BMS1030 - Proteins Flashcards
Describe the general structure of an amino acid. How many amino acids are there?
There are 20 amino acids.
How are amino acids categorised?
By their R-group
e.g. polar/non-polar, positive/negative, aromatic/aliphatic
What is the difference between oligopeptides and polypeptides?
Oligopeptides - 2-20 AAs
Polypeptides - Many AAs
How are peptide bonds formed?
How are sequences of Amino acids written in a polypeptide?
From the Amino (N) end to the carboxyl end.
How many ionizable R groups do peptides contain?
Like amino acids, pepties have their own ______ point.
2
Isoelectric point/pH
Multisubunit protiens have more than 1 polypeptides associated ___________.
If these polypeptides are identical, what is this called?
What re the 2 subunits referred to?
non-covalently
oligometric
protomers
What are conjugated proteins?
Proteins containing other components (e.g. lipids), also known as prothetic groups.
In Alpha helixes, every ___ peptide bonds is bonded with H-bonds.
What groups do these bonds link?
4
C=O of one peptide to the N-H of another. Does not involve R-groups.
In Alpha helixes are the R groups on the inside or outside of the helix?
Do C=O groups point down or up? What does this give to the helix?
Outside
C=O points down. N-H points up.
This gives polarity to the helix.
What amino acid causes a destabalising kink to the alpha helix?
What also destabalises the structure?
What AA has too high flexibility?
Proline
Neg and Pos charged AAs, along with the shape of some uncharged AAs.
Glycine.
Which AA has the greatest tendency to form alpha helices?
Alanine
Describe the strucure of Beta sheets.
Adjacent parallel peptide chains run in opposite directions.
H-bonds form between peptides in different chains (do not involve R groups).
H-bonding is stronger in anti-parallel B-sheets because C=O and N-H groups are better aligned.
How do the folding of proteins allow them to remain stable in an aq environment?
Hydrophobic R groups form a core in the middle of the protein.
Polar R groups on the outside can form H-bonds with H2O.
This stabalises the protein.
What proteins aid folding?
Chaperone proteins
_______ proteins are targeted for degradation.
Misfolded
What types of bonds are involved in tertiary proteins?
Disulfite bonds, salt bridges/ionic bonds and hydrogen bonds.
How are tertiary proteins classified?
Globular or fibrous
What are intrinsically disordered protiens?
Polypeptide chains lacking a stable tertiary struture.
Name 4 things that can be used to denature proteins.
Heat, Changing pH, Detergents, Chaotropic agents (urea)
These disrupt H-bonds and/or ionic bonds.
What are ligands?
Molecules tha bind to proteins at their binding site.
What is the disassociation constant (Kd)?
The lower the Kd the _____ the affinity for the ligand.
The rate of disassociation.
The lower the Kd the STRONGER the affinity for the ligand.
Write an equation for the association constant Ka.
Write an equation for the dissociation constant Kd.
Ka = [PL] / [P][L]
Kd = [P][L]/[PL]
P = protein
L = ligand
What does the term ‘Y’ refer to? (usually seen on graphs)
The fraction of potential binding sites occupied.
