Protein Structure Flashcards
What is the major goal surrounding protein science?
Predict structure from sequence
Predict function
Predict binding partners
Create novel enzymes
Drug design
New protein nanomaterials
What are the major structural classes of proteins? [4]
- Globular
- Membrane
- Fibrous
- Intrinsically disordered proteins (think of it as a ‘floppy noodle’) - an example is casein!
- This is one reason why it is so hard to replicate the structure/function relationship of casein using plants
What are the major functional classes of proteins? [8]
- Enzymes (amylase; pepsin)
- Contractile proteins (myosin; actin; tubulin; kinesin)
- Signal transduction (GPCRs)
- Carrier proteins (hemoglobin; myoglobin; serum albumin)
- Storage proteins (egg & seed proteins; ferritin)
- Structural proteins (collagen; keratin; elastin)
- Antibodies (IgG)
- Hormones (insulin; growth factor)
What is the primary structure of a protein?
- Amino acid sequence
- Proteins are linear, not branched
What is the secondary structure of a protein?
Local interactions
Alpha helices
Beta-pleated sheets
What is the tertiary structure of a protein?
the overall three-dimensional arrangement of its polypeptide chain in space.
What is the quaternary structure of a protein?
the association of several protein chains or subunits into a closely packed arrangement
What defines the physicochemical properties of a protein?
Primary structure
What is a peptide/amide bond?
A peptide bond is a covalent bond that links two amino acids together in a protein or peptide. It forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH₂) of another through a condensation reaction (dehydration synthesis), releasing a molecule of water (H₂O).
Define: polypeptide
Linear chain of L-amino acids, connected via amide bonds.
There are exceptions where branching occurs, but this is rare.
The peptide backbone is […]
Relatively hydrophilic
The functionality of a protein depends on [2] of amino acids.
Composition & sequence
Always read protein chains from N-terminus to C-terminus.
Except for glycine, amino acids are […].
Chiral
Chirality is a property of an object that is non-superimposable on its mirror image.
Which amino acids are ‘small’?
- Glycine - very flexible
- Alanine
What are the ‘nucleophilic/polar’ amino acids?
- Serine
- Threonine
- Cysteine - can form disulfide bonds - important for protein rigidity
The amide amino acids, asparagine and glutamine, are also polar.
What are the hydrophobic amino acids?
- Proline - very rigid because it will covalently bond with protein backbone
What are the aromatic amino acids
?
- Phenylalanine
- Tyrosine
- Tryptophan
What are the acidic amino acids?
- Aspartic acid
- Glutamic acid
What are the basic amino acids?
- Histidine
- Lysine
- Arginine
What are the amide amino acids?
- Asparagine
- Glutamine
These ones are also polar.
Describe the ionization of acidic and basic side chains.
When pH = pKa = pI (so 50/50 proportion of forms)
Acidic amino acids are neutral at pH < pKa.
True or False?
True.
Acidic amino acids are negative at pH < pKa.
True or False?
False.
Acidic amino acids are neutral at pH < pKa.
Acidic amino acids are negative at pH > pKa.
True or False?
True.
Acidic amino acids are neutral at pH > pKa.
True or False?
False.
Acidic amino acids are negative at pH > pKa.
Basic amino acids are positive at pH < pKa.
True or False?
True.
Basic amino acids are neutral at pH < pKa.
True or False?
False.
Basic amino acids are positive at pH < pKa.
Basic amino acids are neutral at pH > pKa.
True or False?
True.
Basic amino acids are positive at pH > pKa.
True or False?
False.
Basic amino acids are neutral at pH > pKa.
pKa values depend on the structural environment around it.
True or False?
True.
pKa values can be shifted up/down in context of folded protein.
pKa values are fixed.
True or False?
False.
pKa values can be shifted up/down in the context of the folded protein
What is protein surface charge?
Depends on which amino acids are external when the protein is fully folded.
What is isoelectric precipitation used for?
Takes advantage of the isoelectric point of the proteins to precipitate proteins out of solution.
Describe the oxidation and reduction of disulfide bonds.
Two cysteine residues can form a disulfide bond
Oxidized (glutathione)
Reducing agents (DTT; ME; TCEP)
List 3 reducing agents.
Added in research/food manufacturing to break disulfide bonds in polypeptide chains.
Discuss disulfide bonds in proteins.
Provides stability to the protein structure.
What defines how amino acids are oriented relative to each other?
Peptide dihedral angles - steric hindrance restricts allowable angles
How are peptide bonds formed?
- Amino group attacks carbonyl and you lose a water molecule in the process
- In the cell, catalytic machinery exists to achieve this - the ribosome.
How are peptide bonds formed in the cell?
- Ribosome synthesizes peptide bonds via condensation reactions
Why is the omega bond more stable than the others? Why is it fixed at 180 degrees?
- Think about resonance structures
- The double bond does spend some time being between the N and C; it spends most time as the carbonyl, but does spend some time between the N-C.
This is why the other two angles will define how the protein folds.
How is a Ramachandran plot interpreted?
- Shaded areas are favourable regions.
- Note even glycine (the smallest amino acid/most flexible) still has regions of unfavourable space due to steric hindrance from the backbone itself
Note proline is the most restricted amino acid because its side chain will bind to its own backbone - phi restricted to -60.
Describe why alpha-helix secondary structure forms.
- Only helix bond with both: (1) Favourable H-bonding and (2) allowed torsion angles
- Stabilized by H-bonds between upstream residues (i + 4)
- 3.6 aa per turn
Relatively local structure; amino acids connected in sequence
Describe why beta-sheets secondary structures form.
- Stabilized by H-bonds between strands
- Strands can be anti-parallel or parallel
Amino acids may be far apart in sequence.
How can helices and sheets be identified in a Ramachandran plot?
Very often phi/psi angles can be found in regions outside of allowed torsional space, very usually they are glycine.
What are supersecondary motifs?
What are domains?
- From motifs → domains → tertiary structure
- Currently only ~1400 unique motifs/domains are known!
- Make up all the known protein structures (>100,000)
What methods are used to determine protein structure? [3]
- X-ray crystallography
- Requires crystals (some proteins do not crystallize well)
- Nuclear Magnetic Resonance (NMR)
- In solution; difficult for proteins > 30 kDa
- Cryo-Electron Microscopy
- Resolution is limiting; no size issue
Cryo-EM makes it possible to […]
2017 Nobel Prize in Chemistry
Portray biomolecules after freezing them very fast (vitrification) so its natural shape is preserved.
What was the first structure of a protein resolved?
What is the protein data bank?
