Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chemistry 438

 Chem 431/8

Final Exam

 Name

 Fall 1994

 (200 pts)
 

(20) 1. For each of the following reactions show all of the cofactors you would expect and name the enzyme type.



a.
Transaminase
or
Amino Transferase
b.

Carboxylase
 c.

Reductase

(Dehydrogenase)
 d.

Dehydrogenase
 e.

Dehydrogenase Complex

(20) 2. What is the P/O ("P to O ratio") for the complete oxidation of hexanoate {CH3(CH2)4COO-}? Show calculations/reasoning for credit! (Set up a table similar to those we've used for ATP equivalents in glycolysis, etc.)

 Reaction Energy Product Factor Multiplier ATP Equiv.

 O's
FACoA Syn. AMP -2 1 -2 0
Flavin DH FADH2 1.5 2 3 2
NAD+ DH NADH 2.5 2 5  2

3 AcCoA's to Kreb's TCA Cycle
Isocit DH (NADH) 2.5 3 7.5  3

 oxoKG DH (NADH)

2.5

3

7.5

3
GTP 1 3 3  0
FADH2 1.5 3 4.5  3
 

Mal DH (NADH)

2.5

3

7.5

3
Total       36  16

P/O = 36/16 = 2.25

(20) 3. a. Write a detailed mechanism for alanine amino transferase (Transaminase).

Where R- = CH3. The mechanism must now be reversed using a second ketoacid (2-oxoglutarate) to give glutamate as the final amino acid product

b. Draw and label a kinetic mechanism diagram for this reaction and name it using Cleland nomenclature.

Ping Pong Bi Bi mechanism

(20) 4. Consider the metabolism of isoleucine in a mammal in the fasting state. Assume the animal needs to make glucose and does not need to use ilu as a direct source of energy. Assume also that the animal needs to keep serum ammonia concentration at a minimum! (ilu = H3+NCH(CO2-)CH(CH3)CH2CH3).

Draw out a pathway whereby the maximum net number of ilu carbons can be incorporated into glucose. Include names &/or structures for all "branchpoint" compounds connecting pathways etc, and show all sites where oxidation/reduction and phoshorylation/dephosphorylation takes place. Indicate tissues, compartmentation and transport for your pathway (is nitrogen involved?)

Muscle cytosol

Blood

Liver cytosol

(25) 5. a. Diagram the electron transport system starting with NADH and glycerol phosphate. Use circles and labels on your diagram to indicate its arrangement into complexes.

b. With which complexes is the phosphorylation of ADP to ATP associated?

Complexes I, III, & IV

c. The main complex involved in energy capture during electron transport in photophosphorylation is analogous to which complex in oxidative phosphorylation?

Complex III (Cytochrome b, c1 complex)

d. How are electrons moved between these complexes? (What links are there between them? Be specific.)

Coenzyme Q transfers between complexes I or II and III

Cytochrome c transfers between complexes III and IV

e. List three types of electron carriers found in both of the electron transport systems we discussed, and give the number of electrons each may carry in the spaces below.

 carrier

 # of electrons carried
a. Iron sulfur complexes(NHI)

1
b. Cytochromes

1 
c. Quinoid or Flavine

2

f. Name the model used to explain the coupling of electron transport to phosphorylation.

Chemiosmotic hypothesis

g. What are the basic premises of this model?

Energy is captured/stored by pumping protons across the mitochondrial inner membrane to form an electrochemical gradient.

ATP is formed by phosphorylating ADP as protons flow back across the gradient though the ATPase "motor."

(20) 6. Consider the process of fatty acid oxidation in mammals.

a. In which tissues is it most important during starvation?

Liver (to make ketone bodies)

Muscle

In which cellular compartment does it occur? ___________________

Mitochondrial matrix

b. What is(are) the oxidizing agent(s) used in this process?

FAD and NAD+

c. What are the metabolic sources of these oxidizing equivalents? Can they be provided anaerobically? Explain briefly.

Ultimatelyprovided by oxygen via the mitochondrial electron transport system, thus it cannot be provided anerobically.

d. How is a fatty acid "activated" prior to oxidation? How much does this "activation" cost (in ATP units)?

An acyl-CoA is formed from the fatty acid and Coenzyme A.

The acyl-CoA is formed via the use of ATP going to AMP, thus two ATP equivalents are used.

(10) 7. Consider the process of Photosynthesis.

a. What pathways are represented in this cycle?

Gluconeogenesis / Glycolysis

Pentose Phosphate Shunt

b. What is the stoichiometry of the light reactions?

8 hn + 2 H2O + NADP+ + 2 ADP + 2 Pi Æ 2 NADPH + ATP + 2 H+ + O2

(4 photons / NADH)

c. Briefly, what occurs in Photosystem II?

Electrons are abstracted from water (releasing oxygen as O2) and raised to a high energy. They then flow down a series of carriers, including a Complex II-like complex and pump protons across the thylacoid membrane.

