Lecture 9: Protein Shape & Structure Part 1

Question 1

How is a protein’s function determined?

Answer 1

• The 3D structure of a protein determines its function

- Chemical properties can also determine function

Question 2

Primary structure

Answer 2

• Linear sequence of amino acid residues
• Determined by mRNA code
• In combination with a protein’s environment, determines the secondary, tertiary, and quaternary structures (these are folded structures)

Question 3

Secondary structure

Answer 3

• Folding and twisting of the peptide backbone (doesn’t include side chains)
• Held together by weak H-bonds between C=O (carbonyl) and N-H (amine) groups in the backbone
• Side chains may involve whether this can form or not
• R-groups stick out from the backbone
• 2 well-known secondary structures: Alpha helices and Beta sheets

Question 4

Alpha helix

Answer 4

• Rigid cylindrical structure
• Forms when H-bonding occurs between a C=O and N-H groups that are 4 amino acids apart on the polypeptide backbone
• Coiling happens in a clockwise direction down the length of the chain

Question 5

Beta sheet

Answer 5

• Flat, sheet-like structure (pleated)
• Forms when H-bonding occurs between a C=O and N-H groups on adjacent polypeptide chains
• Adjacent chains can be parallel (adjacent chains run N-terminal to C-terminal)
• Adjacent chains can also be antiparallel (adjacent chains run in opposite directions)

Question 6

Exception to secondary structures

Answer 6

• Rigid proline residues insert a “kink” in a protein’s backbone and disrupt secondary structures
• Proline has a secondary amine instead of a primary amine, so N-C bond to carbonyl group is rigid
• Can be involved in a beta turn, but not involved in alpha helix or beta sheet structures

Question 7

Tertiary structure

Answer 7

• 3D arrangement of secondary structures
• Mostly held together by noncovalent attractions between:
• > R-groups (side chains)
• > Between R-groups and the surrounding environment (i.e. aqueous or hydrophobic lipid bilayer interior)
• > Between R-groups and polypeptide backbone
• R group interactions lead to the folding of secondary structures into 3D structures
• Unstructured loops (aka random coils) link secondary structures together (don’t have a single defined structure to them)

Question 8

Covalent disulfide bonds

Answer 8

• Can form between cysteine residues to cross-link parts of the polypeptide backbone
• Occur on the lumen of organelles on the secretory pathway and in the extracellular environment since they are oxidizing environments
• They don’t occur in the cytosol as that is a reducing environment
• Not required for tertiary structure to form
• Can stabilize tertiary structures and make them able to withstand harsh conditions

Question 9

What does 3D folding do?

Answer 9

• Results in structures that assume the lowest possible energy state
• Folding doesn’t occur in a vacuum
• The effects of protein folding on the surrounding water solvent must be considered
• Protein stability depends on the free energy change between the folded and unfolded states (deltaG = G FOLDED - G UNFOLDED)
• Proteins become more stable as G UNFOLDED > G FOLDED

Question 10

Molecular chaperones (chaperonins)

Answer 10

• 3D folding doesn’t occur rapidly for all proteins
• Many require ‘molecular chaperones’ called chaperonins that provide an isolated chemical environment in which they can fold
• Chaperonins = “cages” and “lids”
• The protein binds to the chaperonin “cage” and enters it
• A chaperonin “lid” seals the cage
• The protein folds into its appropriate shape and is released

Question 11

Prions

Answer 11

• Evidence that some unusual contagious neurological diseases are caused by proteins alone
• Very controversial for a long time; proved by Stanley Prusiner in the 1980s (Nobel prize in 1997)
• Can adopt an alternative folded state
• Abnormally folded protein causes a normally folded protein to adopt the abnormal conformation (bad apples spoil the other apples)

Question 12

Protein domains

Answer 12

• A region of the protein that folds essentially independently of other regions
• A protein can have a single domain or multiple domains
• Often represents a functional region of the protein - we can think of proteins as molecular, being built up from a “tool box” of domains
• Different domains of a protein often have different functions
• Example: Diptheria Toxin - 3 functional domains
• Catalytic domain: Inhibits host cell protein synthesis
• Receptor binding domain: attaches to cell surface
• Hydrophobic domain: Inserts into membranes

Question 13

Motifs

Answer 13

• Similar domains which occur in many related proteins (e.g. DNA binding motif)
• Drosophila and yeast protein backbones are separated by millions of years of evolution yet share the same DNA-binding domain structure with 3 alpha helices

Question 14

Quaternary structure

Answer 14

• Arrangement of multiple tertiary structures
• Held together by weak bonds and some disulphide bonds
• Homomers: identical subunit polypeptides
• Heteromers: different subunit polypeptides
• Can be simple (hemoglobin: 2 copies each of 2 subunits) or complex (RNA polymerase II contains 17 subunits, 11 different polypeptide chains)
• Represents all essential subunits of a protein - if a subunit gets taken away, it no longer works
• Different from a multi-protein complex (all proteins can work independently)