Sesh 5: Protein Structure and Function Flashcards
What determines the amino acid sequence of a protein?
The nucleotide sequence of the gene encoding that protein.
What does the folding of the protein depend on?
The physical and chemical properties of its amino acid residues.
What 4 things are bonded to the central alpha carbon of an amino acid?
- Amino group
- Carboxyl group
- Hydrogen atom
- R group/ side chain- distinguishes amino acids
What is the ionisation state of an amino acid?
The state the amino acid is in when it is in solution…e.g. NH2 gains and COOH loses protons to form a zwitterion (the deprotonated form).
Why are amino acids classified by the chemical properties of their R groups?
As when joined by peptide bonds, they lose their amino and carboxyl group, so are only amino acid residues with their R group left- this group determines the protein’s structure.
Define an amino acid residue.
What remains of an amino acid after it has been joined by a peptide bond to form a protein.
Name 2 possible PHYSICAL properties of amino acids R chains.
Aliphatic or aromatic (carbon rings).
What is the pKR?
The log of the acid dissociation constant for amino acid R chains. At this pH, there will be equal amounts of the protonated and deprotonated forms.
Amino acids with high pKR values have ___________ charged R groups.
Amino acids with low pKR values have _____________ charged R groups.
- Positively
2. Negatively
If the solution pH is less than the pKR value, the R group will be ____________.
If the solution pH is greater than the pKR value, the R group will be _____________.
- Protonated
2. Deprotonated
Define the primary structure of a protein.
The linear amino acid sequence of the polypeptide chain. ‘Beads on a string’ model.
What is the secondary structure of a protein?
The local spatial arrangement/folding of the polypeptide backbone, forming conformations e.g. Alpha helices, beta pleats
Define the tertiary structure of a protein.
The spatial arrangement of amino acids far apart in the protein sequence to give the overall 3-D configuration of the protein.
What can you infer about a protein if it has a quaternary structure?
It has multiple subunits which associate to form the protein. Not necessarily all protein subunits e.g. Ribosome made of protein and RNA.
Peptide bond formation is a _____________ reaction as it involves the _____ of water.
- Condensation
2. Loss
Why does a protein have polarity?
Because the amino acid at 1 end will have a free amino group- the amino/N terminus- and 1 at the other end will have a free carboxyl group- carboxyl/C terminus.
Name 3 properties of peptide bonds that are important for protein structure.
- They are planar
- They are rigid- form resonance structures, so unable to rotate
- Exhibit a trans conformation to avoid steric clashes
What are the bonds on either side of the peptide bond called, and what property makes them different to a peptide bond?
- Psi bond (C-C)
- Phi bond (C-N)
Unlike the peptide bond, these are free to rotate to give different bond angles….but are still slightly restricted due to steric clashes.
What is the isoelectric point (pI) of a protein?
The pH at which there is no overall net charge on the protein. (Individual amino acids will still be charged, but their charges balance at pI)…
An acidic protein has many _________ charged amino acids, and a basic protein has many ___________ charged amino acids.
- Negatively
2. Positively
The angles of the ___ and ___ bonds determine the conformation of the peptide ________, thus determining how the protein _____.
- Phi
- Psi
- Backbone
- Folds
Describe an alpha helix.
A compact ribbon-like right-handed helix.
Define the ‘pitch’ and the ‘rise’ determined by the protein’s secondary structure.
- Pitch= 1 complete turn of the helix
- Rise= distance between each amino acid
What holds the alpha helix of a protein together?
H bonds between the backbone structure (carbonyl oxygens and amide hydrogens).
Describe the characteristic H bonding in an alpha helix.
H bonds form in the peptide backbone between a carbonyl oxygen and an amide hydrogen 4 amino acids away.
How can primary sequence affect alpha helix stability?
Some amino acids are more likely to form alpha helices than others….
- Small hydrophobic residues are strong helix formers e.g. Ala, Leu
- Pro & Gly= helix breakers due to R group bonding
Is a beta strand more or less compact than an alpha helix/?
Less. More of an extended conformation. Rise= larger (0.35nm vs 0.15 nm)
Describe an anti-parallel beta-sheet.
Adjacent beta strands run in opposite directions, stabilised by many inter-strand H bonds between carbonyl oxygens and amide hydrogens.
Why is a parallel beta sheet slightly weaker than an anti-parallel beta sheet?
Beta strands are running in the same direction, meaning the H bonds are at slightly different angles.
Describe the structure and function of fibrous proteins.
- Simple structure with multiple repeating secondary structures, to form long strands or sheets.
-Stable, so have roles in support, shape and protection.
E.g. Collagen- triple helical arrangement of collagen chains with Gly-X-Y repeating seq.
Describe the structure and function of globular proteins.
- Made up of several different types of secondary structures, to give a compact shape, and give rise to a variety of tertiary structures.
- Roles in catalysis and regulation
E.g. Carbonic anhydrase
What are motifs?
Folding patterns containing 1/more secondary structure elements. Commonly found in globular proteins.
E.g. Beta-barrel, beta-alpha-beta loop
Define a protein domain.
A part of a polypeptide chain that folds up independently into a distinct shape to fulfill a specific functional role.
How does the polypeptide chain of water soluble proteins fold so that they are stable?
Fold so that hydrophobic chains are buried on the inside, and hydrophilic charged residues are on the surface, to interact with water.
Describe the general distribution of amino acids in membrane proteins.
Usually show ‘inside out’ distribution. Hydrophobic residues on surface to interact with hydrophobic fatty acid chains in the membrane, and hydrophilic residues buried on the inside e.g. To form a water filled pore.
What is a protein?
A polypeptide= a macromolecule composed of amino acids covalently joined to give the protein sequence, which can then fold to form the protein structure. Have a role in virtually all biochemical processes.
What are disulphide bonds?
Found in tertiary and quaternary structure of a protein.
Relatively strong covalent bonds between cysteine residues.
Most proteins with them are secreted e.g. Ribonuclease.
What are electrostatic interactions formed between?
Oppositely charged groups on amino acids.
What is a hydrogen bond?
A bond between an electronegative atom and a H bound to another electronegative atom.
What is the hydrophobic effect/ hydrophobic interactions?
Interactions between hydrophobic amino acid side chains that come together to exclude/ displace water.
What type of interactions are Van der Walls forces, and when are they important?
Dipole-dipole interactions that occur due to uneven charge distribution in covalent bonds.
Important for when large molecule come together.
What is a native conformation of a protein?
It is in its normally folded state and is functional.
Briefly describe amyloid fibres and how they are formed.
Misfolded, insoluble forms of a normally soluble protein, that can aggregate and cause amyloidoses.
Have a highly ordered structure- mainly beta sheets. Core beta sheet forms first.
Then get H bonds between aromatic amino acids to stabilise inter-chain assembly.