(15) 8. a. Show the reactions for the following synthesis:

serine + CO2 + NH2 ->Tetrahydrofolate-> 2 glycine

You may use an abbreviated structurefor the H4Folate molecule.

b. Outline (words or symbols) how serine could be used to provide all of the carbons required to synthesis creatine

Serine + H4folate gives 5,10-methylene H4folate + Glycine

5,10-methylene H4folate is reduced with NADH to give 5-methyl H4folate which then transfers its methyl group to homocysteine to give methionine. Methionine is adenylated with ATP to give phophate, pyrophosphate and S-adenosyl Methionine.

Glycine and arginine are combined to give ornithine and Guanidine acetate.

Guanidine acetate is methylated using S-adenosyl Methionine, giving homocysteine and Creatine

(10) 9. a. Under what conditions will "ketone bodies" be formed in the liver?

Under "fasting" conditions, that is when serum (glucose) is low, or, as in diabetes, glucose is unavailable.

b. What is the biological "purpose" for forming ketone bodies?

To provide an alternative source of carbons to peripheral tissues - especially the CNS - when glucose is unavailable.

c. Explain the statement: "Ketonebodies give the liver overall control of fatty acid metabolism."

Ketone bodies are predominantly in the liver, thus although fatty acids are released by adipose, they cannot be used by many tissues, and in fact may be repackaged and returned by the liver. Or, the liver can use them to make into ketone bodies foruse by the CNS, etc.

(25) 10. Briefly describe or discuss the following:

a. (10) The structure of hemoglobin, or a similar multimeric protein, in terms of the various levels and/or elements of protein structure.

The 4º structure of Hb consists of an a2b2 arrangement with 4 subs of 2 different kinds.

The 3º structure of the subunits are all similar, with a single domain of predominantly a-helical 2º structure, with no particular super secondary structure. The a helixes form a box enclosing a heme group in each protomer.

The a helices and random regions in turn result in the folding of the sequence of aa's or primary structures of the two subunit types.

b. (10) The synthesis of fat from glucose, including the sources of reducing equivalents.

Glucose is first phosphorylated to give G-6-P. The G-6-P is now used via glycolysis to provide carbons (and indirectly half the required reducing equivalents, see below) and half of the reducing equivalents via the Pentose Phosphate Shunt.

Pyruvate from glycolysis is now transported into the matrix of the mitochondria where it is oxidized to acetyl CoA by Pyr DH Complex. The AcCoA is next condensed with oxalacetate (beginning of Pyruvate-Malate cycle) to give citrate. Citrate is now transported to the cytosol via an antiport. In the cytosol citrate is cleaved with the input of energy from one ATP to give Acety CoA for use in FA biosynthesis and oxalacetate for recycling via the Pyruvate-Malate cycle.

Oxalacetate is next reduced to malate by NADH, regenerating NAD+ for glycolysis. The malate is then oxidized to pyruvate by NADP+ giving NADPH for use in FA biosynthesis (thus providing the alf of the reducing equivalents form glycolysis). Pyruvate is now transported into the mitochondrial matrix where carbondioxide is added to give oxalacetate and complete the Pyruvate-Malate cycle.

Acetyl CoA is used in FA biosynthesis along with NADPH reducing equivalents from Pyruvate-Malate cycle (1/2) and Pentose Phosphate Shunt (1/4 from each DH reaction).

c. (5) Substrate/co-factor control of the rate of aerobic metabolism.

In TCA and ETS much of important control is due to availability of cofactors NAD+ and ADP respectively. Since the normal [ ]'s of these substances are low these processes will only operate to the extent NADH and ADP are regenerated and available.

(15) 11

a. In our discussion of nitrogen catabolism three excretory products were discussed and their uses rationalized. What are these three products and what reasons were given for their specific uses by different organisms?

1. NH3 - toxic, so only excreted when large reservoir is available for dilution (i.e. for aqueous beasts and plants) least energy to exrete.

2. Urea - relatively non-toxic, water soluable - used when water is available, but restricted (i.e. mammals).

3. Uric acid - very low solubility - used by organisms in a "physiological desert" (i.e. - terrestrial egg layers such as birds and reptiles).

b. Briefly describe/diagram the pathway used by mammals to excrete nitrogen, beginning with amino acids, such as alanine, in the liver.

Alanine is first transaminated using 2-oxoglutarate to give pyruvate and glutamate. The glutamate is then used to provide both urea nitrogens: half of the gultamate is then deaminated by glutamate DH to give back 2-oxoglutarate and ammonia, while the other half is used to transaminate oxalacetate to give 2-oxoglutarate and aspartate.

The ammonia is next combined with carbondioxide and two ATP's to give two ADP's an inorganic phosphate and Carbamyl phosphate. Carbamyl phosphate is now condensed with the carrier, ornithine, to give citrulline.

The aspartate is now condensed with the citrulline to give argininosuccinate with the loss of two ATP equivalents (ATP to AMP). Argininonsuccinate is then cleaved to give fumerate and arginnine. Finally, the arginnine is cleaved to regnerate ornithine with the release of our product, UREA.

However, the fumerate must be processed through the Kreb's Cycle to regenerate oxalacetate, one of our starting materials, in order to complete the biosynthesis.


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Last modified 14 May 2004