Biochemistry: Nucleic Acid Structure, DNA Replication, Transcription, Translation, and Biotechnology

Vocabulary practice flashcards covering nucleic acid biochemistry, DNA replication enzymes and mechanics, transcription initiation and post-transcriptional processing, genetic code mutation types, and molecular biotechnology techniques including PCR, cloning, and microarrays.

Central Dogma

The framework first proposed by Frances Crick in 1958 describing the flow of genetic information within a biological system: DNA (information storage blueprint) to RNA (accessible working copy) to Protein (functional workhorse of the cell).

Hydrophobic Effect

The thermodynamic driving force wherein nonpolar hydrophobic molecules associate and aggregate in aqueous environments to release ordered water cages, thereby increasing the overall entropy of the system.

Hydrogen Bond

A weak non-covalent interaction formed between an electronegative donor atom (such as oxygen, nitrogen, sulfur, or fluorine) bearing a partially positive hydrogen atom ($\delta^+$) and an electronegative acceptor atom ($\delta^-$).

van der Waals Interactions

Transient, weak non-covalent forces that arise from temporary fluctuations and asymmetry in electron distribution around an atom, inducing complementary dipole polarization in adjacent neighboring atoms.

Electrostatic Interactions

Non-covalent ionic attractions or salt-bridges that occur between fully or partially charged chemical groups of opposite electrical charge.

Nucleoside

A unit of nucleic acid structure consisting exclusively of a nitrogenous purine or pyrimidine base covalently linked via a $\beta$-glycosidic linkage to a ribose or deoxyribose five-carbon sugar, lacking phosphate groups.

Nucleotide

The monomeric building block of nucleic acids composed of a five-carbon pentose sugar, a nitrogenous base attached at the $1'$ carbon, and one or more phosphate groups esterified to the sugar (e.g., at the $5'$ carbon).

Purines

A class of nitrogenous bases characterized by a bicyclic fused double-ring system (a six-membered ring fused to an imidazole ring), comprising Adenine and Guanine in nucleic acids.

Pyrimidines

A class of nitrogenous bases characterized by a single six-membered aromatic heterocyclic ring, comprising Cytosine, Thymine (found exclusively in DNA), and Uracil (found in RNA).

Deoxyribose

The five-carbon aldopentose sugar found in DNA nucleotides, distinct from ribose due to the absence of an oxygen atom at the $2'$ carbon position (bearing a hydrogen $-H$ instead of a hydroxyl $-OH$ group).

Phosphodiester Bond

The covalent linkage connecting the $3'$ hydroxyl group of one nucleotide pentose sugar to the $5'$ phosphate group of the adjacent nucleotide, forming the negatively charged sugar-phosphate backbone of nucleic acid polymers.

Melting Temperature ($T_m$)

The specific temperature at which half of the helical double-stranded DNA structure is dissociated (denatured) into single strands, a transition detectable by an increase in optical absorbance at $260\,\text{nm}$.

Histones

A family of small, highly basic proteins (H1, H2A, H2B, H3, and H4) enriched in positively charged arginine and lysine residues that electrostatically bind to the negatively charged DNA backbone to facilitate chromatin compaction.

Nucleosome

The fundamental repeating structural unit of eukaryotic chromatin, consisting of a histone octamer core particle (two copies each of H2A, H2B, H3, and H4) wrapped by double-helical DNA and connected by linker DNA in a 'beads on a string' organization.

Semiconservative Replication

The mechanism of DNA synthesis wherein each of the two parental strands separates and serves as an individual template, resulting in daughter double helices composed of one conserved parental strand and one newly synthesized strand.

Origin of Replication

A specific sequence of DNA enriched in adenine-thymine ($A\text{-}T$) base pairs where DNA double-helix unwinding begins and replication forks assemble.

DnaA Protein

An initiator protein that recognizes and binds specific repeats at the bacterial origin of replication, hydrolyzing ATP to melt and initiate the opening of the DNA double helix.

DNA Helicase (DnaB)

An ATP-dependent enzyme that binds at replication forks and unwinds double-stranded parental DNA ahead of the polymerase by breaking hydrogen bonds between base pairs.

