BIOC 307 EXAM STUDY GUIDE
What are the most abundant amino acids in the liver? What are they a major source of? -
ANSWER Ala and Gln- major source of N in the liver
Ubiquitin is the signal for... - ANSWER protein degradation
How does Ubiquitin bond to other Ubiquitin molecules? - ANSWER 48 Lys attaches to
c-terminus of other molecule
only _____ is sufficient for degradation - ANSWER POLYubiquination
is there a gene for ubitquitin? - ANSWER no
Since there is no gene for ubiquitin, how is it made? - ANSWER many other genes
contain ubiquitin in them; when the peptide is made, the Ub is cleaved to become a part
of the Ub pool
How many steps of ubiquitination and how many enzyme domains do them? - ANSWER 3
and 3
What are the three domains of ubiquitination, their names, and their functions? -
ANSWER E1: ubiquitin-activating enzyme, adenylation and attachment to C-terminus of
Ub
E2: ubiquitin-conjugating enzyme, thioester transfer from E1 to E2
E3: ubiquitin ligase, SUBSTRATE RECOGNITION, specifies substrate
After a protein is ubiquitinated, it is degraded by the... - ANSWER proteasome
What are the domains of the proteasome? - ANSWER two 19S caps and 20S catalytic
core
Functions of the 19S cap - ANSWER recognizes poly-Ub
ATPases that unfold proteins
cleave/release & recycle Ub
Functions of the 20S catalytic core - ANSWER contains actual proteases, 3 types of
subunits that cleave after specific residues
What are the three types of domains in the 20S catalytic core? - ANSWER beta1: cleaves
after acidic residues
beta2: cleaves after basic residues
,beta5: cleaves after hydrophobic residues
under normoxia, HIF-1a is hydroxylated on ______ and is always being... - ANSWER
proline residues; made and destroyed
hydroxyproline on HIF-1a can recruit ____ leading to... - ANSWER hydroxyproline on
HIF-1a can recruit the E3 ubiquitin ligase leading to HIF-1a degredation
under hypoxia, HIF-1a starts to rise in concentration and so... - ANSWER HIF-1a
interacts with HIF-1B which then act as a transcription factor in hypoxia response
protein
what are DUBs? - ANSWER deubiquitinating enzymes
explain how misfolded proteins are a target to degradation - ANSWER misfolding
exposes hydrophobic residues which recruits chaperones, chaperones facilitate
refolding attempts, if a protein is misfolded for too long, the chaperones recruit E3 Ub
ligases for degredation
Dietary protein is enzymatically degraded in the _____. What enzymes facilitate the
degradation? - ANSWER digestive tract
pepsin in the stomach
trypsin in the small intestine
what does transamination do? - ANSWER interconverts amino acids and alpha-keto
acids
what does oxidative deamination do? - ANSWER releases ammonia from glutamate
(toxic) for disposal
hydrolysis of glutamine by the _____ enzyme releases _____ and generates ____. -
ANSWER hydrolysis of glutamine by the glutaminase enzyme releases ammonia and
generates glutamate.
what is the first step of protein degradation? - ANSWER removal of ammonia
what is the universal nitrogen carrier? - ANSWER glutamate
what is the universal nitrogen acceptor? - ANSWER alpha-ketoglutarate
ammonia made in muscles must be transported to the ____ by adding it onto ____ -
ANSWER ammonia made in muscles must be transported to the liver by adding it onto
alanine
what enzyme irreversibly turns glutamate into alpha-ketoglutarate? what are the
substrates/products of this reaction? - ANSWER glutamate+ NAD(P)+ + H2O
--->
, NAD(P)H + NH4
what is the important intermediate of PLP-dependent transamination mechanisms? -
ANSWER schiff's base
What is the source of oxygen when converting an immine to a ketone? - ANSWER water
transferases are... - ANSWER reversible
Explain the ping-pong mechanism overall - ANSWER very reversible
the "ping" step turns an amino acid into an keto-acid
the "pong" step resets PLP by taking the amino group it picked up and placing it on
alpha-ketoglutarate making glutamate
Where does PLP take up the amide during aminotransferase mechanisms? - ANSWER
the amino group replaces the =O on the aldehyde carbon
ammonia is safely transferred from non-liver tissue in the blood as ____. _____ is turned
into this glutamine by the enzyme ______. - ANSWER ammonia is safely transferred from
non-liver tissue in the blood as glutamine. glutamate is turned into this glutamine by the
enzyme glutamine synthytase.
