lecture 1 biochemistry (week 2) Flashcards
(33 cards)
what are the structural levels of proteins?
20 L- amino acids –> polypeptide –> a-helix, b-strand, turns, loops –> globular/fibrous monomer –> multisubunit structure
how are proteins synthesised?
translation of mRNA, always from the N-terminus to the C-terminus
what are structural elements in proteins?
hydrogen bonding between coils
hydrogen bonding between strands of the sheet
C=O and NH groups of the peptide bonds = backbone of the protein
what amino acids tend to be in a-helix?
ala, cys, leu, met, glu, gln, his, lys
what amino acids tend to be in b-strands?
val, ile, phe, tyr, trp, thr
what amino acids tend to be in turns?
gly, ser, asp, asn, pro
what does the 1a structure determine?
the 3a structure
val, leu, ile, met, phe - occur in the interior of a protein, away from the aqueous environment
arg, his, lys, asp, glu - are located on the surface of a protein in contact witt the aqueous solvent
ser, thr, asn, gln - are often on the surface but can occur inside if H-bonded to something else
tyr, trp - are usually buried but can occur on the surface too
what are the most hydrophobic amino acids?
isolecucine - 4.5
valine - 4.2
leucine - 3.8
phenylalanine - 2.8
cysteine - 2.5
what are the most hydrophilic amino acids?
arginine - -4.5
lysine - -3.9
asparagine - -3.5
aspartic acid - -3.5
glutamine - -3.5
what are transmembrane proteins usually?
a-helices of about 20 residues
what is bacteriorhodopsin: a 7TM protein
membrane protein in purple sulphur bacteria
grow in salty conditions
when nutrients are scare they use bacteriorhodopsin to harvest light energy to pump ATP by pumping protons to form a proton gradient
what type of structure do most proteins have?
native structure in which they are stable and fold spontaneously
lowest energy conformation
secondary structural elements pack together neatly to give the tertiary structure
what type of bonds contribute to the stabilisation of protein structure?
salt bridges (ion pairs) - strong attraction between opposite charges - small importance
van der waals (H bonds) - weak attraction between dipoles on neutral groups - quite important - lots of groups that have dipoles
hydrophobic - tendency for non polar groups to cluster together away from water - very important as it is unfavourable for DeltaG to disrupt the H bonding of water
disulphide bridges - only covalent - strong bond between cysteine - important for extracellular proteins
describe the anatomy of a protein
core tightly packed (alpha-beta barrel)
polar residues in the catalytic site
polar residues in wireframe on surface
loops and coils on surface
describe protein movement and flexibility
not rigid
core solid but rest is deformable
loops at the edge of protein often have a lot of mobility
why is protein movment and flexibility important?
essential for catalysis
receptor ligand binding and signalling
contraction or elasticity in fibrous proteins
what functions fo specific motifs have?
helix-loop-helix : asp-asp-asp—–thr-glu - calcium binding loop
zinc-finger : zinc binding domain common in DNA-binding proteins
what are domains?
domains are structurally independent units with the characteristics of small globular proteins
100-200 residues in size
independent functions or activities
kinases and dehydrogenases are good examples of this:
lactate dehydrogenase has a lactate-binding domain that gives it specificity, but the dehydrogenase domain that binds NADH/NAD+ is common to many enzymes
what is alcohol dehydrogenase?
a dimer
each subunit has a substrate binding domain and an NAD+ binding domain
what is the 4a structure?
level of structure above tertiary
association of two or more subunits together to give a multimeric protein within its own 3D structure
therefore monomers has no 4a structure
a molecule is a collection of atoms joined by covalent bonds.
a polypeptide chain is a single molecule; so are 2 peptide chains linked by a disulfide bond
what is the oligomer composition and terminology?
homodimers (a2) and heterodimer (a2b2)
tetramer (a2b2)
octamer (a4b4)
homotrimer (a3)
octamer (a2b2y2s2)
how are interactions of subunits driven in 4a structures?
salt bridge interactions
hydrogen bonding
hydrophobic patches
mainly weak covalent bonding, although interactions are weak, they are numerous and sufficient to drive subunit assembly and stability
covalent bonds may occasionally form between subunits, but in this case the subunits cannot dissociate
what are advantages of multimeric proteins?
large and complex or enzymes can be assembled from simpler units
formation of the cytoskeleton (actin and tubulin polymers) or the mitochondrial respiratory complexes
binding sites or catalytic sites can be formed between the subunits, giving greater versality or structure
the properties of one subunit can be affected by interaction with other subunits which gives a mechanism for regulation
describe allosteric proteins and enzymes
roteins whose ligand binding to subunit 1 (or site) is affected by ligand binding to another subunit (or site)
the binding of the ligand to subunit 1 affects its structure, and hence the structure of an adjacent subunit
usually, binding of a ligand to one subunit increases the affinity of the other subunits for the ligand - positive cooperativity
