L9 - Protein Structure Flashcards
What are proteogenic amino acids?
The 20 naturally occuring a/a found in proteins
- alpha a/a
- all are chiral (except glycine)
How do a/a form peptides and proteins?
Polymerise, linking with peptide (amide) bonds by condensation reaction
How are peptides and proteins synthesised?
N-terminus (amino group) to the C-terminus (a-carboxylate group)
What does the backbone of proteins consist of?
-N-Ca-C-N-Ca-C-
Constant across a/a and form a continuous chain
What is the primary structure of a protein hekd together by?
Covalent bonds
Which properties are determined by protein primary structure?
- molecular mass = yk what atoms are there
- protein shape = determines the shape the seq. folds
- overall electric charge = yk what +ve/-ve charges are present
- hydrophibicity = yk what a/a will be on the inside based on the environment they’re put in
- surface charge = yk what a/a are on the outside
What is the peptide bond like?
Planar (flat)
What does the eq between the 2 isomers of the peptide bond result in?
- partial double bond characteristic = planar bond
- stable bond and modified reactivity of the ketone and amine
- trans isomer most energetically favourable
Who were set out to calculate all H-bonded structures that could be formed from a single polypeptide chain?
Linus Pauling
Robert Corey
Herman Branson
What do a-helices involve?
Non covalent interactions between residues close together in primary sequence
What is some extra info about a-helices?
- they are right handed
- each turn has 3.6 a/a
- the pitch of the helix is 5.4 Å
What are the helices stabilised by?
Hydrogen bonds between the backbone amine (NH) and the bacbone carbonyl (CO) of another a/a 4 residues earlier
What is a H bond?
Non-covalent interaction in which the H covalently attached to one electroneg atoms is shared with another electroneg atom that possesses a lone pair of electrons
What were LRH close about with their structure?
Their calculated structures aren’t quite what we see in protein structures
What were LRH correct on?
That parallel and anti-parallel structures are formed
What do B-sheets involve?
Non-covalent interactions between residues which may be far apart in primary sequence
What are the polypeptide chains like in B-sheets?
- extended
- run parallel or anti-parallel (more common)
What are B-sheets stabalised by?
The backbone of hydrogen bonds between CO and HN in another
What are a-helices and B-sheets commonly connected by in proteins?
Loops or regions of irregular structures
What is the secondary structure of proteins hekd together by?
Non-covalent interactions
What elements of secondary structure found as? And how are they formed?
- regular structure found in proteins
- formed by non-covalent interactions between backbone atoms
What is the secondary structure mostly independent of?
Only involves bacbone atoms
- independent of the detailed primary structure of the protein
What does the tertiary structure encompass?
All non-covalent a/a interactions between a/a of a single polypeptide chain (not included in the definition of the 2nd structure
What interactions are part of the tertiary structure?
Interactions between:
- protein sidechains
- protein sidechains and the backbone
Involves interactions between residues which are far apart in terns of primary sequence
What is the quaternary structure?
Interactions holding multiple polypeptde chains together into one protein
What are the polypeptide chains called in quaternary structure? How are they held together?
Subunits: 2 dimers, 3 trimers, 4 tetramers
Held together by the same non covalent interactions as tertiary stucture
What are the 3D structure of proteins stabilised by?
Large numbers of weak non-covalent interactions
What is secondary structure stabilised by?
Hydrogen bonds
What are the tertiary and quaternary stabilised by?
- hydrogen interactions
- hydrogen bonds
- salt bridges (pairs acidic and basic a/a close together in structure, +ve/-ve charges)
- vdw interactions (permanent or transient delta+/delta- charges)
- disulphide bridges (covalent bond S-S bond between 2 cysteines close in space)
