Biological Molecules, Enzymes, and Cell Transport

Comprehensive vocabulary flashcards covering biological molecules (carbohydrates, lipids, proteins, nucleic acids, water, and ATP), enzyme kinetics and inhibition, and membrane structure and transport mechanisms.

Monomer

A smaller, individual repeating unit from which larger molecules and polymers are synthesized.

Polymer

A large molecule composed of a large number of monomers joined together through the process of polymerisation.

Condensation Reaction

A chemical reaction that links two molecules together with the formation of a chemical bond and the elimination or release of a molecule of water ($H_2O$).

Hydrolysis Reaction

A chemical reaction that breaks a chemical bond between two molecules through the addition of a molecule of water ($H_2O$).

Monosaccharide

A sweet-tasting, soluble single sugar monomer with the general formula $(CH_2O)_n$, such as glucose, galactose, or fructose.

Alpha ($\alpha$) Glucose and Beta ($\beta$) Glucose

Structural isomers of glucose differing by the orientation of the hydroxyl ($-OH$) group on carbon 1: positioned below the plane of the ring in $\alpha$-glucose and above the plane in $\beta$-glucose.

Reducing Sugar

A sugar that can donate electrons and reduce another chemical, such as alkaline copper (II) sulfate in Benedict's reagent to an insoluble red precipitate of copper (I) oxide.

Benedict's Test

A semi-quantitative biochemical test for reducing sugars that involves heating the sample with an alkaline solution of copper (II) sulfate; color changes from blue (none) to green (trace), yellow (low), orange (moderate), and brick-red precipitate (high).

Disaccharide

A carbohydrate formed by the condensation of two monosaccharides linked by a glycosidic bond, including maltose (glucose + glucose), sucrose (glucose + fructose), and lactose (glucose + galactose).

Glycosidic Bond

A covalent chemical bond formed between two monosaccharides during a condensation reaction, commonly between carbon 1 and carbon 4 ($\alpha\text{-1,4-glycosidic bond}$).

Non-Reducing Sugar Test

A procedure for sugars like sucrose that give a negative Benedict's result initially: the sample is boiled with dilute hydrochloric acid to hydrolyse glycosidic bonds, neutralised with solid sodium hydrogen carbonate, and re-tested with Benedict's reagent and heat.

Amylose

An unbranched, helical polymer of $\alpha$-glucose joined by $\alpha\text{-1,4-glycosidic bonds}$; its coiled structure is compact and occupies minimal space, making it ideal for storage in plants.

Amylopectin

A branched polymer of $\alpha$-glucose found in starch, joined by $\alpha\text{-1,4-glycosidic bonds}$ with $\alpha\text{-1,6-glycosidic bonds}$ forming branches, which provide numerous ends for rapid enzyme hydrolysis.

Starch

A plant storage polysaccharide made of amylose and amylopectin ($200\text{--}100{,}000$ $\alpha$-glucose units); it is insoluble, does not affect water potential or osmosis, and turns iodine from orange to blue/black.

Glycogen

The major carbohydrate storage polysaccharide in animals and bacteria, composed of $\alpha$-glucose chains that are shorter and more highly branched than starch to permit rapid glucose release for high metabolic demands.

Cellulose

A structural polysaccharide in plant cell walls formed from straight, unbranched chains of $\beta$-glucose running parallel to each other, cross-linked by numerous hydrogen bonds to provide high tensile strength and rigidity.

Microfibrils

Bundles of parallel cellulose molecules cross-linked by hydrogen bonds that group together to form macroscopic fibres in plant cell walls, preventing cells from bursting when turgid.

Triglyceride

A non-polymer lipid formed by the condensation of one molecule of glycerol ($C_3H_8O_3$) with three fatty acid chains, forming three ester bonds and releasing three molecules of water ($3H_2O$).

Saturated Fatty Acid

A fatty acid hydrocarbon chain containing no carbon-carbon double bonds ($C=C$), leaving all carbon atoms fully bonded to the maximum number of hydrogen atoms; typically found in animal fats and solid at room temperature.

Unsaturated Fatty Acid

A fatty acid whose hydrocarbon chain contains one ($\text{mono-unsaturated}$) or more ($\text{polyunsaturated}$) carbon-carbon double bonds ($C=C$), causing bends that prevent close packing and making them liquid oils at $20\,^\circ\text{C}$.

Phospholipid

A polar lipid molecule consisting of a glycerol molecule bound to two fatty acids (hydrophobic tails) and a phosphate group (hydrophilic head), enabling the formation of bilayers in cell membranes.

