2.4 - Quaternary Structure Flashcards
non-bonded interactions (4)
- electrostatic interactions
- hydrogen bonds
- hydrophobic interactions
- van der waals forces
acid dissociation constant
pH at which charged amino acids carry no net charge
+ve charged R group amino acids (3)
- lysine (Lys, K)
- arginine (Arg, R)
- Histidine (His, H)
what affects basic and acidic amino acid R groups?
pH of the environment
-ve charged R group amino acids (2)
- glutamic acid (Glu, E)
- aspartic acid (Asp, D)
when do salt bridges form?
at neutral pH, when most charged side chain R groups are ionised
how do salt bridges form?
electrostatic interaction occurs between a +ve and -ve side chain (if they are closely arranged in space)
effect of salt bridge formation
charge spread across whole residue
where do H-bonds form between amino acids?
between R groups (as well as main chain)
hydrophobic effect
apolar (non-polar) molecules aggregate in presence of water
where are hydrophobic residues usually found in molecule?
in the centre of the folded molecule
van der waals
weak electrostatic interaction between atoms in close proximity, generated by dipoles from the electron cloud
why cant atoms interacting via van der waals come too close?
-vely charged e- will repel (van der waals radius)
multimeric protein nomenclature: identical chains
homo-
multimeric protein nomenclature: different chains
hetero-
multimeric protein nomenclature: 2 chains
dimer
multimeric protein nomenclature: 3 chains
trimer
multimeric protein nomenclature: 4 chains
tetramer
fibrous proteins
elongated and structural role in nature - provide support, shape or protection
examples of fibrous proteins (3)
- collagen
- keratin
- silk
collagen role
connective tissue
examples of collagen (4)
- tendons
- cartilage
- organic matrix of bone
- cornea
collagen structure
3 intertwined polypeptide chains that form triple helix
how many distinct versions of collagen do humans have?
16 - differ in primary sequence
globular protein structure (2)
- spherical shape
- exist in enormous variety of 3D structures
globular protein frequency vs fibrous proteins
globular much more numerous
classifications of protein interactions (2)
- permanent
- transient
characteristics of permanent protein interactions
tight binding with strong affinities
characteristics of transient protein interactions
weaker and more dynamic
characteristics of protein-protein interaction sites (5)
- hydrophobic
- surface accesible
- protruding
- planar
- specific residue propensities
membrane proteins
interact with lipids and have very specific primary sequences and structures
what is gramicidin A
antibiotic peptide
where is gramicidin found?
DMPC lipid bilayer and water
gramicidin A action (2)
- forms pore in cell wall of bacteria letting out monovalent cations (K+/Na+)
- membrane potential disappears and bacteria dies
gramicidin structure (2)
- 15 amino acids
- helical
how does gramicidin form a channel
head-to-head dimer
types of ion channels (4)
- simple pores
- substrate gated channels
- voltage-gated channels
- pumps
example of simple pore ion channels
GAP junctions
example of substrate gated ion channel
nicotinic receptor
example of voltage-gated ion channel
K+ channel
examples of pump ion channels (2)
- ATP-synthase
- K+/Na+-ATPase
requirements for drug to interact with protein to inhibit/enhance function (3)
- correct size
- right chemical properties to fit active site
- compete with substrate
