L7 - Introduction to Protein Structure and Function Flashcards
(22 cards)
List and describe the four levels of protein structure
- primary
- The amino acid sequence determined by RNA transcript - secondary
- Display Alpha helices and beta strands/sheet - tertiary
- 3D folded protein structure - quaternary
- Association of multiple folded peptide chains into a larger complex
what is the common structure of amino acids
Amino acids consist of an alpha carbon bonded to a carboxyl group (-COOH),
amino group (NH2) and side chain (R-group
what is the common structure of peptide chain
Peptide bond formed by dehydration of two residues to form a peptide backbone of one nitrogen group and two carbon groups
types of physical and chemical properties of amino acid side chains
Physical properties: Size and Shape
Chemical properties: Charged, uncharged, basic, acidic.
how do the physical and chemical properties influence the folding of the peptide chain
the attraction and repulsion of the side chain characteristics to each other form the specialised shapes of proteins as the proteins attempt to pack due to size and shape efficiently (steric hindrance).
what interactions determine or stabilise the secondary and tertiary structure
Folding is driven by attainment of lowest energy state
Folding determined by hydrophobic effect and stabilised by hydrogen bonding interactions
Describe how primary structure relates to secondary and tertiary structure
Primary structure determines the folding of proteins into 2nd and 3rd structures based on the psychical and chemical properties of the AA
Define a protein domain
Are distinct units of a protein that are stably folded independently from the rest of the protein.
Domains often confer a particular function or interaction which contributes to the overall function of the protein.
what is a protein
a macromolecule consisting of a chain of amino acids joined together by a peptide bonds and folded in to 3D structures
TRUTH or FALSE: The 3D structure of a protein determines its function
TRUE
how do we determine structure of protein
x-ray diffraction crystallography, electron density, molecular model, protein crystal
structure model representations of porteins
ball and stick (atoms and bonds)
- active site chemistry
cartoon (secondary structure)
- fold classification
surface (effective shape)
- ligand/substrate binding pockets
what are the 6 colours used to represent these molecules: sulphur, oxygen, hydrogen, nitrogen, carbon, phosphorus
yellow, red, white, blue, green/teal, orange
what’s a supersecondary structure
Specific combinations of secondary structures
- turns and loop are examples
TRUE or FALSE: primary structures have the potential to become any 2nd structure
FALSE: certain amino acids favor the formation of alpha helices or beta sheets e.g. M, A, L, E, K, N - alpha helix
V, I, Y, C - beta sheet
how are alpha helices stabilised
hydrogen bonding between every fourth residue
exists in a dipole
how are beta sheets stabilised
hydrogen bonds
examples of supersecondary structures
beta hairpin
helix-loop-helix
jelly roll
helix hairpin
what are the three types of tertiary structures
globular, fibrous, membranous
what is the free energy landscape model
the journey of a protein from a denatured to native state is driven by lowest free energy, folding will move down this pathways until it achieves a minimal energy state this is the native state
how do chaperone protein assist in protein folding
according to the lowest free energy model chaperone protein ensure that protein dont get caught in local minima
what domains are present on an abl kinase domain and what is their role
SH2 - signal regulation
SH3 - substrate recruitment
Protein-kinase like - catalytic activity
F-actin Binding - subcellular localisation
