Genome I

A comprehensive set of vocabulary flashcards covering genomic techniques, DNA/RNA structures, mapping methods, and molecular biology experiments based on the lecture notes.

SAGE

Stands for Serial Analysis of Gene expression; a sequencing technique used to analyze the transcriptome by isolating short cDNA fragments (tags) from mRNA and linking them together into long chains (concatemers) for simultaneous quantitative analysis.

Transcriptome

The complete collection of RNA molecules (specifically the range of messenger RNA) in a cell or tissue, used to understand when and where genes are turned on or off.

DNA microarray

A technique that uses thousands of short, single-stranded DNA sequences (probes) attached to a chip to detect the expression of thousands of genes simultaneously or to identify specific gene mutations through complementary base pairing.

Alternative splicing

A process carried out by the spliceosome where unique combinations of exons from a single gene are joined together during RNA processing, allowing one gene to produce many mRNA transcripts and increasing protein diversity.

Orthologous gene

Genes in different species that evolved from a common ancestor through speciation and normally retain the same biological function; they are used to deduce unknown gene functions and track evolutionary history.

Paralogous gene

Genes related by gene duplication within a genome that evolve independently and diverge to take on unique but related biological functions.

BLAST program

Stands for Basic Local Alignment Search Tool; a program used to compare biological sequences (DNA, RNA, or proteins) from large databases to predict gene function and observe evolutionary relationships.

Homologous recombination

A process where nucleotide sequences are switched between two identical or similar DNA molecules to repair double strand breaks using a sister chromatid as a template and to create genetic variation during meiosis.

Transposon tagging

A technique used to identify and isolate unknown genes based on phenotypes where a transposon acts as a mobile genetic element that inserts itself near mutation-causing genes to serve as a molecular tag.

RNAi

A process where small pieces of RNA inhibit gene expression or translation by neutralizing mRNA molecules, thereby silencing specific genes without altering the DNA.

Site-directed mutagenesis

A technique used to make intentional changes to a specific DNA sequence, allowing for the insertion, deletion, or substitution of exact nucleotides.

Immunocytochemistry

A technique that uses fluorescently tagged antibodies to bind to antigens, allowing the detection and visualization of the location and abundance of proteins in individual cells under a microscope.

Thermostable DNA polymerase

An enzyme used in PCR to synthesize new DNA by assembling complementary nucleotides; it is capable of withstanding the heat of protein-denaturing temperatures during the denaturation phase.

Fusion PCR

A technique to join two or more different DNA fragments without using restriction enzymes or ligases by utilizing primers with overlapping complementary sequences that hybridize during the annealing step.

RT-PCR

Reverse transcription polymerase chain reaction; a method used to detect and measure RNA by first converting it into cDNA via reverse transcriptase before undergoing standard PCR amplification.

PCR Requisites

The necessary materials for a PCR reaction: template DNA, DNA polymerase, forward and reverse primers, dNTPs, PCR Buffer, magnesium ion, nuclease-free water, thermal cycler, PCR tubes, micropipettes/tips, and micro-centrifuge.

Genetic mapping

The process of determining the positions of genes and other genetic markers on chromosomes to study gene inheritance and traits.

Physical mapping

The determination of exact distance between genes measured in nucleotide base pairs, with units such as $\text{bp}$, $\text{kb}$, and $\text{Mb}$.

Restriction mapping

A technique used to identify the location of recognition sites for specific restriction enzymes on a DNA segment to check plasmid insertion or select enzymes for cutting genes.

Fluorescent in situ hybridization (FISH)

A technique using fluorescently labeled DNA probes to detect sequences on chromosomes, used to identify missing, extra, or rearranged chromosome segments.

STS mapping

Sequence Tagged Site mapping; a technique that uses short DNA sequences with known locations to build physical maps for large-scale genomic sequencing.

