Biochemistry: Nucleic Acids and Enzymes

Comprehensive practice flashcards covering the chemical composition, structure, and functions of nucleic acids, as well as the mechanisms, kinetics, and regulation of enzymes.

Friedrich Miescher

Swiss physiologist who discovered nucleic acids in 1869 while studying the nuclei of white blood cells.

Nucleic Acid

An unbranched biopolymer whose monomer units are nucleotides, essential to all forms of life and responsible for storing and transferring genetic information as well as protein synthesis.

Nucleotide

A three-subunit monomer molecule consisting of a pentose sugar bonded to both a phosphate group and a nitrogen-containing heterocyclic base.

Nucleoside

A two-subunit molecule composed of a pentose sugar bonded to a nitrogen-containing heterocyclic base, lacking a phosphate group.

Ribose

The five-carbon pentose sugar found in ribonucleic acid (RNA), containing a hydroxyl group ($-\text{OH}$) at the $2'$ carbon position.

2'-Deoxyribose

The five-carbon pentose sugar found in deoxyribonucleic acid (DNA), which lacks an oxygen atom at the $2'$ carbon position.

Hydrogen Phosphate Ion ($\text{HPO}_4^{2-}$)

The ionized form of phosphoric acid ($\text{H}_3\text{PO}_4$) that forms under cellular pH conditions when phosphoric acid loses two of its hydrogen atoms, giving nucleic acids their acidic properties.

Pyrimidine

A monocyclic, six-membered nitrogen-containing heterocyclic base found in nucleic acids; includes thymine (T), cytosine (C), and uracil (U).

Purine

A bicyclic nitrogen-containing heterocyclic base consisting of fused five- and six-membered rings; includes adenine (A) and guanine (G).

Thymine (T)

A pyrimidine base found primarily in DNA that pairs complementarily with adenine via hydrogen bonding.

Cytosine (C)

A pyrimidine base found in both DNA and RNA that pairs complementarily with guanine via three hydrogen bonds.

Uracil (U)

A pyrimidine base found exclusively in RNA that replaces thymine and pairs complementarily with adenine.

Adenine (A)

A purine base found in both DNA and RNA that forms complementary base pairs with thymine in DNA and uracil in RNA.

Guanine (G)

A purine base found in both DNA and RNA that forms complementary base pairs with cytosine.

$\beta$-N-Glycosidic Linkage

The covalent linkage formed between the $C\text{-}1'$ position of a pentose sugar in the $\beta$-configuration and nitrogen-9 of a purine or nitrogen-1 of a pyrimidine.

Condensation Reaction (Nucleoside Formation)

The reaction mechanism by which a nitrogenous base and a pentose sugar bond together at the $C\text{-}1'$ position with the release of a water molecule ($\text{H}_2\text{O}$).

-idine

The nomenclature suffix appended to pyrimidine bases to name the corresponding nucleoside (e.g., cytidine, thymidine, uridine).

-osine

The nomenclature suffix appended to purine bases to name the corresponding nucleoside (e.g., adenosine, guanosine).

Deoxythymidine

The specific deoxyribonucleoside formed by the attachment of the pyrimidine base thymine to $2'$-deoxyribose.

Phosphate-Ester Linkage

The covalent bond that connects a phosphate group to the $C\text{-}5'$ hydroxyl position of a pentose sugar during nucleotide formation.

Nucleotide Nomenclature

The system of naming nucleotides by appending the term '5\'-monophosphate' to the name of the parent nucleoside (e.g., adenosine 5\'-monophosphate).

Adenosine 5'-Triphosphate (ATP)

A nucleotide containing adenine, ribose, and three phosphate groups that functions as the primary energy source for cellular activity.

Deoxyribonucleic Acid (DNA)

A double-stranded nucleic acid polymer whose primary function is the storage and transfer of genetic information from existing cells to new cells during cell division.

Ribonucleic Acid (RNA)

A single-stranded nucleic acid polymer occurring in all parts of the cell whose primary biological function is the synthesis of proteins.

Primary Nucleic Acid Structure

The precise linear sequence in which nucleotides are linked together in a nucleic acid polymer.

