Gene Technology and Bioinformatics Review

Flashcards covering key concepts from the lecture notes on gene technology, PCR, DNA profiling, genetic code, recombinant DNA, bioinformatics, sequencing, and GM crops.

What is the primary function of restriction enzymes in gene technology?

To recognize specific DNA sequences and cut the DNA at these sites.

What is the primary purpose of plasmid mapping?

To determine the location and order of restriction enzymes cut sites on a plasmid.

What is the name and typical temperature of the first step in PCR, which separates double-stranded DNA?

Denaturing, which occurs at 94 to 96 degrees Celsius.

What is the name and purpose of the second step in PCR, which occurs at 50 to 55 degrees Celsius?

Annealing, where the forward and reverse primers bind to specific locations on the single-stranded DNA.

What occurs during the extension or elongation step of PCR?

Taq DNA polymerase binds to the primers and synthesizes new complementary DNA strands.

In a PCR reaction, what is the DNA molecule that contains the region to be amplified?

DNA template.

What is the role of Taq DNA polymerase in a PCR reaction?

It is an enzyme that extends and synthesizes the new complementary DNA strand.

What are primers in the context of a PCR reaction?

Short single-stranded DNA sequences that are complementary to a specific region of the template DNA.

What are the building blocks, abbreviated as dNTPs, required for synthesizing a new DNA strand in PCR?

Deoxynucleoside triphosphates (ATGC).

Why are divalent cations like Mg2+ or Mn2+ essential components of a PCR reaction?

They are required for the DNA polymerase to function properly.

Which type of PCR is used to convert mRNA into complementary cDNA to detect gene expression?

Reverse transcriptase PCR.

The PCR technique that uses multiple primer pairs to amplify several different genes in a single reaction is called…?

Multiplex PCR.

Which type of PCR utilizes a fluorescent dye that binds to amplified DNA, allowing for quantification of the product?

Real-time PCR.

What is the key feature of nested PCR?

It uses two sets of primer pairs where the second set amplifies a fragment within the product of the first set.

What is the difference between microsatellites and minisatellites?

Microsatellites are repeats of two to five base pairs, while minisatellites (VNTR) are repeats of 10 to 60 base pairs.

Name the three main techniques used for DNA profiling.

Restriction Fragment Length Polymorphism (RFLP), Variable Number Tandem Repeats (VNTR), and Short Tandem Repeats (STR).

List the three steps of the Restriction Fragment Length Polymorphism technique in order.

DNA isolation, DNA fragmentation with restriction enzymes, separation by electrophoresis, and visualization via Southern blotting.

What is a key feature of the primers used in the Short Tandem Repeats technique?

They are labeled with fluorescent tags to allow for detection after electrophoresis.

What does it mean for a genetic code to be universal?

The same codons specify the same amino acid in nearly all living organisms.

The characteristic of the genetic code where each codon is an independent set of three bases read from a fixed starting point is known as…?

Non-overlapping.

What does it mean that the genetic code is degenerate?

The same amino acid can be coded for by more than one codon.

The property that the genetic code is always read in a fixed 5' to 3' direction is referred to as…?

Polar.

What is meant by the non-ambiguous nature of the genetic code?

A particular codon will always code for the same single amino acid.

What is the second key step in recombinant DNA technology after isolating the target DNA?

Using restriction enzymes to cut both the target DNA and the cloning vector.

What is the term for the process of transferring a recombinant DNA vector into a bacterial cell?

Transformation.

In blue and white screening, why do colonies containing a recombinant plasmid appear white?

The insertion of the recombinant gene disrupts the lacZ gene, preventing the production of functional enzyme.

In colony hybridization, how are successfully transformed colonies identified?

They produce a positive signal because the radiolabeled probe has bound to the gene of interest.

What is the definition of primary database informatics?

Repositories containing raw, unanalyzed DNA and protein sequence datasets accessible to the public.

What is the definition of secondary database informatics?

Databases containing data that has been derived from the analysis of entries in primary databases.

Which BLAST tool would you use to search a nucleotide database using a nucleotide query, for example, when looking for a sequence in similar species?

BLASTn.

Which BLAST tool would you use to search a protein database using a protein query?

BLASTp.

Which BLAST tool is used to search a protein database with a query that is a nucleotide sequence that first gets translated?

BLASTX.

The BLAST tool _ is used to search a translated nucleotide database using a protein query, which is useful for finding genes in distantly related species.

TBlastn.

What is the purpose of the FASTA format in bioinformatics?

It is a standard text-based format for representing nucleotide or protein sequences.

What are bioinformatics tools like ClusterW and ClusterOmega commonly used for?

Performing multiple sequence alignments and phylogenetic analysis.

The Sanger sequencing method developed in 1977 is also known by what name?

The chain termination method.

What is the function of modified dideoxynucleotide triphosphates (ddNTPs) in Sanger sequencing?

They terminate the extension of the DNA strand because they lack a 3'-OH group.

Which second-generation sequencing technology utilizes a process called bridge amplification?

Illumina sequencing.

Which second-generation sequencing technology relies on the detection of hydrogen ions released during nucleotide incorporation?

Ion torrent semiconductor sequencing.

Which third-generation sequencing technology detects the fluorescent signal of a single nucleotide being added to a DNA strand in real-time?

Single molecule real-time sequencing.

Oxford Nanopore technology sequences DNA by monitoring changes to a _ as nucleic acids are passed through a protein nanopore.

Electro current.

What is the primary characteristic of first-generation GM crops?

They possess enhanced traits like herbicide tolerance or insect resistance without significant changes in phenotype, taste, or nutrition.

How do second-generation GM crops differ from first-generation?

They have increased nutrition benefits for consumers, such as higher vitamin or protein levels.

What is a major goal for the development of third-generation GM crops?

To provide resistance to abiotic stress or produce active pharmaceutical products.