Nucleic Acids and Nucleotide Metabolism

Comprehensive practice flashcards covering nucleotide structure, functions, nomenclature, DNA/RNA forms, secondary structures, denaturation, and chemical transformations based on the provided lecture notes.

Gene

A segment of a DNA molecule that contains the information required for the synthesis of a functional biological product, whether protein or RNA.

Ribosomal RNAs (rRNAs)

Components of ribosomes, the complexes that carry out the synthesis of proteins.

Messenger RNAs (mRNAs)

Intermediaries carrying genetic information from one or a few genes to a ribosome for protein synthesis.

Transfer RNAs (tRNAs)

Adapter molecules that translate the information in mRNA into a specific sequence of amino acids.

Nucleobase

The nitrogenous base component of a nucleotide or nucleoside.

Nucleoside

A chemical unit consisting of a nitrogenous base and a pentose sugar.

Nucleotide

A chemical unit consisting of a nitrogenous base, a pentose sugar, and a phosphate group.

Pyrimidines

One of two parent compounds of nitrogenous bases, characterized by a single-ring structure.

Purines

One of two parent compounds of nitrogenous bases, characterized by a double-ring structure.

Adenine (A)

A major purine base found in both DNA and RNA.

Guanine (G)

A major purine base found in both DNA and RNA.

Cytosine (C)

A major pyrimidine base found in both DNA and RNA.

Thymine (T)

A major pyrimidine base found primarily in DNA.

Uracil (U)

A major pyrimidine base found primarily in RNA.

Adenosine

The nucleoside name for adenine in RNA.

Deoxyadenosine

The nucleoside name for adenine in DNA.

Guanosine

The nucleoside name for guanine in RNA.

Deoxyguanosine

The nucleoside name for guanine in DNA.

Cytidine

The nucleoside name for cytosine in RNA.

Deoxycytidine

The nucleoside name for cytosine in DNA.

Thymidine

The nucleoside name for thymine in DNA (also called deoxythymidine).

Uridine

The nucleoside name for uracil in RNA.

Adenylate

The nucleotide name for adenine in RNA.

Deoxyadenylate

The nucleotide name for adenine in DNA.

Guanylate

The nucleotide name for guanine in RNA.

Deoxyguanylate

The nucleotide name for guanine in DNA.

Cytidylate

The nucleotide name for cytosine in RNA.

Deoxycytidylate

The nucleotide name for cytosine in DNA.

Thymidylate

The nucleotide name for thymine in DNA (also called deoxythymidylate).

Uridylate

The nucleotide name for uracil in RNA.

2'-deoxy-D-ribose

The pentose sugar found in DNA nucleotides.

D-ribose

The pentose sugar found in RNA nucleotides.

N-glycosidic bond

The single bond that attaches the pentose ring to the nucleobase in a nucleoside.

N1 in Pyrimidines

The specific nitrogen atom in a pyrimidine ring that forms the N-glycosidic bond with the sugar.

N9 in Purines

The specific nitrogen atom in a purine ring that forms the N-glycosidic bond with the sugar.

Phosphodiester linkage

The covalent bridge joining the 5'-phosphate group of one nucleotide to the 3'-hydroxyl group of the next.

5' end

The end of a nucleic acid strand that lacks a nucleotide at the 5' position.

3' end

The end of a nucleic acid strand that lacks a nucleotide at the 3' position.

ATP

Adenosine 5'-triphosphate, the primary energy currency for cellular metabolism.

NAD+

Nicotinamide adenine dinucleotide, a nucleotide acting as an enzyme cofactor.

cAMP

Adenosine 3',5'-cyclic monophosphate, a nucleotide acting as a signal transduction molecule.

Pi to Pi* transitions

Electronic transitions responsible for the absorption of UV light at $250-270\,nm$ in nucleobases.

Hypochromic effect

The decrease in UV light absorption when bases are stacked or paired in complementary strands.

Hyperchromic effect

The increase in UV light absorption when double-stranded DNA undergoes denaturation into single strands.

Oligonucleotide

A short polymer containing 50 or fewer nucleotides.

Polynucleotide

A longer polymer of nucleic acids, typically exceeding 50 nucleotides.

Watson-Crick base pairing

Specific hydrogen-bonding pattern where A pairs with T (or U) and G pairs with C.

Antiparallel

The orientation in DNA where the two strands run in opposite directions ($5' \rightarrow 3'$ vs $3' \rightarrow 5'$).

DNA polymerase

The class of enzymes that catalyze the synthesis of new DNA strands using a template strand.

Chargaff's Fourth Rule

The relationship in all cellular DNAs where $A = T$ and $G = C$.

B-form DNA (B-DNA)

The most stable right-handed double-helix structure for DNA under physiological conditions.

