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Genetics and Genome Editing Essentials
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1
Question
What is a transposable element (TE) or transposon?
Page 1
Answer
A transposable element (TE) or transposon is a DNA sequence (a “jumping gene”) that can move to a new location in the genome.
2
Question
What are sticky ends and how do they help transposable elements insert?
Page 1
Answer
Sticky ends are short single-stranded overhangs created by staggered cuts in DNA; they help transposable elements insert by base-pairing between complementary overhangs at the insertion site.
3
Question
What is transposase and what is its role?
Page 1
Answer
Transposase is an enzyme that cuts and moves DNA transposons, performing the "cut-and-paste" mobility of many transposable elements.
4
Question
What function does integrase serve in mobile genetic elements?
Page 1
Answer
Integrase is an enzyme that helps integrate DNA into a new genomic site, mediating insertion of DNA sequences into host genomes.
5
Question
How does a cut-and-paste transposon move compared with a copy-and-paste (retrotransposon)?
Page 1
Answer
A cut-and-paste transposon is excised from one site and inserted into another (original copy is removed). A copy-and-paste transposon (retrotransposon) is transcribed to RNA, reverse-transcribed to DNA, and inserted elsewhere so the original copy remains.
6
Question
Who discovered transposons in corn and what recognition did they receive?
Page 1
Answer
Barbara McClintock discovered transposons in corn and was awarded the Nobel Prize in Physiology or Medicine in 1983.
7
Question
What is a provirus or retrovirus and how can it be silenced in the host genome?
Page 1
Answer
A provirus/retrovirus is an RNA virus that is reverse-transcribed into DNA and integrated into the host genome; it is often silenced by host DNA hypermethylation.
8
Question
How can transposable element insertion affect grape color?
Page 1
Answer
Insertion of a transposable element in the promoter of an anthocyanin gene can disrupt its expression, changing purple grapes into white or green grapes by reducing pigment production.
9
Question
Define SNP (single nucleotide polymorphism) and its significance.
Page 1
Answer
A SNP is a single base change between individuals and is a major source of genetic variation; millions of SNPs account for the ~0.1% DNA difference between humans.
10
Question
What is meant by genetic diversity in humans according to the notes?
Page 1
Answer
Humans are about 99.9% similar in DNA; the ~0.1% difference corresponds to millions of SNPs and is the basis for human genetic diversity.
11
Question
What causes lactose persistence in adults at the genetic level?
Page 1
Answer
Lactose persistence is caused by a SNP in the regulatory/promoter region of the lactase gene that allows continued expression of lactase into adulthood.
12
Question
What are GalSafe pigs and why were they engineered?
Page 1
Answer
GalSafe pigs are genetically modified pigs lacking the $alpha$-1,3-galactose surface signature to reduce immune rejection/allergic responses, useful for xenotransplantation and safer animal products.
13
Question
What is $alpha$-1,3-galactose and why is it important in xenotransplantation?
Page 2
Answer
$alpha$-1,3-galactose is a sugar epitope present on most non-human mammal cells that can trigger immune rejection or allergy in humans; removing it from donor animals reduces transplant rejection risk.
14
Question
List common medical/biotech applications of removing $alpha$-1,3-galactose from animals.
Page 2
Answer
Applications include xenotransplantation (cross-species organ transplants), producing safer animal-derived products, and reducing immune rejection in recipients.
15
Question
What do the suffixes '-ose', '-ase', '-in', and '-ol' generally indicate in biology/chemistry terms?
Page 2
Answer
-ose indicates sugars (e.g., glucose, sucrose); -ase indicates enzymes (e.g., polymerase, ligase); -in often indicates proteins (e.g., insulin, actin); -ol indicates alcohols (e.g., ethanol, methanol).
16
Question
What does CRISPR stand for and what is its natural function?
Page 2
Answer
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats; in bacteria it forms DNA repeat arrays containing unique spacer sequences derived from viruses, providing adaptive immunity by recognizing and targeting viral DNA.
17
Question
What are Cas proteins and what is their role in CRISPR systems?
Page 2
Answer
Cas (CRISPR-associated) proteins are nucleases and other enzymes that cut nucleic acids; they work with CRISPR-derived guide RNAs to recognize and cleave target DNA sequences.
18
Question
What is Cas9 and why is it important in gene editing?
Page 2
Answer
Cas9 is a programmable nuclease used for gene editing that makes double-stranded cuts at targeted DNA sequences directed by guide RNA, enabling targeted modification of genomes.
19
Question
What is guide RNA (gRNA) and what does it do in CRISPR-Cas9 editing?
Page 2
Answer
Guide RNA (gRNA) is an RNA molecule that base-pairs with the target DNA sequence and directs Cas9 to a specific genomic "address," thereby specifying where Cas9 will cut.
20
Question
Compare NHEJ and HDR DNA repair pathways and their relevance after a Cas9 cut.
Page 2
Answer
NHEJ (non-homologous end joining) is an error-prone repair pathway that ligates DNA ends and often introduces small indels leading to frameshifts and gene disruption (knockout). HDR (homology-directed repair) is a precise repair pathway that uses a supplied DNA repair template to insert or correct specific sequences (knock-in).
21
Question
How does CRISPR immunity function in bacteria?
Page 2
Answer
Bacteria insert viral DNA fragments into CRISPR loci; these loci are transcribed to RNA, loaded onto Cas proteins, and used to recognize and cut matching viral DNA during subsequent infections.
22
Question
Give examples of foods engineered using CRISPR to reduce browning and explain the target.
Page 2
Answer
Non-browning mushrooms and Arctic apples are engineered to reduce polyphenol oxidase (PPO) activity, the enzyme responsible for browning, so they don’t brown when cut or bruised.
23
Question
What ethical/regulatory controversy was associated with the "CRISPR twins" case?
Page 3
Answer
He Jiankui attempted to edit the CCR5 gene in human embryos to reduce HIV susceptibility, which led to major ethical and regulatory backlash due to concerns about consent, safety, and germline editing implications.
24
Question
Name two diseases for which CRISPR-based therapies have received FDA approval and briefly describe the approach.
Page 3
Answer
CRISPR therapies have been FDA-approved for sickle cell disease and beta-thalassemia by ex vivo editing of patient hematopoietic stem cells to correct or compensate for the defective genes.
25
Question
Define gene expression.
Page 3
Answer
Gene expression is the production of a functional gene product, either RNA or protein, from a gene.
26
Question
If all cells contain the same genome, what determines different cell types and functions?
Page 3
Answer
Which genes are turned on or off (gene expression patterns) determines cell type and function, even though all cells contain the same genome.
27
Question
How does gene expression vary across an organism?
Page 3
Answer
Expression varies spatially (between tissues), temporally (during development or in response to environment), and in response to signals; this dynamic regulation determines cell behavior.
28
Question
What is the gene dosage effect?
Page 3
Answer
The gene dosage effect is the principle that the total amount of gene product depends on the number of active gene copies; more copies generally yield more product.
29
Question
What is a Barr body and why does it form?
Page 3
Answer
A Barr body is the inactive X chromosome in female mammals that forms to compensate for gene dosage differences between XX females and XY males, reducing expression from one X.
30
Question
Explain X chromosome inactivation and X-linked mosaicism with an example.
Page 3
Answer
X chromosome inactivation is the random silencing of one X in each female cell, producing X-linked mosaicism where different cells inactivate different Xs, leading to patchy phenotypes such as the calico coat pattern in cats.