PCR and Forensics – Vocabulary Flashcards (Notes: The Polymerase Chain Reaction)

Vocabulary flashcards covering key concepts, reagents, steps, and technologies described in the PCR lecture notes.

Polymerase Chain Reaction (PCR)

A lab technique developed in the mid-1980s by Kary Mullis to amplify a specific DNA region by cycling denaturation, primer annealing, and extension using a DNA polymerase.

VNTR (Variable Number Tandem Repeat)

A repetitive DNA region used as a target in PCR for forensic analysis.

Target DNA

The DNA region selected for amplification; typically 100–1500 bp, with 100–500 bp common in forensics; shorter targets help with degraded samples.

Denaturation

The process of unzipping DNA by heating to about 95°C to form two single strands.

Annealing

Cooling to about 50–65°C to allow primers to bind to complementary sequences.

Extension

Raising temperature to about 72°C so Taq polymerase extends new DNA strands from the primers.

Taq Polymerase

Thermostable DNA polymerase isolated from Thermus aquaticus that copies DNA during PCR.

DNA Polymerase

Enzyme that reads the DNA sequence and builds the complementary new strand by adding nucleotides.

Nucleotides

The building blocks (A, C, G, T) used to synthesize new DNA strands.

Buffer

Maintains pH and optimizes PCR conditions.

Primers

Short DNA sequences (~20–30 bp) that flank the target region and provide starting points for DNA synthesis.

Forward Primer

Primer that binds to the left-side strand and is read left to right (5’-to-3’).

Reverse Primer

Primer that binds to the opposite strand and is read right to left (5’-to-3’).

5’-3’ Primer Direction

The orientation in which primers are read; forward reads left to right, reverse reads right to left.

Single Cell DNA

A single cell can provide enough DNA for PCR.

Exonuclease Activity / Proofreading

Modern DNA polymerase proofreading ability that corrects mistakes to ensure accurate copies.

Temperature Cycling (Denaturation, Annealing, Extension)

The three main steps repeated in PCR to amplify DNA, typically 25–35 cycles.

Denaturation Temperature

Usually around 95°C; separates DNA into two single strands.

Annealing Temperature

Generally 50–65°C; allows primers to bind to target DNA.

Extension Temperature

Typically 72°C; polymerase extends the new DNA strand from the primer.

Primer Design Temperature Formula

Primer sequence determines the temperature: [2(A+T) + 4(G+C)] - 5 ≈ primer temp (optimal range 50–65°C).

Primer GC Content

G and C should make up about 40–60% of the primer to achieve the desired temperature.

Exponential Amplification

Each PCR cycle doubles (approximately) the number of target DNA molecules, leading to exponential growth.

Capillary Electrophoresis

A highly sensitive method using fine capillaries to separate DNA by size and detect with lasers; can distinguish 1 bp differences.

Gel Electrophoresis

Classical method to separate amplified DNA by size on a gel.

Mastermix

Pre-mixed solution containing primers, nucleotides, buffer, and polymerase prepared to run a reaction; ensures consistent ratios.

Forensics Use of PCR (VNTRs)

PCR amplified VNTRs are analyzed to identify individuals; electrophoresis is used to visualize the results.

DNA Size Ladder / Alignment Marker

A reference set of DNA fragments used to size PCR products and normalize across capillaries.