Single-Stranded DNA-Binding Proteins (SSB)

Proteins that bind cooperatively to unwound, exposed single-stranded template DNA to stabilize it, prevent premature reannealing, and protect it from nucleolytic degradation.

Topoisomerases

Enzymes that transiently cut ('nick') one or both strands of DNA to relieve torsional tension and positive supercoiling created ahead of the unwinding replication fork before resealing the backbone.

Primase

A specialized RNA polymerase that synthesizes a short RNA primer ($5\text{–}15\,\text{nucleotides}$ long) complementary to the DNA template, providing the essential free $3'\text{-OH}$ group required for DNA polymerases to initiate elongation.

DNA Polymerase III

The primary enzyme responsible for prokaryotic DNA replicative chain elongation, synthesizing new complementary DNA strands strictly in the $5' \rightarrow 3'$ direction from a primed template.

DNA Polymerase I

A prokaryotic enzyme responsible for processing Okazaki fragments by excising RNA primers ribonucleotide by ribonucleotide with its $5' \rightarrow 3'$ exonuclease activity and filling the resulting gaps with deoxyribonucleotides, utilizing proofreading capability.

DNA Ligase

An enzyme that catalyzes the formation of a phosphodiester bond to seal single-stranded nicks remaining in the sugar-phosphate backbone between adjacent DNA fragments (such as newly synthesized Okazaki fragments).

Okazaki Fragments

Short, discontinuous segments of newly synthesized DNA formed on the lagging template strand during replication, which are subsequently processed and joined covalently.

Telomeres

Repetitive, non-coding tandem nucleotide sequences capping the ends of linear eukaryotic chromosomes that prevent the loss of critical genetic coding sequences and chromosome degradation during iterative rounds of replication.

Telomerase

A specialized reverse transcriptase enzyme carrying an internal RNA template that lengthens the ends of linear eukaryotic chromosomes to compensate for the end-replication problem.

Licensing Factor Proteins

Proteins that bind eukaryotic origins of replication prior to the S-phase to ensure each chromosomal origin fires precisely once per cell cycle, dissociating immediately once replication commences.

Transcription

The enzymatic copying of specific genetic sequences from a DNA template strand (antisense strand) into a complementary single-stranded RNA molecule, catalyzed by RNA polymerase in the $5' \rightarrow 3'$ direction.

RNA Polymerase Holoenzyme

The fully competent bacterial transcription complex comprising the core catalytic enzyme ($\alpha_2 \beta \beta' \omega$) plus the dissociable sigma ($\sigma$) initiation factor.

Sigma (\sigma) Factor

A bacterial transcription initiation subunit that confers promoter recognition specificity to the RNA polymerase core enzyme by binding consensus elements at $-35$ and $-10$, recycling off the enzyme following initiation.

Promoter

A defined non-transcribed DNA sequence located upstream of a gene (such as the $-35$ region and the $-10$ TATAAT box in prokaryotes) that directs RNA polymerase binding and specifies the exact transcription start site ($+1$).

Intrinsic Transcription Termination

A mechanism of bacterial transcription termination (Rho-independent) signaled by an inverted repeat within the nascent RNA transcript that forms a stable GC-rich hairpin stem-loop followed immediately by a run of uracil ($U$) residues, halting the polymerase and releasing the RNA.

Rho-Dependent Termination

A transcription termination pathway in prokaryotes that requires the Rho protein factor, which binds a recognition signal sequence on the nascent RNA transcript and translocates toward the transcription bubble to release the synthesized RNA.

Transcription Factor IID (TFIID)

A basal eukaryotic transcription factor protein complex containing the TATA-binding protein (TBP) that binds the core promoter to direct the assembly of the RNA Polymerase II pre-initiation complex.

5' Cap (7-methylguanylate cap)

A post-transcriptional modification added to the $5'$ end of eukaryotic pre-mRNA, featuring a 7-methylguanosine linked via an unusual $5'\text{-to-}5'$ triphosphate bridge to protect mRNA from nucleases and facilitate ribosome binding.

Poly(A) Tail

A protective modification comprising approximately $250$ adenylate nucleotides enzymatically added to the cleaved $3'$ end of eukaryotic mRNA by poly(A) polymerase following recognition of the AAUAAA cleavage signal.

