Protein Flashcards
what are the roles of the proteins
- Structural – cytoskeleton
- Catalysts – enzymes (anabolic and catabolic)
- Carrier/storage - haemoglobin
- Protective - antibodies
- Signalling – receptors, intracellular signalling
- Channels – transport through membranes
- Transporters – transport through membranes and barriers
- Cell adhesion – extracellular matrix
structure and function are….
linked, they impact each other
what are the level of structures of proteins
- Primary – sequence of amino acids from the N-terminus to the C-terminus
- Secondary – 2d fold
- Tertiary – 3d fold
- Quaternary – interaction of multiple subunits
what is the function of the protein determined by
- The function of the protein is determined by its chemistry on the outside and the shape, this is determined by the amino acid sequence
- Different amino acids have different R groups which have different properties chemically and structurally
what is the amino acid made out of
- Made out of an amino group NH2
- R group – gives the chemical and physical properties - varies between 20 different amino acids
- H on the carbon
- Carboxyl group COOH
what are the different chemical properties of R groups
- Hydrophobic/hydrophilic
- Polar (have an electrical charge) and non polar(don’t have an electrical charge)
- they have overlapping properties
how do we join amino acids together
peptide bonds
describe the peptide bond
- Impacts structural implications – can be planar and H bonding
- Looses water forms CONH bond, looses H from NH2 and looses OH from COOH
what does planar mean
rigid, cant bend around the peptide bond and therefore this restricts the 3D shapes that are available
whats the minimal number of amino acids in a protein
50
what is the typical number of amino acids in a protein
- 50-2500 amino acids make a typical protein but it can be as many as 5000
describe what determines the secondary structure
- This is determined by the interactions between the peptide bonds via hydrogen bonding
what are the two types of secondary structure
alpha helix and beta pleat
describe the alpha helix
- 3.6 residues per 360deg turn, a 0.54nm pitch - this means residues are travelling forward
- Stabilised by hydrogen bonding between the peptide bonds carboxyl group and amino group further down
- R groups point outwards due to the peptide chain
why is proline not found in an alpha helix
- Proline has problems being in an alpha helix, because most R groups go out from the central carbon and doesn’t reconnect, this means that proline cant twist and bend in the same way that other amino acids can, therefore proline is not in an alpha helix but rather at the beginning and end where it breaks the alpha helix
describe the beta sheet
- Hydrogen bond run across to stabilise it
- Beta sheets can be stacked to form a 3D tertiary structure
- Strands can be parallel or anti-parallel
- forms a flat surface sheet with strands of protein alongside
- Stabilised by hydrogen bonds between amide links
what are the two subclasses of beta sheets
parallel and antiparallel
describe parallel
parallel sheet the strands go in the same direction from N-terminus and C- terminus
describe antiparallel
Antiparallel is where the strands go one way and then another
describe disorder
- third type of secondary structure
- This is a concept of key forming in the lock
- Disordered regions of proteins often involve protein interaction and are often rich in polar residues so they are hydrophilic
- Cant form on its own
- Often on the surface of the protein
- Amino acids tend to be hydrophilic
describe the tertiary structure
- Tertiary structure is the 3D fold of the protein which brings the secondary structure into 3D space
- Held together by interactions between the R groups
- Huge variety of different structures possible
- R group is central
- Can be globular or fibrous
- Globular = water solution for example haemoglobin
- Fibrous = insoluble such as collagen and keratin
describe the quaternary structure
- A fold of 3D folded subunits
- Not all proteins have this some stop at tertiary
- Can be homo or hetero
- Homo – subunits are the same
- Hetero – mixture of subunits
- E.g. haemoglobin and collagen
- Large scale quaternary protein complexes are in a viral capsid e.g. SV40 - can have loads of subunits
what does homo mean
subunits are the same
what does hetero mean
mixture of subunits
describe collagen
- Fibrous
- 3 polypeptides
- Hydrogen bonding
- Triple helix with a large number of prolines in a pro-pro-gly motif
- Collagen has to be strong as it forms part of the structural part of the protein
- Staggering of prolines between three chains helps hydrogen bonding between chains, forms a rigid structure
- Further post translational modification or amino acid side chains enable covalent strand cross links which include disulphide between cysteines and lysine cross linking
- vitamin C is important as it is a cofactor of propyl hydroxyls
- modified proline known as hydroxyproline
- 35% glycine amino acid as every 3rd residue is
what are the two types of proteins
globular and fibrous
describe globular proteins
majority of proteins are globular
- Overall globular shape with a mixture of secondary structures
describe fibrous proteins
- Extensive packing of secondary structure
- Dominated by one type of secondary structure
- Forms structural proteins such as collagen and keratin
what are domains
these are discrete regions of 3D structures
how is folding driven
- the hydrophobic effect
- hydrogen and polar bonding
what does spontaneous folding do
minimises the energy
not all proteins can….
