Protein Structure Flashcards
What is the general structure of an amino acid?
A central carbon has an amino group, carboxyl group, a hydrogen atom and an R group covalently bonded to it
In what state are amino acids usually present as?
Zwitter Ions
What is an amino acid residue?
What remains of an amino acid after it has been joined by a peptide bond to form a protein
If an amino acid has a high PKA value what does that indicate?
It is a basic amino acid
What is pKa?
pKa tells you the strength of an acid, so how likely the groups are to lose or gain protons
If the pH is less than then pKa value what will happen to the side group?
The group is more likely to be protonated
What is the primary structure of a protein?
The amino acid sequence of the polypeptide chain
What is the secondary structure?
The way the chains fold into conformations like helices etc
What is the tertiary structure?
The overall 3D shape
What is the quaternary structure?
The association between different polypeptides to form a multi-subunit protein
In what type of reaction are peptide bonds formed?
A condensation reaction so a molecule of water is released
What does it mean by saying that peptide bonds are planar?
The atoms all lie in the same plane
Why can’t peptide bonds rotate?
Electrons from the C=O bond of the carboxyl group move between the central carbon and nitrogen from the amino group giving it double bond properties (resonance)
Why do peptide bonds also have trans conformations?
By having the central carbon on opposite sides of the peptide bonds, the R groups will be further apart so won’t repel
Why is the amino acid sequence important?
It determines the physical characteristic and the way in which the protein folds
What is the ISO electric point of a protein?
The pH at which there is no overall net charge
What happens if the pH is less than pI?
The amino acids will be protonated
What are conjugated proteins?
Proteins that are covantely linked to other chemical components as well as amino acids e.g. Glycoproteins
What binds hold the alpha helix structure together
Hydrogen bonds between the amino group and the carboxyl group
What 2 arrangements can be made from proteins with a beta sheet secondary structure?
Antiparallel and parallel sheets
Why are parallel beta sheets weaker than antiparallel sheets?
As the beta strands are running in the same direction the hydrogen bonds are at an angle and so are weaker
What is the domain of a globular protein?
Where part of a polypeptide chain folds into a distinct shape and often has a specific role
What are the 2 different types of tertiary structure?
Fibrous and Globular
How can amino acids be classified?
By whether they are:
- hydrophilic/hydrophobic
- polar/non-polar
- basic/acidic/neutral
- aliphatic/aromatic
If an amino acid has a charge will it be hydrophobic or hydrophilic
Hydrophilic
What does it mean if the pKa is equal to pH?
There will be equal amounts of protonated and deprotonated forms
What is the Henderson-Hasselbach equation?
pH = pKa + log(base/acid)
What bonds hold the tertiary structure together?
Ionic, H bonds, covalent, Van der Walls and hydrophobic and disulphide bonds
Between which amino acid residues do disulphide binds form?
Cystine
What properties do disulphide bonds give to proteins
The binds help keep the structure better so they can withstand hostile environments
Between what groups do electrostatic interactions occur
Oppositely charged groups
What is the hydrophobic effect?
Interactions between hydrophobic side chains result in the exclusion of water
What determines how a protein folds?
Primary sequence
How do proteins fold?
There is localised folding to form stable conformations
What is amyloidosis
A condition when their are deposits of amyloid fibres (misfolded, insoluble protein)