Splicing

The post-transcriptional process in eukaryotes where non-coding intervening sequences (introns) are excised from primary RNA transcripts and coding sequences (exons) are joined covalently to generate mature mRNA.

Transfer RNA (tRNA)

Small adaptor RNA molecules that undergo 5' leader cleavage, 3' terminal CCA addition, base modifications, and intron removal to fold into a cloverleaf secondary structure displaying a specific anticodon and amino acid attachment site.

Complementary DNA (cDNA)

Double- or single-stranded DNA synthesized in vitro from a mature RNA template by the enzyme reverse transcriptase, creating a more stable, intron-free DNA copy for molecular analysis.

Reverse Transcriptase

An RNA-dependent DNA polymerase enzyme that synthesizes a complementary DNA (cDNA) strand utilizing an RNA template and a primer (such as an oligo(dT) primer annealed to mRNA poly(A) tails).

Reverse Transcription PCR (RT-PCR)

A molecular biology technique wherein an RNA population is first converted to cDNA by reverse transcription and subsequently amplified via standard polymerase chain reaction for gene expression analysis or cloning.

DNA Microarray

A high-throughput solid substrate (chip) containing thousands of immobilized single-stranded DNA sequences used to assess global gene expression patterns or mutations by hybridizing fluorescently labeled cDNA samples.

Restriction Endonuclease

A bacterial defensive enzyme that recognizes specific short (typically $4\text{–}6\,\text{bp}$) palindromic double-stranded DNA sequences and cleaves the phosphodiester bonds to produce defined restriction fragments with sticky or blunt ends.

Cloning Vector

A DNA molecule (typically a bacterial plasmid) capable of autonomous replication within a host cell, carrying at least one unique restriction enzyme cleavage site and an antibiotic resistance selection marker (e.g., AmpR, TetR).

Polymerase Chain Reaction (PCR)

An in vitro thermal cycling technique used to exponentially amplify ($2^n$) a specific target DNA sequence through repeated cycles of denaturation ($95^\circ\text{C}$), primer annealing ($70^\circ\text{C}$), and enzymatic extension.

Taq DNA Polymerase

A heat-stable DNA polymerase derived from thermophilic bacteria used in PCR reactions to synthesize new DNA strands at elevated temperatures without undergoing thermal inactivation during denaturation.

Gel Electrophoresis

A laboratory technique using an electric field to migrate negatively charged nucleic acids or proteins through a porous matrix (agarose or polyacrylamide) toward the positive electrode, fractionating molecules inversely by molecular size.

DNA Probe

A single-stranded oligonucleotide sequence (typically $20\text{–}30\,\text{nucleotides}$ long) labeled with a radioisotope ($^{32}\text{P}$) or fluorophore that hybridizes specifically to a complementary target sequence among complex DNA mixtures.

Codon

A continuous sequence of three nucleotide bases in mRNA that specifies a single amino acid during protein translation or acts as a signal to initiate (AUG) or terminate (UAA, UAG, UGA) synthesis.

Degeneracy (Redundancy) of the Genetic Code

The structural property of the genetic code wherein multiple distinct triplet codons can encode the same amino acid (with only Methionine and Tryptophan specified by a single codon).

Point Mutation

A genetic mutation involving the alteration of a single nucleotide base pair within a DNA or mRNA sequence, causing silent, missense, or nonsense effects.

Silent Mutation

A point mutation altering a codon base such that the new codon encodes the identical amino acid residue due to genetic code degeneracy, producing an unaltered protein.

Missense Mutation

A point mutation in which a single base substitution generates a codon that specifies a different amino acid than the original sequence.

Nonsense Mutation

A point mutation where a codon specifying an amino acid is converted into a premature stop or termination codon (UAA, UAG, or UGA), causing truncated, nonfunctional proteins.

Frameshift Mutation

A mutation resulting from the insertion or deletion of a number of nucleotides not divisible by three, permanently shifting the translational reading frame and altering all downstream amino acids.

Trinucleotide Repeat Expansion

A mutation characterized by an amplification in the number of tandem copies of a specific three-base sequence; when present in coding regions (e.g., CAG encoding glutamine in Huntington's disease), it causes toxic protein aggregation and neurodegeneration.