Chapter 4: Genes and Genomes

Define:

• 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

Describe 3 roles of DNA other than being informational molecules

• 1) Biofilm structural component

• 2) Nutrient 

• 3) Storage of phosphate

• 4) Used as a defense by multicellular organisms 

Define repeated sequence (or repetitive sequence) and consensus sequence

• Repeated sequence: DNA sequences that exist in multiple copies

  • Repetitive: Same as repeated sequences.

• Consensus sequence: Idealized base sequence consisting of the bases most often found at each position

Describe the difference between SINEs and tandem repeats

• SINEs: Short interspersed element.

  • Almost all nonfunctional

  • Scattered throughout the genome

• Tandem repeats: Repeated sequences of DNA (or RNA) that lie next to each other.

  • Next to each other with no gaps in between 

Describe VNTRs and their use in DNA analysis

• a section of DNA where a short nucleotide sequence is repeated multiple times in a row, and the number of repeats varies significantly between individuals

• They can be used in fingerprint analysis 

Describe the following configurations of DNA:

• 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 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

Describe the correct orientation of the gel in the gel box

• position the side with the wells (sample loading area) towards the negative electrode (cathode), and the opposite end without wells towards the positive electrode (anode)

Describe how DNA migrates and is separated in an agarose matrix

• based on its size due to the negative charge on its phosphate backbone, causing it to move towards the positive electrode when an electric current is applied

Compare and contrast bromophenol blue and xylene cyanol

• Bromophenol blue: travels through the gel similarly to a DNA fragment that is 350 to 400 bp (faster)

• Xylene cyanol: equivalent to a fragment that is 3,000 to 4,000 bp (slower)

Explain the six factors that affect the migration of DNA in an agarose gel

• 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)

  • coated with water and doesn’t fluoresce well