BIOCHEMISTRY EXAM QUESTIONS AND
THEIR EXPECTED ANSWERS
exergonic/endergonic
energy exits/enters the system, negative/positive dG
exothermic/endothermic
heat exits/enters the system, negative/positive dH
entropy
dS is always positive, disorder of universe tends to
increase
enthalpy
dH = dE + PdV, heat
Gibbs free energy
dG = dH - TdS, negative dG means reaction is
spontaneous and favorable, this is determined by both
Keq and Q
dG' = - RTlnK'eq
dG = dG' + RTlnQ, Q = Keq but not at any given time
ATP -> ADP + P, dG = -12
activation energy
energy required to produce the transition state,
catalyst/enzyme stabilize the transition state and reduce
Ea without changing dG
higher Ea means slower reaction rate
,drawing a reaction coordinate graph
enzymes
physiological catalysts
increase reaction rate so it happens in a biologically
relevant time-frame, not used up in reaction, specific to a
reaction (important for regulation)
interact with substrate at active site, always stereospecific
and can form specific stereoisomers from non-chiral
molecules
can interact with different substrates that have similar
chemical linkages
induced-fit model vs. lock-key model
dimers have two similar proteins connected by
hydrophobic amino acids or by disulfide bonds
heterodimer- two different proteins
homodimer- two identical proteins
common types:
1. kinases takes phosphate group from donor (ATP)
2. phosphatases removes phosphate group
3. phosphorylases adds phosphate group
3. ligases combine two molecules
4. lyases break apart a molecule, form double bond
5. isomerases convert between isomers
, 6. transferases transfer functional groups from one
molecule to another (sometimes includes kinases and
phosphatases)
activating enzymes
zymogen is an inactive enzyme that needs to be cleaved
apoenzyme is an inactive enzyme that needs a cofactor
phosphorylation can activate/deactivate
allosteric interactions can regulate
hydrolyzing enzymes
hydrolysis breaks bonds
lipase- hydrolysis of lipids (triacylglycerol breaks apart into
glycerol and 3 fatty acids)
protease- hydrolysis of proteins (proteins are cleaved to
activate subunits)
endonuclease- hydrolysis of nucleotides in middle of a
strand (restriction enzymes cut at palindromes)
exonuclease- hydrolysis of nucleotides at the ends of a
strand
ribonuclease- hydrolysis of RNA (protected from my 5'-
caps and 3'-poly A tails)
amylase, glycosidase- hydrolysis of carbohydrates
enzyme regulation
1. regulated at allosteric site
2. regulated by modifications like phosphorylation
on vs. off states
negative feedback- product inhibits enzyme
THEIR EXPECTED ANSWERS
exergonic/endergonic
energy exits/enters the system, negative/positive dG
exothermic/endothermic
heat exits/enters the system, negative/positive dH
entropy
dS is always positive, disorder of universe tends to
increase
enthalpy
dH = dE + PdV, heat
Gibbs free energy
dG = dH - TdS, negative dG means reaction is
spontaneous and favorable, this is determined by both
Keq and Q
dG' = - RTlnK'eq
dG = dG' + RTlnQ, Q = Keq but not at any given time
ATP -> ADP + P, dG = -12
activation energy
energy required to produce the transition state,
catalyst/enzyme stabilize the transition state and reduce
Ea without changing dG
higher Ea means slower reaction rate
,drawing a reaction coordinate graph
enzymes
physiological catalysts
increase reaction rate so it happens in a biologically
relevant time-frame, not used up in reaction, specific to a
reaction (important for regulation)
interact with substrate at active site, always stereospecific
and can form specific stereoisomers from non-chiral
molecules
can interact with different substrates that have similar
chemical linkages
induced-fit model vs. lock-key model
dimers have two similar proteins connected by
hydrophobic amino acids or by disulfide bonds
heterodimer- two different proteins
homodimer- two identical proteins
common types:
1. kinases takes phosphate group from donor (ATP)
2. phosphatases removes phosphate group
3. phosphorylases adds phosphate group
3. ligases combine two molecules
4. lyases break apart a molecule, form double bond
5. isomerases convert between isomers
, 6. transferases transfer functional groups from one
molecule to another (sometimes includes kinases and
phosphatases)
activating enzymes
zymogen is an inactive enzyme that needs to be cleaved
apoenzyme is an inactive enzyme that needs a cofactor
phosphorylation can activate/deactivate
allosteric interactions can regulate
hydrolyzing enzymes
hydrolysis breaks bonds
lipase- hydrolysis of lipids (triacylglycerol breaks apart into
glycerol and 3 fatty acids)
protease- hydrolysis of proteins (proteins are cleaved to
activate subunits)
endonuclease- hydrolysis of nucleotides in middle of a
strand (restriction enzymes cut at palindromes)
exonuclease- hydrolysis of nucleotides at the ends of a
strand
ribonuclease- hydrolysis of RNA (protected from my 5'-
caps and 3'-poly A tails)
amylase, glycosidase- hydrolysis of carbohydrates
enzyme regulation
1. regulated at allosteric site
2. regulated by modifications like phosphorylation
on vs. off states
negative feedback- product inhibits enzyme