explain the glutamine synthytase reaction - ANSWER turns glutamate into glutamine in
two-steps
uses ATP and free ammonia
produces ADP and Pi
Once in the liver, glutamine is broken down producing ____ to make ____ by the enzyme
_____ - ANSWER Once in the liver, glutamine is broken down producing ammonia to
make urea by the enzyme glutaminase
What are the most abundant amino acids in the liver? What are they a major source of? -
ANSWER Ala and Gln- major source of N in the liver
Ubiquitin is the signal for... - ANSWER protein degradation
How does Ubiquitin bond to other Ubiquitin molecules? - ANSWER 48 Lys attaches to
c-terminus of other molecule
only _____ is sufficient for degradation - ANSWER POLYubiquination
is there a gene for ubitquitin? - ANSWER no
Since there is no gene for ubiquitin, how is it made? - ANSWER many other genes
contain ubiquitin in them; when the peptide is made, the Ub is cleaved to become a part
of the Ub pool
How many steps of ubiquitination and how many enzyme domains do them? - ANSWER 3
and 3
What are the three domains of ubiquitination, their names, and their functions? -
ANSWER E1: ubiquitin-activating enzyme, adenylation and attachment to C-terminus of
Ub
E2: ubiquitin-conjugating enzyme, thioester transfer from E1 to E2
E3: ubiquitin ligase, SUBSTRATE RECOGNITION, specifies substrate
After a protein is ubiquitinated, it is degraded by the... - ANSWER proteasome
What are the domains of the proteasome? - ANSWER two 19S caps and 20S catalytic
core
Functions of the 19S cap - ANSWER recognizes poly-Ub
ATPases that unfold proteins
cleave/release & recycle Ub
Functions of the 20S catalytic core - ANSWER contains actual proteases, 3 types of
subunits that cleave after specific residues
What are the three types of domains in the 20S catalytic core? - ANSWER beta1: cleaves
after acidic residues
beta2: cleaves after basic residues
,beta5: cleaves after hydrophobic residues
under normoxia, HIF-1a is hydroxylated on ______ and is always being... - ANSWER
proline residues; made and destroyed
hydroxyproline on HIF-1a can recruit ____ leading to... - ANSWER hydroxyproline on
HIF-1a can recruit the E3 ubiquitin ligase leading to HIF-1a degredation
under hypoxia, HIF-1a starts to rise in concentration and so... - ANSWER HIF-1a
interacts with HIF-1B which then act as a transcription factor in hypoxia response
protein
what are DUBs? - ANSWER deubiquitinating enzymes
explain how misfolded proteins are a target to degradation - ANSWER misfolding
exposes hydrophobic residues which recruits chaperones, chaperones facilitate
refolding attempts, if a protein is misfolded for too long, the chaperones recruit E3 Ub
ligases for degredation
Dietary protein is enzymatically degraded in the _____. What enzymes facilitate the
degradation? - ANSWER digestive tract
pepsin in the stomach
trypsin in the small intestine
what does transamination do? - ANSWER interconverts amino acids and alpha-keto
acids
what does oxidative deamination do? - ANSWER releases ammonia from glutamate
(toxic) for disposal
hydrolysis of glutamine by the _____ enzyme releases _____ and generates ____. -
ANSWER hydrolysis of glutamine by the glutaminase enzyme releases ammonia and
generates glutamate.
what is the first step of protein degradation? - ANSWER removal of ammonia
what is the universal nitrogen carrier? - ANSWER glutamate
what is the universal nitrogen acceptor? - ANSWER alpha-ketoglutarate
ammonia made in muscles must be transported to the ____ by adding it onto ____ -
ANSWER ammonia made in muscles must be transported to the liver by adding it onto
alanine
what enzyme irreversibly turns glutamate into alpha-ketoglutarate? what are the
substrates/products of this reaction? - ANSWER glutamate+ NAD(P)+ + H2O
--->
, NAD(P)H + NH4
what is the important intermediate of PLP-dependent transamination mechanisms? -
ANSWER schiff's base
What is the source of oxygen when converting an immine to a ketone? - ANSWER water
transferases are... - ANSWER reversible
Explain the ping-pong mechanism overall - ANSWER very reversible
the "ping" step turns an amino acid into an keto-acid
the "pong" step resets PLP by taking the amino group it picked up and placing it on
alpha-ketoglutarate making glutamate
Where does PLP take up the amide during aminotransferase mechanisms? - ANSWER
the amino group replaces the =O on the aldehyde carbon
ammonia is safely transferred from non-liver tissue in the blood as ____. _____ is turned
into this glutamine by the enzyme ______. - ANSWER ammonia is safely transferred from
non-liver tissue in the blood as glutamine. glutamate is turned into this glutamine by the
enzyme glutamine synthytase.
explain the glutamine synthytase reaction - ANSWER turns glutamate into glutamine in
two-steps
uses ATP and free ammonia
produces ADP and Pi
Once in the liver, glutamine is broken down producing ____ to make ____ by the enzyme
_____ - ANSWER Once in the liver, glutamine is broken down producing ammonia to
make urea by the enzyme glutaminase
