biochemistry
Old Biochem Exam 2
Biochemistry 3053 GIFT 2
Possible Questions: BLUE
Possible Answers: RED
From Previous GIFT: Yellow Highlight
Notes: GREEN
1. Which enzyme is considered [REDACTED]?
Part of TCA and ETC?
FADH2 - ubiquinone oxidoreductase
Succinate dehydrogenase
Rate limiting:
Of glycolysis: phosphofructokinase-1 (stronger) or hexokinase
*** hexokinase is important but not rate limiting***
Of TCA: isocitrate dehydrogenase
1. Which enzyme is considered part of TCA and ETC?
A. Malate dehydrogenase
B. Citrate synthase
C. Isocitrate dehydrogenase
D. NADH- ubiquinone oxidoreductase
E. FADH2- ubiquinone oxidoreductase
2. A solution at pH [REDACTED] contains a weak acid, HA. The pKa of the acid is
[REDACTED]. What is the ratio of [A- ]:[HA]?
pH=7 pKa=6.5
pH= pka + log ([A- ]/[HA])
7= 6.5 + log ([A- ]/[HA])
log ([A- ]/[HA])= 0.5
([A- ]/[HA])= 100.5 = 3.16227766017
1
ratio of [A- ]:[HA]= 3.16:1
,3. In mitochondria, what is the expected pH [REDACTED]?
In mitochondria, what is the expected pH of the matrix compared to the intermembrane
space? More basic
Intermembrane space pH is lower than matrix pH = Intermembrane space is more acidic
than the matrix.
4. When Compound C [REDACTED] electrons [REDACTED] Compound D,
[REDACTED]
When Compound C gives electrons to Compound D, then Compound D is the oxidant
and Compound C is the reductant.
Oxidant and reductant
When Compound C removes electrons from Compound D, then Compound C is the
oxidant and Compound D is the reductant
Oxidant and reductant
5. When Compound C [REDACTED] electrons [REDACTED] Compound D,
[REDACTED]
When Compound C gives electrons to Compound D, then Compound D was reduced and
Compound C was oxidized.
Reduced and oxidized
When Compound C removes electrons from Compound D, then Compound C is reduced
and Compound D was oxidized
Reduced and oxidized
6. What provides the energy to the ATP Synthase for the formation of ATP?
Proton Flow *Electrochemical gradient
- ADP + Pi + H+out ⇌ ATP + H2O + H+in
When protons flow back down their concentration gradient (from the intermembrane
space to the matrix)
7. Which of the following describe cristae?
- Cristae do not have pores for movement of proteins
- Their proteins are not found in outer membrane
- Cristae does not seal inner membrane
- Cristae does not anchor f1f0 ATP synthase
- THEY INCREASE SURFACE AREA OF INNER MEMBRANE
, 8. (True / False) The amino acid [REDACTED] at pH 7.4 has [REDACTED] charged
groups.
- Amino acid T at pH 7.4 has two charged groups but net charge of 0. ← True because
Threonine has a polar uncharged side chain
- Amino acid H at pH 7.4 has two charged groups but net charge of 0. ← True because
Histidine’s R group will be deprotonated at a pka of 6.0 (I think)
- Amino acid E at pH 7.4 has two charged groups but net charge of 0. ← False because
Glutamate’s R group will be deprotonated at a pka of approximately 4.25 causing the
amino acid to have an overall charge of -1
-(True / False) The amino acid [aspartic acid or glutamic acid] at pH 7.4 has [a negative
charge on the side chain].
TRUE
(T/F) The amino acid [aspartate] at pH 7.4 has [three] charged groups
T
Congratulations! Due to your success in Dr. Daniel’s Biochemistry class. You have been
selected by NASA to do the biochemical write up on a new organism recovered from a
Martian probe! During your analysis you have discovered a brand new electron transport
chain! The organism appears to use electron transport as its primary source of energy
rather than ATP. This leaves you with a couple of questions to answer: During analysis,
your technician reports a new electron transport chain (always check your technician’s
work! Analyze this carefully!):
Ickygreenone + H+ + 2e- → Ickygreenol [REDACTED] V -0.2 V
Barsool → Barsoom + H+ + 2e- [REDACTED] V 0.03 V
Because the reactions are not originally in the same form we would flip the bottom reaction
to have the oxidized form accepting electrons to become the reduced form so we can
determine which half reaction is the stronger reductant
This would give:
Ickygreenone + H+ + 2e- → Ickygreenol (-0.2 V)
Barsoom + H+ + 2e- → Barsool (-0.03 V)
Both half reactions are now in the same form so we can confirm that the top reaction is the
most negative of the two half reactions and the stronger reductant
Old Biochem Exam 2
Biochemistry 3053 GIFT 2
Possible Questions: BLUE
Possible Answers: RED
From Previous GIFT: Yellow Highlight
Notes: GREEN
1. Which enzyme is considered [REDACTED]?
Part of TCA and ETC?