Emulsion Test

A biochemical test for lipids where the sample is crushed and shaken with ethanol to dissolve any lipids present, followed by the addition of water; the formation of a milky-white cloudy emulsion confirms the presence of lipids.

Amino Acid

The basic monomer of polypeptides and proteins consisting of a central $\alpha$-carbon bonded to an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom ($H$), and a variable chemical group ($R$).

Peptide Bond

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction with the elimination of water ($H_2O$).

Primary Protein Structure

The specific sequence and number of amino acids in a polypeptide chain, determined by DNA, which dictates all higher levels of protein folding and structure.

Secondary Protein Structure

The regular local folding of the polypeptide chain into an $\alpha$-helix or $\beta$-pleated sheet, stabilized by hydrogen bonds between the positively charged $-NH$ group and the negatively charged $-C=O$ group.

Tertiary Protein Structure

The overall specific 3D conformation of a polypeptide chain folded upon itself, maintained by disulphide bridges, ionic bonds between free charged groups, and numerous hydrogen bonds.

Quaternary Protein Structure

The functional biological structure formed by the combination of two or more individual polypeptide chains and optional prosthetic non-protein groups (such as heme).

Fibrous Proteins

Proteins with long, thin, insoluble parallel polypeptide chains cross-linked to provide structural functions, such as keratin in hair and collagen in tendons and connective tissue.

Globular Proteins

Spherical, water-soluble proteins that perform metabolic and biochemical roles in organisms, such as enzymes, antibodies, and transport proteins like myoglobin.

Biuret Test

A biochemical test for proteins where Biuret reagent is added to a sample; a color transition from blue to purple indicates the presence of peptide bonds.

Chromatography Retention Factor ($R_f$)

A ratio used to identify separated compounds, calculated as: $R_f = \frac{\text{distance moved by compound}}{\text{distance moved by solvent}}$.

Nucleotide

The monomer of nucleic acids consisting of three covalently linked components: a pentose sugar (ribose or deoxyribose), a phosphate group, and a nitrogenous organic base (adenine, thymine, cytosine, guanine, or uracil).

Phosphodiester Bond

The covalent bond that links adjacent nucleotides together between the pentose sugar of one mononucleotide and the phosphate group of another in a condensation reaction.

Complementary Base Pairing

The specific pairing of nitrogenous bases in DNA stabilized by hydrogen bonds: adenine pairs with thymine via 2 hydrogen bonds ($A=T$), and guanine pairs with cytosine via 3 hydrogen bonds ($G\equiv C$).

Dipolar Water Molecule

The condition of a water molecule ($H_2O$) having no overall net charge, but possessing an uneven charge distribution with a slight negative charge ($\delta^-$) on oxygen and slight positive charges ($\delta^+$) on hydrogens.

Specific Heat Capacity of Water

The amount of heat energy required to raise the temperature of a given mass of water; water's high value allows it to act as a thermal buffer in organisms and aquatic environments due to extensive hydrogen bonding.

Latent Heat of Vaporisation

The large amount of thermal energy required to evaporate a given mass of liquid water, providing an effective evaporative cooling mechanism (e.g., sweating) in living organisms.

Cohesion and Surface Tension

The physical tendency of water molecules to stick to one another via hydrogen bonds, enabling column transport in xylem, and pulling inward at the air-water interface to form an elastic surface skin.

Adenosine Triphosphate (ATP)

A phosphorylated macromolecule nucleotide consisting of adenine, a ribose sugar, and three phosphate groups, acting as the immediate, manageable cellular energy donor.

ATP Hydrolase

The enzyme that catalyses the single-step hydrolysis of ATP to ADP and inorganic phosphate ($P_i$), releasing energy for cellular processes like active transport and movement.

ATP Synthase

The enzyme that catalyses the condensation reaction combining ADP and inorganic phosphate ($P_i$) with the removal of water to regenerate ATP during photosynthesis or respiration.

pH Formula

A logarithmic scale representing hydrogen ion concentration in solution: $pH = -\log[H^+(aq)]$, where $[H^+(aq)]$ denotes concentration in $\text{mol}\,\text{l}^{-1}$.

Activation Energy ($E_A$)

The minimum amount of initial energy required by colliding reactant molecules to overcome the energetic barrier and initiate a chemical reaction.

Active Site

A small, functional depression of specific amino acids within an enzyme molecule that binds temporarily to a complementary substrate to form an enzyme-substrate complex.

