DNA Structure, Replication, Genome Organization, and Protein Function Flashcards

Comprehensive set of vocabulary flashcards covering basic nucleic acid structure, protein organization, genome compaction, DNA replication machinery, telomeres, and repair pathways.

Nucleotide Chemical Components

The monomeric building block of nucleic acids consisting of a five-carbon sugar, a phosphate group, and a nitrogenous base.

Deoxyribose

The five-carbon sugar component in DNA that lacks a hydroxyl $-OH$ group at the $2'$ carbon position, distinguishing it from ribose.

Purines

A family of nitrogenous bases featuring a double-ring structure, which includes Adenine ($A$) and Guanine ($G$).

Pyrimidines

A family of nitrogenous bases featuring a single-ring structure, which includes Cytosine ($C$), Thymine ($T$), and Uracil ($U$).

Chargaff's Rules

The experimental observation that in DNA, the amount of Adenine equals Thymine ($A = T$), Guanine equals Cytosine ($G = C$), and total purines equal total pyrimidines ($A + G = T + C$).

Phosphodiester Bond

A strong covalent linkage connecting the $3'$ carbon of one sugar to the $5'$ phosphate group of the adjacent nucleotide in a nucleic acid strand.

Antiparallel Strands

The arrangement of two complementary DNA strands running alongside each other in opposite chemical directions ($5' \rightarrow 3'$ and $3' \rightarrow 5'$).

Complementary Base Pairing

Specific hydrogen bonding between nitrogenous bases where Adenine pairs with Thymine via $2$ hydrogen bonds ($A=T$) and Guanine pairs with Cytosine via $3$ hydrogen bonds ($G \rightleftharpoons C$).

Major Groove

The larger and wider helical space in double-stranded DNA that exposes detailed chemical features, allowing sequence-specific recognition by regulatory proteins.

B-DNA Structural Parameters

The standard, predominant right-handed conformation of standard cellular DNA featuring a helix width of $20$\text{ nm} ($2.0$\text{ nm}), $10.5$\text{ base pairs per turn}, a turn length of $3.4$\text{ nm}, and $0.34$\text{ nm} spacing between adjacent bases.

Base Stacking

Hydrophobic and $\pi-\pi$ interactions among the planar nitrogenous bases stacked inside the double helix, serving as a primary contributor to overall DNA thermodynamic stability.

Denaturation

The separation of double-stranded DNA into single strands via disruption of hydrogen bonds and base stacking interactions without severing the phosphodiester backbone.

Melting Temperature ($T_m$)

The specific temperature at which $50\%$ of double-stranded DNA in a sample becomes denatured into single strands.

G-Quadruplex

A secondary nucleic acid structure formed in guanine-rich regions, composed of four-stranded planar G-tetrads stacked together via Hoogsteen base pairing.

Ribozyme

A catalytic RNA molecule capable of accelerating specific biochemical reactions, such as self-splicing or peptide bond formation in the ribosome.

Primary Structure of Protein

The unique, linear sequence of amino acids linked by covalent peptide bonds, synthesized in the $N\text{-terminus} \rightarrow C\text{-terminus}$ direction.

Secondary Structure of Protein

Localized regular folding patterns within a polypeptide backbone, primarily $\alpha$-helices and $\beta$-pleated sheets, stabilized by backbone hydrogen bonding.

Tertiary Structure of Protein

The complete three-dimensional spatial conformation of a single polypeptide chain, maintained by hydrophobic interactions, electrostatic forces, hydrogen bonds, and disulfide bridges.

Quaternary Structure of Protein

The structural arrangement resulting from the non-covalent or covalent association of multiple polypeptide subunits into a single functional protein complex.

Degenerate Genetic Code

The feature of the genetic code where multiple distinct triplet codons (out of $61$ coding codons) specify the same amino acid.

Wobble Hypothesis

The non-rigid pairing flexibility at the $3'$ position of an mRNA codon (and $5'$ position of a tRNA anticodon) allowing one tRNA to recognize multiple synonymous codons.

Induced Fit

The structural modification of an enzyme's active site upon substrate binding to achieve optimal complementary fit and promote catalysis.

Kinase

An enzyme that catalyzes the transfer of a phosphate group from ATP onto a target molecule or specific amino acid residue (such as Serine, Threonine, or Tyrosine).

Phosphatase

An enzyme that removes a phosphate group from a phosphorylated target protein via hydrolysis.

Molecular Chaperones

Proteins (such as Hsp70 and Hsp90) that facilitate correct folding of polypeptide chains, prevent improper non-specific aggregation, and assist in refolding or degradation.

