Biochemistry - Chemical Foundations, Water, Amino Acids, and Protein Structure

A set of vocabulary flashcards covering foundational chemical, physical, and structural concepts from biochemistry lectures, including thermodynamics, water properties, amino acid classification, peptide bond chemistry, and the hierarchy of protein structure.

Biochemistry

The study of chemistry inside living cells, applying principles from general chemistry, biology, and organic chemistry to living organisms to describe how cells extract, store, and channel energy into homeostasis.

Bulk Elements

Elements required by living organisms in large quantities, including $H$, $C$, $N$, $O$, $P$, $S$, $Na$, $Mg$, $K$, $Ca$, and $Cl$.

Trace Elements

Elements present in small amounts in cells that are essential to life, such as $Mn$, $Fe$, $Co$, $Ni$, $Cu$, and $Zn$.

Stereoisomer

Molecules that share the same chemical formula and bond connections but differ in their three-dimensional spatial configurations.

Enantiomers

Stereoisomers that are non-superimposable mirror images of one another.

Diastereomers

Stereoisomers that are not mirror images of one another.

Gibbs Free Energy Change (delta G)

The amount of energy associated with a chemical reaction that is available to do work, defined as changed in G = change in enthalpy - temp x change in entropy

Exergonic Reaction

A reaction with a negative free energy change ($\Delta G < 0$) that releases free energy and occurs spontaneously.

Endergonic Reaction

A reaction with a positive free energy change ($\Delta G > 0$) that requires an input of energy to proceed.

Hydrogen Bond

A weak non-covalent interaction between an electronegative atom and a hydrogen covalently bonded to another electronegative atom, with a bond dissociation energy of $\sim 23\,kJ\,mol^{-1}$.

Hydrophobic Interactions

The association of non-polar molecules in an aqueous environment to minimize the ordered cage of water molecules around them, driven by an increase in entropy.

Van der Waals Interactions

Weak, non-specific, transient electrostatic attractions between any two uncharged atoms in very close proximity, with an interaction energy of $\sim 4\,kJ\,mol^{-1}$.

Buffer

An aqueous system consisting of a weak acid and its conjugate base that resists changes in $pH$ when small amounts of acid or base are added.

Henderson-Hasselbalch Equation

An equation relating $pH$, $p K_a$, and the concentrations of a weak acid and its conjugate base: $pH = p K_a + \log\left(\frac{[A^-]}{[HA]}\right)$.

Zwitterion

A dipolar molecule containing spatially separated positive and negative charges with an overall net electrical charge of zero.

Isoelectric Point

The specific $pH$ at which a molecule or amino acid carries no net electrical charge.

Peptide Bond

A substituted amide linkage formed through a condensation reaction between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another.

Disulfide Bridge

A covalent $S-S$ linkage formed by the oxidation of the sulfhydryl (thiol) groups of two cysteine residues.

Post-Translational Modifications (PTM)

Covalent additions or alterations made to a protein after ribosomal synthesis, such as phosphorylation, glycosylation, or ubiquitination, which modify protein function, structure, or localization.

Primary Structure

The linear sequence of amino acid residues in a polypeptide chain joined by covalent peptide bonds.

Secondary Structure

The local, regularly repeating spatial arrangement of the polypeptide backbone atoms, such as $\alpha$-helices and $\beta$-sheets, stabilized by hydrogen bonds.

Tertiary Structure

The complete three-dimensional folded conformation of a single polypeptide chain, stabilized by non-covalent interactions and disulfide cross-links.

Quaternary Structure

The spatial arrangement and non-covalent or covalent interactions of multiple folded polypeptide subunits in a multi-subunit protein complex.

Paralogs

Genes or proteins present within the same species that arose via gene duplication and often evolve distinct functional roles.

Orthologs

Genes or proteins in different species that evolved from a common ancestral gene via speciation and typically perform the same biological function.

Ramachandran Plot

A two-dimensional plot displaying the backbone dihedral angles $\phi$ (phi) and $\psi$ (psi) of amino acid residues to show sterically allowed and forbidden secondary structure conformations.

alpha-Helix

A rigid, right-handed helical secondary structure with $3.6$ amino acid residues per turn and a pitch of $5.4\,\text{\AA}$, stabilized by intrachain hydrogen bonds between backbone carbonyl oxygens and amide nitrogens.

beta-Sheet

A secondary structure composed of multiple adjacent extended $\beta$-strands arranged parallel or antiparallel to each other, stabilized by inter-strand hydrogen bonds.

beta-turn

A $180^\circ$ turn in a polypeptide chain involving four amino acid residues, usually located on protein surfaces and stabilized by a hydrogen bond between the first and fourth residues.

