Molecular Biology (BIOL 475): DNA & RNA

Vocabulary flashcards covering key structural features, components, conformations, and biological functions of DNA and RNA from Chapter 2.

Photo 51

The X-ray diffraction pattern of DNA produced by Rosalind Franklin and Maurice Wilkins that revealed crucial structural information about the double helix.

Purines

Nitrogenous bases containing a double carbon-nitrogen ring structure, including Adenine ($A$) and Guanine ($G$).

Pyrimidines

Nitrogenous bases containing a single carbon-nitrogen ring structure, including Cytosine ($C$), Thymine ($T$), and Uracil ($U$).

Nucleoside

A compound formed by a nitrogenous base linked to the $C1'$ carbon of a pentose sugar via a glycosidic bond.

Nucleotide

A building block of nucleic acids consisting of a nitrogenous base, a pentose sugar, and one or more phosphate groups attached to the $C5'$ carbon.

Phosphodiester bond

The covalent bond linking the $3'$ hydroxyl group of one pentose sugar to the phosphate group attached to the $5'$ hydroxyl group of the adjacent sugar in a nucleic acid polymer.

Chargaff's rules

The structural rules establishing that in double-stranded DNA, $[A] = [T]$, $[G] = [C]$, and the total amount of purines equals the total amount of pyrimidines ($[A] + [G] = [T] + [C]$).

Tautomers

Isomeric forms of nitrogenous bases created by the migration of a proton, occurring in less than $0.01\%$ of bases and capable of causing base-pairing misincorporations during DNA replication.

Base stacking

The hydrophobic and Van der Waals interactions between planar nitrogenous bases stacked inside the double helix that exclude water and stabilize DNA tertiary structure.

B-DNA

The predominant right-handed double-helical conformation of DNA under normal physiological conditions, characterized by $10.5\,\text{base pairs/turn}$, a $3.4\,\text{\AA}$ distance between base pairs, a $20\,\text{\AA}$ diameter, and a $C2'$-endo sugar pucker.

A-DNA

A right-handed double helix conformation with $11.6\,\text{base pairs/turn}$, a $26\,\text{\AA}$ diameter, and $C3'$-endo sugar pucker, which occurs under low humidity/high salt and is adopted by double-stranded RNA regions.

Z-DNA

A left-handed double-helical DNA structure featuring $12\,\text{base pairs/turn}$ and an alternating purine-pyrimidine sequence, associated with relieving torsional strain during active transcription.

Slipped structure

An unusual DNA secondary structure formed at tandem/direct repeat sequences that can cause expansion or deletion of repeats during replication, leading to neurological triplet repeat disorders.

DNA Unwinding Elements (DUEs)

$\text{A-T}$-rich regions of DNA associated with replication origins that undergo localized unwinding.

Cruciform structure

A four-way junction structure formed by intrastrand base pairing at inverted repeat sequences to create paired stem-loops.

Triplex H-DNA

A three-stranded nucleic acid complex formed when a single strand binds to a Watson-Crick duplex along polypurine-polypyrimidine mirror repeats via Hoogsteen hydrogen bonding.

Linking number ($Lk$)

A topological property of closed circular DNA defined as the sum of twist ($Tw$) and writhe ($Wr$), expressed as $Lk = Tw + Wr$.

Topoisomerase I

An enzyme that alters DNA supercoiling by transiently cleaving and resealing a single strand of the DNA double helix without requiring ATP.

Topoisomerase II

An enzyme that cuts and reseals both strands of a DNA double helix to relieve torsional strain, condense chromosomes, or segregate daughter chromosomes.

Sugar pucker

The non-planar ring conformation of ribose or deoxyribose, predominantly existing as $C3'$-endo in A-form helices and $C2'$-endo in B-form helices.

Ribozyme

An RNA molecule with catalytic activity that increases the rate of specific chemical reactions without being consumed in the overall process.

Pseudoknot motif

An RNA tertiary structure formed when single-stranded nucleotides in a hairpin loop pair with a complementary sequence outside the loop, folding via coaxial stacking.

