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Amino acids
Uni of Notts, Genes, Molecules and Cells, first year
| Term | Definition |
|---|---|
| Origin of eukaryotes + how this was discovered | Originate from a branch of Archaea called Asgard. This was discovered by analysing similarities in amino acids between RNA polymerases in both organisms |
| Current paradigm about viruses | They're obligate cellular parasites since they can't produce ATP or translate mRNA. Although some viruses are capable of this to an extent & are recognised as living mimiviruses |
| Why only L-amino acids are used in the biosphere | Biology evolved to incorporate only L-amino acids so that all proteins are homochiral & uniform so that a large amount can be made identically to make many identical proteins. Alpha helices will always twist right handedly |
| Amino acid: pKa pI pKR | Likelihood of an amino acid absorbing a proton in solution Isoelectric point, pH at which the amino acid is amphoteric acid dissociation constant of R group, when side chain is 50% protonated & deprotonated |
| Hydropathy index | Measure of -hydrophobicity or +hydrophilicity of an amino acid, this is important for behaviour in non-covalent binding |
| Unusual covalent bonds: proline & cysteine | Proline - cyclic imino acid with R group connected covalently to N terminal, causes peptide backbone to kink allowing for twists in tertiary structure Cysteine - forms covalent disulphide bridges which strongly crosslinks amino acids |
| Unusual amino acids: desmosine & selenocystein | Some amino acids can have their R groups altered to serve different purposes, they don't have DNA codons. Desmosine has 4 crosslinking ports, is used in elastin; selenocysteine replaces S with Se for blood clotting enzymes |
| Non-covalent fundamental forces: Electrostatic/ionic | Attraction between oppositely formally or partially charged groups, between ionic R groups this is known as a salt bridge. Is weaker in aqueous environments which makes proteins semi-fluid |
| Ionic protein interactions in biological systems: ATP hydrolysis & DNA separation | ATP hydrolase uses positively charged R groups to form salt bridges with phosphates. DNA helicase forms salt bridges with nitrogenous bases to overcome their hydrogen bonds |
| Coulomb's law | The magnitude of electrostatic force between 2 points is proportional to the product of their charges & inversely proportional to the square of the distance between them |
| Coulomb's law equation | F = k[q1.q2]/r^2 F = Magnitude of electrostatic force k = Coulomb's constant: 8.99 x 10^9 x m^2 x C^-2 q = charges of each point r = distance between them |
| Non-covalent fundamental forces: Polar bond | Stabilising interactions between partially charged groups forming hydrogen bonds & dipole-dipole interactions |
| Solvation shell | Polar R groups form hydrogen bonds with water creating a stable shell around the protein allowing it to persist in aqueous environments, usually contains a hydrophobic core |
| Non-covalent fundamental forces: Van Der Waals | Weak transient fluctuation of electron cloud causing temporary poles in electron density between molecules which allows non-polar residues to be packed into the protein core |
| Non-covalent fundamental forces: Hydrophobic interactions | Hydrophobic R groups don't repel each other but are repelled by polar groups causing them to group together. This happens with purely hydrocarbon R groups |
| Thermodynamics affecting hydrophobic interactions | More energetically favourable in water as aggregates release water which increases entropy & drives molecular movement. Interactions become stronger as temperature increases unlike other interactions |
| Order of hydrophobicity of R groups | Isoleucine, valine, leucine, glycine, & methionine |
| How peptide bond affects structure & bonding | The peptide bond forms a resonance hybrid with 40% double bond characteristic keeping it rigid, coplanar & slightly formally charged allowing hydrogen bonding which stabilises tertiary structures |
| Thermodynamics of protein folding | Proteins fold from primary structures into conformations with the lowest energy using fundamental forces between R groups and surrounding substances, a change in this causes a conformational shape change |
| Amino acid rotational flexibility | Some flexibility in the backbone due to N-C (psi) & C-C (phi) dihedral angles. However, electrostatic repulsion & steric clashes from R groups coming too close together restrict the possible angles keeping it rigid |
| How secondary structures form | Different amino acid chains prefer to form these structures based on lowest energy conformations & steric hinderances. Turns & loops are neither helices nor sheets but allow the protein to change directions |
| Special function of alpha helices with electrons | Since alpha helices have oppositely charged ends, it allows them in certain circumstances to pass electrons between ends |
| Super secondary structures | Structural combinations of different secondary structures to form compact functional motifs playing key roles in protein structure & function. An example is supercoiling alpha helices or double stranded beta sheets |
Created by:
Beech47
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