FADH2 - ubiquinone oxidoreductase
Succinate dehydrogenase
Rate limiting:
Of glycolysis: phosphofructokinase-1 (stronger) or hexokinase
*** hexokinase is important but not rate limiting***
Of TCA: isocitrate dehydrogenase
1. Which enzyme is considered part of TCA and ETC?
A. Malate dehydrogenase
B. Citrate synthase
C. Isocitrate dehydrogenase
D. NADH- ubiquinone oxidoreductase
E. FADH2- ubiquinone oxidoreductase
2. A solution at pH [REDACTED] contains a weak acid, HA. The pKa of the acid is
[REDACTED]. What is the ratio of [A- ]:[HA]?
pH=7 pKa=6.5
pH= pka + log ([A- ]/[HA])
7= 6.5 + log ([A- ]/[HA])
log ([A- ]/[HA])= 0.5
([A- ]/[HA])= 100.5 = 3.16227766017
1
ratio of [A- ]:[HA]= 3.16:1
,3. In mitochondria, what is the expected pH [REDACTED]?
In mitochondria, what is the expected pH of the matrix compared to the intermembrane
space? More basic
Intermembrane space pH is lower than matrix pH = Intermembrane space is more acidic
than the matrix.
4. When Compound C [REDACTED] electrons [REDACTED] Compound D,
[REDACTED]
When Compound C gives electrons to Compound D, then Compound D is the oxidant
and Compound C is the reductant.
Oxidant and reductant
When Compound C removes electrons from Compound D, then Compound C is the
oxidant and Compound D is the reductant
Oxidant and reductant
5. When Compound C [REDACTED] electrons [REDACTED] Compound D,
[REDACTED]
When Compound C gives electrons to Compound D, then Compound D was reduced and
Compound C was oxidized.
Reduced and oxidized
When Compound C removes electrons from Compound D, then Compound C is reduced
and Compound D was oxidized
Reduced and oxidized
6. What provides the energy to the ATP Synthase for the formation of ATP?
Proton Flow *Electrochemical gradient
- ADP + Pi + H+out ⇌ ATP + H2O + H+in
When protons flow back down their concentration gradient (from the intermembrane
space to the matrix)
7. Which of the following describe cristae?
- Cristae do not have pores for movement of proteins
- Their proteins are not found in outer membrane
- Cristae does not seal inner membrane
- Cristae does not anchor f1f0 ATP synthase
- THEY INCREASE SURFACE AREA OF INNER MEMBRANE
, 8. (True / False) The amino acid [REDACTED] at pH 7.4 has [REDACTED] charged
groups.
- Amino acid T at pH 7.4 has two charged groups but net charge of 0. ← True because
Threonine has a polar uncharged side chain
- Amino acid H at pH 7.4 has two charged groups but net charge of 0. ← True because
Histidine’s R group will be deprotonated at a pka of 6.0 (I think)
- Amino acid E at pH 7.4 has two charged groups but net charge of 0. ← False because
Glutamate’s R group will be deprotonated at a pka of approximately 4.25 causing the
amino acid to have an overall charge of -1
-(True / False) The amino acid [aspartic acid or glutamic acid] at pH 7.4 has [a negative
charge on the side chain].
TRUE
(T/F) The amino acid [aspartate] at pH 7.4 has [three] charged groups
T
Congratulations! Due to your success in Dr. Daniel’s Biochemistry class. You have been
selected by NASA to do the biochemical write up on a new organism recovered from a
Martian probe! During your analysis you have discovered a brand new electron transport
chain! The organism appears to use electron transport as its primary source of energy
rather than ATP. This leaves you with a couple of questions to answer: During analysis,
your technician reports a new electron transport chain (always check your technician’s
work! Analyze this carefully!):
Ickygreenone + H+ + 2e- → Ickygreenol [REDACTED] V -0.2 V
Barsool → Barsoom + H+ + 2e- [REDACTED] V 0.03 V
Because the reactions are not originally in the same form we would flip the bottom reaction
to have the oxidized form accepting electrons to become the reduced form so we can
determine which half reaction is the stronger reductant
This would give:
Ickygreenone + H+ + 2e- → Ickygreenol (-0.2 V)
Barsoom + H+ + 2e- → Barsool (-0.03 V)
Both half reactions are now in the same form so we can confirm that the top reaction is the
most negative of the two half reactions and the stronger reductant
