Biochemistry: Proteins, Amino Acids, Nucleic Acids, and DNA Replication

Comprehensive vocabulary flashcards generated from lecture notes covering amino acid chemistry, protein secondary and tertiary structures, hemoglobin/myoglobin dynamics, nucleic acid conformations, RNA types, and core DNA replication mechanisms.

Isoelectric Point ($pI$) of Hydrophobic Amino Acids

The pH value at which a hydrophobic amino acid carries net zero charge, calculated as the average of its two $pK_a$ values (the carboxyl functional group and the amine functional group).

Isoelectric Point ($pI$) of Polar and Charged Amino Acids

The pH value at which a polar or charged amino acid carries net zero charge, calculated by taking the average of its three $pK_a$ values using the formula $\frac{pK_{a1} + pK_{a2} + pK_{a3}}{3}$.

Aspartate

A negatively charged amino acid that contains two carboxylic functional groups and one amine functional group.

Lysine

A positively charged polar amino acid that contains two amine functional groups and one carboxylic functional group.

Antiparallel $\beta$\text{-Pleated Sheet}

A protein secondary structure in which adjacent sheets run in opposite directions and intermolecular hydrogen bonds are vertically arranged, making it stronger than the parallel arrangement.

Parallel $\beta$\text{-Pleated Sheet}

A protein secondary structure in which adjacent polypeptide sheets run in the same direction and intermolecular hydrogen bonds are slanted in one direction to pair with corresponding molecules.

Fibrous Proteins

Proteins composed entirely of a single type of secondary structure throughout their entire length (e.g., exclusively $\beta$\text{-pleated sheets} or exclusively $\alpha$\text{-helices}).

Globular Proteins

Proteins whose overall structure contains more than one type of secondary protein structure.

Collagen

A glycoprotein composed of three right-handed $\alpha$\text{-chains} twisted into a left-handed helical structure, with a basic amino acid composition of Glycine ($35\%$), Alanine ($11\%$), and Proline plus Hydroxyproline ($21\%$).

Scurvy

A condition caused by Vitamin C deficiency, which prevents the hydroxylation of proline residues to hydroxyproline, resulting in weakened collagen fibers and symptoms such as a smelly mouth.

Methemoglobin (MetHb)

A form of hemoglobin in which iron is oxidized to its ferric ($Fe^{3+}$) state, preventing oxygen ($O_2$) from reversibly binding.

Myoglobin

A monomeric oxygen storage protein with high affinity for oxygen that yields a rectangular hyperbolic oxygen-binding curve.

Hemoglobin

A tetrameric oxygen carrier protein that displays cooperative oxygen binding, yielding a sigmoidal oxygen-binding curve.

Carbamino-hemoglobin

A complex formed when carbon dioxide binds to the N-terminal amine groups of the T form of hemoglobin, without competing with oxygen for the heme active site.

2,3-Diphosphoglycerate (2,3-BPG)

A negatively charged allosteric regulator that binds to positively charged residues (2 His, 2 Lys, 2 N-termini) in the central cavity of hemoglobin, shifting the curve toward the T state to facilitate $O_2$ release.

His E7 (Distal Histidine)

A histidine residue on the oxygen-binding side of heme that sterically hinders bound carbon monoxide ($CO$), forcing it to tilt away from its preferred perpendicular orientation and reducing its binding affinity relative to $O_2$.

Perutz Mechanism

A model describing cooperativity in hemoglobin, wherein oxygen binding to one heme group induces conformational changes in secondary, tertiary, and quaternary structures that increase the affinity of remaining heme groups.

Purines

Nitrogenous bases containing a fused 5-membered and 6-membered ring system, comprising Adenine and Guanine.

Pyrimidines

Nitrogenous bases containing a single 6-membered ring, comprising Cytosine, Uracil, and Thymine.

$\beta$\text{-N-Glycosidic Linkage}

The covalent bond connecting the $1'$ carbon of a pentose sugar to a nitrogenous base in nucleotides, configured in the $\beta$ position to prevent cleavage by human digestive enzymes.

Sugar Pucker

The three-dimensional conformation of the pentose sugar ring (ribose or deoxyribose) in nucleotides, defined by the out-of-plane displacement of either the $C_2'$ or $C_3'$ carbon relative to the other four ring atoms.

$C_2'$\text{-endo Pucker}

A sugar pucker conformation where the $C_2'$ carbon is displaced out of the plane on the same side as the $C_5'$ carbon, representing the major sugar conformation in B-DNA.

$C_3'$\text{-endo Pucker}

A sugar pucker conformation where the $C_3'$ carbon is displaced out of the plane on the same side as the $C_5'$ carbon, representing the predominant conformation in A-DNA and double-stranded RNA.

A-DNA

A short, broad, right-handed double helix of DNA featuring $C_3'$\text{-endo} sugar puckers, which exists physiologically under dehydrated conditions.

B-DNA

The standard hydrated, right-handed double-helical conformation of DNA with $C_2'$\text{-endo} sugar puckers, a helix pitch of $3.4\,\text{nm}$, and $10\,\text{bp}$ per turn.

Z-DNA

An elongated, thin, left-handed double helix with a zig-zag sugar-phosphate backbone containing alternating $C_2'$\text{-endo} and $C_3'$\text{-endo} puckers and a high frequency of G-C repeats.

Heterogeneous Nuclear RNA (hnRNA)

The initial eukaryotic pre-mRNA transcript produced in the nucleus that contains coding exon regions interrupted by non-coding intron sequences.

Poly(A) Tail

A string of $100\text{--}200$ adenylic acid residues appended to the $3'$ end of eukaryotic mRNA post-transcriptionally to enhance molecular stability.

Transfer RNA (tRNA)

An adaptor RNA molecule featuring an acceptor stem ($CCA\text{-}3'\text{-OH}$), D loop (containing dihydrouridine), anticodon loop, and $\text{T}\psi\text{C}$ loop (containing pseudouridine) that carries specific amino acids to the ribosome.

Small Nuclear RNA (snRNA)

A class of eukaryotic nuclear RNA molecules present in stable ribonucleoprotein complexes that process precursor pre-mRNA (hnRNA) into mature mRNA for cytoplasmic export.

Vicinal $2'$\text{-OH} Group

The hydroxyl group on the $2'$ carbon of ribose in RNA that makes the adjacent $3'$\text{-phosphodiester} linkage vulnerable to nucleophilic cleavage and alkaline hydrolysis, causing RNA to be less stable than DNA.

Kornberg Polymerase

DNA Polymerase I, the first DNA-synthesizing enzyme discovered, named in honor of Arthur Kornberg.

Semiconservative Replication

The mode of DNA replication wherein each new daughter double helix consists of one intact original parental strand and one newly synthesized daughter strand.

Bidirectional Replication

DNA replication that progresses in both directions simultaneously from an origin of replication via two active replication forks.

DNA Polymerase Priming Requirement

The prerequisite that all DNA polymerases require a pre-existing RNA primer providing a free $3'$\text{-OH} group to perform nucleophilic attack on incoming dNTPs and synthesize DNA in the $5' \rightarrow 3'$ direction.