Protein Structure Flashcards
How can amino acids act as acids/bases?
The carboxyl and amino groups can ionize
Amino group acts a base acting as a proton acceptor
Carboxyl group as an acid, being a proton donor
Why are amino acids classified per the properties of their R groups?
because rest of it is the same
Amino acid residue definition
What remains of an amino acid after a peptide bond has been formed, forming a protein
Acidity of proteins with side chains containing positively charged R groups?
Positively charged = (proton acceptor) = weakly acidic = high pKa = less likely to donate protons
Acidity of proteins containing side chains with negatively charged R groups?
Negatively charged = more likely to donate/ lose a proton = low pKa value = strongly acidic
By looking at pH and pKa, how can you identify whether a group will be protonated/ deprotonated??
If pHpKa, group is deprotonated (solution is more basic so group loses a proton)
Secondary structure
Local spatial arrangement of polypeptide backbone
alpha helicies, B pleated sheets
What are the properties of peptide bonds?
- they’re planar (C-N bond unable to rotate)
- they are rigid, as C-N bond has partial double bond characteristics.
- exhibit a trans conformation (if cis, there would be steric clashes)
Isoelectric point definition
The pH of a protein at which there is no overall net charge
Using pH and pI, how can you identify as to whether a protein is protonated/deprotonated??
?
PHpI, protein is deprotonated
What are conjugated proteins
Some proteins that contain covalently bonded chemical compounds, not including amino acids
why may some polypeptide sequences not have alpha helix conformations?
- Some amino acid residues can act as helix breakers, if hydrophobic eg Leu and Ala
- Pro is a helix breaker as rotation around C-N is impossible
- Gly is a helix breaker as the tiny R group supports other conformations
What is the conformation of the B strand like and how can these be arranged?
Amino acid residues in B strands are more widely spaced, having an extended conformation.
0.35nm between adjacent amino acid residues, with R groups alternating
Can be arranged (to make a B sheet) antiparallel or parallel.
How to fibrous and globular proteins differ?
Fibrous has functions of support, shape and protection, whilst Globular is involved in catalysis and regulation.
Fibrous has long strands or sheets, whilst globular is more compact.
Fibrous has a single repeating secondary structure whilst globular can have many types.
Collagen arrangement?
Triple helical arrangement of collagen chains
What are the different types of tertiary structures of globular proteins
Motifs; folding patterns containing 1 or more elements of secondary structure
Domains; part of polypeptide chain folding into a distinct shape. Often has a specific functional role
Why are some amino acid side chains charged at physiological pH
If pHpI, protein is deprotonated
What does the pKa value of an amino acid side chain tell you about that chemical group?
Higher the pKa, the less acidic it is and higher the pH and less likely to donate protons POSITVELY CHARGED R GROUP
Lower the pKa, the more acidic, more likely to donate a proton and lower the pH NEGATIVELY CHARGED R GROUP.
When may disulphides bonds form within protein structure?
Between cys residues (have a sulphur in R group)
Proteins with disulphide bonds are often secreted
214 kJ/mol
Can be broken with reducing agents
Electrostatic attraction and van der waals energies
Electrostatic attractions; 10-30Kj/mol
Van der waals 4kJ/mol
When may the hydrophobic effect be present in protein structure and what is it?
Interaction between hydrophobic side chains, due to water displacement.
10Kj/mol
Urea disrupts reactions
How may proteins denature (no longer in native conformation)
Heat; inc vibrational energy
PH; ionisation states of a.a residues altered, ionic, H-bonds interfered with
Adding detergents/organic solvents; interferes with hydrophobic interactions
How do proteins fold
Folding process is ordered, using localised folding, to find most stable conformation
Example of how protein misfolding can cause disease
Amyloid fibres; misfolded, insoluble form of a normally soluble protein
Lots of B sheets (core sheets form first out of whole protein)
Hydrophobic interactions between aromatic amino acids
