Nucleotides, Nucleic Acids, and Genetic Information

Vocabulary practice flashcards covering nucleic acid structures, nucleotide functions, historical DNA experiments, sequencing technologies, and molecular biology tools.

Purines vs Pyrimidines Ring Structures

Purines consist of a fused bicyclic ring system (e.g., Adenine, Guanine); Pyrimidines consist of a single six-membered ring (e.g., Cytosine, Uracil, Thymine).

Adenine (Ade, A) Chemical Structure

A purine nitrogenous base containing an amino group ($\text{-NH}_2$) attached to position 6 of the bicyclic ring system.

Guanine (Gua, G) Chemical Structure

A purine nitrogenous base containing a carbonyl oxygen at position 6 and an amino group at position 2.

Cytosine (Cyt, C) Chemical Structure

A pyrimidine nitrogenous base containing an amino group at position 4 and a carbonyl group at position 2.

Uracil (Ura, U) Chemical Structure

A pyrimidine nitrogenous base found in RNA containing carbonyl oxygen groups at positions 2 and 4.

Thymine (Thy, T) Chemical Structure

A pyrimidine nitrogenous base found in DNA containing carbonyl groups at positions 2 and 4, and a methyl group ($\text{-CH}_3$) at position 5.

Ribose vs Deoxyribose 2' Carbon Difference

Ribose possesses a hydroxyl group ($\text{-OH}$) attached to the 2' carbon, whereas deoxyribose possesses a hydrogen atom ($\text{-H}$) at the 2' carbon.

Nucleoside Definition

A chemical compound comprising a nitrogenous base covalently linked to a ribose or deoxyribose sugar at the 1' position, lacking phosphate groups.

Nucleotide Definition

A monomeric subunit of nucleic acids consisting of a nitrogenous base, a pentose sugar, and one or more phosphate groups attached to positions such as 5' or 3'.

Ribonucleoside of Adenine

Adenosine ($\text{Ado}$ or $\text{A}$).

Deoxyribonucleoside of Adenine

Deoxyadenosine ($\text{dAdo}$ or $\text{dA}$).

Ribonucleotide of Guanine

Guanylic acid or Guanosine monophosphate ($\text{GMP}$).

Nucleoside of Thymine

Deoxythymidine ($\text{dThd}$ or $\text{dT}$).

Nucleotide of Cytosine in DNA

Deoxycytidylic acid or Deoxycytidine monophosphate ($\text{dCMP}$).

Six Major Cellular Functions of Nucleotides

1. Activation of intermediates, 2. Enzyme coenzymes, 3. Intracellular signaling, 4. Allosteric enzyme regulation, 5. Energy transfer, 6. Monomeric units of nucleic acids ($\text{RNA/DNA}$).

UDP-Glucose Functional Role

An activated nucleotide-sugar intermediate used in glycogen biosynthesis and cellular carbohydrate metabolism.

Structure of Nicotinamide Adenine Dinucleotide ($\text{NAD}^+$)

A coenzyme composed of two nucleotides joined by phosphate groups, containing a nicotinamide ring and an adenine ring each linked to a ribose sugar.

Redox Reaction Mechanism of $\text{NAD}^+$ and $\text{NADH}$

$\text{NAD}^+$ (oxidized form) accepts two electrons and one proton ($\text{H}^+$) on its nicotinamide ring to form reduced $\text{NADH}$.

Flavin Mononucleotide ($\text{FMN}$) Structure

A biomolecule containing an isoalloxazine ring system attached to ribitol and a single phosphate group.

Flavin Adenine Dinucleotide ($\text{FAD}$) Biosynthesis

Synthesized from $\text{FMN}$ and $\text{ATP}$ by $\text{FAD}$ pyrophosphorylase, producing $\text{FAD}$ and inorganic pyrophosphate ($\text{PP}_i$).

Coenzyme A ($\text{CoA}$) Structural Components

Contains 3'-phospho-AMP linked via pyrophosphate to pantothenic acid and a terminal cysteamine sulfhydryl ($\text{-SH}$) group.

Cyclic AMP ($\text{cAMP}$) Functional Role

A key nucleotide second messenger that relays extracellular receptor signals to intracellular effectors.

Allosteric Regulation Mechanism by Modulator Nucleotides

Binding of a modulator ($\text{M}$) to the regulatory subunit induces a conformational change in the catalytic subunit, enabling substrate ($\text{S}$) binding.

