Nucleic Acid

Which molecules store and transfer genetic information across cellular generations?

Nucleic Acids

Which nucleotide derivative acts as the universal cellular energy currency?

ATP

Which metabolic coenzymes contain nucleotide-derived structural components?

NAD+ and FAD

Which cyclic nucleotides serve as metabolic regulators and second messengers?

cAMP and cGMP

Which one- or two-ring nitrogenous aromatic compounds are fundamental building blocks of nucleic acids?

Nucleobases / Nitrogenous Bases

Which base class makes up the bulk of DNA and RNA, in contrast to unusual or modified bases?

Major Bases

Which base class consists of unusual or modified bases with specialized regulatory, structural, and metabolic functions?

Minor Bases

Which nitrogenous-base class has two rings resembling pyrimidine and imidazole and nitrogen atoms at positions 1, 3, 7, and 9?

Purines

Which nitrogenous-base class has a six-membered heterocyclic aromatic ring containing two nitrogen atoms?

Pyrimidines

Which two purines are major nitrogenous bases of DNA and RNA?

Adenine and Guanine

Which major purine has an amino group at C6 without an oxo group?

Adenine

Which major purine has an amino group at C2 and an oxo group at C6?

Guanine

Which major pyrimidine has an amino group at C4 and an oxo group at C2?

Cytosine

Which RNA pyrimidine has oxo groups at C2 and C4 without a C5 methyl group?

Uracil

Which DNA pyrimidine has oxo groups at C2 and C4 and a methyl group at C5?

Thymine

Which major pyrimidine is shared by DNA and RNA, and which additional major pyrimidine does each contain?

Shared: Cytosine; DNA: Thymine; RNA: Uracil

Which unusual bases exemplify the minor nucleobases found in DNA and RNA?

5-methylcytosine, N4-acetyl cytosine, N6-methyladenine, N6, N6-dimethyl adenine, and Pseudouracil

What role are unusual nucleic-acid bases believed to play in enzyme interactions?

Recognition of specific enzymes

Which free minor purines are metabolic intermediates, and which is the end product?

Hypoxanthine and Xanthine; Uric acid

Which phenomenon allows a molecule to exist in keto (lactam) and enol (lactim) forms?

Tautomerism

Which functional groups participate in proton shifting between keto and enol forms of purines and pyrimidines?

Oxo functional groups (C=O)

Which compounds consist of a nitrogenous base and pentose sugar without a phosphate group?

Nucleosides

Which bond joins purine N9 or pyrimidine N1 to pentose C1′ in a nucleoside?

N-Glycosidic Bond

What suffixes distinguish purine and pyrimidine nucleoside names, respectively?

-sine and -dine

Which ribonucleosides form from ribose combined with adenine, guanine, uracil, and cytosine, respectively?

Adenosine, Guanosine, Uridine, and Cytidine

Which ribonucleosides form from hypoxanthine and xanthine, respectively?

Inosine and Xanthosine

Which deoxyribonucleosides form from deoxyribose combined with adenine, guanine, cytosine, and thymine, respectively?

Deoxy adenosine (d-adenosine), d-guanosine, d-cytidine, and d-thymidine

How are nitrogenous-base atoms and sugar carbons distinguished in nucleoside numbering?

Cardinal numbers; Primed numbers

Which nucleoside conformation rotates the base away from the sugar and predominates in standard DNA and RNA structures?

Anti Conformation

Which nucleoside conformation rotates the base over the sugar and is less common?

Syn Conformation

Which nucleoside component accounts for greater water solubility than that of free bases?

Sugar moiety

How do nucleosides respond to alkaline conditions?

Highly stable and resistant

How do purine and pyrimidine nucleosides differ in acid hydrolysis?

Purine hydrolyze easily to free base and pentose; pyrimidine are resistant

Which compounds contain a nitrogenous base, pentose sugar, and phosphate group?

