unit 3 test

• mRNA synthesis in the nucleus

  1. DNA

  2. Transcription

  3. mRNA

  4. Movement of mRNA into cytoplasm via nuclear pore

  
• Protein synthesis in the cytoplasm

  1. Ribosome

  2. Amino acids

  3. Polypeptide synthesis
• "Central Dogma of Biology"

  DNA -> RNA -> Proteins

  
• DNA replication - a simple outline

  1. Open

  2. Copy

  3. Untangle

  4. Close

  5. Repair

  
• Comparison of DNA and RNA

  • DNA: Double stranded, Sugar = deoxyribose, Thymine, Stable, One function: storage of genetic information
  • RNA: Single stranded, Sugar = ribose, Uracil, Reactive, Multiple functions: mRNA, tRNA, rRNA, miRNA

  
• The lagging strand is synthesized in pieces
• Another example of DNA repair: Excision repair


  Damaged region is removed and replaced by DNA synthesis
• DNA Repair


  • There are many pathways, we talked about 3 examples
  • Recognize the terms mismatch repair and excision repair and have a basic understanding of what they are
• Eukaryotic Replication


  • Larger amount of DNA in multiple chromosomes
  • Complex packaging
  • Linear structure

  
• Eukaryotic replication


  1. Multiple origins on each chromosome- not sequence specific

  2. Priming is done by DNA polymerase (alpha) α and primase

  3. DNA pol ε (epsilon) copies the leading strand

  4. DNA pol δ (delta) copies the lagging strand

  5. Sliding clamp is PCNA (proliferating cell nuclear antigen)

  6. Helicase moves in the opposite direction along DNA

  
• Telomerase


  Enzyme makes telomere section of lagging strand using an internal RNA template (not the DNA itself)

  
• Bacterial Cell Division


  • Bacteria divide by binary fission
  • No sexual life cycle
  • Reproduction is clonal
  • Single, circular bacterial chromosome is replicated
• Eukaryotic Chromosomes- every species has a different number of chromosomes in their somatic cells (10-50 typically)
• Chromatin organization


  • Chromatin is organized into territories
  • Territories contain individual chromosomes
  • Compartments exist within each chromosome
  • Formed by TADs (topologically associated domains)
• TADs


  • Loops of DNA in nucleosomes
  • Anchored by CTCF and Cohesins
  • Organization may affect the control of gene expression

  
• How to study for mitosis


  • Know all of the stages and a 1 sentence description for what happens at each stage
  • Know the general shape and organization of the DNA at each stage
  • Think about what would happen if there are mutations in proteins involved

  
• Overview of M phase

  1. Prophase

  2. Prometaphase

  3. Metaphase

  4. Anaphase

  5. Telophase
• Eukaryotic Cell Cycle


  • G1 (gap phase 1)
  • S (synthesis)
  • G2 (gap phase 2)
  • M (mitosis)
  • C (cytokinesis)
• Important terms to remember

  • Chromosome
  • Homologue
  • Sister Chromatid
  • Centromere
  • Kinetochore
  • Cohesin
  • Condensin

  
• Cell cycle control


  3 Checkpoints: G1/S, G2/M, Late metaphase (spindle)

  
• How cyclins work


  • By changing in concentration
  • By complexing with a cyclin-dependent kinase

  
• Genetic Code


  • The order of nucleotides in DNA encoded amino acid sequence
  • Codon – block of 3 DNA nucleotides corresponding to an amino acid
• Characteristics of the genetic code

  • Made up of codons (triplets of bases)
  • Codons do not overlap
  • Includes "stop" codons
  • Degenerate or redundant code
  • Read from a fixed starting point (AUG)
  • Read from 5' to 3' end
  • Mutations can change the message
• Specialized Codons


  • Starting protein synthesis: AUG (methionine)
  • Stopping protein synthesis: TGA, TAA, TAG (don't encode anything)

  
• Reading Frame


  • Only one strand of DNA encodes protein for most genes
  • Template strand vs Coding strand
  • Three possible start points when reading a coding strand or RNA sequence

  
• Transcription Initiation


  1. RNA polymerase binds to DNA

  2. Transcription bubble forms

  3. RNA synthesis begins

  
• Transcription Elongation


  1. Ribonucleotides added to 3' end

  2. Transcription bubble moves along DNA

  
• Transcription Termination


  1. Happens at terminator sequence

  2. Phosphodiester bond formation stops

  3. RNA-DNA hybrid dissociates

  4. RNA polymerase releases DNA
• Eukaryotic pre-mRNA splicing


  1. Introns removed

  2. Exons joined together

  3. Small ribonucleoprotein particles (snRNPs) recognize intron-exon boundaries

  4. snRNPs form spliceosome to remove introns
• Alternative splicing


  Single primary transcript can be spliced into different mRNAs by including different sets of exons
• Basic Gene Structure


  • Promoter: Control region, not transcribed
  • Transcription Unit: Portion of gene transcribed into RNA

  
• Eukaryotic Transcription


  • 3 different RNA polymerases: I, II, III
  • Each recognizes its own promoter

  
• Types of RNA


  • Messenger RNA (mRNA)
  • Ribosomal RNA (rRNA)
  • Transfer RNA (tRNA)
  • Small nuclear RNA (snRNA)
  • Signal recognition particle RNA (SRP RNA)
  • Micro-RNA (miRNA)

  
• Control region


  NOT transcribed
• Control region


  • Contains conserved regions
  • Bases numbered negatively from right to left
• Transcription Unit


  • Portion of gene transcribed into RNA
  • Bases numbered positively from first base

  
• Eukaryotic Transcription


  • RNA polymerase I transcribes rRNA
  • RNA polymerase II transcribes mRNA and some snRNA
  • RNA polymerase III transcribes tRNA and some other small RNAs

  
• Each RNA polymerase recognizes its own promoter
• RNA


  • Messenger RNA (mRNA)
  • Ribosomal RNA (rRNA)
  • Transfer RNA (tRNA)
  • Small nuclear RNA (snRNA)
  • Signal recognition particle RNA (SRP RNA)
  • Micro-RNA (miRNA)

  
• All RNA is synthesized from DNA template by transcription