Structure of Adenosine Triphosphate ($\text{ATP}$)

An adenosine nucleoside bound to three phosphate groups ($\alpha$, $\beta$, $\gamma$) connected by high-energy phosphoanhydride bonds.

Energy Transfer Mechanism of $\text{ATP}$ Hydrolysis

Cleavage of the terminal phosphoanhydride bond ($\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i$) yields free energy to drive endergonic processes.

Phosphodiester Bond Linkage in Polynucleotides

A covalent ester bond linking the 3' hydroxyl group ($\text{-OH}$) of one sugar to the 5' phosphate group of the adjacent nucleotide sugar.

Directionality of Nucleic Acid Strands

Polynucleotide chains are synthesized and read in the 5' to 3' direction, beginning at a free 5' end and terminating at a free 3' end.

Erwin Chargaff's Key Discovery (1940s)

Quantitated DNA composition and demonstrated that double-stranded DNA contains equal amounts of adenine and thymine, and equal amounts of guanine and cytosine.

Chargaff's Rules Equations

$\text{A} = \text{T}$, $\text{G} = \text{C}$, and total purines equal total pyrimidines ($\text{A} + \text{G} = \text{C} + \text{T}$).

Jerry Donohue's Contribution to DNA Structure

Demonstrated that nitrogenous bases exist predominantly in their keto (rather than enol) tautomeric forms under physiological conditions.

Enol vs Keto Tautomeric Forms in Base Pairing

Keto forms feature carbonyl ($\text{C=O}$) groups required for standard Watson-Crick hydrogen bonding; enol forms feature hydroxyl ($\text{-C-OH}$) groups.

Rosalind Franklin's Contribution to Molecular Biology

Biophysicist who produced X-ray diffraction images (Photo 51) revealing the helical geometry, dimensions, and hydrated states of DNA.

Maurice Wilkins's Role in DNA Discovery

Physicist who studied DNA structure via X-ray crystallographic methods and shared critical X-ray data with Watson and Crick.

1962 Nobel Prize Recipients for DNA Structure

James Watson, Francis Crick, and Maurice Wilkins.

Watson and Crick Landmark Publication

Published in Nature on April 25, 1953 (Volume 171, pages 737-738), proposing the antiparallel double-helix model of DNA.

Handedness of B-DNA Double Helix

Right-handed double helix.

Diameter of B-DNA Double Helix

$20\,\text{Å}$ ($2.0\,\text{nm}$).

Distance per Complete Helical Turn in B-DNA

$34\,\text{Å}$ ($3.4\,\text{nm}$), spanning 10 base pairs per repeat.

Distance Between Adjacent Base Pairs in B-DNA

$3.4\,\text{Å}$ ($0.34\,\text{nm}$).

Helical Twist Angle per Residue in B-DNA

$36^\circ$ of rotation between consecutive base pairs on the same chain.

Major Groove Width in B-DNA

$22\,\text{Å}$ wide, serving as a primary site for sequence-specific protein binding.

Minor Groove Width in B-DNA

$12\,\text{Å}$ wide.

Hydrogen Bonding in Adenine-Thymine Pairs

Held together by 2 hydrogen bonds (purine position 1 to pyrimidine position 1, and purine position 6 to pyrimidine position 6).

Hydrogen Bonding in Guanine-Cytosine Pairs

Held together by 3 hydrogen bonds, conferring higher thermal stability than A-T pairs.

Base Stacking Interactions in DNA

Hydrophobic and van der Waals interactions between stacked parallel aromatic base rings oriented perpendicular to the fiber axis.

Antiparallel Strand Alignment in DNA

One strand runs 5' to 3' while the complementary strand runs in the opposite 3' to 5' direction.

Complementary Sequence Determination

Due to strict $\text{A-T}$ and $\text{G-C}$ base pairing rules, knowing the base sequence on one strand automatically dictates the sequence on the opposite strand.

Nucleosome Core Structure

The structural unit of chromatin, composed of double-stranded DNA wrapped around an octamer core of histone proteins.

Chromosomal Structural Hierarchy

DNA double helix $\rightarrow$ Nucleosomes $\rightarrow$ Chromatin loops $\rightarrow$ Chromatid $\rightarrow$ Metaphase chromosome.

