Standard Level Biomolecules: Water, Organic Compounds, Nucleic Acids, Carbohydrates, Lipids, and Proteins

Comprehensive vocabulary flashcards covering the core biochemistry concepts of water, organic compounds, carbohydrates, lipids, nucleic acids, and proteins.

Polarity (Water)

The slight charge difference across a water molecule caused by unequal electron sharing, where the oxygen atom has a higher electronegativity and carries a partial negative charge ($\delta^-$) while the hydrogen atoms carry a partial positive charge ($\delta^+$).

Hydrogen Bond (Water)

A relatively strong polar intermolecular association formed between the slightly positive ($\delta^+$) hydrogen dipole of one water molecule and the slightly negative ($\delta^-$) oxygen dipole of an adjacent water molecule.

Hydration Shell

A dispersive cluster of oriented water molecules surrounding a charged ion or polar solute surface, allowing water to dissolve and dissociate ionic compounds.

Cohesion (Water)

The tendency of water molecules to stick to one another via hydrogen bonding, giving rise to high surface tension that allows small insects to glide across water surfaces.

Adhesion (Water)

The property of water molecules to stick to polar or charged materials, enabling phenomena like meniscus formation in glass cylinders and capillary action.

Capillary Action

The flow of water in opposition to gravitational forces along a narrow polar or charged passage under tension, enabling the transport of water up plant stems via xylem vessels.

Specific Heat Capacity (Water)

The amount of thermal energy required to raise the temperature of $1\,\text{g}$ of water by $1\,^\circ\text{C}$ ($4.186\,\text{J}\,\text{g}^{-1}\,{^\circ\text{C}}^{-1}$), providing a stable internal and external homeostatic thermal buffer for aquatic organisms.

Thermal Conductivity (Water)

A measure of a medium's capacity to transfer heat across a temperature gradient, which is high in water ($0.58\,\text{W}\,\text{m}^{-1}\,\text{K}^{-1}$) compared to air ($0.024\,\text{W}\,\text{m}^{-1}\,\text{K}^{-1}$).

Buoyancy

The upward force applied to an object immersed in a fluid medium, determined by fluid density; water is approximately $1000\times$ denser than air and provides greater buoyant support.

Viscosity

A fluid's internal resistance to flow, caused by frictional intermolecular interactions such as hydrogen bonding; water is approximately $50\times$ more viscous than air.

Black-Throated Loon (Gavia arctica)

An Arctic aquatic bird possessing solid bones that are less dense than those of typical terrestrial animals to allow diving while maintaining buoyancy, rear-located legs for water propulsion, and interlocking waterproof feathers to minimize heat loss.

Ringed Seal (Pusa hispida)

An Arctic marine mammal adapted to cold water through dense bones for staying submerged, a streamlined body to overcome viscosity, fur that traps air for waterproofing, and a thick blubber layer for thermal insulation.

Organic Compound

A compound containing carbon that is synthesized by living things, with notable exceptions such as carbon dioxide ($\text{CO}_2$) and carbonates.

Metabolism

The totality of chemical reactions and processes occurring within a cell or organism in order to maintain life, maintain cellular materials, and supply metabolic energy.

Anabolism

The set of metabolic pathways that build larger, complex macromolecules from smaller monomers via condensation reactions, releasing water ($\text{H}_2\text{O}$) as a by-product.

Catabolism

The set of metabolic reactions that break down larger polymeric compounds into simpler monomeric subunits via hydrolysis reactions, consuming water ($\text{H}_2\text{O}$) in the process.

Nucleotide

The monomer of nucleic acids, consisting of a 5-carbon pentose sugar, a phosphate group joined at the $5'\text{-carbon}$, and a nitrogenous base joined at the $1'\text{-carbon}$.

Sugar-Phosphate Backbone

The structural chain of a polynucleotide strand formed by condensation reactions connecting the $5'\text{-phosphate}$ of one nucleotide to the $3'\text{-position}$ of an adjacent sugar.

Purines

A class of double-ringed nitrogenous bases found in nucleic acids, consisting of adenine ($\text{A}$) and guanine ($\text{G}$).

Pyrimidines

A class of single-ringed nitrogenous bases, consisting of cytosine ($\text{C}$), thymine ($\text{T}$) in DNA, and uracil ($\text{U}$) in RNA.

Complementary Base Pairing

The specific hydrogen bonding between purines and pyrimidines across antiparallel strands: adenine pairs with thymine/uracil via $2$ hydrogen bonds, and guanine pairs with cytosine via $3$ hydrogen bonds.

Antiparallel (DNA)

The structural arrangement in double-stranded DNA where the two polynucleotide chains run parallel to each other but in opposite directions.

Messenger RNA (mRNA)

A single-stranded transcript synthesized from a DNA gene template that delivers instructions to ribosomes to direct the synthesis of a polypeptide chain.

Transfer RNA (tRNA)

A specialized RNA molecule that binds and carries specific amino acids to the ribosome corresponding to codons on an mRNA strand during translation.

Ribosomal RNA (rRNA)

The structural and catalytic RNA component of the ribosome that enables interaction with both mRNA and tRNA during polypeptide synthesis.

