Chapter 15 BIO 1306

• coding strand


  The strand of a DNA duplex that is the same as the RNA encoded by a gene. This strand is not used as a template in transcription; it is complementary to the template.

  
• translation 


  the process by which the information stored in mRNA is read and used to make polypeptides that fold into proteins.
• codons


  groups of 3 nucleotides in the mRNA
• what do codons do?

  they are read to determine the amino acid sequence of the protein.
• messenger RNA (mRNA) 


  The RNA transcribed from structural genes; RNA molecules complementary to a portion of one strand of DNA, which are translated by the ribosomes to form protein.
• transfer RNA (tRNA)


  link between the messenger RNA (mRNA) molecule and the growing chain of amino acids that make up a protein.
• If an arginine nutritional mutant can grow on minimal media, supplemented with ornithine, we can conclude that...

  This mutant has a mutation in the argE gene.
• A mutant for the argG gene will be able to grow on minimal media supplemented with

  arginine

  arginosuccinate
• messenger RNA

  an intermediate is needed to carry the information in DNA to the ribosome in the cytoplasm. 
• transcription


  process of creating RNA from a DNA template.

  takes place in the nucleus

  1. RNA polymerase splits the double helix
  2. RNA nucleotides match to the unpaired DNA
  3. RNA exits the nucleus to a ribosome
• translation

  process of building a protein

  takes place at a ribosome

  1. ribosome reads 1 mRNA codon at a time - AUG start codon begins the process
  2. tRNA delivers the proper amino acid - anticodon match prevents delivery of the wrong amino acid
• frameshift mutation 


  a mutation in which a base is added to or deleted from the DNA sequence. Changes alter the reading frame downstream of the mutation.
• reading frame 


  how the nucleotides in a nucleic acid molecule are grouped into codons, with each codon containing three nucleotides. Established by the 1st codon in the sequence.
• stop codons

  UAA, UGA, UAG

  they signal "stop"

  
• start codon

  AUG

  signals "start"

  
• Crick and Brenner performed a set of experiments with viral DNA designed to determine the nature of the genetic code. What were their conclusions?

  • The genetic code has no punctuation.
  • The genetic code is read in increments of three nucleotides.
• how was the genetic code deciphered?

  by using cell-free biochemical systems to produce proteins based on synthetic mRNAs
• what happened when a single deletion or two occurred in a gene?

  the genetic message shifted and all amino acids after the deletion were altered.
• 3′ poly-A tail


  protects mRNA from degradation, aids in exporting the mature mRNA to the cytoplasm, and is also involved in binding proteins to initiate translation.
• Eukaryotic RNA polymerases

  RNA polymerase I

  RNA polymerase II

  RNA polymerase III
• RNA polymerase I

   Synthesizes ribosomal RNA (rRNA) and Recognizes species-specific promoter.
• RNA polymerase II

   Synthesizes messenger RNA (mRNA) and some small nuclear RNAs (snRNAs).Recognizes core promoter with multiple elements.
• RNA polymerase III

  Synthesizes transfer RNA (tRNA) and other small RNAs. Recognizes promoter internal to the gene.
• RNA polymerases II Transcription process

  • Requires additional factors for elongation.
  • Modifying enzymes act during transcription for:
  • Capping the 5' end.
  • Adding poly-A tail to the 3' end.
  • Splicing introns out of pre-mRNA.
• How do eukaryotic transcription factors help form the initiation complex?

  They recruit RNA polymerase to the promoter.
• what is the strongest evidence that all organisms share a common evolutionary heritage?

  the universality of the genetic code
• the components of the eukaryotic initiation complex

  promoter

  RNA polymerase II

  transcription factors
• In the transcription elongation complex of eukaryotes, what is the function of the CTD?

  It act as a platform, which recruits elongation factors and RNA-modifying enzymes,
• the primary transcript of a gene in eukaryotes...

  has to be extensively modified (include addition and removal of elements) before it can be translated.
• Before it can bind to the promoter, a eukaryotic RNA polymerase II has to be recruited by ...

  several transcription factors
• introns


  noncoding sections of an RNA transcript, or the DNA encoding it, that are spliced out before the RNA molecule is translated into a protein. 
• exon 


  coding DNA sequences expressed in mRNA and protein
• small nuclear ribonucleoprotein particles (snRNP)

  a complex composed of snRNA and protein that clusters together with other snRNPs to form the spliceosome, which removes introns from the primary transcript.
• spliceosome 


  snRNPs cluster with other proteins to form a larger complex.

  responsible for removing introns during splicing (pre-mRNA splicing.)
• transcriptome


  all RNAs produced from a genome
• proteome 


  all proteins produced from a genome
• alternative splicing


  A single gene's primary transcript can be spliced into different mRNAs using different exon combinations
• In the transcription elongation complex of eukaryotes, what is the carboxy terminal domain of RNA polymerase II made of...

  7 amino acids repeated many times.
• The poly-A tail of most mature eukaryotic mRNAs is found 

  at the 3' end of the transcript
• all modifications of eukaryotic transcripts

  addition of a 5' cap

  removal of introns

  addition of a 3' poly-A- tail