Biological Molecules and Enzyme Action

Comprehensive practice flashcards covering bonding, biological monomers and polymers, carbohydrates, lipids, protein structure, enzyme kinetics, factors affecting enzyme activity, and inhibition mechanisms.

How do covalent, ionic, and hydrogen bonds differ in the formation of biological molecules?

In covalent bonding, atoms share a pair of electrons in their outer shells to form a stable molecule. In ionic bonding, electrostatic attraction forms between oppositely charged ions (e.g., $Na^+$ and $Cl^-$), which is weaker than a covalent bond. In hydrogen bonding, an uneven distribution of charge makes a molecule polar, creating a weak electrostatic attraction between the negative region of one polarised molecule and the positive region of another.

What is the difference between a condensation reaction and a hydrolysis reaction?

A condensation reaction joins monomers to form polymers and produces a molecule of water each time a new sub-unit is attached. A hydrolysis reaction breaks down polymers into constituent sub-units by adding water molecules to split the chemical bonds.

How is a mole defined, and what is the value of the Avogadro constant?

A mole (abbreviated mol) is the SI unit for measuring the amount of a substance and contains the same number of particles as there are in $12\,g$ of carbon-12 atoms ($^{12}C$). This number is $6.022 \times 10^{23}$, known as the Avogadro number or Avogadro constant.

What is a molar solution ($M$), and what mass of sodium chloride is dissolved in a $1\,M$ solution?

A molar solution ($M$) contains one mole of solute in each litre of solution. Since the atomic mass of sodium (Na) is 23 and chlorine (Cl) is 35.5, the molecular mass of $NaCl$ is $58.5$. Therefore, a $1\,M$ solution contains $58.5\,g$ of sodium chloride in $1\,\text{litre}$ of solution.

What is the definition of metabolism?

Metabolism is the collective term for all the chemical processes that take place in living organisms.

What is the general formula of monosaccharides, and which three examples are given?

Monosaccharides have the general formula $(CH_2O)_n$, where $n$ can be any number from 3 to 7. Common examples are glucose, galactose, and fructose.

How do the structures of $\alpha$-glucose and $\beta$-glucose differ?

Both are hexose isomers with the molecular formula $C_6H_{12}O_6$, but they differ in the spatial orientation of the hydroxyl ($-OH$) and hydrogen ($-H$) groups on carbon atom 1.

How is the Benedict's test for reducing sugars carried out?

Add $2\,cm^3$ of the food sample (ground in water if solid) to a test tube, add an equal volume ($2\,cm^3$) of Benedict's reagent, and heat the mixture in a gently boiling water bath for 5 minutes. An insoluble orange-brown or red precipitate of copper(I) oxide confirms the presence of a reducing sugar.

Why is the Benedict's test described as semi-quantitative?

The colour and amount of precipitate formed vary according to the concentration of reducing sugar present (ranging from green for very low, to yellowish green, yellowish brown, dark brown, and red for high concentrations), allowing an approximate estimate of concentration.

Which monosaccharides combine to form maltose, sucrose, and lactose?

Glucose joined to glucose forms maltose; glucose joined to fructose forms sucrose; glucose joined to galactose forms lactose.

What bond links monosaccharide monomers together, and how is it formed and broken?

Monosaccharides are linked by a glycosidic bond. It is formed by a condensation reaction (removal of a water molecule) and broken by a hydrolysis reaction (addition of a water molecule).

What is the procedure for testing for a non-reducing sugar such as sucrose?

First, test the sample with Benedict's reagent; if it remains blue, heat a new $2\,cm^3$ sample with $2\,cm^3$ dilute hydrochloric acid in a gently boiling water bath for 5 minutes to hydrolyse the disaccharide into monosaccharides. Slowly add sodium hydrogencarbonate until alkaline (checked with pH paper), then re-test by heating with $2\,cm^3$ Benedict's reagent for 5 minutes. An orange-brown precipitate indicates a non-reducing sugar was originally present.

How is the iodine test for starch conducted, and what indicates a positive result?

Place $2\,cm^3$ of the sample into a test tube or spotting tile at room temperature and add two drops of iodine in potassium iodide solution, shaking or stirring. A colour change from yellow to blue-black indicates the presence of starch.

How is the molecular formula of sucrose deduced from its constituent monosaccharides ($C_6H_{12}O_6$)?

