Chapter 4: Genes and Genomes

Genome

The entire genetic information from an individual.

Chromosome

Structure containing a cell's genes and made of a single molecule of DNA.

Intergenic DNA

Noncoding DNA that lies between genes.

Intron

Segment of a gene that does not code for protein but is transcribed and forms part of the primary transcript.

Exon

Segment of a gene that codes for protein and that is still present in the messenger RNA after processing is complete.

Pseudogene

Defective copy of a genuine gene.

Fill in the Blank: A role of DNA as a biofilm structural component is that it acts as __________.

Biofilm structural component.

Fill in the Blank: DNA serves as a __________, providing essential nutrients.

Nutrient.

Fill in the Blank: DNA storage of __________ is another of its roles.

Storage of phosphate.

Repeated sequence

DNA sequences that exist in multiple copies.

Consensus sequence

Idealized base sequence consisting of the bases most often found at each position.

SINEs

Short interspersed elements; almost all nonfunctional and scattered throughout the genome.

Tandem repeats

Repeated sequences of DNA (or RNA) that lie next to each other with no gaps in between.

VNTRs

A section of DNA where a short nucleotide sequence is repeated multiple times in a row and varies significantly between individuals; used in fingerprint analysis.

Hairpin

A double-stranded base-paired structure formed by folding a single strand of DNA or RNA back upon itself.

Stem-loop

Structure made by folding an inverted repeat sequence.

A-tracts

Bending of DNA that occurs to the 3’-side.

G-quadruplex

A four-stranded structure that forms in DNA due to the presence of multiple G tracts.

Supercoiled

Higher-level coiling of DNA that is already a double helix.

Correct Orientation of Gel

Position the side with the wells towards the negative electrode (cathode) and the opposite end without wells towards the positive electrode (anode).

DNA Migration in Agarose Matrix

DNA migrates based on its size due to the negative charge on its phosphate backbone, moving towards the positive electrode when an electric current is applied.

Bromophenol blue

A dye that travels through the gel similarly to a DNA fragment that is 350 to 400 bp (faster).

Xylene cyanol

A dye equivalent to a fragment that is 3,000 to 4,000 bp (slower).

Factors Affecting DNA Migration

1. The composition of the electrophoresis buffer 2) The direction of the electrical field 3) The applied voltage 4) The concentration of the agarose 5) The conformation of the DNA 6) Intercalating dyes – Ethidium Bromide (EtBr)