Expressed sequence tags (EST)

Short strands of nucleotides from a cloned cDNA sequence derived from mRNA, representing portions of genes actively expressed in a cell.

SSLPs

Simple Sequence Length Polymorphisms; variable repeated DNA sequences used as genetic markers in mapping and DNA fingerprinting.

Clone contig

A physical map created by matching overlapping segments of cloned DNA to build a continuous stretch of a chromosome.

Sanger method

Also known as the chain-termination method; a technique to determine the order of nucleotide bases by stopping DNA replication at determined bases using modified nucleotides.

Maxam-Gilbert method

Also known as chemical sequencing; a method of determining nucleotide order by using chemicals that modify and cleave DNA at specific bases.

Pyrosequencing

A method of sequencing that detects flashes of light triggered by the luciferase-mediated oxidation of luciferin whenever a new nucleotide is added to a growing DNA chain.

Chromosome walking

A technique used to map and sequence large chromosome segments by using a known marker to find overlapping clones until a specific target gene is reached.

Sequence gap

A gap in sequencing where the general order and orientation of DNA fragments are known, but the specific nucleotide letters are unclear due to repetitive regions or low quality data.

Physical gap

An unsequenced region that lacks any information to connect DNA pieces together, occurring when a gap was not recorded or included in the data.

Reading frame

A continuous sequence of non-overlapping nucleotide triplets (codons) in DNA or RNA; a single sequence can have three possible reading frames.

Intergenic DNA

Non-coding DNA sequences located between separate genes, involved in gene regulation, non-coding RNA production, and structural organization.

Codon bias

The preference of certain organisms or genes for specific synonymous codons over others to encode the same amino acid.

Exon-intron boundary

Also called a splice junction; the point where an exon joins an intron, recognized by the cell's splicing machinery for intron removal.

Synteny

The conservation of gene order across different species that share a common evolutionary ancestor.

Zoo-blotting

A variation of Southern blotting used to detect whether a specific DNA sequence or exon is conserved across different organisms.

Genome

The complete set of DNA in an organism, including all genes and non-coding sequences.

Proteome

The whole set of proteins expressed by an organism at a certain time in a specific cell or tissue type.

System biology

An integrative approach to biology studying the relationships between mathematics, engineering, and computer science to see how different biological parts work together.

Avery experiment

A 1944 experiment that proved DNA is responsible for heredity and bacterial transformation by treating bacteria with proteases, RNase, and DNase.

DNA structure

A double helix consisting of two antiparallel strands of nucleotides, each made of deoxyribose, a phosphate group, and a nitrogenous base ($A$, $T$, $C$, or $G$).

RNA structure

A single-stranded molecule composed of nucleotides containing ribose, a phosphate group, and nitrogenous bases ($A$, $U$, $G$, and $C$).

Protein structure

Formed by chains of $20$ different amino acids; it progresses through primary, secondary, tertiary, and quaternary levels to form a functional complex.

Reverse transcriptase

An enzyme that uses an RNA molecule as a template to synthesize complementary DNA ($\text{cDNA}$).

Type II restriction endonuclease

A prokaryotic enzyme that cuts DNA at a specific site, used widely because the cut position is consistent and predicted by the recognition site.

Southern hybridization

A technique developed by Edwin Southern in $1975$ to detect specific DNA sequences by size and abundance using restriction enzymes, gel electrophoresis, and blotting.

Western blot

A technique used to separate proteins by molecular weight via SDS-PAGE and identify them using antibody incubation and fluorescence.

DNA ligase

An enzyme that joins DNA fragments together by forming phosphodiester bonds, essential for sealing Okazaki fragments and repairing DNA nicks.

Selectable marker

A gene (such as Ampicillin resistance) inserted into a cell by a vector to allow for artificial selection of cells containing the desired traits.

YAC

Yeast Artificial Chromosome; a human-engineered DNA molecule used as a shuttle vector to clone and amplify DNA sequences in yeast cells.