Lock and Key Hypothesis

An early scientific model proposing that an enzyme's active site has a fixed, rigid geometric shape that is precisely complementary to the substrate prior to binding.

Induced Fit Model

The modern enzyme action model where the flexible active site moulds around the substrate upon binding, changing shape to become fully complementary and putting strain on substrate bonds to lower activation energy.

Denaturation (Enzymes)

A permanent structural change occurring when high temperatures ($>45\,^\circ\text{C}$ to $60\,^\circ\text{C}$) or extreme pH break hydrogen and ionic bonds stabilizing tertiary structure, disrupting active site shape so substrates can no longer bind.

Optimum Temperature

The temperature at which an enzyme-controlled reaction reaches its maximum rate; for most human body enzymes, this occurs at approximately $37.0\,^\circ\text{C}$.

Optimum pH

The specific hydrogen ion concentration at which an enzyme's active site maintains the ideal charge distribution and complementary shape for maximum rate of reaction.

Competitive Inhibitor

A molecule with a shape similar to that of the substrate that competes for and temporarily occupies the enzyme's active site, whose inhibitory effect is reduced by increasing substrate concentration.

Non-Competitive Inhibitor

A molecule that binds to an enzyme at an allosteric site other than the active site, altering the enzyme's tertiary structure and active site shape so substrate cannot bind, unaffected by substrate concentration.

Allosteric Site

A specific binding site on an enzyme distinct from the catalytic active site, to which non-competitive inhibitors or regulatory molecules attach to alter enzyme conformation.

End-Point Inhibition

A homeostatic control mechanism where the final product of a metabolic pathway acts as an allosteric inhibitor on the first enzyme ($E_1$) in the sequence (e.g., isoleucine inhibiting threonine deaminase).

Fluid Mosaic Model

A biological membrane model where individual phospholipid molecules can move relative to one another (fluid) and proteins embedded within vary in shape, size, and pattern (mosaic).

Phospholipid Bilayer

A double-layered sheet of phospholipids with hydrophilic heads facing outwards towards water and hydrophobic tails tucked inwards, serving as a barrier to water-soluble ions while allowing lipid-soluble molecules to cross.

Cholesterol (Membrane Component)

A hydrophobic lipid component embedded in membranes that adds strength, limits lateral movement of phospholipids without rigidity, prevents leakage of water/ions, and reduces fluidity at elevated temperatures.

Glycolipid

A membrane molecule formed of a carbohydrate covalently bonded to a lipid, extending into the extracellular environment to serve as a cellular recognition site, aid cell attachment, and enhance membrane stability.

Glycoprotein

A cell surface protein with attached branching carbohydrate chains that acts as a cell surface receptor for hormones and neurotransmitters, and aids cell adhesion and cell recognition.

Diffusion

The passive net movement of molecules or ions from a region of higher concentration to a region of lower concentration down a concentration gradient until distributed evenly, driven by innate kinetic energy.

Facilitated Diffusion

Passive movement of polar molecules and charged ions across a plasma membrane down a concentration gradient via specific transmembrane channel or carrier proteins.

Channel Proteins

Water-filled hydrophilic transmembrane protein tubes that selectively open or close to allow specific water-soluble ions to diffuse passively across the membrane.

Carrier Proteins

Transmembrane proteins that bind specifically to a molecule (such as glucose or an amino acid), undergo a conformational shape change, and release the substance across the membrane.

Water Potential ($\Psi$)

The pressure created by water molecules, measured in kilopascals ($\text{kPa}$); pure water has a potential of $0\,\text{kPa}$ at standard temperature and pressure, and the addition of solute makes it progressively more negative.

Osmosis

The passage of water from a region of higher water potential (less negative) to a region of lower water potential (more negative) across a selectively permeable membrane.

Plasmolysis

The shrinking and pulling away of the plant cell protoplast/cytoplasm from the rigid cell wall when placed into a hypertonic solution with a more negative water potential.

Turgid Cell

A plant cell placed in a hypotonic solution where water enters by osmosis, causing the protoplast to swell and push against the rigid cellulose cell wall, generating inward pressure.

Active Transport

The movement of molecules or ions across a membrane against a concentration gradient using carrier proteins and metabolic energy derived from ATP hydrolysis.

Co-Transport

A secondary active transport mechanism where the active transport of sodium ions out of epithelial cells establishes a gradient that drives the simultaneous uptake of glucose and sodium from the ileum lumen into the cell.