A-form DNA (A-DNA)

A wider right-handed helix with 11 base pairs per turn, favored in solutions devoid of water.

Z-form DNA (Z-DNA)

A left-handed helical DNA structure with 12 base pairs per turn and a zigzag backbone appearance.

Hoogsteen positions

Functional groups in the major groove that allow nucleotides to form additional hydrogen bonds in triplex DNA.

Palindrome

Regions of DNA with inverted repeats of base sequence having twofold symmetry across two strands.

Mirror repeat

An inverted repeat occurring within an individual strand of DNA, incapable of forming hairpins.

Hairpin

A secondary structure formed by intrastrand base pairing when a single DNA or RNA strand is involved.

Cruciform

A cross-shaped structure formed when both strands of a duplex DNA participate in intrastrand base pairing.

Denaturation (Melting)

The process of unwinding the DNA double helix into two single strands by disrupting hydrogen bonds and base stacking.

Annealing (Renaturation)

The spontaneous rewinding of separated complementary DNA strands to reform an intact duplex.

Melting point ($T_m$)

The characteristic temperature at which a specific species of DNA denatures.

DNA Bubbles

Specific denatured regions rich in $A = T$ base pairs that can be visualized with electron microscopy.

Hybridization

The technique of pairing complementary DNA/RNA strands from different species to detect sequence similarity.

Pyrimidine dimers

Covalent linkages between adjacent pyrimidine bases induced by UV light, linked to skin cancer.

Oxidative DNA damage

Damage caused by excited-oxygen species such as hydrogen peroxide, superoxide, and hydroxyl radicals.

Hydroxyl radicals

The specific excited-oxygen species responsible for most oxidative DNA damage.

Superoxide dismutase

An enzyme that converts reactive oxygen species to harmless products as part of a cell's defense system.

Monocistronic mRNA

An mRNA molecule that carries the code for only one polypeptide chain.

Polycistronic mRNA

An mRNA molecule that codes for two or more different polypeptides.

Transcription

The process of forming a single-stranded mRNA on a DNA template.

Ribozyme

An RNA molecule with enzymatic activity, such as RNase P.

Dicer

An enzyme that cleaves double-stranded RNA into oligonucleotides for viral protection and RNA interference.

Mutations

Permanent alterations in DNA structure that change the encoded genetic information.

Deamination

The spontaneous loss of exocyclic amino groups from nucleotide bases.

DNA Methylation

The enzymatic addition of methyl groups to bases (usually adenine or cytosine) for protection or regulation.

Nucleotide-binding fold

A single protein domain that binds adenosine, found in many enzymes that use ATP or cofactors.

Adenylyl cyclase

The enzyme associated with the plasma membrane that catalyzes the formation of cAMP from ATP.

Second messenger

An intracellular molecule, often a nucleotide like cAMP, produced in response to extracellular signals.

Hydrophobic stacking interactions

Parallel positioning of base rings to minimize contact with water and stabilize nucleic acid structure.

Aromacity

A property of purines and pyrimidines that results in electron delocalization and near-planar structures.

C-2' endo conformation

The specific pucker of the furanose ring found in the deoxyribose of Watson-Crick B-DNA.

Major groove

The larger of the two grooves created by the offset pairing of DNA strands on the duplex surface.

Minor groove

The smaller of the two grooves produced by the offset orientation of the DNA double helix.

G tetraplex

A stable quadruplex structure formed by four DNA strands in sequences high in guanosine residues.

Beta configuration (β)

The specific orientation of the N-glycosidic bond formed at the anomeric 1' carbon of the sugar.

Energy for metabolism

A function of nucleotides exemplified by ATP.

Processing of genetic information

A function of nucleic acids performed by ribozymes.

Storage of genetic information

The primary biological function of DNA.

Radiationless transitions

The process by which excited states of nucleobases decay rapidly, providing photoprotection.

S-RNase

An enzyme found in plants used to prevent inbreeding by degrading RNA.

RNase P

A ribozyme that processes tRNA precursors.

H-bond length (A-T primary)

$2.8\,\text{\AA}$ between Adenine and Thymine.

H-bond length (G-C primary)

$2.9\,\text{\AA}$ between Guanine and Cytosine.

Total span of A-T pair

$11.1\,\text{\AA}$.

Total span of G-C pair

$10.8\,\text{\AA}$.

Hoogsteen pairing

Non-Watson-Crick pairing involving atoms in the major groove, named after Karst Hoogsteen (1963).

Triplex DNAs

Triple-helical DNA structures formed through Hoogsteen pairing, most stable at low pH.

Inverted repeat

A sequence of DNA that is self-complementary and can form hairpins or cruciforms.

Electrophoresis

A method for separating DNA strands based on size, using agarose or polyacrylamide gels.

Agarose

A gel matrix typically used for the electrophoresis of longer pieces of DNA.