Proteins Flashcards
What does it mean if a cell is polarised?
It means that each end of the cell has a different function.
How is a prokaryotic cell different to a eukaryotic cell?
It has no distinct nucleus, it has fewer organelles and it has a cell wall as well as a plasma membrane.
What is a monomeric unit? And what forces are involved in the making of a macro molecular complex?
It is a simple molecule. These are joined together by covalent bonds to form macromolecules which then combine to form macro molecular complexes. The complexes are held together by weaker non-covalent interactions.
List the four types of weak interaction (non-covalent).
Hydrogen bonds (between dipoles on neutral groups) Ionic interactions (between charged particles) Hydrophobic interactions (exclusion of water) Van dear waals forces.
What must a molecule be able to form in order to be soluble?
Hydrogen bonds. This means soluble molecules often contain large numbers of OH groups or =O. Non polar molecules cannot form hydrogen bonds, and therefore are insoluble.
What is an amphipathic molecule?
A molecule which has both polar and non polar regions
What type of molecules form micelles and why?
Amphipathic molecules form micelles because the hydrophobic groups cluster together to exclude water and water surrounds the hydrophilic parts of the molecules.
What is the fluid mosaic model for a plasma membrane?
This is where the phospholipid molecules form a bilayer with their hydrophobic tails pointing inwards and the hydrophilic heads pointing outwards.
If cells all have the same DNA, how can we get different specialised cells?
Different cells have different proteins expressed and therefore carry out different functions.
What is a protein?
A protein is a polypeptide. A polymer of covalently bonded amino acids.
How does the amino acid sequence affect the protein function?
The amino acid sequence affects the way in which the protein folds, and therefore ultimately its shape. The shape of the protein determines it’s function.
What is the structural state of an amino acid in water in the body?
Amino acids are dissolved in water in the body and so they are in their zwitterion form.
What charge does an amino acid have?
Amino acids can act as both a base and an acid depending on their environment. The NH2 amine group can accept protons whilst the COOH group can donate protons.
What determines the acid base behaviour of a protein?
The R groups. All the COOH and NH2 groups are contained within the peptide linkages which form when the protein forms.
What are the three classes of amino acids?
Non-polar amino acids
Polar uncharged amino acids
Polar charged amino acids
How can we estimate the effect that a mutation will have on a protein?
Look at the size and structure of the change in R groups. Large changes will have a bigger effect than small ones.
What is pK and what does it tell us?
pK is how likely a group is to dissociate and donate a proton.
If pK pH : the group accepts a proton - is protonated
What are the key properties of a peptide bond?
The peptide bond is C-N. This is a planar bond with the H and R groups above and below the plane. Electrons dissociate into the bond from C-O and this gives it partial double bond properties, preventing rotation.
What is the Isoelectric point of a protein?
This is the point where there is no overall charge.
Will a basic protein contain mostly positively or negatively charged amino acids?
Positively charged.
The basic protein has already accepted protons, and now it can act as an acid and donate protons.
In what state will a protein be if pH
Protonated, because if pH is lower then it will of acted as a base and accepted a proton.
What is an oligopeptide?
A peptide of only a few amino acids in length.
What is the secondary structure of a protein and what two forms can it take?
The secondary structure is the spatial arrangement of the polypeptide backbone. This can take the form of either an a helix or a B sheet.
What is the tertiary structure of a protein?
It is the 3D arrangement off all the atoms in the polypeptide.
What is the quarternary structure of a protein?
It is the arrangement of multiple subunits within space.
Describe the secondary protein structure: a helix
It is a right handed helix with 3.6 amino acid residues per turn. Hydrogen bonds form between every fourth amino acid residue.R groups are all on the outside of the helix and have no impact on formation.
Can all polypeptides form a helixes?
No. Those will small R groups form strong helixes because these do not interact, however Proline acts as a helix breaker because the bond angles are impossible.
What is a B sheet?
This is the fully extended conformation for a protein with R groups lying alternately on either side of the chain.
What is the difference between a parallel and an anti-parallel B sheet?
In a parallel B sheet all strands run in the same direction, whilst in an anti parallel sheet they run in opposite directions. It is also possible to have mixed sheets.
What are the three functions of a fibrous protein?
Support, shape, protection
Give two properties of a fibrous protein.
They tend to have long strands or sheets and are made from a single repeating secondary structure.
What type of proteins are involved in catalysis and regulation?
Globular
What is a domain? (Think proteins)
A domain is a polypeptide chain which folds into a specific shape and has a functional role.
What is a motif? (Think proteins)
A motif is a folding pattern which contains multiple secondary structures, for example a BaB loop.
Where are hydrophobic R groups normally found when a protein folds?
They are normally buried within the protein to protect them from water.
Between which amino acids do covalent disulphide bonds form and what type of proteins do these tend to be?
They are found between Cys residues. They tend to occur in proteins to be secreted. Particularly in the gut because here strong bonds are needed due to uncontrollable conditions.
What are reasons for protein denaturation and why?
Heat due to increased vibrational energy
pH due to altered ionisation states
Solvents disrupt hydrophobic interactions.
In protein folding, what is a Chaperone?
It holds the protein molecule to prevent misfolding.
Define an amyloidose.
It is a disease that occurs due to the misfolding of proteins. Amyloid fibres form when normally soluble proteins are insoluble.
What is the relationship between H+ and pH?
[H+] = 10^(-pH)
What is the equation for pH which includes pKa?
Henderson-Hasselbalch equation.
pH = pKa + log([base]/[acid])
