Amino Acids, the Peptide Bond and Protein Structure: every key term you need (+ practice quiz)
25 flashcard terms for Biochemistry Topic 2, written to match the course framework. Study them here, then drill them as interactive flashcards, or test yourself with the 8-question quiz — free, no account needed.
The central carbon of an amino acid bearing the amino group, carboxyl group, hydrogen and side chain. With four different substituents it is a chiral centre in every residue except glycine.
Side chain
The variable group attached to the alpha carbon that determines a residue's chemistry: charge, polarity, size and reactivity all come from here rather than from the backbone.
Nonpolar aliphatic residues
Side chains built from hydrocarbon such as alanine, valine, leucine, isoleucine and methionine. They are typically buried in the protein core to satisfy the hydrophobic effect.
Aromatic residues
Phenylalanine, tyrosine and tryptophan. Their rings stack and absorb ultraviolet light near 280 nanometres, which is how protein concentration is routinely measured.
Glycine
The residue whose side chain is a single hydrogen. It is achiral, unusually flexible in the backbone, and therefore common at tight turns and in tightly packed helices.
Proline
A residue whose side chain loops back onto the backbone nitrogen, removing the amide hydrogen. It cannot donate a backbone hydrogen bond and disrupts regular helices.
Cysteine
A thiol-bearing residue that can be oxidized to form a covalent disulfide bridge. Such bridges are common in secreted proteins and rare in the reducing cytosol.
Histidine
The only residue whose side chain pKa sits near physiological pH, so it can gain or lose a proton under normal conditions. This makes it the standard acid-base catalyst in active sites.
Basic residues
Lysine and arginine carry positive charge across the physiological range. They dominate nucleic-acid binding surfaces and often anchor phosphate groups in substrates.
Acidic residues
Aspartate and glutamate carry negative charge at neutral pH. They frequently coordinate metal ions and act as general bases in catalysis.
Peptide bond
The amide linkage joining the carboxyl group of one residue to the amino group of the next. Resonance gives it partial double-bond character, so it is planar and rigid.
Trans configuration
The arrangement in which successive alpha carbons sit on opposite sides of the peptide bond. It is strongly favoured because it avoids steric clash, with proline the main exception.
Phi and psi angles
The two rotatable backbone torsion angles flanking each alpha carbon. Because the peptide bond itself cannot rotate, these two angles define the backbone conformation.
Ramachandran plot
A map of allowed phi and psi combinations. Its permitted regions correspond to the common secondary structures, and unusual points flag either strain or a modelling error.
Primary structure
The covalent sequence of residues written from amino to carboxyl terminus. It encodes every higher level of structure and is the level altered by a point mutation.
Alpha helix
A right-handed coil with roughly 3.6 residues per turn, stabilized by backbone hydrogen bonds between each carbonyl and the amide four residues ahead. Side chains project outward.
Helix dipole
The summed alignment of peptide bond dipoles along a helix, leaving partial positive charge at the amino end. Negatively charged ligands such as phosphates often bind there.
Beta sheet
An extended structure in which strands hydrogen bond side by side. Parallel sheets have angled bonds and are less stable than antiparallel sheets with their straight bonds.
Beta turn
A short four-residue reversal of chain direction, usually stabilized by a single hydrogen bond and often containing glycine or proline.
Tertiary structure
The complete three-dimensional fold of a single chain, held by hydrophobic packing, hydrogen bonds, ion pairs and any disulfides.
Quaternary structure
The assembly of two or more folded chains into a functional complex. It permits cooperativity and allosteric regulation that a single subunit cannot achieve.
Protein domain
A compact region that folds independently and often carries one function. Domains recur across unrelated proteins, which is why sequence modules predict function.
Motif
A small recurring arrangement of secondary structure elements, such as a helix-turn-helix, that is smaller than a domain and typically tied to one binding task.
Denaturation
Loss of native folding without breaking peptide bonds, caused by heat, extreme pH, urea or detergent. Function is lost even though the sequence is intact.
Edman degradation
Sequentially removes and identifies the amino-terminal residue of a peptide, allowing a short sequence to be read directly from the intact chain.