Nucleotides

Which pentose in RNA has a hydroxyl group at its 2′ carbon?

Ribose

Which pentose in DNA lacks the 2′ hydroxyl group?

Deoxyribose

Where does phosphate attach to the pentose sugar in nucleotides?

C5′ or C3′

Which nucleotide classes include AMP/GMP/CMP/TMP/UMP, ADP/GDP, and ATP/GTP, respectively?

Monophosphates, Diphosphates, and Triphosphates

Which nucleotide arrangement esterifies one phosphate to both the 3′ and 5′ hydroxyl groups of a pentose?

Cyclic Nucleotides / Cyclic Phosphodiesters

Which linkage joins phosphate groups in ADP and ATP?

Phosphoric anhydride linkage

How are ATP’s phosphate groups designated from the sugar outward?

alpha, beta, and gamma

What products form when phosphate is added to AMP and ADP, respectively, in condensation reactions?

ADP + Water; ATP + Water

Which bond connects the 3′ carbon of one nucleotide sugar to the 5′ carbon of the next?

3′, 5′-Phosphodiester Bond

Which repeating hydrophilic framework supports the nitrogenous bases in nucleic-acid strands?

Sugar-Phosphate Backbone

Which nucleic acid is a polymer of deoxyribonucleotides?

DNA

Which four deoxyribonucleotides make up DNA?

Deoxyadenylate (A), Deoxyguanylate (G), Deoxycytidylate (C), and Thymidylate (T)

Which free groups define the 5′ and 3′ ends of a nucleic-acid strand, respectively?

Free phosphate; Free hydroxyl

What term describes the opposite 5′→3′ and 3′→5′ orientations of the two DNA strands?

Antiparallel Directionality

Which arrangement consists of two polydeoxyribonucleotide strands twisted around a common axis?

DNA Double Helix

Which DNA groove is approximately 22 Å wide and accessible for transcription-factor binding?

Major Groove

Which DNA groove is approximately 12 Å wide and binds some drugs and proteins?

Minor Groove

Which complementary DNA base pairs have two and three hydrogen bonds, respectively?

Adenine–Thymine and Guanine–Cytosine

Why does DNA pair a purine with a pyrimidine rather than two purines?

Two purines would not fit the allowable helical dimensions

What is the approximate uniform span of a purine–pyrimidine DNA base pair?

11 Å

What forces stabilize DNA structure?

Hydrogen bonding; base stacking through hydrophobic and van der Waals interactions; the hydrophobic effect; electrostatic interactions and cations

Which DNA form predominates under physiological conditions of low salt and high hydration?

B-DNA

Which right-handed DNA form commonly occurs in DNA–RNA hybrid molecules?

A-DNA

Which DNA form is a left-handed zigzag helix favored by high cation concentrations and G- and C-rich regions?

Z-DNA

What are the helix diameters and pitches of A-DNA, B-DNA, and Z-DNA, respectively?

26 Å and 28 Å; 20 Å and 34 Å; 18 Å and 45 Å

How many base pairs occur per turn in A-DNA and Z-DNA, respectively?

11 and 12

What are the rise per base pair and base tilt of A-DNA, B-DNA, and Z-DNA, respectively?

2.6 Å and 20°; 3.4 Å and 6°; 3.7 Å and 7°

How do the sugar puckers of A-DNA, B-DNA, and Z-DNA differ?

C3'; C2'; purine: C2' and pyrimidines: C3'

How do glycosyl-bond conformations differ among A-DNA, B-DNA, and Z-DNA?

Anti; Anti; Anti in pyrimidines and Syn in purines

Which cross-shaped DNA structure forms from inverted repeat sequences?

Cruciform DNA

Which DNA structure forms when a single strand folds back and base-pairs with itself?

Hairpin DNA

Which three-stranded DNA structure forms in purine/pyrimidine-rich regions and plays a role in gene regulation?

