Molecular Genetics: Transcription and CRISPR-CAS Systems

A set of vocabulary flashcards covering the mechanisms of transcription in prokaryotes and eukaryotes, the central dogma, and the CRISPR-CAS adaptive immunity system based on lecture notes.

Central Dogma of Molecular Genetics

The flow of genetic information in cells typically followed as: DNA \rightarrow Transcription \rightarrow RNA (mRNA, rRNA, tRNA) \rightarrow Translation \rightarrow Protein.

Transcription Unit

A segment of DNA that encodes an RNA molecule, consisting of a promoter, the RNA-coding region (the gene), and a terminator.

Transcription

The transfer of genetic information from DNA by the synthesis of a complementary RNA molecule copied from the DNA template.

Transcription Requirements

A DNA template (a gene), RNA polymerase enzyme, and free NTPs; notably, no primers are required.

Phosphodiester Bond Formation Equation

$$\text{NTP-NMP}_n + \text{NTP} \rightarrow \text{NTP-NMP}_{n+1} + \text{P-P}$$

Template Strand

The transcribed strand of DNA, also referred to as the antisense strand.

Non-template Strand

The DNA strand that is not transcribed, also referred to as the sense strand.

Transcription Bubble

The region of locally unwound DNA where, during elongation, the last $8$ nucleotides added remain base-paired with the DNA template.

Promoter

The binding site for RNA polymerase on the DNA molecule, located right before the $+1$ site, which is not itself transcribed.

Sigma factor ($\sigma$)

A factor found only in prokaryotes that recognizes the promoter and directs RNA polymerase to it, dissociating after transcription initiation.

Transcription Initiation Site ($+1$)

The first base of the DNA sequence to be transcribed into RNA.

Bacterial Transcription Rate

Transcription continues at approximately $50$ nucleotides/second at $37^\circ\text{C}$ until reaching the terminator sequence.

Roger Kornberg

The scientist who described eukaryotic RNA polymerase II.

Rat1

A $5' \rightarrow 3'$ RNA exonuclease in eukaryotes that binds to the unprotected $5'$ end of trailing RNA and degrades it to terminate transcription.

CRISPR RNA (crRNA)

Small RNA molecules used for adaptive immunity in prokaryotes, derived from the cleavage of a long CRISPR precursor RNA by CAS proteins.

CRISPR Array

DNA arrays in bacteria and archaea consisting of short palindromic sequences separated by spacer sequences derived from invading DNA like bacteriophages.

Acquisition (CRISPR stage)

The first stage where foreign dsDNA enters the cell, is processed, and a piece is inserted into the CRISPR array as a new spacer.

Expression (CRISPR stage)

The stage where the CRISPR array is transcribed into a precursor RNA and cleaved by CAS proteins into individual crRNAs containing one spacer.

Effector Complex

A functional unit formed by the combination of crRNA and a CAS protein used to identify and cleave foreign DNA.

Interference (CRISPR stage)

The stage where the effector complex recognizes foreign DNA via base-pair complementarity to the crRNA and the CAS protein cleaves it.