA Polymerases


  • The DNA sequence to which RNA polymerase binds to initiate transcription of a gene is called the promoter
  • RNA-PolII: TATA box (85% genes), 20-200 nucleotides

  
• Type of RNA synthesized by each RNA polymerase

  • mRNA (Pol II)
  • tRNA (Pol III)
  • rRNA (Pol I and III)
  • snRNA and scRNA (Pol II and IIIa)

  
• Major steps of transcription

  1. Promoter recognition

  2. Initiation

  3. Elongation

  4. Termination

  
• Processing of RNA

  1. Splicing

  2. 5' CAPPING and polyadenylation

  
• Alternative splicing

  A process that enables mRNA to direct synthesis of different protein variants (isoforms) that may have different cellular functions or properties. It occurs by rearranging the pattern of intron and exon elements that are joined by splicing to alter the mRNA coding sequence.

  
• Characteristics of the genetic code

  • The genetic code is universal. All known living organisms use the same genetic code.
  • The genetic code is unambiguous. Each codon codes for just one amino acid (or start or stop).
  • The genetic code is redundant. Most amino acids are encoded by more than one codon. This is known as the degenerate code.

  
• Advantage of the degenerate code

  Mistakes happen! On occasions either at replication or transcription the nucleotide sequence can change – this is called a mutation. With a degenerate code a change in a nucleotide will either: The new codon will code for the same a.a or The new codon will code for a different a.a. What effect will the different a.a have on the resulting polypeptide structure?