Ubiquitin-Proteasome System (UPS)

A major eukaryotic protein degradation pathway where target misfolded or regulatory proteins are covalently tagged with a Lys48-linked polyubiquitin chain by E1, E2, and E3 enzymes for proteasomal destruction.

Prion

An infectious protein particle ($PrP^{Sc}$) possessing an abnormal three-dimensional conformation that self-propagates by inducing normal host proteins ($PrP^C$) to misfold.

Nucleosome

The basic structural repeating unit of eukaryotic chromatin, consisting of approximately $147$\text{ base pairs} of DNA wrapped $1.67$ times around a core histone octamer.

Histone Octamer

The protein core of a nucleosome comprising two copies each of the four core histone proteins: H2A, H2B, H3, and H4.

Euchromatin

A less-condensed, transcriptionally active form of chromatin that allows regulatory proteins access to DNA.

Heterochromatin

A highly condensed, transcriptionally silent form of chromatin where DNA remains inaccessible to gene expression machinery.

Condensin

A ring-shaped protein complex that drives the higher-order structural organization and condensation of chromosomes during cell division.

Cohesin

A multiprotein ring complex that physically holds sister chromatids together from DNA replication until anaphase separation.

CENP-A

A specialized histone H3 variant that replaces normal H3 at centromeres, serving as a landmark for kinetochore assembly.

C-Value Paradox

The observation that total haploid genome size (C-value) does not correlate with the evolutionary complexity of an organism.

Lateral Gene Transfer

The direct transfer of genetic material between distinct organisms or species, independent of vertical parent-to-offspring inheritance.

Heteroplasmy

The presence of a mixture of distinct mitochondrial DNA genomes (wild-type and mutant) within a single cell or individual.

Semidiscontinuous Replication

The mechanism of DNA replication in which synthesis proceeds continuously on the leading strand ($5' \rightarrow 3'$) and discontinuously on the lagging strand ($5' \rightarrow 3'$).

Okazaki Fragments

Short, newly synthesized DNA segments generated discontinuously on the lagging strand template during DNA replication.

Processivity

The ability of an enzyme (such as DNA polymerase) to catalyze consecutive reactions along a substrate strand without falling off.

Origin Recognition Complex (ORC)

A multi-protein complex that binds to origins of replication to initiate the assembly of pre-replication complexes (pre-RCs).

Replication Protein A (RPA)

A eukaryotic single-stranded DNA-binding protein that stabilizes unwound single strands during replication, preventing reannealing or secondary structure formation.

Topoisomerase

An enzyme that relieves supercoiling and torsional strain ahead of the advancing replication fork by transiently cleaving and resealing DNA strands.

PCNA (Proliferating Cell Nuclear Antigen)

A ring-shaped sliding clamp protein that encircles DNA and locks replicative DNA polymerases onto the template, dramatically increasing processivity.

Proofreading

The $3' \rightarrow 5'$ exonuclease activity of DNA polymerases that recognizes, excises, and replaces incorrectly incorporated nucleotides during synthesis.

DNA Ligase

An enzyme that joins DNA fragments (such as Okazaki fragments) by catalyzing the formation of a phosphodiester bond to seal single-strand nicks.

Telomere

A repetitive G-rich DNA structure (human sequence $5'\text{-TTAGGG}-3'$) located at the ends of linear chromosomes that guards against structural degradation and end-to-end chromosome fusion.

Telomerase

A specialized ribonucleoprotein reverse transcriptase (comprising TERT and TERC) that extends the $3'$ end of telomeres using an intrinsic RNA template.

Hayflick Limit

The finite maximum number of mitotic cell divisions that a normal somatic cell population can undergo before entering permanent senescence.

Silent Mutation

A nucleotide substitution that changes a codon without altering the coded amino acid sequence in the resulting protein.

Missense Mutation

A single base substitution that alters a codon, leading to the incorporation of a different amino acid in the polypeptide chain.

Nonsense Mutation

A base substitution that converts an amino acid codon into a premature stop codon ($UAA$, $UAG$, or $UGA$), causing premature translation termination.

Frameshift Mutation

An insertion or deletion of nucleotides in numbers not divisible by three, shifting the reading frame of the mRNA downstream of the mutation.

Thymine Dimer

A lesion caused by ultraviolet radiation where adjacent thymine bases in a DNA strand form abnormal intra-strand covalent bonds, causing helical distortion.

Translesion Synthesis (TLS)

A DNA damage bypass mechanism where specialized error-prone DNA polymerases synthesize DNA past template lesions to prevent replication fork arrest.

Photoreactivation

A direct repair process in which the enzyme DNA photolyase absorbs visible light energy to break covalent bonds in pyrimidine dimers and restore intact bases.