Protein Structure Flashcards
What is an oligopeptide
3-10 amino acids joined together
What is the primary structure and what does it affect
Made up of covalent (peptide) bonds between amino acids
What is the secondary structure
Made up of hydrogen bonds between parallel strands in the beta sheet
How can polypeptides adapt the lowest energy conformation possible
why is the backbone of a polypeptide rigid
Due to restricted rotation around pi bonds (so around the peptide bond rotation can’t occur)
However, rotation can occur around the sigma bonds in an amino acid
What is a beta pleated sheet and its structure
Dipole-dipole interactions aka hydrogen bonds
What is an alpha helix
Same angles over and over again (regular structure)
R groups all stick out
When H bonds form every 3 residues the dipoles line up
What is the tertiary structure of a protein
Formed from hydrophobic effect and van der Waals interactions
Where are residues wit hydrophobic and residues with hydrophilic side chains found and why
What is the quaternary structure of a protein
2 types- fibrous and globular
Is the interaction of multiple polypeptides
What is a disulphide bond
What is a fibrous and globular protein
What happens if there’s a small change in polypeptide sequence
There would be a big change in protein structure and folding
Where is keratin found in the body
Skin
Hair
Nails
What is the structure of keratin
2 alpha helices put into bundles
What is an anti parallel beta pleated sheet
When the starting point of the row alternates between being the C and N terminus
What are loops and turns and what is the difference
What is the role of aromatic amino acids in a protein
They make the protein more rigid and stable (stops things from moving around)
This is because the rings are flat and stable
They are found on the inside of a protein (along with the hydrophobic non polar amino acids)
Why can glycine fit in places that other amino acids can’t fit inside a protein
It’s side chain is absent locally so can make tight turns while the amino acids maintain its planar shape
It’s side chain is absent because if it was present there would be steric clash
So glycin is always involved in turns (when the polypeptide turns in a protein- turn regions ) since it has no side chain
What is collagen
The structural protein in cartilage and bone
What is the distance between each residue in collagen
2.9 angstroms
What is the structure of collagen
Every third amino acid used is glycine which allows the formation of fibrous proteins
However, this would make the protein flexible
How is the problem of a fibrous protein being flexible due to the presence of glycine every third amino acid overcome
Proline is used as it forms a ring with its side chain (since it bonds to the nitrogen in the amino group)
This helps to provide rigidity to counteract the flexibility of glycine
This makes the overall structure of the protein stable
What is a Ramachandran plot
What are phi and psi angles
They involve 2 amino acids
What is a phi angle
Rotation around the bond from the alpha carbon to nitrogen (this bond is called the phi bond)
Is the angle between 2 carbonyl carbon atoms on the 2 separate amino acids
What is the psi angle
Rotation around the bond from the alpha carbon to the carbonyl group (this is the psi bond)
The angle between the two nitrogen atoms on the two separate amino acids
What is the omega angle
This bond refers to the dihedral angle around the peptide bond (C-N bond) that links two amino acids together. The omega angle is usually either 0° (for cis configuration) or 180° (for trans configuration), with the trans configuration being far more common in proteins.
Label the psi, phi and omega angles and bonds on a diagram
What happens when you look down the alpha C-N bond (to measure the phi angle) and what would this look like diagrammatically
Nitrogen will be hidden behind the alpha carbon
alpha carbon would be at the front
What happens when you look down the alpha C- carbonyl C bond (to measure the psi angle) and what would this look like diagrammatically
The carbonyl carbon would be hidden
What is meant by a staggered conformation
All atoms are equally spaced out
What is meant by an eclipsed conformation
Carbons are aligned so that the hydrogens line up with eachother
Forms steric hinderance/ steric clash
What is the range for dihedral angles . Explain using the clock analogy
-180 degrees to + 180 degrees
What is the angle is the 2 carbonyl carbons are eclipsed
The angle is 0
How can rotation occur around a peptide bond
Would have to break the bond
Explain the Ramachandran plot
What is the distance between each residue in an alpha helix
1.5 angstroms
What is the width of an alpha helix
5 angstroms
What do you see if you look down at the top of an alpha helix
What is the distance between 2 R groups of an amino acid in a beta strand
7 angstroms
What are the regular secondary structures
Alpha helix
Beta sheet
What is a parallel beta sheet
What is regular secondary structure and what it is regulated by
Repeating the same psi and phi bonds over and over
Regulated by:
- ideal peptide geometry
- ideal van der Waals interactions
- ideal H bonds in backbone
What charge do acidic amino acids side chains have with the example of aspartate and glutamate
They are Negatively charged
So their names ending is -ate
What is the ratio of [A-]/[HA] for acidic amino acids
The acidic amino acids are aspartic acid and glutamic acid. They have carboxylic acid side chains that can lose a proton , forming an anionic form
Show the distribution of electrons/ resonance forms of the carboxyl group when acidic amino acids are missing the hydrogen attached to the oxygen in the carboxyl group
