Flashcards in Protein Structure Deck (57):
what are proteins used for in biochemical processes?
Ligands in cell signalling
What are proteins made up of?
What bonds form in proteins?
What determines the amino acid sequences of a protein?
The nucleotide sequence of a gene
What does the folding of a protein depend on?
3D shape depends on the chemical and physical properties of the amino acid
What is an amino acid made up of?
An amino group -NH2
A carboxyl group- COOH
A hydrogen atom
An R group
What is a zwitterion?
Ionised form of an amino acid
E.g. NH3+ and COO-
How are amino acids classified?
According to the chemical properties of the r group:
Hydrophobic or hydrophilic
Polar or non-polar
Acidic, basic or neutral
Aliphatic or aromatic
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 e.g. HNCHCH3CO
If the pK value is lower is the side chain more likely to be acidic or basic?
If pK value is higher is the side chain more likely to be acidic or basic?
If the pH of the solution is lower than the pK them what will happen to the group?
It will be protonated
If the pH of the solution is greater than the pK value then what will happen to the group?
It will be deprotonated
What is primary structure?
The linear amino acid sequence of the polypeptide chain
What is secondary structure?
Local spatial arrange of polypeptide backbone e.g. Alpha helix
What is tertiary structure?
The overall 3D configuration of the protein
What is the quaternary structure?
Association between different polypeptides to form multi-subunit proteins
How are peptide bonds formed?
Linking of two amino acids by the abstraction of a water molecule
How do peptide bonds lie?
All lie in the same plane
Why are peptide bonds so rigid?
Has a partial double bond characteristic
Unable to rotate
Are peptide bonds cis or trans?
Which bonds in a peptide bond are free to rotate?
Bond on either side of the bond
What does the amino acid sequence of a protein determine?
The way in which the polypeptide chain folds and the physical characteristics of the protein
What is the isoelectric point of a protein?
The pH at which there is no overall net charge
What would the isoelectric point of basic proteins be?
Greater than 7
What would the isoelectric points of acidic proteins be?
Less than 7
If the pH is less than the isoelectric point of a protein is the protein protonated or deprotonated?
If the pH is more than the isoelectric point of a protein is the protein protonated or deprotonated?
What does the sequence determine for a protein?
What does the structure determine for a protein?
What bonds are present in the primary structure of a protein?
What bonds are present in the secondary structure of a protein?
Hydrogen bonds between NH and CO
How does an alpha helix form?
The CO group of one residue hydrogen binds to a NH of a residue 4 amino acids away
What do Ala and Leu have in common?
Small and hydrophobic
Strong helix formers
What does Pro do?
Helix breaker as rotation around N-C bond is impossible
Why does Gly do?
Helix breaker as tiny R group supports other conformations
How does a beta sheet form?
R groups alternate between opposite sides of the chain and hydrogen bonds form
What is an example of an alpha helix?
What is an example of a beta sheet?
Fatty acid binding protein
What is an example of tertiary structure?
What is a fibrous protein?
Support, shapes and protects
Long strands or sheets
Single type of repeating secondary structure
What is a globular protein?
Several types of secondary structure
What is collagen?
Triple helix arrangement
Gly- X- Y
Hydrogen bonds stabilise interactions between chains
What is a motif?
Folding patterns containing 1 or more elements of secondary structure
What is a domain?
Part of a polypeptide chain that folds into a distinct shape. Often has a specific functional role
How do polypeptide chains fold?
So that hydrophobic side chains are buried and polar charged chains are on the surface
Except membrane proteins which are the opposite
What are 2 examples of quaternary structures?
Haemoglobin and ribosomes
What forces are present in tertiary and quaternary structures?
Covalent, ionic, H bonds, van see walls, hydrophobic
What are disulphide bonds?
Formed between sys residues between two sulphurs
What are electrostatic interactions?
Formed between charged groups e.g. Glu- or arg+
What are hydrogen bonds?
Bonds formed between electronegative atoms and a hydrogen bound to another electronegative atom
What is hydrophobic effect?
Interactions between hydrophobic side chains due to displacement of water
What is a van dear waals force?
Dipole dipole interactions
Important when surfaces of two large molecules come together
How can proteins be denatured?
Disruption of protein structure can be done by breaking of forces holding the proteins together e.g. Heat (increased vibration energy) and pH ( alters ionisation states and changes bonds)
How do proteins fold?
Each step Localised folding and with stable conformations maintained
Driven by the need to find the most stable conformation
What can protein misfolding cause?