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Bio 201 Lessons 14-15

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  • What is the most economical rate limiting step in gene expression?

    Transcription initiation

  • Study of changes in gene activity that can be transmitted through cell divisions but cannot be explained by changes in the DNA sequence

    Epigenetics

  • Set of chemical modifications to the DNA and DNA-associated proteins in the cell, which alter gene expression, and are heritable via DNA replication

    Epigenome

  • What are the two types of chemical modifications to the DNA and DNA-associated proteins in the cell?

    DNA Methylation and Histone Modification

  • What characteristics indicate that a gene is transcriptionally active?

    DNA that is open and loosened from histones

  • What characteristics indicate that a gene is not transcriptionally active?

    DNA that is closed and tight around histones

  • Why do the chemical modifications of DNA methylation and histone modification occur?

    They occur as a natural process of development and tissue differentiation

  • True or False: DNA methylation and histone modification can be altered in response to environmental exposures or disease

    True

  • Where will methylated cytosine nucleotides be found?

    5' to guanosine nucleotides

  • Pairs of mCG found in clusters

    CpG Islands

  • Where can CpG islands be found relative to the promoter?

    Upstream of the promoter

  • Why is it negative that CpG islands can be found upstream of promoters?

    They prevent transcription factors from binding to control elements

  • True or False: Cells/tissues have unique gene expression patterns transcribing only the genes needed for their specific functions

    True

  • What does it mean for a gene if the promoter is highly methylated?

    The gene is off

  • In a cancer cell, a gene that normally functions to suppress cell division would likely have ______ methylation than in a wildtype cell

    More

  • What is the phenotype of a cell in which a gene that promotes cell division is hypomethylated?

    Cell division is enhanced

    (Low Methylation --> Active Transcription)

  • Would a positive or negative amino acid more likely to be prevalent in the histone tail?

    Positive amino acids because positive charged R groups can bind to negatively charged DNA

  • How does acetylation cause opening of the DNA?

    Acetylation neutralizes the positively charged lysine in the histone tail, thus loosening the ionic interaction with negatively charged DNA

  • What characteristics mean that a gene is transcriptionally active?

    DNA with a low amount of methyl group and histones with a high amount of acetyl groups

  • What characteristics mean that a gene is transcriptionally inactive?

    1) DNA with a high amount of methyl groups and histones with a high amount of acetyl groups

    2) DNA with a high amount of methyl groups and histones with a low amount of acetyl groups

    3) DNA with a low amount of methyl group and histones with a low amount of acetyl groups

  • Technique used to measure specific mRNAs based on primer design

    RT-PCR

  • What is the purpose of using RT-PCR?

    To know if a gene is being transcribed

  • True or False: Small non-coding RNAs (snRNAS) are made into proteins

    False

  • RNAs that silence genes post transcriptionally by targeting mRNA

    Small non-coding RNAs

  • Process in which different sized mRNAs and proteins can be made from the same pre-RNA

    Alternative Splicing

  • True or False: The different mRNAs in alternative splicing can have different tissue specific functions

    True

  • Are the differences in splicing due to cis or trans factors in the different cell types?

    Trans factors

  • In old school Sanger sequencing, what did each of the 4 tubes contain?

    Template DNA, a primer, DNA polymerase, and nucleotides to be modified

  • What does dideoxy nucleotide (ddNTP) sequencing begin with?

    DNA polymerase adding nucleotides to the 3' OH group of a primer

  • What happens when modified nucleotides are added to the 3' end of the growing strand?

    Polymerase stops and short segments are made

  • In a gel electrophoresis, which end do the smaller fragments represent?

    5'

  • In a gel electrophoresis, which end do the larger fragments represent?

    3'

  • In modern Sanger sequencing, what does the DNA fragment end with in each tube?

    A fluorescently labeled ddNTP

  • Number of base pairs that can be accurately read in a single sequencing run in DNA sequencing

    Read Length

  • What do cells endogenously repair to preserve genome integrity?

    Double-strand DNA breaks (DSB)

  • Term used to described DNA sequences that share the same or very similar nucleotide sequences (High level of complementarity)

    Homology

  • Why is important for the homologous strand to be available?

    Acts as a template to direct repair

  • How do CRISPR associated protein Cas9 and restriction endonucleases differ?

    A restriction enzyme only cuts one specific sequence while Cas9 can cut any sequence it is directed to

  • How can Cas9 be directed to cut a specific DNA sequence?

    By using a short nucleic acid molecule complementary to the target

  • True or False: A normal version of the gene in the donor is needed for an insertion using a donor template

    False, the insert can be anything

  • How many polypeptides make up hemoglobin?

    4

  • What causes sickle cell anemia?

    A single point mutation in the beta-hemoglobin gene

  • What is the function of dCas9 fusion proteins

    To repress and activate genes

  • Method used to recruit corepressors that drive histone methylation and chromatin condensation, thereby silencing target genes

    CRSPR Interference (CRISPRi)

  • Method used to recruit transcriptional co-activators that enhance chromatin accessibility and promote robust transcriptional activation of target genes

    CRISPR Activation (CRISPRa)