Nucleic Acid Backbone

The constant structural framework of a nucleic acid strand composed of alternating pentose sugar and phosphate units.

3',5'-Phosphodiester Linkage

The ester bonds that link the nonterminal phosphate group to the $3'$ carbon of one sugar and the $5'$ carbon of the next sugar in a polynucleotide chain.

5' End

The terminus of a polynucleotide chain that has a free, unattached phosphate group at the $5'$ carbon position of its terminal sugar.

3' End

The terminus of a polynucleotide chain that has an unreacted, free hydroxyl group ($-\text{OH}$) at the $3'$ carbon position of its terminal sugar.

Directionality of Nucleic Acid Reading

The rule establishing that a nucleic acid polymer's primary sequence is written and read from the free $5'$ end to the free $3'$ end using the letters of its bases (e.g., $5'\text{-A-C-G-T-}3'$).

Chargaff's Rule

The empirical biochemical principle stating that in DNA, the amount of adenine is identical to thymine ($\text{A} = \text{T}$) and the amount of cytosine is identical to guanine ($\text{C} = \text{G}$).

Secondary Nucleic Acid Structure

The three-dimensional conformation of the sugar-phosphate backbone and base pairing between complementary nucleotides, exemplified by the DNA double helix.

Complementary Base Pairing

The specific hydrogen bonding pairing rule in nucleic acids where adenine pairs exclusively with thymine (or uracil) and guanine pairs exclusively with cytosine.

Complementary DNA Strand

A polynucleotide strand running antiparallel to another strand, wherein each nitrogenous base aligns opposite its complementary base partner.

Base Stacking Interactions

Hydrophobic interactions occurring between the parallel planar rings of adjacent nitrogenous bases that help stabilize the DNA double helix.

Pi-pi Interactions

Noncovalent electrostatic forces that occur between the delocalized aromatic electrons of planar nitrogenous bases within stacked nucleic acid structures.

DNA Double Helix Diameter

The uniform spatial width across the double-stranded DNA structure, measuring exactly $2\,\text{nm}$.

DNA Base-Pair Distance

The vertical distance separating adjacent stacked base pairs along the axis of the DNA double helix, measuring $0.34\,\text{nm}$.

Major and Minor Grooves

The asymmetrical helical indentations on the exterior surface of a DNA double helix resulting from the geometric arrangement of the antiparallel sugar-phosphate backbones.

Tertiary Nucleic Acid Structure

The overall three-dimensional folding and spatial arrangement of atoms in a nucleic acid, accommodating steric and geometric constraints (such as supercoiling).

Quaternary Nucleic Acid Structure

The higher-order structural interaction and association of nucleic acids with other macromolecules, such as histone proteins.

Nucleosome

The basic structural repeating unit of chromatin consisting of DNA wound around an octameric core of histone proteins, appearing as a 'bead'.

Linker DNA

The segment of continuous double-stranded DNA that connects adjacent nucleosome beads, resembling the 'string' in a 'beads on a string' chromatin fiber.

30-nm Fiber

A tightly coiled cord of nucleosomes measuring $30\,\text{nm}$ in diameter that forms an intermediate stage of chromatin condensation.

Looped Domains

Higher-order chromatin structures formed as a dividing cell condenses its $30\text{-nm}$ fiber into loops anchored to a non-histone protein scaffold.

Transfer RNA (tRNA)

The smallest RNA type (size range between 73 and 93 nucleotides, averaging 75) that folds into a warped cloverleaf shape and delivers a specific amino acid to the ribosome during protein synthesis.

Ribosomal RNA (rRNA)

The most abundant RNA type (constituting 80% of total cellular RNA, rich in guanylic acid) that associates with proteins to form eukaryotic $60\text{S}$ and $40\text{S}$ ribosomal subunits and initiates polypeptide synthesis.

Messenger RNA (mRNA)

An unstable, short-lived RNA product constituting about 5% of cellular RNA that carries genetic instructions from DNA in the nucleus to the ribosomes for protein synthesis.

Heterogeneous Nuclear RNA (hnRNA)

The direct transcriptional RNA precursor synthesized in the cell nucleus that undergoes processing to yield mature messenger RNA.

