Molecular Biology: Nucleic Acids, Replication, Gene Expression, and Proteins

Vocabulary practice flashcards covering core concepts of molecular genetics and biochemistry, including translation, transcription, DNA replication, nucleic acid structure, chromatin packaging, and protein structure and function.

Ribosome

A ribonucleoprotein complex composed of large and small subunits and rRNA that promotes interaction between tRNAs and mRNA to synthesize proteins; found in the cytoplasm of prokaryotes and in the cytoplasm and rough endoplasmic reticulum of eukaryotes.

A Site (Aminoacyl Site)

The tRNA binding site on the ribosome where an incoming charged tRNA carrying a specific amino acid binds during translation elongation.

P Site (Peptidyl Site)

The ribosomal binding site that holds the tRNA attached to the growing polypeptide chain.

E Site (Exit Site)

The ribosomal binding site through which uncharged tRNAs leave the ribosome after donating their amino acid to the growing peptide chain.

Degeneracy of the Genetic Code

The characteristic of the triplet genetic code whereby $18$ of the $20$ standard amino acids are specified by more than one codon.

Aminoacyl-tRNA Synthetase

An enzyme that uses ATP to covalently attach a specific amino acid to the 3' end of its cognate tRNA during protein synthesis

Shine-Dalgarno Sequence

A conserved sequence found on prokaryotic mRNA adjacent to the start codon (AUG) that binds the small ribosomal subunit ($30\text{S}$) to initiate translation.

Peptidyl Transferase

A catalytic RNA molecule (ribozyme) within the large ribosomal subunit that catalyzes peptide bond formation via condensation between the amino acid in the A site and the peptidyl-tRNA in the P site.

Release Factor

A regulatory protein that recognizes and binds to a stop codon (UAA, UAG, or UGA) in the ribosomal A site, prompting peptidyl transferase to cleave the polypeptide from the P-site tRNA and disassembling the translation complex.

Polyribosome (Polysome)

A structure formed by multiple ribosomes simultaneously translating the same mRNA molecule in a sequential manner.

Chromatin Remodeling

The cellular process of altering chromatin condensation via DNA methylation, histone modification (acetylation and methylation), and chromatin remodeling complexes to regulate transcriptional access to genes.

Missense Mutation

A point mutation in DNA that changes a single codon in mRNA, resulting in the substitution of one amino acid for another in the synthesized protein.

Nonsense Mutation

A point mutation that converts a sense codon specifying an amino acid into a premature stop codon, terminating translation prematurely.

Frameshift Mutation

A mutation resulting from the insertion or deletion of a number of nucleotides not divisible by three, shifting the reading frame and altering all subsequent codons.

Philadelphia Chromosome

An abnormal chromosome 22 discovered by Nowell and Hungerford in 1960 that arises from a reciprocal translocation between chromosomes 9 and 22, producing a constitutively active BCR-Abl fusion protein that drives chronic myeloid leukemia (CML).

Central Dogma of Molecular Biology

The foundational principle explaining the directional flow of biological sequence information: DNA is transcribed into RNA, and RNA is translated into functional proteins.

Promoter

A specialized DNA sequence located at the 5' end upstream of a gene that is recognized and bound by RNA polymerase to initiate transcription, but is not itself transcribed.

Sigma ($\sigma$) Factor

A prokaryotic accessory protein subunit that associates with RNA polymerase to identify and bind the $-35$ and $-10$ promoter consensus sequences; it dissociates after approximately $9$ nucleotides are transcribed.

Pre-Initiation Complex (PIC)

The multi-protein complex in eukaryotes formed by RNA polymerase II and general transcription factors (including TFIID, TBP, TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH) assembled at the core promoter (TATAA box at $-30$).

Rho-Dependent Termination

A bacterial transcription termination mechanism where the Rho helicase protein binds the nascent mRNA strand and unwinds the RNA-DNA hybrid to release the RNA transcript.

Rho-Independent Termination

A bacterial transcription termination mechanism where a region of symmetry in the nascent RNA forms a hairpin loop structure that stalls RNA polymerase and causes release of the transcript.

Polycistronic mRNA

A prokaryotic mRNA transcript that carries coding sequences for multiple distinct proteins from clustered genes functioning in the same metabolic pathway.

5' Cap

A modified guanine nucleotide added to the 5' end of eukaryotic pre-mRNA when the nascent strand is approximately $25\,\text{bp}$ long; required for nuclear export, protection from enzymatic degradation, and ribosome binding.

Poly(A) Tail

A tract of several hundred adenylic acid residues added to the 3' end of eukaryotic pre-mRNA by poly(A) polymerase, essential for cytoplasmic export and mRNA stabilization.

Alternative Splicing

A regulated eukaryotic process in which different combinations of exons from a single pre-mRNA are spliced together, producing distinct protein isoforms from a single gene.

Semiconservative Replication

The mechanism of DNA duplication, confirmed experimentally by Meselson and Stahl using $^{15}\text{N}$ and $^{14}\text{N}$ isotopes, wherein each daughter DNA double helix contains one original parental strand and one newly synthesized strand.

DNA Helicase

An enzyme that breaks hydrogen bonds between complementary base pairs to unwind the double helix at the replication fork.