Anatomy of Metaphase Chromosomes

Consists of a short $p$ arm, a long $q$ arm, a central centromere, and terminal telomeres.

Telomere Structure & Function

Repetitive DNA caps located at the ends of linear chromosomes that protect genomic ends from degradation and end-to-end fusion.

Messenger RNA (mRNA) Function

Single-stranded RNA carrying protein-coding genetic sequences transcribed from DNA to the ribosome for translation.

Ribosomal RNA (rRNA) Function

Structural and catalytic RNA components that assemble with ribosomal proteins to form functional ribosomes.

Transfer RNA (tRNA) Function

Adaptor RNA molecules containing an anticodon loop and an amino acid attachment site that deliver specific amino acids during translation.

Small Nuclear RNA (snRNA) Function

Non-coding nuclear RNA involved in eukaryotic pre-mRNA processing and intron splicing.

Ribonuclease P (RNase P) Function

A catalytic RNA enzyme (ribozyme) that cleaves precursor sequences from the 5' end of tRNA molecules.

Griffith Experiment Setup (1928)

Tested living virulent (S), living non-virulent (R), heat-killed S, and heat-killed S plus living R pneumococcal strains in mice.

Griffith Experiment Outcome & Conclusion

Mice injected with heat-killed S and living R strains died and yielded living S bacteria, demonstrating bacterial genetic transformation.

Avery-MacLeod-McCarty Experiment Strategy (1944)

Treated heat-killed virulent bacterial extract with specific enzymes (Protease, RNase, Lipase, Carbo-ase, or DNase) prior to transformation.

Avery-MacLeod-McCarty Landmark Result

Bacterial transformation failed only when the extract was treated with DNase, proving DNA is the transforming principle.

Hershey-Chase Experiment Radioisotopes (1952)

Used Sulfur-35 ($^{35}\text{S}$) to label bacteriophage protein capsids and Phosphorus-32 ($^{32}\text{P}$) to label bacteriophage DNA.

Hershey-Chase Key Finding

Only $^{32}\text{P}$-labeled DNA entered infected E. coli host cells, confirming DNA as the hereditary genetic material.

Meselson-Stahl Experiment Nitrogen Isotopes (1958)

Grew E. coli in heavy nitrogen ($^{15}\text{N}$) medium, shifted to light nitrogen ($^{14}\text{N}$) medium, and monitored DNA density over successive generations.

Meselson-Stahl Analytical Technique

Cesium chloride ($\text{CsCl}$) density gradient ultracentrifugation.

Meselson-Stahl Generational Density Results

Gen 0 gave heavy DNA ($^{15}\text{N-}^{15}\text{N}$), Gen 1 gave hybrid DNA ($^{15}\text{N-}^{14}\text{N}$), and Gen 2 gave hybrid and light DNA ($^{14}\text{N-}^{14}\text{N}$), proving semiconservative replication.

Semiconservative DNA Replication Concept

Mechanism where each replicated double helix consists of one intact parental strand and one newly synthesized strand.

Central Dogma Information Flow

The directional transmission of biological information: DNA replication $\rightarrow$ Transcription into RNA $\rightarrow$ Translation into Protein.

Transcription Process Definition

Enzymatic synthesis of a complementary single-stranded RNA transcript using a double-stranded DNA template strand.

Translation Process Definition

Ribosome-catalyzed peptide bond formation reading mRNA codons to assemble specific amino acid sequences into proteins.

Codon Definition in mRNA

A triplet sequence of 3 adjacent nucleotides in mRNA specifying a single amino acid or translation stop signal.

Endonuclease vs Exonuclease Activity

Endonucleases cleave internal phosphodiester bonds within nucleic acid chains; Exonucleases remove terminal nucleotides from 3' or 5' ends.

Snake Venom Phosphodiesterase Specificity

An exonuclease that sequentially cleaves nucleotides from the 3' end of polynucleotides to produce mononucleotides.

Restriction Endonuclease Function

Bacterial site-specific endonucleases that recognize specific double-stranded DNA sequences and cleave phosphodiester bonds on both strands.

Palindromic DNA Sequence Definition

A sequence that reads identically 5' to 3' on both complementary DNA strands due to twofold rotational symmetry.

Sticky Ends vs Blunt Ends

Sticky ends possess single-stranded overhangs from staggered cuts; Blunt ends possess flush double-stranded ends from straight cuts.