Cellular Locations of DNA

The specific compartments within a eukaryotic cell where DNA is found, comprising the nucleus, mitochondria, and chloroplasts.

Enzyme

A biological catalyst, usually a globular protein, that accelerates chemical reaction rates in cells by providing an alternative pathway with a lower activation energy.

Catalyst

A substance that accelerates the rate of a chemical reaction without undergoing any permanent chemical alteration or consumption in the process.

Activation Energy ($\Delta G^{\ddagger}$)

The minimum initial input of free energy required to convert reactant molecules into an unstable, high-energy transition state complex.

Transition State

The transient, high-energy molecular configuration achieved during a chemical reaction that possesses sufficient energy to convert into reaction products.

Net Free Energy Change ($\Delta G^\circ$)

The thermodynamic difference in free energy between reactants and products, which remains completely unchanged by the presence of an enzyme catalyst.

Simple Enzyme

An enzyme composed entirely of amino acid protein chains without any non-protein components.

Conjugated Enzyme (Holoenzyme)

A fully active, intact enzyme consisting of a protein component (apoenzyme) combined with a non-protein component (cofactor).

Apoenzyme

The inactive protein portion of a conjugated enzyme that requires a non-protein cofactor to function catalytically.

Cofactor

A non-protein chemical compound (inorganic ion or organic molecule) that binds tightly or loosely to an apoenzyme and is required for catalytic activity.

Prosthetic Group

A cofactor, usually a small inorganic atom or metal ion (e.g., zinc, manganese, iron), that is tightly bound to an apoenzyme.

Coenzyme

A large organic cofactor (often a vitamin derivative) that is loosely bound to an apoenzyme and assists in catalytic group transfers.

Active Site

A small, crevice-like region of an enzyme's three-dimensional structure formed by protein folding that directly binds the substrate and participates in catalysis.

Substrate

The specific reactant molecule that binds to an enzyme's active site and is converted into a product during a chemical reaction.

Enzyme-Substrate Complex ($ES$)

The intermediate molecular entity formed when a substrate reversibly binds to the active site of an enzyme through noncovalent interactions.

-ase

The standard nomenclature suffix identifying a biochemical substance as an enzyme (e.g., urease, sucrase, lipase).

-in

The historical suffix retained in the names of several classical digestive enzymes, including trypsin, chymotrypsin, and pepsin.

Oxidoreductase (EC 1)

An enzyme class that catalyzes oxidation-reduction reactions, such as glucose oxidase, peroxidase, catalase, and lactate dehydrogenase.

Transferase (EC 2)

An enzyme class that catalyzes the transfer of a functional group (e.g., methyl, acyl, amino, or phosphate) from one molecule to another.

Hydrolase (EC 3)

An enzyme class that catalyzes the hydrolytic cleavage of chemical bonds using water as an acceptor for the transferred group.

Lyase (EC 4)

An enzyme class that catalyzes the cleavage of bonds by means other than hydrolysis and oxidation, often adding or removing groups to form double bonds.

Isomerase (EC 5)

An enzyme class that catalyzes geometric or structural rearrangements within a single molecule, including mutase reactions and $\text{L}$-to-$\text{D}$ isomerizations.

Ligase (EC 6)

An enzyme class that catalyzes the joining of two molecules with covalent bonds coupled to the energy released from ATP hydrolysis.

Enzyme Commission (EC) Number

A systematic four-digit classification number assigned by the I.U.B. designating an enzyme's class, subclass, sub-subclass, and specific serial identifier (e.g., EC 2.7.1.1 for hexokinase).

Lock-and-Key Model

An enzyme-substrate binding model proposing that the active site has a rigid, pre-existing shape perfectly complementary to that of the substrate.

Induced-Fit Model

An enzyme-substrate binding model proposing that the active site is flexible and alters its conformation upon substrate binding to maximize geometric and chemical fit.

Absolute Specificity

The property of an enzyme to catalyze only one single chemical reaction for a single specific substrate (e.g., urease catalyzing only urea hydrolysis).

Group Specificity

The property of an enzyme to act on a group of distinct substrates that share similar functional groups (e.g., hexokinase phosphorylating hexoses).

