Please enable JavaScript.
Coggle requires JavaScript to display documents.
W3 Enzymes, carbon hydrates and Glycobiology, polysaccharides, 下載 (4),…
W3 Enzymes
7 steps of Chrymotrypsin Mechanism
water comes in
incoming water molecule deprotonated by base, second intermediate ,oxyanion hole
water attacks
short lived intermediate to acyl-enzyme intermediate
substrate Cleavage
collapse of tetrahedral intermediate , reform double bond C and amino group and break peptide bond .
break-off from enzyme
enzyme-product 2 complex
nucleophilic attack
Ser and His both conduct and form a tetrahedral acyl-enzyme
substrate binding
substrate binds, side chain adjacent to peptide bond
product dissociates
turn back to chymotrypsin and go on and on
regulate enzyme
covalent modification
pphosphorylation
irreversible
trypsin chymotrypsin
blood clotting
noncovalent modification(allosteric)
small chemicals that can be positive or negative
reversible
Catalysis
decrease activation barriers lower the energy of transition state
uncatalyzed uni molecular reactions
catalysis reactions
covalent
covalent bond between enzyme and substrate
metal ion
oxidation reactions
acid base
proton transfer to and rom H20
uncatalyzed bimolecular
Linus Pauling:enzymes bind transition states best
Imaginary Stickcase
酵素完全貼合
只影響速率
increase k
DO NOT effect K,free energy
Chymotrypsin
cleave the peptide bond adjacent to aromatic aa
substrate
proteases that cuts peptides at specific locations
peptidoglycan and lysozyme
peptidoglycan: bacterial cell walls
lysozyme:antibacterial enzyme
2 successive models of the cleavage
Glu interact
Glu and Asp both interact
Glu first act acid Asp act as covalent catalyst
Glu then act as base
Equations
Michaelis-Menten equation
enzyme efficiency: kcat/Km
kinetic mechanism
two substrate reactions
sequential mechanism
ping pong mechanism
constraints and assumptions
total concentration is constant
steady state assumption
enzyme inhibition
uncompetitive inhibition
decrease in Vmax Km
lines parallel
no change in Km/Vmax
親和力變大
mixed inhibition
lines intersect left from y-axis
noncompetitive inhibitors:no change in Km
competitive inhibition
increase Km
interact at y axis
no change in Vmax
親和力變低
Enzyme mechanism
Substrate Selectivity
substrate complex drives selectivity
carbon hydrates and Glycobiology
Carbonhydrates
common carbonhydrates
ribose
glucose
galatose
glucose epimer
mannose
glucose epimer
fructose
ketose of glucose
aldehyde親電 alcohol 親核=>hemiacetal
stereoisomers
enantiomers對掌
L and D isomers are enantiomers and have the same water solubility
epimers
epimers are diastereomers (非鏡像異構）have different physical properties(water solubility )
ketone親電 alcohol親核=>hemiketal
functional group
aldose 醛糖
ketose酮糖
cyclization of monosaccharides
alchohol attacks carbonyl carbon allowing formation of a hemiacetal
linear C forms a ring
pyranoses
furanoses
former carbonyl become new chiral anomeric carbon
trans
cis
conformational formulas
chair
boat
important hexose derivatives
deoxy sugar
acidic sugar
amino sugar
functions
cell wall and exoskeleton
cell cell signal
energy source
reducing sugar
reduce Ag+ to Ag
colorimetric
測吸光值
reduce Cu+2 to Cu+
electrochemical
nonreducing disaccharides
two acetal groups and no hemiacetal
no reducing sugar
joined via glycosidic bond
glycosidic bond
stable and less reactive
2 glucose => matose
2 sugar molecules joined via a glycosidic bond
glycosaminoglycans
negatived charged : uronic acids and sulfate essters
extended hydrated molecule
one monomer is either N-acetyl=glucosamine or N-acetyl-galactosamine
extracellular matrix
repeating of disaccharides
heparin
heparan sulfate is heparin-like polysaccharide but attached to protein
prevent blood clotting
linear 3-40kDa
regulates development and formation of blood vessels
decrease virus and bacteria virulence
glycoprotein
viral proteins evade immune system
half of mammal proteins
a protein with small oligosaccharsides attached
glycolipids
determine blood group in vertebrates
gramnegative lipopolysaccharides cover the peptidoglycan layer
cell membrane
proteoglycans
syndecans
glypicans
sulfated glycosaminoglycans attached to a large shaped protein
interact with a variety of receptors from neighboring cells and regulate cell growth
aggrecan
aggregates
low friction material
articular cartilage
hold water
ECM
barrier in tissues
components: proteoglycan aggregates, collagen fibers, elastin
material outside the cell
barrier for tumor cells
cell growth ,mobility, apoptosis ,wound healing
syndecans and intergins
polysaccharides
category
heteropolysaccharides
agar
composed of agarose and agaropectin
agar solutions form gels for growing bacteria
agarose solutions form gels used for separate DNA
homopolysaccharides
glycogen
branch points
store polysaccharide in animal
glucose monomers
insoluable
(one reducing end and many no reducing end)
starch
mixture of amylose (one redicung end)and amylopectin (one reducing end and many no reducing end)
main storage in plants
reducing ends and branch points
insoluable
cellulose
tough water insoluble hard to substrate
most abundant polysaccharides
hydrogen bonds
linear glucose beta 1-4 polysaccharides
ruminants and termites symbiotically
fungi bacteria and protozoa secrete cellulase
chitin
in mushrooms cell walls and insects' exoskeleton
hard insoluble but flexible
linear of N-acetylglucosamine b1-4chain
no dsfined molecule weight