Protein Motif

A recognizable folding pattern comprising two or more connected secondary structure elements, such as a helix-loop-helix or $\beta\alpha\beta$ unit.

Protein Domain

A distinct, independently stable structural and functional region of a single polypeptide chain that can fold autonomously.

alpha Keratin

A tough, fibrous structural protein composed of right-handed $\alpha$-helices intertwined into two-chain coiled coils and cross-linked by disulfide bonds.

Collagen

A fibrous structural protein consisting of a right-handed triple superhelix of three left-handed helical chains containing a repeating Gly-Pro-4-Hyp amino acid sequence.

Biochemistry

The study of chemistry inside living cells, applying principles from general chemistry, biology, and organic chemistry to living organisms to describe how cells extract, store, and channel energy into homeostasis.

Bulk Elements

Elements required by living organisms in large quantities, including $H$, $C$, $N$, $O$, $P$, $S$, $Na$, $Mg$, $K$, $Ca$, and $Cl$.

Trace Elements

Elements present in small amounts in cells that are essential to life, such as $Mn$, $Fe$, $Co$, $Ni$, $Cu$, and $Zn$.

Stereoisomer

Molecules that share the same chemical formula and bond connections but differ in their three-dimensional spatial configurations.

Enantiomers

Stereoisomers that are non-superimposable mirror images of one another.

Diastereomers

Stereoisomers that are not mirror images of one another.

Gibbs Free Energy Change (delta G)

The amount of energy associated with a chemical reaction that is available to do work, defined as $\Delta G = \Delta H - T\Delta S$.

Standard Free Energy Change (delta G)

The free energy change of a reaction calculated under standard conditions ($1\text{ M}$ concentrations, $1\text{ atm}$, and $25\,^\circ\text{C}$), mathematically related to the equilibrium constant by $\Delta G^\circ = -RT\ln(K_{eq})$.

Equilibrium Constant (Keq)

The ratio of product concentrations to reactant concentrations at chemical equilibrium, where a value of $K_{eq} > 1$ indicates that products are favored.

Exergonic Reaction

A reaction with a negative free energy change ($\Delta G < 0$) that releases free energy and occurs spontaneously.

Endergonic Reaction

A reaction with a positive free energy change ($\Delta G > 0$) that requires an input of energy to proceed.

Energy Coupling

The process of driving an endergonic reaction ($\Delta G > 0$) by pairing it with an exergonic reaction ($\Delta G < 0$) so that the combined free energy change is negative.

Hydrogen Bond

A weak non-covalent interaction between an electronegative atom and a hydrogen covalently bonded to another electronegative atom, with a bond dissociation energy of $\sim 23\,kJ\,mol^{-1}$.

Hydrophobic Interactions

The association of non-polar molecules in an aqueous environment to minimize the ordered cage of water molecules around them, driven by an increase in entropy.

Van der Waals Interactions

Weak, non-specific, transient electrostatic attractions between any two uncharged atoms in very close proximity, with an interaction energy of $\sim 4\,kJ\,mol^{-1}$.

Ionic Interactions

Electrostatic forces of attraction or repulsion between charged groups or ions, such as salt bridges formed between oppositely charged amino acid side chains.

pKa

The negative logarithm of the acid dissociation constant ($pK_a = -\log(K_a)$), where smaller values represent stronger acids.

Buffer

An aqueous system consisting of a weak acid and its conjugate base that resists changes in $pH$ when small amounts of acid or base are added.

Henderson-Hasselbalch Equation

An equation relating $pH$, $pK_a$, and the concentrations of a weak acid and its conjugate base: $pH = pK_a + \log\left(\frac{[A^-]}{[HA]}\right)$.

Essential Amino Acids

Amino acids that cannot be synthesized by the human body and must be obtained through dietary intake.

Aromatic Amino Acid UV Absorbance

The property of phenylalanine, tyrosine, and tryptophan to absorb ultraviolet light near $280\,nm$ due to their conjugated aromatic ring systems.