Linkage Specificity

The property of an enzyme to catalyze a reaction on a specific chemical bond type regardless of the rest of the molecular framework (e.g., chymotrypsin hydrolyzing peptide bonds).

Stereochemical Specificity

The property of an enzyme to distinguish between stereoisomers due to the inherent chirality of its active site (e.g., L-amino acid oxidase acting only on L-amino acids).

Optimum Temperature

The temperature at which an enzyme catalyzes a reaction at its highest rate (approximately $40\,^\circ\text{C}$ for most human enzymes).

Optimum pH

The specific pH value at which an enzyme exhibits maximum catalytic activity, reflecting the optimal ionization states of active site amino acid residues.

Pepsin

A digestive protease located in the stomach that hydrolyzes peptide bonds, operating with an optimum pH of 2.

Arginase

A liver enzyme in the urea cycle that requires a $\text{Mn}^{2+}$ cofactor and hydrolyzes arginine at an alkaline optimum pH of 9.7.

Saturation Point

The condition in an enzyme-catalyzed reaction where all active sites are continuously bound to substrate molecules, causing the reaction velocity to reach $V_{\max}$.

Water-Soluble Vitamins

Vitamins (B-complex and Vitamin C) that absorb directly into the bloodstream, circulate in water-filled compartments, are excreted by the kidneys in urine, and function as coenzymes.

Fat-Soluble Vitamins

Vitamins (A, D, E, and K) that enter the lymph system, require protein carriers, are stored in fat-associated tissues, and generally do not function as coenzymes.

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

A coenzyme derived from Vitamin $\text{B}_3$ (niacin) that accepts a hydride ion ($\text{H}^-$) or electrons, functioning as an oxidizing agent in metabolic redox reactions.

Flavin Adenine Dinucleotide (FAD)

A coenzyme derived from Vitamin $\text{B}_2$ (riboflavin) that accepts a hydride ion and a proton ($\text{H}^+$) to become $\text{FADH}_2$, acting as an electron donor in cellular respiration.

Coenzyme A (CoA)

A coenzyme synthesized from Vitamin $\text{B}_5$ (pantothenic acid) that binds and transfers acyl and acetyl groups via a reactive sulfhydryl ($-\text{SH}$) group.

Coenzyme $\text{Q}_{10}$ (Ubiquinone)

A lipid-soluble, vitamin-like electron carrier that transfers electrons between complexes in the mitochondrial electron transport chain.

Thiamin Pyrophosphate (TPP)

A coenzyme derived from Vitamin $\text{B}_1$ that participates in decarboxylation and carboxyl group transfer reactions in the citric acid cycle.

Enzyme Inhibitor

A substance that binds to an enzyme and decreases the rate of the catalyzed reaction without permanently destroying the enzyme protein.

Competitive Inhibition

A reversible inhibition mode where an inhibitor structurally resembles the substrate, competes for the active site, and can be overcome by increasing substrate concentration.

Noncompetitive Inhibition

An inhibition mode where an inhibitor binds to an enzyme at a site other than the active site, altering the enzyme's conformation so that substrate binding or catalysis cannot proceed effectively.

Uncompetitive Inhibition

An inhibition mode where the inhibitor binds exclusively to the enzyme-substrate ($ES$) complex, preventing product formation.

Negative Allosteric Regulator

A regulatory substance that binds to a non-active allosteric site and alters active site geometry, making it less receptive to the substrate and decreasing reaction rate.

Positive Allosteric Regulator

A regulatory substance that binds to an allosteric site and alters active site shape, enabling it to accept substrate more readily and increasing reaction rate.

Aspartate Transcarbamoylase

An allosteric enzyme organized into two catalytic trimers and three regulatory dimers that is allosterically inhibited by cytidine triphosphate (CTP) and activated by ATP.

Feedback Inhibition (Feedback Control)

A metabolic regulatory mechanism in which the end product of a multi-step pathway binds to and inhibits an early regulatory enzyme in that same pathway.

Alanine Aminotransferase (ALT)

A liver transferase enzyme whose elevated concentration in the blood serves as an important diagnostic clinical indicator of liver damage or disease.