Molecular Genetics: Structure of DNA/RNA, Chromosomes, Replication, Transcription, and Lab Techniques

Vocabulary flashcards covering the molecular structure of DNA and RNA, bacterial and eukaryotic chromosome organization, transposable elements, semiconservative replication mechanisms, transcription initiation and termination, and molecular lab techniques.

Nucleoside

A molecular structure composed only of a sugar and a nitrogenous base.

Nucleotide

The structural building block of nucleic acids, consisting of a sugar (deoxyribose in DNA), a nitrogenous base, and a phosphate group.

Griffith's Experiment

An experiment showing that heat-killed virulent smooth (S) bacteria can transform live nonvirulent rough (R) bacteria into virulent S bacteria.

Avery, MacLeod, and McCarty Experiment

An experiment that used enzymes to systematically destroy specific molecules, demonstrating that transformation stopped when DNA was destroyed and identifying DNA as the transforming substance.

Hershey-Chase Experiment

An experiment using $^{32}\text{P}$ to label DNA and $^{35}\text{S}$ to label protein in T2 bacteriophages infecting E. coli, showing that DNA enters host cells and serves as the genetic material.

Chargaff's Rules

The observation of base composition in DNA where the amount of adenine equals thymine ($A = T$) and cytosine equals guanine ($C = G$).

B-DNA

The predominant right-handed helical form of DNA in living cells, characterized by base pairs oriented perpendicular to the central axis, with $10$ base pairs per $3.4\,\text{nm}$ complete turn.

Z-DNA

A left-handed conformation of DNA that forms under certain conditions, characterized by a zigzag sugar-phosphate backbone.

Intergenic Region

Nontranscribed DNA segments located between genes in bacterial chromosomes.

Nucleoid

The region within a bacterial cell where the chromosome is located.

Nucleoid-Associated Proteins (NAPs)

Bacterial proteins that bend DNA, connect distant DNA regions, and organize and compact the bacterial chromosome.

Negative Supercoiling

The twisting of DNA to compact it, which aids in DNA organization and promotes strand separation during replication and transcription.

Topoisomerase I

An enzyme that relaxes negative supercoils in bacterial chromosomes.

DNA Gyrase

Also known as Topoisomerase II, an enzyme that introduces negative supercoils, relaxes positive supercoils, and untangles bacterial DNA.

Kinetochore

A group of proteins associated with the centromere that connects the chromosome to the spindle apparatus for segregation.

Telomeres

Specialized structures located at the ends of eukaryotic chromosomes that maintain chromosome length and prevent translocations.

Exons

The protein-coding regions of eukaryotic genes.

Introns

Noncoding intervening sequences within eukaryotic genes that are removed during RNA processing.

Transposition

The process by which a DNA segment moves or is inserted into a new location within the genome.

Transposable Elements (TEs)

DNA sequences, also known as jumping genes, that can move to different locations within a genome; first discovered by Barbara McClintock in corn.

Simple Transposition

A cut-and-paste mechanism carried out by transposons in which the original DNA segment is physically removed and inserted elsewhere.

Retrotransposition

A transposition mechanism using an RNA intermediate, where the transposable element is transcribed to RNA and copied into a new DNA segment by reverse transcriptase before insertion.

Transposase

An enzyme that facilitates the excision and insertion of transposable elements during transposition.

Integrase

An enzyme responsible for inserting reverse-transcribed retrotransposon DNA into a new genomic location.

Reverse Transcriptase

An enzyme that synthesizes a complementary DNA (cDNA) strand using an RNA molecule as a template.

Insertion Element (IS)

The simplest type of transposable element, characterized by inverted repeats at its ends and potentially encoding a transposase gene.

Meselson and Stahl Experiment

An experiment using $^{15}\text{N}$ and $^{14}\text{N}$ isotopes in E. coli to confirm that DNA replicates in a semiconservative manner.

DnaA

A bacterial replication initiation protein that binds to DnaA boxes at the origin of replication (ORI).