Two hexose molecules ($C_6H_{12}O_6 + C_6H_{12}O_6 = C_{12}H_{24}O_{12}$) combine via a condensation reaction that eliminates one water molecule ($H_2O$), yielding the formula $C_{12}H_{22}O_{11}$.

How does the molecular structure of starch relate to its function as a storage polysaccharide in plants?

Starch is an unbranched or branched chain of $\alpha$-glucose. It is insoluble (does not draw water by osmosis or diffuse from cells), compact (coils into a tight helix held by hydrogen bonds to store large amounts in small spaces), forms readily transportable and respirable $\alpha$-glucose when hydrolysed, and its branched form has many ends for rapid simultaneous enzyme action.

How does glycogen differ structurally from starch, and why is this advantageous for animals?

Glycogen has shorter chains and is more highly branched than starch. This provides many more branch ends that can be acted on simultaneously by enzymes, allowing faster breakdown into glucose monomers to support the higher metabolic and respiratory rates of mobile animals.

How does the molecular arrangement of cellulose differ from starch?

Cellulose is made of $\beta$-glucose monomers rather than $\alpha$-glucose, forming straight, unbranched chains. Adjacent glucose molecules are rotated by $180^\circ$, allowing hydroxyl ($-OH$) groups on both sides of the chain to form hydrogen bond cross-links with parallel adjacent chains.

How do cellulose microfibrils provide support and rigidity to plant cells?

Parallel cellulose chains are cross-linked by numerous hydrogen bonds to form microfibrils, which group into fibres. These exert an inward wall pressure that prevents the plant cell from bursting as water enters by osmosis, keeping cells turgid and maintaining semi-rigid stems and leaves for photosynthesis.

What are the main biological roles of lipids?

Lipids serve as components of cell membranes (phospholipids provide flexibility and transfer lipid-soluble substances), energy sources (releasing more than twice the energy per mass of carbohydrates upon oxidation and producing metabolic water), waterproofing (waxy cuticles in plants/insects and mammalian sebaceous secretions), thermal and electrical insulation (subcutaneous fat and myelin sheath), and physical protection around delicate organs like the kidneys.

How is a triglyceride formed from glycerol and fatty acids?

A triglyceride is formed when three fatty acid molecules combine with one glycerol molecule through condensation reactions, each forming an ester bond and releasing three water molecules.

What distinguishes saturated, mono-unsaturated, and polyunsaturated fatty acids?

A saturated fatty acid has no carbon-carbon double bonds in its hydrocarbon chain. A mono-unsaturated fatty acid has one carbon-carbon double bond. A polyunsaturated fatty acid has more than one carbon-carbon double bond, which causes kinks that prevent tight packing and make them liquid (oils) at room temperature.

How does the structure of a phospholipid differ from a triglyceride, and what property does this create?

In a phospholipid, one of the three fatty acids is replaced by a phosphate molecule. This creates a polar molecule with a hydrophilic phosphate 'head' that attracts water and two hydrophobic fatty acid 'tails' that repel water and mix with fats.

How is the emulsion test for lipids performed, and what causes the cloudiness in a positive result?

Add $5\,cm^3$ of ethanol to $2\,cm^3$ of sample in a dry, grease-free tube, shake thoroughly to dissolve lipid, then add $5\,cm^3$ of water and shake gently. A milky-white emulsion indicates lipids. The cloudiness is caused by dispersed lipid droplets refracting light as it passes between oil droplets and water.

What four chemical groups are bonded to the central carbon atom of an amino acid?

An amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom ($-H$), and a variable side group ($R$ group).

How is a peptide bond formed between two amino acids?

A condensation reaction combines the $-OH$ from the carboxyl group of one amino acid with the $-H$ from the amino group of another, releasing a water molecule and forming a peptide bond between the carbon and nitrogen atoms ($-CO-NH-$).

What defines the primary, secondary, tertiary, and quaternary structures of a protein?

Primary: sequence of amino acids in a polypeptide chain. Secondary: folding or coiling of the chain (such as an $\alpha$-helix) due to hydrogen bonding between $-NH$ and $-C=O$ groups. Tertiary: overall 3-D folding held by disulfide bridges, ionic bonds, and hydrogen bonds. Quaternary: combination of multiple polypeptide chains and associated non-protein prosthetic groups.

How is the Biuret test for proteins conducted, and what constitutes a positive result?