spontaneously fold for example the entire protein may need to be present
describe the hydrophobic effect
- wants to reduces the surface of a fat that interacts with water, this drives the folding to happen
- It creates a Hydrophobic centre
what is the exception to the hydrophobic effect
membrane protein
- inside the membrane you want hydrophobic effect works in reverse and it folds in the opposite way
what is nomenclature
the naming of proteins and 3D structures
what would make the protein unfold
- temperature
- pH
- detergent - destroys hydrophobic effect
- electric field
- Putting energy into the system, this changes the bonding and causes the protein to unfold
whats another word for heat shock proteins
chaperones
what do chaperone proteins do
- help proteins refold when they are under stress
- some proteins need them to help them fold normaly
what causes chaperones to increase
- Helper proteins – molecular chaperones which helpd fold many proteins
- Levels of chaperones increase when the cell is subjected to stress such as heat shock, but there present most of the time anyway
how do chaperone proteins help refold
HSP70 - heat shock protein 70
- Some act to protect the folding protein from the cytoplasm – ie a unique environment such as GroEL
- Chaperones often use ATP to provide energy to the folding process
what are the causes of protein folding and diseases
- inherited mutation
- environmental stress
what is the mechanism of protein folding and disease
- Loss of function
- Toxic gain of function
- Dominant negative
what are the diseases associated with a malfunction in protein folding
Neurodegeneration - Alzheimers - Parkinsons Metabolic disorders - Monogenic obesity Cancer - P53
what is post translational modification
- process of adding more things to protect it
what are the types of post translation modification
phosphorylation disulphide bridge cleavage membrane anchors ublinquitination deamindation
describe phosphorylation
- Process of adding phosphate group to the protein this is catalysed by phosphorylation kinase causes ATP to become ADP
- Dephosphorylation phophastase catalyses the removal of a phosphate from a protein
- Allows you to have an on and off swtich, in one state protein is on and in another state protein is off
describe disulphides
- Covalent link between cystine residues, cysteine contains sulfur
- Go from two chains that did not have a covalent link together to chains that do have a covalent link
- Stabilises a 3D structure
- Requires specific environment to form, often found extracellularly
describes cleavage
- Insulin as a long polypeptide
- Cleave it twice to form two separate chains
- Have insulin forms disulphide bridges, cut out a chain and then leaves 2 chains together that give insulin its shape and allows it to carry out its function
describe membrane anchors
- Add lipids to proteins modifies them
describe ubiquitnation
- Small protein added to another protein
- added ubiquitin to lysine.
- Acts in signalling and in degradation (disposes of the cells)
describe deamination
- Unavoidable chemical reaction in physiological conditions – can be reduced by removing reactive species from the cytosol
- Results in structural changes and therefore protein damage therefore we want to degrade it – do this in ubiquitination
what are the types of post translational modification descriptions
Addition of other functional groups - Acetate, phosphate and lipids, Addition of other proteins/peptides - Ubliquitination, SUMOylation, Neddylation Changing the chemical nature of amino acids - Deamination, eliminylation Structural changes - Disulphide, cleavage
What is the bond between two amino acids caused by
A condensation reaction in which water is lost
what is the carbon in the middle of the amino acid called
known as a chiral carbon as it is attached to four different groups (apart from glycine)
- have two different structures which are mirror images of each other but are non superimposable
- two forms are D and L
- we use L in cells
what are the bonds holding the tertiary structure together
- hydrogen bonding
- ionic bonding
- disulphide bridges
- hydrophobic and hydrophilic interactions
globular is ..
soluble because they have hydrophilic R groups surrounding the outer aspect that can interact with water
fibrous is ..
insoluble
- made up of many polypeptide chains such as keratin
name some examples of chaperone proteins
Hsp70
Hip90
what is the primary structure
- Chain of amino acids connected by peptide bonds
- Protein is greater than 50 amino acids joined together, there are 20 different amino acids
- Ribosome come out of the N-terminus
- Leaves from C-terminus
