Cellular Energetics, Molecular Biology, and Microbial Genetics

Vocabulary flashcards covering cellular energetic pathways, central dogma, prokaryotic transcription/translation, bacterial gene transfer, and DNA repair mechanisms based on lecture notes.

Central Dogma

The flow of genetic information: Genes (DNA) to transcript (RNA) to protein (Function).

RNA Polymerase

An enzyme that synthesizes RNA during transcription.

Sigma Factor ($\sigma$)

A protein factor needed only for the initiation of RNA synthesis that guides RNA polymerase to the promoter's $-10$ and $-35$ regions.

Holoenzyme

The complex formed by the core enzyme plus the sigma factor.

Rho-Dependent Termination

A transcription termination mechanism in which the Rho protein binds mRNA and releases the mRNA and RNA polymerase from DNA.

Rho-Independent Termination

A transcription termination mechanism where an RNA hairpin followed by U bases causes mRNA and RNA polymerase to detach from RNA.

Codons

Triplets of nucleotides consisting of 61 codons encoding 20 amino acids and 3 stop codons.

16S rRNA

A ribosomal RNA molecule found in the $30\text{S}$ small ribosomal subunit of bacteria and archaea, used for the identification of unknown bacteria.

Shine-Dalgarno Sequence

The ribosome binding site on mRNA that allows binding to the $30\text{S}$ ribosomal subunit during translation initiation.

Transformation

A form of genetic transfer in which free naked DNA is taken up from the environment and integrated into the genome.

Conjugation

The transfer of DNA from one bacterium to another cell via cell-cell contact.

Transduction

DNA transfer between bacteria mediated by a bacteriophage.

DNA Methylation (Bacterial Defense)

A process where bacteria add methyl groups to their own DNA to protect it from restriction enzymes.

Restriction Enzymes

Enzymes that recognize and destroy unmethylated foreign DNA.

Mutation

Heritable changes in the nucleic acid bases in the genome of an organism.

Point Mutations

Mutations that involve a change in a single base.

Missense Mutation

A mutation that leads to an amino acid charge.

Silent Mutation

A mutation that does not change the amino acid due to the degeneracy of the genetic code.

Nonsense Mutation

A mutation that produces a stop codon.

Non-Homologous End Joining

A mechanism that repairs double-strand DNA breaks without requiring homologous DNA, utilizing Ku-family proteins to bind broken ends and ligase to join the ends.

Proofreading

A mechanism where DNA polymerase catches and fixes mistakes during DNA replication.

Nucleotide Excision Repair

A repair pathway that recognizes damages causing distortion in DNA structure.

Base Excision Repair

A repair pathway that recognizes and repairs bases that do not distort DNA structure.

Methyl Mismatch Repair

A repair pathway that recognizes mismatches missed by proofreading.