Biological Molecules: Proteins, Enzymes, and Nucleic Acids

Comprehensive vocabulary flashcards covering proteins, protein structure levels, enzyme action and inhibition, DNA and RNA structures, and semi-conservative DNA replication based on lecture mind maps.

Amino Acids

Nitrogen-containing monomers that join together to form polypeptides and make up proteins, consisting of an amino group, a carboxyl group, a hydrogen atom, and a variable $R$ group.

Polymerise

The process in which many monomers join together to form a polymer, such as joining amino acids together to form a polypeptide.

Condensation Reaction (Proteins)

A chemical reaction that forms a peptide bond between amino acids by releasing a water molecule, removing an $-OH$ group from the carboxyl group ($-COOH$) of one amino acid and an $-H$ from the amine group ($-NH_2$) of another.

Hydrolysis Reaction (Proteins)

A chemical reaction in which water is added to break chemical bonds, such as breaking a peptide bond in a polypeptide.

Dipeptide

A molecule formed when two amino acids are joined together by a single peptide bond.

Biuret Test

A biochemical test for proteins where an equal volume of sodium hydroxide solution is added to a sample at room temperature followed by a few drops of very dilute ($0.05\%$) copper(II) sulfate; a purple colouration indicates the presence of peptide bonds, while the solution remains blue if no protein is present.

Primary Structure

The unique sequence of amino acids in a polypeptide chain, held together by strong covalent peptide bonds.

Secondary Structure

The twisting and folding of long polypeptide chains into a 3D shape, forming either an alpha ($\alpha$) helix or a beta ($\beta$) pleated sheet, held together by hydrogen bonds between the $H$ in $-NH_2$ and the $O$ in $-COOH$.

Tertiary Structure

The precise 3D folding of a polypeptide chain into a specific functional shape, maintained by disulfide bridges, ionic bonds, hydrogen bonds, and hydrophobic interactions between variable $R$ groups.

Disulfide Bridge

A very strong covalent bond formed between the variable $R$ groups of amino acids in a protein's tertiary structure that is not easily broken.

Ionic Bond (Protein Structure)

A relatively strong electrostatic attraction between oppositely charged $R$ groups in a polypeptide that is not involved in peptide bonds and is easily broken by changes in pH.

Hydrophobic Attraction

Weak interactions between non-polar $R$ groups that repel water to help maintain the 3D shape of a protein; weaker than ionic or disulfide bonds, but not as weak as hydrogen bonding.

Quaternary Structure

A protein structure formed only when two or more polypeptide chains interact together, held by the same types of bonds that maintain tertiary structure (e.g., collagen and haemoglobin).

Globular Protein

A smaller, spherical protein that can easily be secreted from a cell and carries out metabolic functions such as enzymes, hormones, and haemoglobin, often containing a non-amino prosthetic group.

Fibrous Protein

A protein made of long, unbranched chains tightly wound together to carry out structural functions (e.g., collagen), typically stopping at secondary structure.

Enzymes

Biological catalysts made of proteins that speed up anabolic and catabolic chemical reactions without being consumed or changed, functioning by lowering the activation energy.

Activation Energy

The minimum amount of energy needed for a chemical reaction to happen.

Active Site

The specific spatial arrangement of amino acids within an enzyme's tertiary structure that is complementary in shape to only one specific substrate.

Induced Fit Model

The model of enzyme action where substrate binding induces a conformational change in the enzyme's active site, distorting or breaking bonds in its tertiary structure to become complementary to the substrate and lower the activation energy.

Competitive Inhibitor

A substance with a similar shape to the substrate that binds directly to an enzyme's active site, preventing substrate binding; its inhibitory effect can be overcome by increasing substrate concentration (e.g., Methotrexate).

Non-Competitive Inhibitor

A substance that binds to an allosteric site on an enzyme, altering the tertiary structure and disrupting the active site so it is no longer complementary to the substrate; its effect cannot be overcome by adding more substrate (e.g., Cyanide).

Allosteric Site

A binding site on an enzyme distinct from the active site where a non-competitive inhibitor binds to alter the enzyme's tertiary structure and active site shape.

DNA (Deoxyribonucleic Acid)

A double-helix polymer consisting of two polynucleotide strands made of nucleotides, which makes up chromosomes and stores genetic information.

Gene

A section of a chromosome made of DNA that codes for a polypeptide, which is used to make proteins that determine characteristics.

Nucleotide

The monomer of nucleic acids composed of three components: a pentose sugar (deoxyribose in DNA or ribose in RNA), a phosphate group, and a nitrogenous base.

Phosphodiester Bond

A strong covalent bond formed via a condensation reaction between the phosphate group of one nucleotide and the pentose sugar of the adjacent nucleotide, forming the sugar-phosphate backbone.

Complementary Base Pairing (DNA)

The specific pairing of nitrogenous bases in DNA based on their shapes: Adenine pairs with Thymine ($A-T$) via $2$ hydrogen bonds, and Cytosine pairs with Guanine ($C-G$) via $3$ hydrogen bonds.

Messenger RNA (mRNA)

A single-stranded RNA molecule that contains codons and carries a copy of the genetic information from the nucleus to ribosomes for protein synthesis, possessing uracil instead of thymine.

Transfer RNA (tRNA)

A single-stranded RNA molecule folded back into a cloverleaf shape held by hydrogen bonds, carrying an amino acid attachment site at its $3'$ end and an anticodon loop to transfer specific amino acids to ribosomes.

Anticodon

A sequence of three bases on a tRNA molecule that is complementary to a specific codon on an mRNA strand.

Ribosomal RNA (rRNA)

The form of RNA that combines with proteins to construct ribosomes (consisting of a large subunit and a small subunit with an mRNA binding site) to translate mRNA into polypeptides.

Semi-Conservative Replication

The mechanism of DNA replication in which each newly formed DNA molecule consists of one original (template) strand and one newly synthesised strand, ensuring genetic continuity.

DNA Helicase

An enzyme that unwinds and separates the two strands of the DNA double helix during replication by breaking the hydrogen bonds between complementary base pairs.

DNA Polymerase

An enzyme that synthesises a new DNA strand in the $5' \text{ to } 3'$ direction by adding free DNA nucleotides to a primer via complementary base pairing.

Meselson-Stahl Experiment (1958)

An experiment using Escherichia coli grown in heavy nitrogen ($^{15}\text{N}$) and light nitrogen ($^{14}\text{N}$) separated by density gradient centrifugation that confirmed the semi-conservative mechanism of DNA replication.