Chemical Constituents of Cells: Water, Acids, Bases, and Proteins

Vocabulary practice flashcards covering the chemical properties and molecular structure of water, acids, bases, biological buffers, and the four levels of protein architecture from Foundation in Science Biology.

Polarity of Water

The asymmetric charge distribution within a water molecule ($H_2O$) caused by oxygen's high electronegativity, which pulls shared electrons closer to create a partially negative ($\delta^-$) oxygen region and partially positive ($\delta^+$) hydrogen regions.

Water Molecular Geometry

The bent or 'V' shape formed by a water molecule, arranged at a bond angle of approximately $104.5^\circ$.

Hydrogen Bond (Water)

A weak intermolecular electrostatic attraction formed between the partially positive ($\delta^+$) hydrogen atom of one water molecule and the partially negative ($\delta^-$) oxygen atom of another; each water molecule can form up to $4$ hydrogen bonds.

Universal Solvent

A property of water derived from its dipolar nature that allows it to dissolve ionic compounds and polar substances by surrounding them with spheres of hydration.

Spheres of Hydration

Hydration shells of water molecules that cluster around dissolved ions, with the negative oxygen ends oriented toward cations ($Na^+$) and the positive hydrogen ends oriented toward anions ($Cl^-$).

Cohesion (Water)

The tendency of water molecules to stick to one another as a result of hydrogen bonding, generating internal pulling forces essential for the movement of water through xylem.

Surface Tension (Water)

The cohesive force that holds molecules at the surface of a liquid together into a membrane-like 'skin,' enabling droplet, bubble, and meniscus formation, as well as allowing organisms such as water striders to walk on water.

Specific Heat Capacity (Water)

The amount of heat energy required to raise the temperature of a substance; water has a high specific heat capacity because substantial energy is consumed breaking hydrogen bonds, preventing rapid fluctuations in aquatic habitats and cellular temperatures.

Latent Heat of Vaporisation

The amount of heat energy required to convert a liquid into vapour; in organisms, this property provides an effective evaporative cooling mechanism through sweating.

Latent Heat of Fusion

The amount of heat energy that must be removed from liquid water to transform it into ice.

Density Anomaly of Water

The property wherein water reaches its maximum density at $4^\circ\text{C}$ and expands upon freezing into a rigid hexagonal crystal lattice, causing ice to float and insulate aquatic organisms during winter.

Viscosity of Water

The relatively low resistance to flow exhibited by liquid water due to the continual breaking and reforming of hydrogen bonds, facilitating fluid transport in xylem, blood flow in capillaries, and locomotion in moist environments.

Acid

A substance that donates hydrogen ions ($H^+$) in an aqueous solution, such as hydrochloric acid ($HCl \rightleftharpoons H^+ + Cl^-$), resulting in a higher concentration of hydrogen ions than hydroxide ions.

Base

A substance that accepts hydrogen ions ($H^+$) in an aqueous solution, such as ammonia ($NH_3 + H^+ \rightleftharpoons NH_4^+$), resulting in a lower concentration of free hydrogen ions.

Skin pH

The slightly acidic physiological pH of normal human skin, measured at approximately $\text{pH } 5.5$, which serves to prevent bacterial growth.

Normal Blood pH

The narrow physiological range of human blood pH between $7.35$ and $7.45$, below which acidosis occurs, above which alkalosis occurs, and outside the range of $7.0\text{--}7.8$ results in death.

Buffer

A solution consisting of a weak acid and its conjugate base, or a weak base and its conjugate acid, that resists changes in pH by donating $H^+$ when pH increases and accepting $H^+$ when pH decreases.

Carbonic Acid Buffer System

The primary physiological buffer system in the blood that stabilizes pH according to the equilibrium: $H_2O + CO_2 \rightleftharpoons H_2CO_3 \rightleftharpoons HCO_3^- + H^+$.

Monomer

The smallest single repeating molecular unit (micromolecule), such as an amino acid or glucose, that covalently links with others to form a larger polymer.

Polymer

A large macromolecule composed of multiple structural monomer units connected together by covalent bonds.

Protein

A biological polymer composed of amino acid monomers joined by peptide bonds, consisting of carbon, hydrogen, oxygen, and nitrogen (and sometimes sulfur and phosphorus), accounting for more than $50\%$ of a cell's dry mass.

Amino Acid

The fundamental monomer of proteins, consisting of an $\alpha\text{-carbon}$ covalently bonded to a hydrogen atom, an amino group ($-NH_2$), a carboxyl group ($-COOH$), and a variable side chain (R group).

Non-Polar Side Chains (Amino Acids)

Hydrophobic amino acid R groups containing pure hydrocarbon alkyl chains or aromatic benzene rings (e.g., glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline).

Polar Side Chains (Amino Acids)

Hydrophilic amino acid R groups containing neutral functional groups like alcohols, amides, or sulfhydryl groups (e.g., serine, threonine, cysteine, tyrosine, asparagine, and glutamine).

Electrically Charged Side Chains

Hydrophilic amino acid R groups that ionize in water, categorized into acidic side chains carrying negative charges (aspartic acid, glutamic acid) and basic side chains carrying positive charges (lysine, arginine, histidine).

Peptide Bond

A covalent linkage formed between the carboxyl group ($-COOH$) of one amino acid and the amino group ($-NH_2$) of another through a dehydration synthesis (condensation) reaction that eliminates a water molecule.

Dipeptide

A molecule consisting of two amino acids linked together by a single peptide bond.

Polypeptide

A linear, unbranched chain of multiple amino acid residues connected by peptide bonds, possessing an amino end (N-terminus) and a carboxyl end (C-terminus).

Primary Structure (Protein)

The linear sequence of amino acids in a polypeptide chain, determined by genetic information and stabilized entirely by covalent peptide bonds.

Secondary Structure (Protein)

The localized folding of a polypeptide chain into $\alpha\text{-helices}$ or $\beta\text{-pleated}$ sheets, stabilized by hydrogen bonding between the $C=O$ and $N-H$ groups of the polypeptide backbone.

Tertiary Structure (Protein)

The overall three-dimensional conformation of a single polypeptide chain, stabilized by interactions among R groups, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulphide bridges.

Disulphide Bond

A strong covalent bond formed by the oxidation of sulfhydryl ($-SH$) groups between two cysteine residues within a polypeptide chain.

Quaternary Structure (Protein)

The structural level produced by the combination and association of two or more polypeptide chains, stabilized by non-covalent interactions and covalent bonds between their R groups and backbones.

Haemoglobin

A quaternary, oxygen-carrying globular protein made of four subunits: two alpha chains ($141$ amino acids each) and two beta chains ($146$ amino acids each), each associated with a heme group.

Fibrous Protein

A class of stable, water-insoluble proteins composed of long, parallel polypeptide chains linked into strong fibers with predominantly non-polar R groups, providing structural and mechanical support (e.g., keratin and collagen).

Globular Protein

A class of water-soluble, spherical proteins whose chains fold with hydrophobic R groups facing inward and hydrophilic R groups facing outward, performing dynamic metabolic functions (e.g., enzymes, antibodies, and hormones).

Conjugated Protein

A globular protein joined to a permanent non-protein component termed a prosthetic group, exemplified by haemoglobin bound to its iron-containing heme groups.