Single-Strand DNA-Binding Proteins (SSBs)

Proteins that bind to separated single-stranded template DNA behind the replication fork to stabilize the strands and prevent them from reannealing.

Topoisomerase

An enzyme (also known as gyrase in bacteria) that cuts and rejoins DNA to relieve twisting forces and torsional strain ahead of the advancing replication fork.

DNA Primase

An RNA polymerase that synthesizes a short RNA primer ($10\text{--}60\,\text{nt}$ in prokaryotes; $10\,\text{nt}$ in eukaryotes) complementary to the DNA template to provide a free 3'-OH group for DNA polymerase extension.

Okazaki Fragments

Short, discontinuous segments of newly synthesized DNA formed on the lagging strand that begin with an RNA primer and are extended in the 5' to 3' direction.

DNA Polymerase I

A bacterial DNA polymerase that utilizes 5' to 3' exonuclease activity to excise ribonucleotides of RNA primers and replaces them with deoxyribonucleotides during replication.

DNA Ligase

An enzyme that seals nicks in the sugar-phosphate backbone by forming phosphodiester linkages between adjacent deoxyribonucleotides, connecting Okazaki fragments into a continuous strand.

Telomerase

A ribonucleoprotein reverse transcriptase enzyme carrying its own internal RNA template that extends the 3' overhanging end of linear chromosomes in gametes and stem cells to prevent chromosome shortening.

Nucleotide

The monomeric subunit of nucleic acids, consisting of a five-carbon pentose sugar, an inorganic phosphate group attached to the 5' carbon, and a nitrogenous base attached to the 1' carbon.

Purines

Double-ringed nitrogenous bases containing nine atoms; includes adenine (A) and guanine (G) in both DNA and RNA.

Pyrimidines

Single-ringed nitrogenous bases; includes cytosine (C) in DNA and RNA, thymine (T) exclusively in DNA, and uracil (U) exclusively in RNA.

Phosphodiester Bond

The covalent linkage formed by a condensation reaction between the 3'-OH group of one pentose sugar and the 5'-phosphate group of an adjacent nucleotide in a nucleic acid strand.

Chargaff's Rules

The biochemical observation that double-stranded DNA maintains an equal ratio of purines to pyrimidines, specifically where percentage adenine equals thymine ($\%A = \%T$) and percentage guanine equals cytosine ($\%G = \%C$).

Photo 51

The historic X-ray diffraction photograph of DNA taken in 1952 by Rosalind Franklin and Raymond Gosling at King's College London, demonstrating the helical structure, base spacing of $0.34\,\text{nm}$, and pitch of $3.4\,\text{nm}$ that enabled Watson and Crick's model.

C-Value

The total amount of DNA present in the haploid ($N$) genome of a species, which does not correlate with an organism's morphological or structural complexity.

Nucleosome

The basic structural repeating unit of eukaryotic chromatin, comprising $146\,\text{base pairs}$ of DNA wrapped approximately twice around an octameric histone core (two each of H2A, H2B, H3, and H4).

Euchromatin

The decondensed, transcriptionally active form of eukaryotic chromatin that is accessible to RNA polymerases and regulatory proteins.

Heterochromatin

The highly compacted, condensed form of eukaryotic chromatin that restricts access to the transcriptional machinery and silences gene expression.

Ribozyme

An RNA molecule with a stable three-dimensional catalytic structure and active site capable of catalyzing chemical reactions, including phosphodiester bond cleavage and formation.

Amino Acid

A molecular monomer of proteins featuring an $\alpha$-carbon bonded to an amino group ($\text{NH}_3^+$), a carboxyl group ($\text{COO}^-$), a hydrogen atom, and a distinctive side chain (R-group).

Peptide Bond

A planar, non-rotatable covalent bond formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing a water molecule ($\text{H}_2\text{O}$).

Primary Protein Structure

The unique, linear sequence of amino acid residues joined by peptide bonds that forms the polypeptide backbone encoded by a gene.

Secondary Protein Structure

Localized conformational patterns ($\alpha$-helices and $\beta$-pleated sheets) within a polypeptide backbone stabilized by hydrogen bonding between carbonyl and amino backbone groups.

Tertiary Protein Structure

The overall three-dimensional folding of a single polypeptide chain, stabilized by interactions among amino acid R-groups (hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces, and disulfide bonds).

Quaternary Protein Structure

The multi-subunit spatial arrangement formed by the non-covalent or covalent association of two or more distinct polypeptide chains into a single functional protein complex.

Disulfide Bond

A covalent cross-link formed between the sulfhydryl (-SH) functional groups of two proximate cysteine residues, providing structural stability to tertiary and quaternary protein structures.

Molecular Chaperone

A specialized helper protein that assists in the proper folding of nascent or denatured polypeptides by preventing inappropriate interactions between exposed hydrophobic residues.

Induced Fit

The mild conformational shape adjustment that an enzyme undergoes upon substrate binding to place its catalytic amino acid residues in precise alignment with the substrate.

Coenzyme

An organic, non-protein enzymatic cofactor typically derived from dietary vitamins that binds reversibly or tightly within the active site to aid catalytic function.