Hemoglobin, Myoglobin, and Nucleic Acids Practice

Vocabulary practice flashcards based on lecture notes covering Myoglobin, Hemoglobin, and fundamental Nucleic Acid chemistry and techniques.

Dissociation constant ($Kd$)

A measurement where a lower value indicates a higher affinity or stronger binding relationship between a protein and its ligand.

Globin fold

A structural motif shared by both myoglobin and hemoglobin characterized by $8$ $\alpha$-helices folded around a prosthetic heme group.

Fractional saturation ($\theta$) of $0.5$

The state achieved when the partial pressure of oxygen ($pO_2$) is equal to the $Kd$ (or $p50$) of myoglobin.

Proximal Histidine (His F8)

The specific amino acid residue that acts as a 'lever' to communicate the movement of the $Fe^{2+}$ atom to the rest of the protein subunit and provides the fifth coordination bond to the iron.

T-state (Deoxyhemoglobin)

The 'tense' structural state of hemoglobin where the $Fe^{2+}$ is slightly too large to fit in the porphyrin ring, sitting out of the heme plane, and stabilized by ion pairs.

\alpha_1̡_1 and \alpha_2̢_2 dimer interfaces

Quaternary interfaces in mammalian hemoglobin dominated by strong hydrophobic interactions that do not shift or break during the transition between structural states.

Dimer-dimer interface

The hemoglobin interface stabilized by ionic and hydrogen bonds that breaks and reforms during the shift between the T and R states.

R-state (Relaxed state)

The structural state of hemoglobin initiated by oxygen binding, leading to the narrowing and constriction of the central cavity, which forces the release of $2,3\text{-BPG}$.

Carbonic Anhydrase

An enzyme found in red blood cells that accelerates the conversion of $CO_2$ and $H_2O$ into $H_2CO_3$ to facilitate the Bohr Effect.

Carbamates

Chemical products formed when $CO_2$ reacts with the N-terminal amino groups of hemoglobin subunits, stabilizing the T-state through salt bridge formation.

$2,3\text{-BPG}$ ($2,3\text{-Bisphosphoglycerate}$)

An allosteric effector that increases in concentration to facilitate oxygen unloading in tissues as an adaptation to low oxygen partial pressures at high altitudes.

Hill plot slope $n = 1$

The observation at very low and very high partial pressures of oxygen where hemoglobin acts non-cooperatively, supporting the 'two-state' model.

Nucleotide

A chemical structure composed of a nitrogenous base, a sugar, and a phosphate group (which is missing in a nucleoside).

$2'\text{-OH}$ group

The structural feature of the ribose sugar in RNA that allows for nucleophilic attack under basic conditions, making RNA less resistant to alkaline hydrolysis than DNA.

Thymine ($5\text{-methyl uracil}$)

The base used in DNA instead of uracil to allow repair enzymes to distinguish between natural bases and deaminated cytosine.

Euchromatin

A less condensed chromatin structure accessible for transcription, formed when histone tails are modified with acetyl or methyl groups.

Ribozyme

A specific class of RNA molecule that possesses intrinsic enzymatic activity.

Actinomycin D

An intercalating agent that inhibits transcription by binding DNA at the initiation complex and preventing elongation by RNA polymerase.

Sticky ends

Single-stranded overhangs generated by a restriction endonuclease when it cleaves DNA at offset positions within a recognition sequence.

0.5 kb DNA fragment

A small DNA fragment that will migrate the greatest distance from the sample well during electrophoretic analysis.

Ethidium Bromide

An intercalating agent used to aid in the visualization of DNA fragments after electrophoresis by fluorescing under UV light.

Dideoxynucleotides (ddNTPs)

Chain-terminating analogs used in automated DNA sequencing, each labeled with a unique colored fluorescent tag for identification.

Polyacrylamide

A gel matrix with smaller pores than agarose, appropriate for separating very small DNA fragments or for DNA sequencing.

Distal Histidine (His E7)

The residue that provides a critical stabilizing hydrogen bond to the oxygen molecule bound as the sixth ligand to the heme iron.

Nucleation

The slow, second-order reaction step in the thermal renaturation of DNA involving the random collision of complementary strands.

Histone H1

The 'linker' histone known for anchoring DNA as it enters and leaves the nucleosome.