Genetics and DNA
True or false: A centimorgan is the length of an interval where there is a 1% chance that two markers on a chromosome will separate during mitosis.
False - there is no recombination during mitosis
True or false: Allosteric modulators induce conformational changes in proteins that affect their function.
True
True or false: Fluorescence resonance energy transfer, or FRET, is a technique used to identify protein-nucleic acid interactions.
False - This is used for protein-protein interaction
True or false: The Svedberg unit is a measure of sedimentation rate, which reflects the rate at which particles sediment in a centrifuge.
True
Unlike linear eukaryotic DNA, bacterial DNA is most typically this.
Circular
A nucleotide consists of a _________ linked to a phosphate group.
Nucleoside
Describe secondary structure of proteins.
Regions of folding patterns made stable by hydrogen bonds
This early microscopy technique allowed for the identification of different organelles and different types of cells.
Light microscope
This technique to identify interactions between a DNA-binding protein and its target DNA sequence is abbreviated as EMSA.
Electrophoretic mobility shift assay
True or False: H2 histones interact with linker DNA to allow chromatin to condense further.
False - H1 histones do this
The Meselson-Stahl experiment, which used a heavy isotope to differentiate between parental and newly synthesized DNA, demonstrated that DNA replication is ____________.
Semiconservative
These are regions of proteins that lack a fixed three-dimensional structure and instead remain flexible and dynamic.
Intrinsically disordered domains
The TWO methods among these are NOT used to quantify gene expression: qRT-PCR, ELISA, nanoStrings, qPCR, microarrays, ATAC-seq
ELISA, ATAC-seq
X-ray diffraction is best used to visualize this level of protein structure.
Tertiary (also quaternary)
This structure consists of a nucleosome core particle and one bound histone H1, further compacting DNA in chromatin.
Chromatosome
Define transition and transversion mutations. Explain which has a stronger impact on function and why.
Transitions - purine/purine or pyrimidine/pyrimidine Transversions - purine/pyrimidine or vice versa. Transversions have a stronger impact because they change the chemical structure more drastically.
Name two ways proteins can bind to nucleic acids.
Possible answers: Noncovalent bonds, van der Waals interactions with bases, electrostatic interactions between basic groups on proteins and nucleic acid phosphates
Name three different ways to assess chromatin accessibility across the genome.
ATAC-seq, DNase-seq, FAIRE-seq
You are interested in finding regions across the genome that are associated with a specific methyl mark on histones. What technique should you use?
Histone modification ChIP-seq (using an antibody that binds to your methyl mark of interest)
Much of the gene diversity in eukaryotes is due to ________ ________, which allows for exon skipping, the use of an alternative start codon, internal deletions and frameshifts, and intron retention.
Alternative splicing
Mendel’s second law states that ________________________________.
During gamete formation, the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair
List three examples of major DNA-binding domains.
Helix-turn-helix, zinc fingers, leucine zippers
Name 3 differences between microarrays and RNA-sequencing.
Possible answers: Compared to RNA-seq, microarrays have a lower sensitivity, lower dynamic range, can only detect known genes, cannot identify alternative isoforms (splice variants), and lower cost.
Nanostrings depend on fluorescence to label and identify different transcripts. However, unlike other gene expression techniques such as qPCR and in situ hybridization that also use fluorescence, nanostrings are able to quantify the expression of up to 800 genes in one reaction. Why?
Nanostrings use fluorescent BARCODES (found on the reporter probe) that use a combination of fluorophores in a specific order. These barcodes are unique to each gene and allow for independent quantification of many transcripts.
A histone associated with a repressor binding site for GeneX is acetylated. GeneX will most likely see (higher/lower) gene expression. Why?
Lower - the repressor binding site will become more accessible to a repressor protein, resulting in gene expression becoming repressed