Triplex DNA (Triple-helical DNA)

Which DNA structure forms in guanine-rich sequences and occurs in telomeres and regulatory regions?

G-quadruplex DNA

Which process separates the two DNA strands through heat or a change in pH?

Denaturation

Which effect is the increase in UV absorbance at 260 nm used to monitor DNA strand separation?

Hyperchromic Effect

What term denotes the temperature at which 50% of DNA is denatured?

Melting Temperature (Tm)

Why does greater G≡C content increase DNA melting temperature?

G≡C pairs have three hydrogen bonds, compared with two in A=T pairs

Which process re-associates complementary DNA strands during slow cooling?

Renaturation (Annealing)

Which hybridization techniques rely on reassociation of complementary nucleic-acid strands?

PCR and Southern blotting

Which double-stranded nucleic-acid molecule pairs complementary strands from different sources, including DNA–DNA or DNA–RNA combinations?

Hybrid Duplex

Which structural modification twists a DNA double helix upon itself to help compact approximately 2 meters of DNA into a micrometer-scale nucleus?

DNA Supercoiling

Which underwound DNA state is most common in living cells and facilitates strand separation, replication, and transcription?

Negative Supercoiling

Which overwound DNA state tightens the molecule and makes strand separation more difficult?

Positive Supercoiling

Which enzyme relieves DNA supercoiling by cutting one strand without requiring ATP?

Topoisomerase I

Which ATP-requiring enzyme cuts both DNA strands to introduce or remove supercoils?

Topoisomerase II

Which bacterial type II enzyme introduces negative supercoils and is a target for quinolones?

DNA Gyrase

Which nucleic acid is an unbranched, single-stranded linear polymer of ribonucleotides?

RNA

Which three major cellular RNA types participate in protein synthesis?

mRNA, tRNA, rRNA

What proportions of total cellular RNA are mRNA, tRNA, and rRNA, respectively?

5–10%; 10–20%; about 80%

Which RNA carries genetic information in codons and serves as the template for protein biosynthesis?

Messenger RNA (mRNA)

Which nuclear RNA serves as the precursor of mRNA?

Heterogeneous nuclear RNA (hnRNA)

Which compound caps the 5′ end of mRNA to facilitate recognition during protein biosynthesis and protect against 5′-exonucleases?

7-methyl-guanosine triphosphate

Which 3′ mRNA structure consists of adenylate residues and protects against 3′-exonucleases?

Poly(A) Tail

Which RNA carries amino acids in an activated form to the ribosome?

Transfer RNA (tRNA)

Which RNA comprises 74–95 nucleotides and folds into a characteristic cloverleaf secondary structure?

Transfer RNA (tRNA)

Which tRNA arm attaches the amino acid and terminates in CCA at the 3′ end?

Acceptor Arm

The D arm of tRNA arm contains?

dihydrouridine

Which tRNA arm base-pairs with the codon on mRNA?

Anticodon Arm

The TψC Arm of tRNA arm contains _______ and _______?

ribothymidine and pseudouridine

Which tRNA arm lies between the anticodon and TψC arms?

Extra Arm (Variable Arm)

How do Class I and Class II tRNAs differ in variable-arm length, and which class predominates?

Class I: 3–5 base pairs, about 75%; Class II: 13–20 base pairs

Which RNA maintains ribosomal structure, binds mRNA to the ribosome, and provides catalytic activity during protein synthesis?

Ribosomal RNA (rRNA)

What term describes an RNA molecule with enzymatic activity?

Ribozyme

What are the subunits and rRNA components of a prokaryotic 70S ribosome?

50S large subunit; 30S small subunit: 16S rRNA

What are the subunits and rRNA components of a eukaryotic 80S ribosome?

60S large subunit: 28S, 5.8S, and 5S rRNAs; 40S small subunit: 18S rRNA

Which specialized RNA excises introns and splices exons?

Small nuclear RNA (snRNA)