All the atoms in the carboxyl group at sp2 hybridised
Grey = pi orbitals
White= sigma orbitals
What charge do amino acids with basic side chains have with the example of lysine (plus its name)
They are positively charged
What are the different resonance forms of arginine and why does it have so many resonance forms
Is very basic due to its guanodino group
Show the distribution of electrons across the atoms in arginines side chain for this version of arginines resonance form
Red arrows= movement. Of electrons
Purple = pi bond = where double bond is
Show the distribution of electrons across the atoms in arginines side chain for this version of arginines resonance form
Show the distribution of electrons across the atoms in arginines side chain for this version of arginines resonance form
Explain the formation of arginines different resonance forms
2 pi orbitals have one electron in them while the other 2 pi orbitals have 2 electrons in them
The two pi orbitals with only one electron in them form a pi bond between them, and this is where the double bond would be in arginines side chain
The an electron from the p orbital with 2 electrons can move to a p orbital that has only one electron in it
Therefore the p orbital that the electron moved from can overlap with the other p orbital with only one electron in it to form the double bond between those atoms
This can happen for all of the p orbitals so the double bond can occur between different atoms depending on where the electron moved from
Show the distribution of electrons between the orbitals of the atoms in this version of arginines side chain
What type of bond can help stabilise quaternary structures
Disulphide bonds between cysteine amino acids
How do beta sheets come together
Due to the hydrophobic effect which puts hydrophobic amino acids on the inside
What are the properties of amino acids with amide groups such as ASN and GLN
All atoms in the amide group are sp2 hybridised so they all have pz orbitals
These amino acids have resonance forms
The atoms in the amide group have strong dipoles
These amino acids can form 3 hydrogen bonds due to the strong dipoles of the atoms in the amide group
Amides don’t undergo chemical reactions
These amino acids aren’t charged as they don’t protonate/deprotonate
What is serine protease Chymotrypsin
It’s an enzyme (protease)
They break peptide bonds
What are DNA-binding proteins
They bind to specific parts of DNA
What is a modular protein
They are folded into units
They are made of domains. Each domain has its own function and can carry that function out independently
What are the two examples of post translational modifications which involve amino acids
Reversible reaction with serine to produce phosphoserine
Irreversible reaction which converts glutamic acid to gamma-carboxyglutamic acid
Give the post translational modification reaction of serine
Give the post translational modification of glutamic acid and the function of the product as well as the form that the product is found naturally
What is this group called
Ether
What is this group called
Thioether
Give the reaction between two cysteine side chains and the name of this reaction + the name of the product
This is another example of a post translational modification
What is the difference between cysteine and cystine
Cysteine is in the cytoplasm and doesn’t have disulphide bonds
Cystine is formed when proteins go down the secretory pathway
What is protein folding
When polypeptide forms secondary or tertiary structure
The folded protein would have native tertiary structure
What is a denatured protein and what can it also be called
It is an unfolded polypeptide which has no defined structure
It can have many conformation s
Phi and psi angles changes constantly
It is also known as a random coil, which has no native structure
How is a loop different to a random coil
A loops structure wouldnt change
The polypeptide would always fold the same way as the sequence of amino acids in the polypeptide would be the same, so the loops would stay the same
What is denaturation
When a protein unfolds
What is an oligomeric structure/ quaternary structure
2 or more polypeptides to make up the protein
What is a subunit in an oligomer
Individual polypeptides
What does it mean if a protein has one subunit/monomer
The protein is monomeric
What does it mean if a protein is dimeric
It has 2 subunits (2 polypeptide chains)
What does it mean if a protein is homo dimer
Composed of 2 identical polypeptides
Can be represented by lowercase alpha 2 (show in image)
What does it mean if a protein is heterodimer
Composed of 2 different polypeptides
Represented by lowercase alpha beta
What is meant by a protein being heterotetromer
Has 2 of the same polypeptides, 2 different polypeptides
Represented by :
What is meant by heterotrimer
A protein which has 3 different subunits/polypeptides
Represented by alpha beta gamma
What are the two ways to make hetero oligomers
What are the long range interactions which stabilise protein structures
The long-range interactions in protein structure include disulfide bond and many non-bond interactions, such as electrostatic interaction, hydrophobic interaction, van der Waals interaction, and hydrogen bond
what are functional sites on proteins
Protein functional sites are amino acid residues, or groups of residues, that perform functional roles in proteins. Examples of functional sites include catalytic sites in enzymes, ligand-binding sites for small molecules, metal ions, nucleic acids and other proteins and protein–protein interaction sites.
