PHRD5025 Biochem - Lecture 2 Protein Function
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molecule bound reversibly by a protein
structural adaptation that occurs between ligand and protein to make the binding site more complementary to the ligand
# of polypeptide chains Hb contains (& types)
what binds to O2 in Hb?
each polypeptide chain contains 1 heme group that binds
If a ligand specifically binds to one of the 2 states, equilibrium between those states will be shifted in favor of the state with bound ligand with the increase of ligand concentration
Wyman Linkage relationship
cyclic organic ring structure bound to Fe to generate heme
what state of Fe binds to oxygen?
what prevents the conversion of ferrous iron Fe2+) to ferric (Fe3+)?
the 4 nitrogen atoms bound to Fe in heme
2 conformations of Hb
- 1) T state - low O2 affinity
- 2) R state - high O2 affinity
conformational change in Hb R state
subunit pairs slide past each other and rotate, narrowing the pocket between the
2 axial ligands to Fe in heme
- 1) sidechain N of a His residue
- 2) O2 binding site
equation for the fraction of total binding sites occupied in Hb
protein in which the binding of a ligand to one site affects the binding properties of another site in the same protein
Hill coefficient nH>1
ligand binding at one site promotes the ligand binding at another site
Hill coefficient nH=1
binding of one ligand impedes the binding of others
any molecule capable of eliciting an immune response
percentage of blood protein made up of antibodies
5 classes of antibodies
- 1) IgG
- 2) IgA
- 3) IgD
- 4) IgE
- 5) IgM
major class of antibody
antibody found in saliva, tears, and milk
3 fragments of IgG when cleaved by papain
- 1) Fc (constant Ab stem)
- 2) 2 Fab's (antigen-binding fragments
a particular molecular structure within an Ag that binds to an individual antibody or TCR
what is binding specificity of an antibody determined by?
amino acid sequences in the variable domains
what activates the macrophage to engulf a foreign body?
IgG binding to an antigen -> receptors on the macrophage surface recognize and bind the Fc region of IgG
proteins that interact with partially folded or improperly folded polypeptides, facilitating correct folding pathways
what to chaperones bind to on improperly folded proteins?
regions rich in hydrophobic residues
do chaperones actively promote folding of a protein?
no, they just prevent aggregation
what is the difference between chaperones and chaperonins?
chaperonins provide a cavity for the folding of an isolated substrate (ex: GroEL/GroES)
double donut shaped protein, with 7 polypeptide chains per donut (14 total)
during 1 cycle, 2 substrate molecules are folded
when does the conformational change occur in the GroEL/ES system?
GroES binding to one of the GroEL rings
where is the chemical energy for muscle contraction derived from?
percentage of protein mass of muscle actin and myosin make up
motor domain that makes muscle contraction possible
myosin head group (globular domain)
- - 2 heavy chains
- - 4 light chains
myosin heavy chain structure
@ C-term: extended
helices, wrapped around each other in a left-handed coiled coil
@N-term: each chain has a large globular domain containing an ATP hydrolysis site
location of myosin light chains
associated with the globular domains of heavy chains
myosin aggregates in muscle cells
bipolar structure of a thick filament
several hundred myosin molecules associate their fibrous tails, with globular domains projecting from either end
thin filament makeup
F-actin (+ other proteins)
associated globular actin (G-actin) proteins
binds ATP and hydrolyzes it to ADP, which helps in the assembly of filaments
G-actin (globular actin)
binds tightly and specifically to 1 myosin head group
each actin monomer in the thin filament
slide along actin thin filaments during contraction
myosin thick filaments
what causes dissociation of myosin head from actin?
ATP binding to myosin head
conformational change in the myosin head that moves actin and myosin filaments relative to one another
triggers power stroke
Pi release from the myosin head
structure serving as an anchor to which thin filaments are attached
arises from the thick filament
arises from the thin filaments
during contraction, Z disks in neighboring __bands draw closer together
# heme groups in myoglobin
nH=1, since there is only 1 ligand binding site
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