A-minor motif

A prominent RNA tertiary interaction in which single-stranded adenosine residues insert into the minor groove of an RNA double helix.

Ribose zipper motif

An RNA tertiary motif held together by hydrogen bonding between the $2'$-\text{OH}$group of a ribose in one helix and the$2$$-oxygen of a pyrimidine base in an adjacent helix.

Kink-turn motif

An asymmetric internal loop motif in an RNA double helix characterized by a sharp bend in the phosphodiester backbone near a $3$-nucleotide bulge.

Hammerhead ribozyme

A small self-cleaving catalytic RNA motif featuring three base-paired stems in a T-shape that uses the $2'$-\text{OH}$$ group as an attacking nucleophile for phosphodiester bond cleavage.

Retrovirus

An RNA virus containing a single-stranded RNA genome that replicates through a double-stranded DNA intermediate integrated into the host genome using reverse transcriptase.

Nucleotide coenzymes

Non-nucleic acid derivatives of nucleotides, such as $ATP$, $NAD^+/NADH$, $FAD/FADH_2$, and $Coenzyme\,A$, that perform essential cellular functions in energy transfer, redox reactions, and group transfers.

Caffeine

A psychoactive xanthine alkaloid and adenosine receptor antagonist that acts as a central nervous system stimulant with an elimination half-life of approximately $4.9\,\text{hours}$.

Triplet repeat expansion diseases

A group of neurological disorders, including Fragile X syndrome, Myotonic dystrophy, and Friedreich's ataxia, caused by the unstable expansion of tandem repeat sequences during DNA replication.

Major groove

The wider ($13\,\text{\AA}$) region of B-DNA where sugar-phosphate backbones are further apart, exposing base pair edge chemical groups that serve as the primary binding sites for sequence-specific regulatory proteins.

Minor groove

The narrower ($9\,\text{\AA}$) region of B-DNA where sugar-phosphate backbones are closer together; binding by proteins here typically induces unwinding or bending of the DNA helix.

tRNA functional loops

Structural domains of transfer RNA comprising the D-loop, T-loop, and anticodon loop, which collectively facilitate aminoacyl-tRNA synthetase recognition, ribosome binding, and mRNA codon pairing.

Inosine ($I$)

A modified purine nucleoside found in tRNA formed by the deamination of adenosine, which possesses neuroprotective properties by neutralizing peroxynitrite.

Pseudouridine ($\Psi$)

The first identified modified nucleoside found in RNA, formed by the isomerization of uridine where the ribose sugar attaches to the $C5$ carbon instead of the $N1$ nitrogen of the uracil ring.

Coaxial stacking

A tertiary structural arrangement in RNA where two separate base-paired stems align end-to-end to form a continuous pseudo-helix, such as the acceptor stem stacking on the T-stem in tRNA.

Tetraloop motif

A common RNA secondary structure motif consisting of a four-nucleotide stem-loop stabilized by base-stacking interactions, such as the sequence $UUUU$.

Kissing hairpin loop

An RNA tertiary interaction formed when single-stranded nucleotides in two separate hairpin loops base pair with each other, creating a pseudo-continuous backbone.

Ribonuclease P (RNase P)

A catalytic ribonucleoprotein endoribonuclease that cleaves precursor tRNA to generate its mature $5'$ end, whose RNA component (M1 RNA in E. coli) possesses intrinsic catalytic activity.

Plus-strand ($+\text{RNA}$) viruses

Eukaryotic RNA viruses whose genome consists of positive-sense coding RNA that can be directly translated into viral proteins by host ribosomes upon cell entry.

Minus-strand ($-\text{RNA}$) viruses

Eukaryotic RNA viruses whose genome consists of non-coding antisense RNA that must be transcribed into a complementary positive strand by a viral RNA polymerase prior to translation.

Hoogsteen hydrogen bonding

Non-Watson-Crick base pairing that utilizes the $N7$ position and major groove face of a purine base, enabling the formation of triplex H-DNA structures.