Genophore

The single circular, unpackaged (naked) DNA chromosome located within the nucleoid region of prokaryotic cells.

Nucleosome

A structural unit of eukaryotic chromatin formed by DNA wrapping around a core of histone proteins to permit compact supercoiling into linear chromosomes.

Monosaccharide

A carbohydrate monomer typically adopting a cyclic ring structure with the empirical formula $(\text{CH}_2\text{O})_n$, classified as pentoses ($5\,\text{C}$) or hexoses ($6\,\text{C}$).

Glucose

A 6-carbon hexose monosaccharide utilized preferentially by cells as a source of chemical energy; exists as $\alpha\text{-glucose}$ and $\beta\text{-glucose}$ isomers differing in the orientation of the $1'\text{-hydroxyl}$ group.

Ribose

A 5-carbon pentose sugar that forms a core component of RNA nucleotides and ATP, differing from deoxyribose by possessing an oxygen atom at the $2'\text{-carbon}$.

Glycosidic Linkage

The covalent bond that connects monosaccharide subunits via a condensation reaction, releasing a water molecule as a by-product.

Amylose

An unbranched, helical plant energy storage polysaccharide composed exclusively of $\alpha\text{-glucose}$ monomers connected via $1'\text{--}4'$ glycosidic linkages.

Amylopectin

A branched plant energy storage polysaccharide composed of $\alpha\text{-glucose}$ monomers connected by $1'\text{--}4'$ glycosidic linkages and occasional $1'\text{--}6'$ branch linkages.

Glycogen

A highly branched animal storage polysaccharide composed of $\alpha\text{-glucose}$ monomers, characterized by more frequent $1'\text{--}6'$ branching linkages than amylopectin.

Cellulose

A linear, mechanically stable structural polysaccharide in plant cell walls made of alternating inverted $\beta\text{-glucose}$ subunits cross-linked by hydrogen bonds.

Glycoprotein

A membrane-bound protein covalently linked to a carbohydrate chain that functions as a cell surface marker or identification antigen, such as in ABO blood groupings.

Simple Lipids

Esters composed of fatty acids linked to an alcohol, with common biological examples being waxes and triglycerides.

Compound Lipids

Lipids consisting of a simple lipid joined to an additional functional group, such as the polar phosphate group in phospholipids.

Derived Lipids

Lipids consisting of hydrocarbon ring assemblies produced from the hydrolysis of simple lipids, exemplified by steroids.

Saturated Fatty Acid

A fatty acid chain lacking carbon-carbon double bonds, resulting in straight chains that pack tightly together with high melting points to form solid fats at room temperature.

Unsaturated Fatty Acid

A fatty acid chain containing one (monounsaturated) or more (polyunsaturated) double bonds, resulting in kinked chains that pack loosely and remain liquid oils at room temperature.

cis-Isomer (Fatty Acid)

An unsaturated fatty acid configuration where the hydrogen atoms attached to the carbon double bond are located on the same side, producing a structural kink in the hydrocarbon chain.

trans-Isomer (Fatty Acid)

An unsaturated fatty acid configuration where hydrogen atoms attached to the double bond are on opposite sides, preventing kinking and giving it linear packing properties similar to saturated fats.

SODA (Lipid Properties)

A mnemonic summarizing why triglycerides excel at long-term energy storage over carbohydrates: Solubility (insoluble in water), Osmosis (exerts less osmotic pressure), Digestion (harder to rapidly mobilize), and ATP production (produces roughly twice as much energy per gram).

Adipose Tissue

A subcutaneous animal connective tissue that stores triglycerides, providing long-term metabolic energy storage, buoyancy in marine mammals, and thermal insulation due to low thermal conductivity.

Phospholipid

An amphipathic compound lipid composed of a central glycerol linked to two fatty acid tails and one polar phosphate head group, forming the bilayer basis of cellular membranes.

Steroid

A derived, non-polar lipid composed of four fused carbon rings that can cross the phospholipid bilayer to bind intracellular receptors as signalling hormones, such as testosterone and oestradiol.

Amino Acid

The monomer of a protein, featuring a central alpha carbon bound to an amine group ($\text{NH}_2$), a carboxyl group ($\text{COOH}$), a hydrogen atom, and a variable side chain ($\text{R}$ group).

Essential Amino Acids

Amino acids that cannot be synthesized by human metabolic pathways and must be obtained directly through diet ($9$ essential and $7$ conditionally essential amino acids in humans).

Peptide Bond

A covalent linkage formed between the carboxyl group of one amino acid and the amine group of another through a condensation reaction that releases a water molecule.

Denaturation

A structural change in a protein caused by thermal disruption of hydrogen bonds or pH-induced alterations of zwitterion charges, leading to protein unfolding and a permanent loss of biological activity.

Proteome

The complete set of proteins expressed by a cell, tissue, or organism under specific environmental conditions and time, predicted to contain roughly $100{,}000$ proteins in humans.

Zwitterion

A dipolar, overall neutral molecule possessing distinct positively charged ($\text{NH}_3^+$) and negatively charged ($\text{COO}^-$) functional regions, characteristic of free amino acids.