L-Amino Acids

The specific stereoisomeric form of $\alpha$-amino acids that exclusively comprises naturally occurring proteins.

Zwitterion

A dipolar molecule containing spatially separated positive and negative charges with an overall net electrical charge of zero.

Isoelectric Point (pI)

The specific $pH$ at which a molecule or amino acid carries no net electrical charge.

Peptide Bond

A substituted amide linkage formed through a condensation reaction between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another.

Partial Double-Bond Character of Peptide Bonds

The resonance phenomenon that restricts rotation around the $\text{C-N}$ peptide bond, constraining its dihedral angle $\omega$ to a planar $180^\circ$ configuration.

Disulfide Bridge

A covalent $S-S$ linkage formed by the oxidation of the sulfhydryl (thiol) groups of two cysteine residues.

Post-Translational Modifications (PTM)

Covalent additions or alterations made to a protein after ribosomal synthesis, such as phosphorylation, glycosylation, or ubiquitination, which modify protein function, structure, or localization.

Primary Structure

The linear sequence of amino acid residues in a polypeptide chain joined by covalent peptide bonds.

Secondary Structure

The local, regularly repeating spatial arrangement of the polypeptide backbone atoms, such as $\alpha$-helices and $\beta$-sheets, stabilized by hydrogen bonds.

Tertiary Structure

The complete three-dimensional folded conformation of a single polypeptide chain, stabilized by non-covalent interactions and disulfide cross-links.

Quaternary Structure ($4^\circ$)

The spatial arrangement and non-covalent or covalent interactions of multiple folded polypeptide subunits in a multi-subunit protein complex.

Backbone Dihedral Angles

The three rotational angles defining polypeptide backbone conformation: $\omega$ for the $\text{C-N}$ peptide bond, $\phi$ for the $\text{N-C}_{\alpha}$ bond, and $\psi$ for the $\text{C}_{\alpha}\text{-C}$ bond.

Ramachandran Plot

A two-dimensional plot displaying the backbone dihedral angles $\phi$ (phi) and $\psi$ (psi) of amino acid residues to show sterically allowed and forbidden secondary structure conformations.

alpha-Helix

A rigid, right-handed helical secondary structure with $3.6$ amino acid residues per turn and a pitch of $5.4\,\text{\AA}$, stabilized by intrachain hydrogen bonds between backbone carbonyl oxygens and amide nitrogens.

beta-Sheet

A secondary structure composed of multiple adjacent extended $\beta$-strands arranged parallel or antiparallel to each other, stabilized by inter-strand hydrogen bonds.

Antiparallel vs. Parallel beta-Sheets

Conformations where adjacent strands run in opposite directions with linear hydrogen bonds (antiparallel), or in the same direction with distorted hydrogen bonds (parallel).

beta-Turn

A $180^\circ$ turn in a polypeptide chain involving four amino acid residues, usually located on protein surfaces and stabilized by a hydrogen bond between the first and fourth residues.

Intrinsically Disordered Regions

Polypeptide segments that lack a fixed three-dimensional structure and remain flexible and dynamic under physiological conditions.

Protein Motif

A recognizable folding pattern comprising two or more connected secondary structure elements, such as a helix-loop-helix or $\beta\alpha\beta$ unit.

Protein Domain

A distinct, independently stable structural and functional region of a single polypeptide chain that can fold autonomously.

Protein Family vs. Superfamily

Classifications where families share clear sequence homology, structure, and function, whereas superfamilies share similar structural motifs and functions without significant sequence homology.

Paralogs

Genes or proteins present within the same species that arose via gene duplication and often evolve distinct functional roles.

Orthologs

Genes or proteins in different species that evolved from a common ancestral gene via speciation and typically perform the same biological function.

alpha Keratin

A tough, fibrous structural protein composed of right-handed $\alpha$-helices intertwined into two-chain coiled coils and cross-linked by disulfide bonds.

Collagen

A fibrous structural protein consisting of a right-handed triple superhelix of three left-handed helical chains containing a repeating Gly-Pro-4-Hyp amino acid sequence.

Scurvy

A disease resulting from Vitamin C deficiency, which impairs the hydroxylation of proline residues to 4-hydroxyproline, weakening the collagen triple superhelix.