Protein structure
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128 Terms
What is a peptide bond?
A covalent bond formed between amino acids by a condensation reaction
Which groups react to form a peptide bond?
C=O and N-H groups
Why is the peptide bond rigid?
It has partial double bond character
Why does the peptide bond have partial double bond character?
Electron delocalisation
Why is the peptide bond planar?
Double bonds are planar
Can peptide bonds rotate?
No
Where can rotation occur in a polypeptide backbone?
Bonds either side of the peptide bond
Why are most peptide bonds trans?
To avoid steric clashes between r groups
Which amino acids commonly form exceptions to trans peptide bonds?
glycine and proline
Why is glycine more flexible than other amino acids?
It has only hydrogen as its side chain
How does glycine affect protein structure?
Increases flexibility
Why does proline restrict protein flexibility?
Its side chain bonds to the backbone
Why can proline disrupt alpha helices?
It makes the backbone rigid
What are torsion angles?
Angles around rotatable backbone bonds
Which bonds define protein torsion angles?
cα-n and cα-c bonds
What is phi (φ)?
Torsion angle around the cα-n bond
What is psi (ψ)?
Torsion angle around the cα-c bond
Why are torsion angles restricted?
Steric hindrance
What are the phi and psi angles in a fully extended polypeptide?
180°
What is a ramachandran plot?
A plot showing allowed phi and psi angles
Why are only certain torsion angles allowed?
To avoid steric clashes
Where should amino acid residues fall on a ramachandran plot?
In allowed regions
What happens in disallowed regions of a ramachandran plot?
Steric clashes occur
Why is the ramachandran plot important?
It predicts allowed protein conformations
What is a residue?
An amino acid within a polypeptide
What is a dipeptide?
Two amino acids joined together
What is an oligopeptide?
A short chain of amino acids
What is a polypeptide?
A chain of many amino acids
In which direction is an amino acid sequence written?
n terminus to c terminus
What is the monomer of a protein?
A polypeptide chain
What is the protein backbone?
The main chain containing peptide bonds
What do side chains contain?
r groups
What determines amino acid properties?
The side chain
What is primary structure?
The amino acid sequence
How are amino acids linked in primary structure?
By peptide bonds
What catalyses peptide bond formation?
Ribosomes
What is secondary structure?
Local backbone folding stabilised by hydrogen bonds
What are the two main secondary structures?
Alpha helices and beta sheets
What stabilises secondary structure?
Hydrogen bonds between backbone groups
How many amino acids are in one turn of an alpha helix?
3.6
What is the pitch of an alpha helix?
5.4 å
What direction does an alpha helix coil?
Right-handed
Why are natural alpha helices right-handed?
Proteins contain l-amino acids
What stabilises an alpha helix?
Hydrogen bonds
Which residues form hydrogen bonds in an alpha helix?
i and i+4
Which groups form hydrogen bonds in alpha helices?
nh and c=o groups
What charge is found at the n terminus of an alpha helix?
Partial positive
What charge is found at the c terminus of an alpha helix?
Partial negative
Where do side chains project in an alpha helix?
Outwards from the helix
Why can alpha helices be amphipathic?
They contain hydrophobic and hydrophilic faces
What is a beta sheet?
A secondary structure made of beta strands
How many strands make up a beta sheet?
Two or more
Can beta strands be parallel or antiparallel?
Yes
How long can a beta strand be?
Up to 15 residues
How many strands can occur in a beta sheet?
2-22
What is an antiparallel beta sheet?
A beta sheet with strands running in opposite directions
Why are antiparallel beta sheets more stable?
They have straighter hydrogen bonds
What is a parallel beta sheet?
A beta sheet with strands running in the same direction
Why are parallel beta sheets slightly less stable?
Their hydrogen bonds are staggered
Can beta sheets contain both parallel and antiparallel strands?
Yes
Why are beta sheets amphipathic?
Side chains alternate above and below the sheet
Why are beta sheets twisted?
l-amino acids are chiral
What connects secondary structure elements?
Loops and turns
What is a loop?
A flexible connecting region lacking regular angles
What is a turn?
An ordered connecting region
Where are loops and turns often found?
On the protein surface
Why are loops and turns important?
They can affect protein function
What is tertiary structure?
The overall 3d structure of a polypeptide
What causes tertiary structure?
Interactions between side chains
What is a monomeric protein?
A protein with one polypeptide chain
What is a domain?
A self-stabilising functional region of a protein
What is quaternary structure?
The arrangement of multiple polypeptide chains
What is an oligomeric protein?
A protein containing multiple polypeptide chains
What is a tetramer?
A protein with four polypeptide chains
What is a hetero-oligomer?
An oligomer containing different polypeptides
What is a homo-oligomer?
An oligomer containing identical polypeptides
What stabilises primary structure?
Covalent peptide bonds
What stabilises secondary structure?
Hydrogen bonds
What stabilises tertiary structure?
Side chain interactions
What stabilises quaternary structure?
Side chain interactions between subunits
What non-covalent interactions stabilise proteins?
Electrostatic, hydrogen bonding, van der waals and hydrophobic interactions
What are electrostatic interactions?
Attractions between charged groups
Which residues can form hydrogen bonds?
Polar residues
What are van der waals interactions?
Weak attractions between nearby atoms
Why do van der waals interactions occur in proteins?
Atoms are packed closely together
How do hydrophobic interactions stabilise proteins?
Hydrophobic residues are buried inside
What covalent bond stabilises tertiary structure?
Disulfide bond
Between which amino acids do disulfide bonds form?
Two cysteines
Why are disulfide bonds important?
They increase stability
Where are disulfide bonds most commonly found?
Extracellular proteins
Why don't disulfide bonds usually form in the cytosol?
The cytosol is reducing
What are the two categories of membrane proteins?
Integral and peripheral
How are membrane proteins arranged differently from soluble proteins?
Hydrophobic residues face the membrane
Where are hydrophilic residues found in membrane proteins?
Outside the membrane
What is an integral membrane protein?
A protein embedded in the membrane
Do integral membrane proteins span the membrane?
Usually yes
What membrane protein structure is common in receptors?
Single alpha helix
What membrane protein structure is common in transporters and enzymes?
Helical bundle
What membrane protein structure is common in channel proteins?
Beta barrel
What is a peripheral membrane protein?
A protein loosely associated with the membrane