Ch8: DNA/RNA and Biotechnology

Comprehensive vocabulary flashcards covering DNA/RNA structure, replication mechanisms, and modern biotechnology techniques including PCR, sequencing, and genome editing.

Central Dogma

The flow of genetic information from DNA to RNA to proteins.

Nucleic Acids

Long linear polymers that carry genetic information; includes DNA and RNA.

Purines

Biopolymers comprising Adenine and Guanine.

Pyrimidines

Biopolymers comprising Cytosine, Uracil, and Thymine.

B-Glycosidic linkage

The bond that joins the nitrogenous base to either a Ribose or Deoxyribose sugar.

Nucleoside

A chemical unit composed of a nitrogenous base and a sugar.

Nucleotide

A chemical unit composed of a nitrogenous base, a sugar, and a phosphate group.

B-form DNA

The right-handed, anti-parallel 'Default' DNA Form held together by Watson–Crick base pairs.

A-form DNA

A DNA structure similar to B-form but wider, shorter, and with tilted base pairs; seen in RNA double helices and RNA–DNA hybrids.

Z-form DNA

A left-handed double helix with zigzagged phosphoryl groups and an unknown biological role.

Chargaff’s Rule

The observation by Erwin Chargaff that in a variety of organisms, the A:T and G:C ratios are each nearly $1:1$.

Stem-loop

A common structural motif in nucleic acids where two complementary sequences within a single strand form a double helix.

DNA polymerase

An enzyme that catalyzes phosphodiester-bridge formation by the formula: (DNA)n + dNTP ightarrow (DNA){n+1} + PPi.

Primase

An RNA polymerase that synthesizes a short RNA strand ($\sim 5$ nucleotides) to serve as a primer for DNA synthesis.

Okazaki fragments

Small fragments of $\sim 1,000$ nucleotides synthesized discontinuously to form the lagging strand.

Helicase

An ATP-requiring ring-like enzyme of six subunits that catalyzes the separation of the two strands of the double helix.

Topoisomerases

Enzymes that can directly alter DNA winding and supercoiling to manage torsional stress.

Linking number (Lk)

A description of DNA topology calculated by the formula $Lk = Tw + Wr$.

Processivity

The ability of an enzyme to catalyze many consecutive reactions without releasing its substrate; facilitated in E. coli by the $\beta 2$ sliding clamp.

Trombone model

A replication mode where the lagging strand is looped so it passes through the polymerase active site in the 3' ightarrow 5' direction, allowing synthesis in the 5' ightarrow 3' direction.

Restriction enzymes

Prokaryotic endonucleases that recognize specific palindromic base sequences and cleave both strands at specific places.

Southern blotting

A technique to identify restriction fragments containing specific sequences by hybridizing them with a labeled complementary DNA probe.

Northern blotting

A technique for the analysis of RNA analogous to Southern blotting.

Polymerase chain reaction (PCR)

A method for amplifying specific DNA sequences involving cycles of heating ($95^ ext{o}C$), cooling ($54^ ext{o}C$), and elongation ($72^ ext{o}C$).

cDNA

Double-stranded DNA generated from an mRNA template by reverse transcriptase.

Quantitative PCR (qPCR)

A technique using SYBR Green I to determine the quantity of mRNA transcripts based on the threshold cycle ($C_T$).

Non-homologous end joining (NHEJ)

An error-prone genome editing repair process that often results in gene knockout through insertions or deletions.

CRISPR-Cas9 system

A system derived from bacterial immune responses that uses a single guide RNA (sgRNA) and Cas9 nuclease to enable custom sequence-specific DNA cleavage.

Protospacer adjacent motif (PAM)

A short DNA sequence recognized by Cas9 that must be adjacent to the target sequence for cleavage to occur.

RNA interference (RNAi)

A technique for gene knockdown where Dicer cleaves double-stranded RNA into siRNA, which then guides the RISC complex to cleave complementary mRNA.