proteins Flashcards
protein chain folds
3d conformation depends on the constituent amino acids
due to non-covalent interactions
protein function
Function depends on 3D structure
- 3D structure depends on sequence
- Sequence is determined genetically
protein organisation
primary: amino acid sequences
secondary: local packing, regular occurring
arrangements
tertiary: 3d packing of secondary structure elements
quaternary: number and position of polypeptide subunits
structure of amino acids
Peptide bonds form between the amino & carboxyl groups of amino acids
Uncharged polar side chains
Methionine
(Met or M)
Cysteine
(Cys or C
Methionine
relatively unreactive but always at the beginning of a protein (tRNA charged with methionine binds to the translation start signal)
Cysteine
form complexes with various metal ions can form disulfide binds
disulfide bonds
form in between two cysteine residues to form cystine: very stable
oxidation and reduction
peptide bond
One loses a hydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This reaction produces a molecule of water (H2O) and two amino acids joined by a peptide bond (-CO-NH-). The two joined amino acids are called a dipeptide
Delocalisation of π electrons over entire peptide bond, rather than simply over the C=O bond= planar structure
partial double bond character because of the restricted rotation
peptide bond conformation
trans or cis conformation (one of the infinite number of possible spatial arrangements of atoms in a molecule )
secondary structure overview
described as the local organisation of polypeptide backbone (excluding constituent’s side-chains).
α-helix & β-sheet
Strands are normally 5-10 amino acids in length
2 strands
Side chains point alternatively up and down
favorises hydrogen bonds between adjacent strands for sheet and amino acids close together for helix
parrallel or antiparallel strands
n-c n-c or n-c c-n
tertiary structure
refers to its exact 3D structure, and the packing of secondary structural elements within it
domains
Polypeptides greater than 200 amino acids often display multiple ‘Domains’
- Often serve as independent units of function
modular structures
Proteins are made up from combinations of structural & functional folds/domains that can be repeated within the same protein structure and found in other proteins
structural motifs
building blocks many domains are composed of: super-secondary structures, can be found in a wide variety of related or unrelated polypeptides
ex: the greek key: linked by loops in a specific 3d structure
stabilisation of structure
domains are achieved after biosynthesis: conformation attained depends on the amino acids present+folding constraints and extent of secondary structure
major stabilising forces:
hydrophobic interactions electrostatic interactions (salt bridge, hydrogen bounding) covalent linkages
hydrophobic interactions
occur between 2 or more non polar molecules when they are in polar environments: non polar residues are buried inside of a polypeptides interior
very powerful interactions
hydration shell
form an order : polar, main chain, hydrophobic
electrostatic attractions
van der walls forces
hydrogen bonds
ionic interactions: slat bridges+ between oppositely charged amino acid side chains
proteins movement
0.2 mm
evolution
optimised protein for it’s role
mutations
deleterious:
leading to an absent/ 1.dysfunctional protein
2.cutting a metabolic pathway
3.dysfunction of a regulatory protein or receptor
4. protein aggregation(alzheimers)
5.impairment or loss of defence against infection
sickle cell anaemia
sickle cells obstruct capillaries causing intense pain and organ damage:
normal haemoglobin: molecules do not interact
exposed hydrophobic pocket (consequence of mutation): Hb molecules associate to form fibres under low oxygen condition
