Lecture 6 Flashcards
the function of nearly all proteins depend on their ability to bind to molecules (ligands or substrates) with a
high degree of specificity
region of a protein that associates with a ligand
binding ste
protein-ligand interaction is mediated by
noncovalent bonds
protein-ligand interaction can be measured by
velocity, affinity (binding strength), and specificity (binding preference)
level of affinity and specificity depends on –
molecular complementaries
– identify crucial ligand-binding sites
evolutionary tracing method
most common way two proteins bind with each other
surface-surface
antibodies can directly – or mark it for destruction
inactivate target protein
T/F: antibodies can distinguish between proteins that differ by only one AA
true
foreign substance that elicits production of an antibody
antigen
subunits/polypeptides of an antibody
2 heavy chains and 2 light chains
the chains of an antibody are held together by
disulfide bonds
each polypeptide chain of an antibody can be divided into 2 domains
variable and constant
the – domains interact with the antigen
variable
ligand binding site in antibodies
hypervariable loop
interaction between antibody and epitope of antigen is
complementary
enzymes binds 2 molecules and – them to encourage a reaction to occur between them
precisely orients
binding of substrate to enzyme rearranges electrons in the substrate that –
favor a reaction
enzymes strains the bound substrate molecule, forcing it toward a – to favor a reaction
transition state
enzyme that catalyze a hydrolytic cleavage
hydrolase
break down nucleic acids by hydrolyzing bonds between nucleotides
nucleases
break down proteins by hydrolyzing bonds between AA
proteases
synthesize molecules in anabolic reactions by condensing two smaller molecules together
synthase
join together two molecules in an energy-dependent process
ligase
catalyze rearrangement of bonds within a single molecule
iosmerase
catalyze polymerization reactions such as synthesis of DNA and RNA
polymerases
catalyze the addition of phosphate groups to molecules
kinases
hydrolyze ATP
ATPases
GTPase
hydrolyze GTP
dissociation rate
Koff * [AB]
association rate
Kon * [A][B]
dissociation rate = association rate at
equilibrium
Vmax
all enzymes are used
Km
substrate concentration at 0.5 Vmax
low Km
enzyme binds to substrate very tightly
enzyme’s active site is made up of
catalytic site and binding pocket
trypsin-like serene proteases’ catalytic site
serine, histidine, aspartate, oxyanion hole
trypsin-like serene proteases’ catalytic site - serine
break peptide bond
trypsin-like serene proteases’ catalytic site - histidine
stabilize (accept proton)
trypsin-like serene proteases’ catalytic site - aspartate
orient histidine at right location by H bonding
trypsin-like serene proteases’ catalytic site - oxyanion hole
stabilize intermediates
trypsin-like serene proteases’ catalytic site - the binding site
is general
trypsin-like serine proteases’ catalytic site - has a – binding pocket
side chain specificity
Trypsin (Asp)
Arg and Lys (positive side chains)
Chymotrypsin (Ser)
Phe, Tyr, Trp (large hydrophobic side chains)
Elastase (Val)
Gly and Ala (small side chains)
substrate of lysozyme
6-sugar oligosaccharide
lysozyme breaks uses – to break between the 4th and 5th sugar
glutamate and aspartate
final products of lysozyme are
4-sugar oligosaccharide and a disaccharide
proteins often use – to carry functions that would be difficult using AA alone
small non-protein molecules
change conformation –> change function examples
allosteric walking and ABC transporter
enzymes in a common pathway are often –
physically associated with one another
– hold related enzymes
scaffold
regulation of protein activity by kinase/phosphatase switch is an example of – protein modification
covalent
T/F: kinase can only turn on proteins
false
Which amino acids are used in the kinase/phosphatase switch?
serine, threonine, tyrosine (hydroxyl group)
receptro tyrosine kinase is activated by –
dimerization
once RTK is active, they –
phosphorylate each other
Src-type kinase as –
signal-integrating device
refers to the changes of protein conformation and activity upon binding to a ligand
allosteric regulation
allosteric regulation is an example of – protein modification
noncovalent
T/F: allosteric regulation can be positive or negative
true
active PKA has lost its
catalytic site
in allosteric regulation, the activity of an enzyme is either inhibited to activated by a regulatory molecule that binds to the allosteric site that is – from the active site
distinct
the binding to the allosteric site produces a – of the active site either simulating or inhibiting the enzyme to catalyze a reaction
conformational change
the binding of tryptophan changes the conformation of the –
repressor
allosteric switch of calmodulin is
noncovalent
GTP bound
ON
GDP bound
OFF
GAP (GTPases Activating Protein)
help turn off faster
GEF (Guanine Exchange Factor)
help turn on faster
when the amount of the – is high it inhibits an enzyme that functions early in the reaction pathway
end product
three conformations of the acetylcholine receptor
unoccupied and closed
occupied and open
occupied and closed
most stable form of the acetylcholine receptor
occupied and closed (inactivated)
tryptophan repressor is an examples of – modification
noncovalent
when there’s a lot of tryptophan, it will bind to the – which binds to the DNA and turns it off
tryptophan repressor
enzymatic cleavage of a backbone peptide bond, resulting in the removal of residues from the polypeptide chain
proteolytic cleavage
proteolytic cleavage is a common mechanism for activating enzymes that function in
programmed cell death
proteolysis also generates active peptide hormones such as – from larger precursor polypeptides
insulin
proteolytic cleavage – inactivates or activates proteins
irreversibly
Ubiquitin is a – amino acid polypeptide that marks proteins for degradation
76
ubiquitin can be covalently linked to other proteins via a covalent bonds between an internal – and its C-terminal
lysine on the substrate protein
monoubiquitylation
histone regulation
multiubiquitylation
endocytosis
polyubiquitylation (Lys 48)
proteosomal degradation
polyubiquitylation (Lys 63)
DNA repair
ubiquitin activating enzyme (E1) uses – to attach ubiquitin to itself via a high energy thioester bond
ATP hydrolysis
E1 passes activated ubiquitin to –
E2 ubiquitin-conjugating enzymes
E2 works with E3 (ubiquitin ligases) which has the – for the target protein
binding site
