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