Add an equal volume of sodium hydroxide solution to the test sample at room temperature, then add a few drops of very dilute ($0.05\%$) copper(II) sulfate solution and mix gently. A purple coloration indicates peptide bonds (protein present); otherwise, it remains blue.

What structural adaptations make collagen suitable for its function in tendons?

Collagen has a primary structure rich in glycine for close packing, wound tightly into an $\alpha$-helix, twisted into a second helix, and formed into a quaternary structure of three polypeptide chains wound together like a rope. Cross-links between adjacent chains and staggered ends throughout the fibre provide high tensile stability without weak points.

How do enzymes speed up chemical reactions in living organisms?

Enzymes act as catalysts by lowering the activation energy barrier, allowing reactions to proceed rapidly at relatively low physiological temperatures (such as $37\,^\circ\text{C}$ in the human body).

How does the induced fit model explain enzyme catalysis compared to the lock and key model?

Unlike the rigid lock and key model, the induced fit model states that the active site is flexible and changes shape to mould around the substrate upon collision. This shape change puts strain on specific substrate bonds, lowering the activation energy needed to break them.

What two variables are most commonly measured over time to determine the rate of an enzyme-catalysed reaction?

The volume or mass of product formed (e.g., volume of oxygen produced by catalase acting on hydrogen peroxide) or the disappearance of substrate (e.g., reduction in concentration of starch acted on by amylase).

How can the rate of an enzyme reaction be calculated at a specific point on a curved time-course graph?

By drawing a tangent that touches the curve at that specific point without crossing it (using a normal line at $90^\circ$ to aid accuracy) and calculating the gradient of the tangent (change in $y$ divided by change in $x$).

Why does an enzyme denature at high temperatures?

Excess thermal energy causes molecules to vibrate excessively, breaking the hydrogen and other bonds that maintain the tertiary structure and active site. The substrate no longer fits into the altered active site, permanently halting enzyme activity (typically around $60\,^\circ\text{C}$).

Why has human body temperature evolved to be $37\,^\circ\text{C}$ rather than the enzyme optimum of around $40\,^\circ\text{C}$?

Maintaining a higher temperature requires more food energy, higher temperatures risk denaturing non-enzyme proteins, and further temperature increases during illness (fever) could denature critical enzymes.

How does a change in pH affect enzyme action?

Changes in hydrogen ion concentration alter the charges on amino acids in the active site, preventing substrate binding, and can disrupt ionic and hydrogen bonds that maintain the tertiary structure, causing the active site to change shape or denature.

What is the pH of a solution with a hydrogen ion concentration of $0.0001\,M$?

Using the formula $\text{pH} = -\log_{10}[H^+]$, for $[H^+] = 1 \times 10^{-4}\,M$, the pH is $-\log_{10}(10^{-4}) = 4$.

What is the effect of increasing enzyme concentration on the rate of reaction when substrate is limiting?

If substrate is limiting, increasing enzyme concentration has no effect on the rate of reaction; the rate levels off because there are already enough active sites to accommodate all available substrate molecules.

According to the provided diagram, how does substrate concentration affect the rate of an enzyme-controlled reaction at a fixed enzyme concentration?

At low substrate concentration, the reaction rate increases in proportion to substrate concentration because active sites are free. At intermediate concentration, all active sites become occupied and the rate reaches maximum ($V_{\max}$). At high substrate concentration, the rate levels off because all active sites are saturated and excess substrate molecules must wait for free sites.

How do competitive inhibitors reduce enzyme activity, and how can their effect be overcome?

Competitive inhibitors have a molecular shape similar to the substrate and bind reversibly to the active site, blocking substrate molecules. Their effect can be overcome by increasing substrate concentration, which outcompetes the inhibitor for free active sites.

How do non-competitive inhibitors reduce enzyme activity, and why does increasing substrate concentration have no effect?

Non-competitive inhibitors attach to the enzyme at an allosteric binding site away from the active site, altering the enzyme's tertiary structure and the shape of the active site so substrates cannot bind. Because they do not compete for the active site, adding more substrate cannot overcome the inhibition.

How does end-product inhibition control a metabolic pathway?

The end product of a metabolic pathway acts as an inhibitor (usually non-competitive) of an enzyme at the start of the pathway (e.g., enzyme A). If end-product levels rise above normal, inhibition increases to slow production; if levels drop, inhibition decreases, maintaining a steady concentration via negative feedback.