DnaB

A helicase enzyme in bacteria that breaks hydrogen bonds between bases to unwind and separate DNA strands.

Single-Strand Binding Proteins

Proteins that bind to separated single strands of DNA at the replication fork to prevent them from reannealing.

Primase

An RNA polymerase that synthesizes short RNA primers to provide a free $3'\text{-OH}$ group for DNA polymerases.

DNA Polymerase III

The primary bacterial enzyme responsible for synthesizing new DNA strands in the $5'$ to $3'$ direction at a rate of approximately $750$ nucleotides per second.

DNA Polymerase I

A bacterial DNA polymerase that removes RNA primers via its $5'$ to $3'$ exonuclease activity and replaces them with DNA.

DNA Ligase

An enzyme that catalyzes the formation of phosphodiester bonds to join adjacent DNA fragments together.

Processivity

The ability of DNA polymerase to remain associated with the template strand and continuously synthesize nucleotides without dissociating.

Proofreading

The error-correcting mechanism of DNA polymerases utilizing $3'$ to $5'$ exonuclease activity to excise mismatched nucleotides.

DNA Polymerase Alpha ($\alpha$)

A eukaryotic DNA polymerase that associates with primase to initiate DNA replication.

DNA Polymerase Epsilon ($\epsilon$)

The eukaryotic DNA polymerase primarily responsible for synthesizing the leading strand during replication.

DNA Polymerase Delta ($\delta$)

The eukaryotic DNA polymerase primarily responsible for synthesizing the lagging strand during replication.

DNA Polymerase Gamma ($\gamma$)

The eukaryotic DNA polymerase responsible for replicating mitochondrial DNA.

Flap Endonuclease

An enzyme in eukaryotic DNA replication responsible for removing RNA primers.

Pribnow Box

The $-10$ consensus sequence (TATAAT) found in bacterial promoters, where DNA unwinding begins to form an open complex.

Sigma Factor

A bacterial protein subunit that binds to the core RNA polymerase enzyme to recognize promoter sequences at the $-35$ and $-10$ regions.

Rho-Dependent Termination

Bacterial transcription termination requiring the external ATP-powered Rho protein to chase paused RNA polymerase and unwind the RNA-DNA hybrid.

Rho-Independent Termination

Intrinsic bacterial transcription termination mediated by the formation of an RNA hairpin loop structure followed by a uracil-rich tract, causing the RNA transcript to release.

Cis-Acting Elements

DNA sequences located on the same molecule as the gene they regulate (e.g., TATA box, enhancers, silencers).

Trans-Acting Factors

Regulatory molecules encoded anywhere in the genome that diffuse through the cell to bind cis-acting DNA elements.

TFIID

A general transcription factor in eukaryotes that recognizes and binds specifically to the TATA box in the promoter.

TFIIH

A general eukaryotic transcription factor that acts as a helicase to unwind DNA and phosphorylates the carboxyl-terminal domain of RNA Polymerase II.

Allosteric Model of Termination

A model of eukaryotic transcription termination where cleavage near the poly-A signal alters the conformation of RNA polymerase II, leading to dissociation of elongation factors and release from DNA.

Torpedo Model of Termination

A model of eukaryotic transcription termination in which an exonuclease degrades the remaining RNA transcript from the $5'$ end after cleavage, ultimately catching and dissociating RNA polymerase II.

Denaturation (PCR)

The first step in a polymerase chain reaction cycle, typically conducted at $95^\circ\text{C}$, which breaks hydrogen bonds to separate double-stranded DNA into single strands.

Annealing (PCR)

The second step of PCR in which temperature is lowered to allow forward and reverse primers to hybridize to their target sequence.

Oligo (dT) Primers

Short synthetic deoxythymidine sequences that bind specifically to the poly-A tail of eukaryotic mRNA to prime cDNA synthesis.

no-RT Control

A negative control in RT-PCR containing RNA and PCR reagents without reverse transcriptase, used to detect genomic DNA contamination.