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Bio 201 Lessons 12-13

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  • Process by which information encoded in DNA directs the synthesis of proteins

    Gene Expression

  • Cis Regulatory DNA sequences

    Regulatory Control Elements

  • What do regulatory control elements bind to in order to increase gene transcription above basal?

    Activator

  • What do regulatory control elements bind to in order to decrease gene transcription below basal?

    Repressor

  • Method used to produce easily detectable signals to track expression

    Repressor Genes

  • What are repressor genes used for?

    1) Determine if specific DNA sequences are regulatory

    2) Observe gene expression from a specific gene

    3) Manipulate a tissue or cells of interest

  • Segments of noncoding DNA with particular nucleotide sequences that serve as binding sites for transcription factors

    Control Elements (enhancers)

  • True or False: Eukaryotes use operons

    False

  • True or False: Each eukaryotic gene has its own promoter

    True

  • What do eukaryotes have that allows them to bind to the promoter and are essential for basal transcription?

    General Transcription Factors

  • True or False: Eukaryotes do not have specific transcription factors

    False, eukaryotes have both general and specific transcription factors

  • What purpose do specific transcription factors serve in eukaryotes?

    1) Regulate expression of a gene

    2) Bind to control elements and serve as a binding platform

    3) Involved in protein complexes that interact with other proteins

  • True or False: Eukaryotic specific transcription factors can be either activators or repressors

    True

  • What are the two domains that specific transcription factors have?

    DNA binding domain and activation/repressor domain

  • What do specific transcription factors bind to? What does this binding accomplish?

    They bind to control elements with the same chromosome and modulate levels of expression

  • What regions of the genome contain the majority of genetic changes linked to human disease?

    Non-coding regions

  • True or False: Cells have the same set of DNA instructions, but different sets of transcription factors

    True

  • What causes the ability for a gene to be transcribed?

    Location of nucleosomes along a gene's promoter and the sites where the promoter DNA attaches

  • Why is the structural organization of chromatin important?

    Packs a cell's DNA into a compact form that fits inside the nucleus and regulates gene expression

  • True or False: Genes with heterochromatin (highly condensed chromatin) are not usually expressed

    True

  • What influences chromatin structure and gene expression?

    Chemical modifications to the histone proteins and DNA nucleotides

  • What is the 1st level of control for eukaryotic gene expression?

    Chromatin Modification (DNA Unpacking)

  • What is the 2nd level of control for eukaryotic gene expression?

    Transcription

  • What is the 3rd level of control for eukaryotic gene expression?

    RNA Processing

  • What is the 4th level of control for eukaryotic gene expression?

    Transport to the Cytoplasm

  • What is the 5th level of control for eukaryotic gene expression?

    Degradation of mRNA

  • What is the 6th level of control for eukaryotic gene expression?

    Translation

  • What is the 7th level of control for eukaryotic gene expression?

    Protein Processing

  • What is the 8th level of control for eukaryotic gene expression?

    Degradation of Protein

  • What is the 9th level of control for eukaryotic gene expression?

    Transport of Protein to Cellular Destination

  • What levels of control for eukaryotic gene expression are unique to eukaryotes?

    Chromatin Modification, RNA Processing, and Transport to Cytoplasm

  • What levels of control for eukaryotic gene expression are the most economical rate limiting steps?

    Chromatin Modification and Transcription

  • Because eukaryotes don't use operons, where are genes that need coordination of expression?

    They are scattered through the genome

  • True or False: Cis and trans control elements of eukaryotes can coordinate expression of genes with related functions

    True

  • True or False: The estrogen receptor is a general transcription factor

    False, the estrogen receptor regulates expression of many genes, binds to specific control elements, and has both a DNA binding domain and a hormone binding activation domain

  • RNA that transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome

    Transfer RNA (tRNA)

  • True or False: tRNA can read the mRNA codon and interpret it as an amino acid

    True

  • What is tRNA classified as and what is it transcribed from?

    Non-Coding RNAs that are transcribed from tRNA genes

  • What stabilizes the secondary structures of tRNA?

    Intramolecular Hydrogen Bonding

  • Flexibility in the base-pairing rules in which the nucleotides at the 5' end of a tRNA antibody can form hydrogen bonds with more than one kind of base in the 3' end of a codon

    Wobble

  • Proteins that recognize stop codons

    Release Factors

  • Essential binding sites for proteins that designate the RNA as a mRNA

    Untranslated Regions (UTRs)

  • What is the function of the proteins that bind to UTRs?

    They help the mRNA get out of the nucleus and recruit the ribosome to initiate translation

  • 5' or 3' UTRs: Regulatory sequences that help ribosomes bind and initiate translation at the right location

    5' UTRs

  • 5' or 3' UTRs: poly-A tail included in eukaryotes

    3' UTRs

  • 5' or 3' UTRs: 5' methylguanine cap included in eukaryotes

    5' UTRs

  • What components are involved in the process of charging a tRNA?

    aminoacyl-tRNA synthetase enzyme and energy from ATP hydrolysis

  • True or False: Each aminoacyl-tRNA synthetase recognizes all the tRNAs that correspond to that one amino acid

    True

  • Why is the high energy bond created from charging a tRNA important?

    Powers peptide bond formation during translation

  • Site that holds the tRNA carrying the growing polypeptide chain

    P Site

  • Site that holds the tRNA carrying the next amino acid to the chain

    A Site

  • Site where discharged tRNAs leave the ribosome

    E Site

  • What does the ribosome binding site align with?

    P site

  • True or False: Transcription and translation can be coupled in eukaryotes

    False, this can only happen in bacteria

  • What does translation termination require?

    Antiparallel and complementary base pairing between two RNA molecules

  • True or False: UTRs are always part of the/processed mRNA

    True

  • True or False: Bound ribosomes are always bound to the ER and free ribosomes are always free in the cytosol

    False

  • What are reading frames set by and when do they get aligned?

    Start codons get aligned during translation initiation

  • What are the three steps in the translation cycle?

    Initiation, Elongation, and Termination

  • What are the three steps in the elongation phase of translation?

    Codon Recognition, Peptide Bond Formation, Translocation

  • Bacteria or Eukaryotes: Ribosome binding site in the mRNA

    Bacteria

  • Bacteria or Eukaryotes: Ribosome scans mRNA to find AUG

    Eukaryotes

  • Bacteria or Eukaryotes: Start codon aligned with P Site

    Both

  • Bacteria or Eukaryotes: GTP required for assembly

    Both

  • Bacteria or Eukaryotes: Proteins required for assembly of translation initiation complex

    Both

  • Bacteria or Eukaryotes: Ribosome reads the mRNA 5' --> 3'

    Both

  • What are the 1st and 3rd steps of translation powered by?

    Energy of GTP hydrolysis provided by elongation factors

  • What is the 2nd step of translation powered by?

    High energy bond betwen the amino acid and tRNAs that was created during the charging of ATP

  • What is true about the anticodon of a particular tRNA molecule?

    It must be complementary to the mRNA codon

  • True or False: Water and salt are less likely to bind to each other than proteins binding to water

    False, water and salt are more likely to bind together