Genomics and Molecular Applications Lecture Notes

Flashcards covering genomics, Hardy-Weinberg equilibrium, molecular disease applications, and gene editing technologies based on lecture materials.

Physical map

A map showing the exact location of genes on DNA measured in base pairs ($bp$), kilobases ($kb$), or megabases ($Mb$).

Cytological map

Shows chromosome banding patterns under a microscope to locate genes to specific chromosome regions, such as $7q31$.

Genetic (linkage) map

A map showing the relative positions of genes based on recombination frequency, measured in centimorgans ($cM$).

GenBank

A database that stores DNA and RNA sequences.

PubMed

A database of scientific and medical research articles.

Primer Pick

A tool used to design PCR primers.

BLAST

A tool used to compare DNA or protein sequences to known sequences.

Hardy-Weinberg allele frequency formula

The formula is $p + q = 1$.

Hardy-Weinberg genotype frequency formula

The formula is $p^2 + 2pq + q^2 = 1$, where $q^2$ is the recessive phenotype frequency.

Hardy-Weinberg Assumptions

The four assumptions are no mutation, no natural selection, random mating, and large population (no genetic drift or migration).

Pedigree symbols

Square represents male, Circle represents female, Shaded represents affected individuals, and Half-shaded represents carriers.

PCR (Polymerase Chain Reaction)

A method used to amplify DNA; gel electrophoresis is then used to separate the DNA by size.

Huntington disease (HD) mutation

A $CAG$ trinucleotide repeat expansion in the $HTT$ gene located on chromosome 4; it is autosomal dominant and causes anticipation.

Fragile X syndrome

A disease characterized by $CGG$ repeats.

Myotonic dystrophy

A disease characterized by $CTG$ repeats.

Friedreich ataxia

A disease characterized by $GAA$ repeats.

Chromosome walking

A technique using overlapping DNA clones to move step-by-step along a chromosome to locate a gene.

Cystic fibrosis (CF) mutation

The most common mutation is the $\Delta F508$ deletion in the $CFTR$ gene, inherited in an autosomal recessive manner.

Sickle cell disease (SCD) mutation

A missense mutation ($Glu \rightarrow Val$) in $\beta$-globin, inherited in an autosomal recessive manner.

Northern blot

A technique used to detect mRNA, show tissue expression of a gene, and confirm gene transcription.

Gene therapy

Treating disease by adding or modifying genes.

Transgene

A foreign gene inserted into an organism.

Transgenic

An organism that carries a transgene.

Somatic cell gene therapy

Gene therapy performed in body cells that is not inherited.

Vector

A carrier, such as a virus or plasmid, used to deliver genes.

BAC

Bacterial Artificial Chromosome.

Contig

A set of overlapping DNA segments that represent a consensus region of DNA.

Shotgun sequencing

A sequencing method; Venter used whole-genome shotgun sequencing for faster assembly.

Sanger sequencing

A method of DNA sequencing; Collins used a clone-by-clone (BAC) approach.

Exon

A sequence of DNA that codes for proteins.

Intron

A noncoding sequence of DNA that is removed during splicing.

GFP (Green Fluorescent Protein)

A reporter gene that glows green under UV/blue light to indicate promoter activity or monitor gene expression.

Mitochondrial DNA

Circular DNA located in mitochondria that is inherited only from the mother.

Microarray

A tool that measures the expression of thousands of genes simultaneously; overexpressed genes show an increased signal.

VNTR

Variable Number Tandem Repeats; long repeat sequences detected by Southern blot.

STR

Short Tandem Repeats; short repeat sequences detected by PCR and fluorescent analysis.

rHGH in E. coli

Recombinant human growth hormone produced in $E. coli$ using human cDNA because $E. coli$ cannot splice introns.

Pronuclear injection

One of the two mechanisms used to engineer transgenic mice.

NeoR

A positive selectable marker (neomycin resistance) used in knockout gene creation to identify successful insertions.

HSV-tk

A negative selectable marker used to remove random insertions during the creation of a knockout gene.

CRISPR/Cas9

A DNA editing tool that uses a guide RNA (gRNA), Cas9 nuclease, and PAM sequence to make permanent changes to DNA.

RNAi (RNA interference)

A system that degrades mRNA to temporarily silence gene expression; deduced by Andrew Fire and Craig Mello.

Ti plasmid

A plasmid found in Agrobacterium used to transfer genes (T-DNA) into plants.