EcoRI Recognition Sequence & Cut Pattern

Recognizes $5'\text{-G}\downarrow\text{AATTC-3'}$ and cuts between G and A to generate 5' sticky overhangs.

EcoRV Recognition Sequence & Cut Pattern

Recognizes $5'\text{-GAT}\downarrow\text{ATC-3'}$ and cuts directly between T and A to produce blunt ends.

Agarose Gel Electrophoresis Separation Basis

Separates DNA molecules according to size as negatively charged fragments migrate through an agarose gel toward the positive electrode.

DNA Migration Direction in Electrophoresis

DNA moves from the negative electrode (cathode) to the positive electrode (anode) due to its negatively charged phosphate backbone.

Gel Matrix Sieving Effect on DNA Size

Shorter DNA fragments pass through gel matrix pores rapidly, while longer fragments are retarded and move more slowly.

Ethidium Bromide Mechanism of Action

A planar hydrophobic molecule that intercalates between stacked base pairs of DNA and fluoresces under ultraviolet ($\text{UV}$) illumination.

2',3'-Dideoxynucleoside Triphosphate (ddNTP) Structure

A modified nucleotide analogue missing hydroxyl groups ($\text{-OH}$) at both the 2' and 3' position carbons of the ribose ring.

ddNTP Chain Termination Mechanism

Incorporation of a ddNTP stops DNA extension because the lacking 3'-OH group prevents formation of a 3'-5' phosphodiester bond.

Essential Reaction Components of Sanger Sequencing

Single-stranded DNA template, oligonucleotide primer, DNA polymerase, standard dNTPs, and chain-terminating ddNTPs.

Modern Automated Sanger Sequencing Method

Employs 4 distinct dye-labeled ddNTPs, capillary gel electrophoresis, and laser fluorescence detection.

Pyrosequencing Light Emission Reaction

Detects light generated by luciferase when inorganic pyrophosphate ($\text{PP}_i$) released by DNA polymerase is converted to ATP by ATP sulfurylase.

Enzymes Involved in Pyrosequencing

DNA Polymerase, ATP Sulfurylase, Luciferase, and Apyrase.

Plasmid Cloning Vector Definition

A small circular double-stranded extrachromosomal DNA molecule capable of autonomous replication in bacterial host cells.

pUC18 Vector Features

A $2.69\,\text{kb}$ plasmid containing an ampicillin resistance gene ($\text{amp}^R$), a $\text{lacZ}$ gene, and a multiple cloning polylinker region.

Polylinker (Multiple Cloning Site) Function

A synthetic sequence within a cloning vector containing multiple unique restriction endonuclease recognition sites.

Selectable Marker Function ($\text{amp}^R$)

Confers ampicillin resistance, enabling survival of plasmid-transformed bacterial cells on ampicillin-containing selective media.

Chimeric (Recombinant) DNA Formation

Created when foreign insert DNA and vector DNA cut by the same restriction enzyme anneal and are joined by DNA ligase.

DNA Ligase Role in Gene Cloning

Catalyzes covalent phosphodiester bond formation between 3'-OH and 5'-phosphate sugar-phosphate backbones of DNA fragments.

CRISPR Acronym Expansion

Clustered Regularly Interspaced Short Palindromic Repeats.

Natural Biological Function of Bacterial CRISPR-Cas Systems

Prokaryotic adaptive immune mechanism that stores phage DNA segments to identify and destroy invading viral DNA.

Key Components of CRISPR-Cas9 Gene Editing

Cas9 endonuclease enzyme and a guide RNA (gRNA/sgRNA) that targets Cas9 to a specific genomic locus.

Protospacer Adjacent Motif (PAM) Requirement

A short conserved DNA sequence ($\text{5'-NGG-3'}$ for Cas9) adjacent to the target site necessary for Cas9 recognition and cleavage.

2020 Nobel Prize in Chemistry Awardees for CRISPR

Jennifer Doudna and Emmanuelle Charpentier.

Direct vs Cell-Based Transgene Delivery Methods

Direct delivery injects packaged viral vectors straight into patient organs; Cell-based delivery modifies patient stem cells in vitro prior to reinfusion.

He Jiankui Bioethics Affair (2018)

Unsanctioned CRISPR editing of the CCR5 gene in human embryos leading to live births, driving global overhauls of gene-editing governance.