DNA Structure, Replication, Transcription/Translation, and Microbial Growth Concepts

Flashcards covering key terms, definitions, and concepts from DNA structure, replication, transcription/translation, operons, biofilms, and microbial growth.

Phosphodiester bond

Covalent link between the sugar of one nucleotide and the phosphate of the next, formed in a condensation reaction that releases water.

Condensation reaction (DNA context)

Reaction that forms a phosphodiester bond and releases a molecule of water (H2O) in nucleotide linkage.

3' end

End of a nucleic acid strand with a free 3' hydroxyl group, the site where the next nucleotide is added.

5' end

End of a nucleic acid strand with a free phosphate group on the 5' carbon.

Antiparallel

Two DNA strands running in opposite directions (one 5' to 3', the other 3' to 5').

Leading strand

The DNA strand synthesized continuously toward the replication fork.

Lagging strand

The DNA strand synthesized discontinuously away from the replication fork.

Okazaki fragment

Short DNA segments formed on the lagging strand during discontinuous replication.

Primase

Enzyme that lays down RNA primers to start DNA synthesis; synthesizes RNA in the 5' to 3' direction.

DNA polymerase III

Main enzyme that adds DNA nucleotides to a primer during replication; highly processive.

DNA polymerase I

Enzyme that replaces RNA primers with DNA and fills in gaps between Okazaki fragments.

DNA ligase

Enzyme that seals nicks between DNA fragments by forming phosphodiester bonds.

Helicase

Enzyme that unwinds the DNA double helix by breaking hydrogen bonds between bases.

Single-stranded binding proteins (SSB)

Proteins that stabilize separated DNA strands to prevent re-annealing during replication.

Origin of replication

Specific DNA sequence where DNA replication begins.

Nucleoid

Region in prokaryotes where the chromosome is located; not membrane-bound.

Plasmid

Small circular DNA molecule in bacteria that is separate from the chromosome.

Histone

Protein around which eukaryotic DNA is wrapped to form chromatin.

Chromosome

Structure containing DNA; packaged for cell division, either linear (eukaryotes) or circular (some prokaryotes).

Backbone (DNA/RNA)

Sugar-phosphate chain that forms the structural framework of nucleic acids.

Deoxyribose

Sugar in DNA lacking the 2' hydroxyl group (2' H).

Ribose

Sugar in RNA with a 2' hydroxyl group (2' OH).

DNA bases (A, T, C, G)

A pairs with T; G pairs with C in DNA via hydrogen bonds.

RNA bases (A, U, C, G)

A pairs with U; G pairs with C in RNA; RNA contains uracil instead of thymine.

Transcription

Process of copying DNA into an RNA molecule using RNA polymerase.

RNA polymerase

Enzyme that synthesizes RNA from a DNA template during transcription; does not require a primer.

Promoter

DNA sequence where RNA polymerase binds to initiate transcription.

Pre-mRNA

Immature mRNA in eukaryotes that includes introns and exons before processing.

Intron

Non-coding segment of RNA that is removed during RNA splicing.

Exon

Coding segment of RNA that remains in mature mRNA after splicing.

Spliceosome

Molecular machinery that removes introns and joins exons during RNA processing.

Coding strand

DNA strand with sequence identical to the mRNA (thymine in DNA vs uracil in RNA).

Template strand

DNA strand used by RNA polymerase to synthesize the RNA transcript; complementary to the mRNA.

Start codon (AUG)

Codon that initiates translation and codes for methionine.

Stop codon (UAA/UAG/UGA)

Codon that signals termination of translation.

Codon

A three-nucleotide word in mRNA that specifies an amino acid or stop signal.

Anticodon

Three-nucleotide sequence on tRNA that pairs with a corresponding mRNA codon.

tRNA

Transfer RNA; carries an amino acid and anticodon to the ribosome during protein synthesis.

Ribosome

RNA-protein complex that reads mRNA and synthesizes proteins.

Central dogma

Concept that genetic information flows DNA -> RNA -> protein via transcription and translation.

Constitutive gene

Gene that is expressed continuously under normal conditions.

Facultative gene

Gene that is expressed only under certain conditions or stimuli.

Operon

Cluster of genes under a shared promoter and operator; can be inducible or repressible.

Lac operon

Inducible operon for lactose metabolism; repressed by LacI and induced by allolactose.

Repressor

Protein that binds the operator to block RNA polymerase and gene transcription.

Allolactose

Inducer of the lac operon that binds the repressor and relieves repression.

TRP operon

Repressible operon for tryptophan biosynthesis.

Biofilm

Structured microbial community attached to a surface, embedded in a matrix and protected from environment.

Capsule vs slime layer

Capsule is a tight, organized layer; slime layer is loose; both aid in adhesion and biofilm formation.

Quorum sensing

Cell-density–dependent regulation of gene expression via autoinducers.

Autoinducer

Small diffusible molecule used to gauge population density in biofilms.

Osmosis

Movement of water across a membrane to balance solute concentrations.

Osmotic pressure

Pressure exerted by water movement due to solute concentration differences.

Isotonic/hypotonic/hypertonic

Isotonic: equal solute; hypotonic: lower outside, hypertonic: higher outside; affects cell volume.

Oxygen requirements (five categories)

Obligate aerobe, facultative anaerobe, obligate anaerobe, aerotolerant, microaerophile.

Superoxide dismutase (SOD)

Enzyme that converts superoxide radicals into oxygen and hydrogen peroxide.

Catalase

Enzyme that decomposes hydrogen peroxide into water and oxygen.

Obligate aerobe

Microorganism that requires oxygen to grow.

Facultative anaerobe

Can grow with or without oxygen; usually grows better with oxygen.

Obligate anaerobe

Cannot tolerate oxygen; often dies in its presence.

Aerotolerant anaerobe

Does not utilize oxygen but can tolerate its presence.

Microaerophile

Requires oxygen but only at low (micro) concentrations.