Proteins Flashcards
Which AA is actually an imino acid?
Proline (P)
What’s supersecondary structure?
The close association of more than one piece of secondary structure into a functional unit.
What parts of a protein interact to stabilise the tertiary structure of a protein?
The side chains of the amino acids
Which area of the Ramachandran plot are the phi-psi angles mostly found in:
- beta sheet
- alpha helix
- beta = top left
2. alpha = bottom left quadrant (closer to centre)
Where are hydrophobic amino acids commonly found in a protein?
In the core
What do the hydrophobic bonds that non polar AAs form provide energy for?
Protein folding
What do chaperones do?
Bind to proteins and help with the correct folding of a protein (incl. preventing incorrect folding)
What type of bond found in a protein is planar and rigid?
Peptide bond
What was the key finding from Afinson’s experiment on protein folding?
All information required for a protein to fold correctly is found in the primary AA sequence.
Which AA is commonly found in a beta-turn?
Proline
What is quaternary structure?
The association of more than one polypeptide chain in a functional protein
What is the Ramachandran plot?
A prediction of allowed rotations of phi and psi
Phosphorylation is a common posttranlational modification catalysed by what?
Kinases
How does phosphorylation regulates protein activity?
By introducing a conformational change
What vitamin is a required cofactor in gamma carboxylation?
Vitamin K
What is the insulin receptor regulated by?
Phosphorylation
Define primary protein structure.
Amino acid sequence
Define secondary protein structure.
3D arrangement of AAs over a short stretch of sequence.
Define tertiary protein structure.
Collection of secondary structures, which make up a 3D structure
Define quaternary structure.
Made up of 2 or more tertiary structures
Which rotation angle does phi represent?
N-C bond (alpha carbon)
Which rotation angle does psi represent?
C-C bond
What are the two Phi-Psi restrictions? (due to steric hinderance)
- Phi rotation can lead to O-O collisions
2. Psi rotation can lead to NH-NH collisions
Which rotation angle does omega represent?
C-N bond (peptide bond)
What are the 2 characteristics of a peptide bond?
- Planar
- Trans (side chains alternating sides w/ carboxyl group)
What rotation angle does chi represent?
Side chain angles
What are the 2 types of protein secondary structure?
- Alpha helix
2. B-strand/B-sheet
What are the properties of the alpha-helix?
- 3.6 residues/turn
- H-bond b/w n & n+4 AA
- Side chains point out from helix (polar on one side, non-polar on the other)
Which 2 AA are unfavourable for alpha-helix formation?
- Proline (too bulky, introduces sharp turn)
2. Glycine (too flexible)
What is the approximate pKa for:
- NH3+ groups
- COO- groups
- > 8
2. < 3
What are secondary structures stabilised by …? Formation of these are called?
Hydrogen bonds
Nucleation
What is the beta structure?
Adjacent peptide chains (B-strands) that have an extended type structure that allows for H-bonding b/w chains
What are the two types of interaction in a B sheet?
- Parallel (B-strands in same direction)
2. Antiparallel (B strands in opposite direction)
Properties of beta structure
- pleated w/ right hand twist
- side chains above and below the sheet (polar on one side, non-polar on the other)
What is the direction of a beta-strand?
N –> C
What are the bonds which stabilise the tertiary structure of a protein? (4 weak, 1 strong)
- H-bonds
- Electrostatic interactions
- Metal ion coordination
- Hydrophobic interactions
- Disulfide bonds
What type of bonds hold quaternary protein structures together?
Weak/non-covalent
What are 4 examples of quaternary structure? I.e. combinations
- homodimer
- heterodimer
- homotetramer
- hetertetramer
Define super secondary structure
Combinations of secondary structures that form recognisable patterns. Connected by loops, turns and coils.
Define domains/motifs.
What is the difference b/w them?
- Combinations of super secondary structures that form independently folded regions that have a specific function.
- Domains have a hydrophobic core (due to being larger/having more super secondary structures)
What are the 3 protein types w/ regard to chaperones?
What is protein folding driven by?
- Chaperone-independent
- Chaperone-dependent (doesn’t require energy)
- Chaperonin-dependent (requires energy)
Driven by hydrophobic interactions
What is the order of protein folding?
- Formation of short secondary structures
- Several/many nuclei come together to form domains
- Several/many domains come together to form the ALMOST final 3D tertiary configuration
- Small conformational adjustments take place to give the final native tertiary structure
What are the 5 steps of the Afinsen experiment?
- Native protein
- Add denaturing agents
- Denature protein
- Remove denaturing agents
- Protein re-folded correctly
Which enzyme is involved in phosphorylation?
Which enzyme removes the phosphate group?
- Kinase
- Phosphatase
What is the importance of phosphorylation?
It introduces a conformational change that either activates or inactivates protein function.
Bc the -vely charged phosphate will attract/repel nearby +ve/-ve groups
What are 2 examples of phosphorylation?
- Insulin receptor
2. Na+/K+ pump
Which enzyme is involved with hydroxylation?
Which cofactors does the enzyme need?
- Hydroxylases
- Vitamin C and Fe2+
What is the importance of hydroxylation?
Facilitates H-bond formation
What is an example of hydroxylation?
Collagen (contains high proportion of hydroxy proline and hydroxy lysine)
What condition does vitamin C deficiency lead to?
Scurvy
What enzyme is involved in Gamma carboxylation?
What cofactor does it need?
Carboxylase
Vitamin K
What is the importance of gamma carboxylation?
Allows two COO- groups to bind to a Ca2+ ion
–> conformational change
(active form (Gla residue) differs from inactive form (Glucose residue))
What is an example of gamma carboxylation?
blood clotting pathway
What is the structure of Hb?
Tetramer
Which has a higher affinity for oxygen: Haemoglobin or myoglobin?
Myoglobin
What does the binding of oxygen do to Hb?
Changes its shape (deoxy-Hb has larger central cavity)
What is the function of myoglobin?
Store oxygen in muscle cells
What is the function of haemoglobin?
Transfer oxygen in blood