Proteins Flashcards
(13 cards)
What are amino acids? And what is their structure?
Amino acids are the building blocks of proteins.
They contain an amino group (NH3+) on one end, a carboxyl group on the other end (COO-) and an α-carbon in the middle, which is also chiral.
Chirality occur when an α-carbon is bonded to four different groups:
1. amino group NH3+
2. carboxyl group COO-
3. hydrogen H
4. side chain R, which is different for all amino acids and it is responsible for the chemical and physical properties of the amino acid.
If a carbon is chiral, then two enantiomers can be formed:
- L: used in mammalian cells
- D: rare and poorly digested by enzymes
Amino acids can be either positively charged (NH3+) or negatively charged (COO-), but at intermediate pH (at iso-electric point) amino acids can occur as zwitter ions, thus having both negative and positive charge.
In which groups amino acids can be discriminated?
- Non-polar, aliphatic
R contains only H and C and single bond C-C- linear chain: Glycin (gly, G); Alanine (ala, A); Proline (pro, P)
- branched-chain: Valine (val, V); Leucine (leu, L); Isoleucine (ile, I)
- Aromatic R contain a 6C ring with single bonds alternated by double bonds, causing the delocalisation of electrons.
: Phenylalanine (phe, F); Tyrosine (tyr, T); Tryptophan (trp, W) - Polar, uncharged
R contains OH or NH2 that can form H-bonds- NH2: Aspargine (asn, N); Glutamine (gln, Q)
- OH: Serine (ser, S); Threonine (thr, T)
- Sulfur-containing R contain S.
: Methionine (met, M); Cysteine (cys, C) - Charged
- negative (acidic): Aspartate (asp, D); Glutamate (glu, E)
- positive (basic): Arginine (arg, R); Lysine (lys, K); Histidine (his, H)
What is the Primary structure of a protein?
The primary structure of a protein is the linear chain of amino acids, that is directly encoded in genes.
The amino acids are linked via peptide bond, through condensation reaction between a carboxyl group and amino group, in which water is released.
What is the Secondary structure of a protein?
The secondary structure of a protein is the regular, recurring arrangements in space of adjacent amino acid residues in a polypeptide chain.
1. α-helix: intramolecular H-bonds between one a.a. and the a.a. found four a.a. further. The R of these a.a point outwards to prevent steric hindrance.
2. β-sheet: a.a. chains are side-by-side linked by H-bonds
- anti-parallel: neighbouring chains have opposite orientation,
causing the H-bonds to be straight.
- parallel: a.a. chains run all in the same direction, causing the H-
bonds to be slightly skewed.
3. β-turn: sharp turn that connect two strands of anti-parallel β-sheet.
What is the Tertiary structure of a protein?
The tertiary structure of a protein is the pattern of secondary structure elements that fold into a three-dimentional conformation.
The secondary elements are connected by loops or coils.
What is the Quaternary structure of a protein?
The quaternary structure of a protein is the arrangement of multiple protein molecules into a larger structural and functional unit.
What are some groups in which proteins can be discriminated into?
- Globular: spherical, water soluble proteins that have a hydrophobic inside.
- Fibrillar:
- keratin (α-keratin): coiled coils of two α-helices cross linked to
other coils by disulfide bonds and kept together by hydrophobic
residues. - fibroin (β-keratin): micro-crystalline array of β-sheets.
- keratin (α-keratin): coiled coils of two α-helices cross linked to
Why is the shape of a function so important?
For the Anfinsen’s Dogma, proteins are functionally active only when folded, and the folded structure must be stable, unique and kinetically accessible. The folded structure is encoded in the primary sequence.
The interactions involved in protein folding are:
- H-bonds
- Salt bridges
- Van der Waals forces
If the folded state is the only one that is active, why the unfolded state is more entropically favourable and, thus, spontaneous?
The unfolded state is more entropically favourable compared to the folded one, because, when unfolded, proteins can assume various shape.
The presence of the disulfide bond between tertiary components stabilise the structure, reducing entropy, shifting the equilibrium towards the folded state.
What is the Native structure of proteins?
The native structure of proteins is the folded state they assume in the tertiary structure.
The Levinthal’s paradox says that there must be local favourable interactions that remain stable after formation, since the random search for the correct structure would take longer than the lifetime of the universe.
Why do proteins unfold?
Proteins denature at high temperature, due to their stability being temperature dependant: the higher the temperature is, the less negative ΔG becomes.
Often denatured proteins can’t be re-folded due to aggregation, an irreversible process in which unfolded proteins inetract with other chains.
What are chaperons?
Chaperons are proteins that can assist in the folding process of other proteins.
They don’t actively fold proteins, but provide a space and time to allow proteins to find their native state, by preventing aggregation.
What are Ligand? How does Ligand binding occur?
Ligand is the general name for any molecule that the protein binds to, in a reversible way.
K is the measure of the strength of ligand binding, while Kb express the affinity of the protein for the ligand: the higher Kb is, the faster is the forward rate and the slower is the reversed rate.
