Module 10 Biomolecules: Enzymes and Nucleic Acids

Comprehensive vocabulary flashcards covering enzyme kinetics, mechanism of action, inhibition, medical assays, nucleic acid structures, replication, and protein synthesis from Module 10.

Enzyme

A protein that acts as a biological catalyst, increasing the reaction rate by lowering the activation energy without being consumed in the reaction.

Carbonic anhydrase

An enzyme that catalyses the reaction $CO_2 + H_2O \rightarrow H_2CO_3$ to remove carbon dioxide from cells, producing $36\text{ million}$ molecules per minute.

Absolute specificity

A condition in which an enzyme will catalyse only one specific reaction of a single substance, such as urease catalysing the hydrolysis of the amide bond in urea.

Relative specificity

A condition in which an enzyme catalyses the reactions of any structurally related substances, such as proteases catalysing the hydrolysis of proteins.

Stereochemical specificity

A condition where an enzyme will only catalyse reactions of a molecule with a specific 3D shape or optical configuration, such as D-amino acid oxidase acting only on D-amino acids.

International Enzyme Commission (IEC) naming system

A systematic classification system that groups enzymes into six classes and assigns names based on the substrate, the functional group acted upon, and the reaction type catalysed.

Active site

The specific 3D region of an enzyme where the substrate binds to form the enzyme-substrate complex and the catalytic chemical reaction takes place.

Lock-and-key model

An enzyme action model proposing that an enzyme's active site is rigid and possesses a fixed shape that matches only a substrate of the exact complementary geometry.

Induced-fit model

An enzyme action model proposing that the enzyme has a flexible structure that modifies or adapts the shape of its active site to fit the incoming substrate.

Co-factor

A small non-protein molecule or ion that an enzyme requires in order to function properly.

Co-enzyme

An organic molecule that acts as a cofactor required for an enzyme to carry out its catalytic function.

Apoenzyme

The inactive protein portion that remains when co-factors or co-enzymes are removed from an enzyme.

Effect of enzyme concentration on reaction rate

Under conditions of unlimited substrate, the reaction rate increases linearly and directly with an increase in enzyme concentration.

Effect of substrate concentration on reaction rate

Reaction rate increases as substrate concentration rises until all enzyme active sites become saturated, after which the rate plateaus and remains constant.

Effect of pH on enzyme activity

Most enzymes display optimum catalytic activity around physiological pH, and activity declines sharply at extreme pH levels due to denaturation.

Effect of temperature on enzyme activity

Enzymes operate at peak activity around physiological temperature ($37\,^\circ\text{C}$), but become denatured and inactive at temperatures above $60\,^\circ\text{C}$ and below $0\,^\circ\text{C}$.

Irreversible inhibition

Inhibition in which an inhibitor permanently binds to a specific functional group of an enzyme, such as cyanide ($CN^-$) binding iron in cytochrome oxidase or heavy metals ($Hg^{2+}$, $Pb^{2+}$) binding cysteine $-SH$ groups.

Competitive inhibition

A form of reversible enzyme inhibition in which an inhibitor has a structure similar to the substrate and competes directly for binding at the active site.

Non-competitive inhibition

A form of reversible enzyme inhibition in which an inhibitor binds to the enzyme at a site other than the active site, altering the 3D shape of the active site so substrate cannot bind.

Assay

A clinical laboratory procedure used to measure the specific amount or activity of an enzyme present in bodily fluids.

Alanine aminotransferase (ALT)

A serum enzyme whose elevated concentration in blood serum is used clinically to diagnose hepatitis.

Creatine phosphokinase (CK)

A serum enzyme measured in medical assays to assist in diagnosing a heart attack.

Nucleotide

The monomer unit of nucleic acids, consisting of a heterocyclic base, a monosaccharide, and a phosphate group.

Pyrimidine

A single-ring heterocyclic aromatic amine whose derived bases found in nucleic acids include cytosine (C), thymine (T), and uracil (U).

Purine

A two-ring heterocyclic aromatic amine whose derived bases found in nucleic acids include adenine (A) and guanine (G).

D-deoxyribose

The five-carbon monosaccharide component found in DNA, which lacks one oxygen atom compared to D-ribose and adopts a $\beta$-configuration at the anomeric carbon.

DNA primary structure

The linear sequence of heterocyclic bases attached to an alternating phosphate-to-monosaccharide backbone, written conventionally in the $5'$ to $3'$ direction.

DNA secondary structure

The 3D right-handed double-helix conformation of DNA, consisting of two antiparallel strands with outward-facing backbones and inward-pointing, hydrogen-bonded bases displaying major and minor grooves.

Complementary base pairs

The specific pairing of bases in DNA wherein adenine pairs with thymine via two hydrogen bonds (A-T) and guanine pairs with cytosine via three hydrogen bonds (G-C).

Replication fork

The Y-shaped region where the double-stranded DNA helix begins unwinding and separating into single strands during DNA replication.

Helicase

The enzyme responsible for catalysing the unwinding and separation of the two strands of the DNA double helix during replication.

Leading strand

The newly synthesised DNA strand that grows continuously in the $5'$ to $3'$ direction moving toward the replication fork.

Lagging strand

The newly synthesised DNA strand formed discontinuously in small segments away from the replication fork.

Okazaki fragments

The short segments of newly synthesised DNA formed discontinuously along the lagging strand during replication.

Semiconservative replication

The mode of DNA replication where each newly generated DNA double helix is composed of one original parental strand and one newly synthesised complementary strand.

Protein synthesis

The overall two-step process consisting of transcription of genetic information from DNA into mRNA within the nucleus, followed by translation of mRNA into a polypeptide chain at the ribosome.

Transcription

The process by which RNA polymerase unwinds DNA to synthesise a complementary single strand of messenger RNA (mRNA) from a DNA template strand.

Messenger RNA (mRNA)

The short-lived RNA molecule that carries transcribed genetic instructions from nuclear DNA to the ribosomes for protein assembly.

Ribosomal RNA (rRNA)

The RNA component that makes up approximately $65\%$ of a ribosome's structure, providing the cellular site where translation occurs.

Transfer RNA (tRNA)

The RNA molecule that delivers specific amino acids from the cytoplasm to the ribosome by matching its complementary anticodon sequence with codons on mRNA.

Codon

A sequence of three adjacent nucleotide bases on mRNA that codes for a specific amino acid or acts as a termination signal during protein translation.

Stop codons

The three specific mRNA codons (UAG, UAA, and UGA) that do not code for any amino acid and cause termination of protein synthesis.

Peptidyl site (P-site)

The site on the ribosome that holds the tRNA carrying the growing polypeptide chain during translation.

Aminoacyl site (A-site)

The site on the ribosome that receives and positions the incoming tRNA molecule carrying the next amino acid to be added to the growing peptide chain.

Translation elongation

The translation stage in which an incoming tRNA binds to the A-site, a new peptide bond forms with the existing polypeptide, and the peptide shifts positions as the ribosome moves along the mRNA.

Mutation

Any change in the DNA base sequence, occurring on average at an error rate of one base in every $10^{10}$ during replication.