Biochemistry Assignment 1

BIOCHEMISTRY ASSIGNMENT

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 Biochemistry Assignment 2

Question 1: Bioenergetics and Oxidative Phosphorylation

The reaction to convert Adenosine triphosphate (ATP) to adenosine diphosphate (ADP) and
inorganic phosphate (Pi) is exergonic.
Table 1. Concentrations (μM) of ATP, ADP, Pi, and phosphocreatine (PCr) in rat
myocytes.

Cell type ATP ADP Pi PCr

Rat myocyte 8045 945 7881 27900

(a)
[ ADP ] [P i]
∆ G P=∆ G '0+ RT ln
[ ATP]

∆ G P=∆ G'0+ RT ln ( 9458045

×7881
)
Under standard conditions has ΔG° = ‐31 kJ/mole.

( )
−4 −3
9.45 × 10 ×7.881 ×10
¿−31.0 kJ /mol+( 8.314 kJ /mol ∙ K )(298 K) ln −3
8.045× 10
−17.33 kJ /mol

(b)
As a result, a reaction's standard free-energy change (G°) establishes its chemical equilibrium
and determines the direction of the reaction under a set of conditions. The standard free-
energy change for biological processes is commonly represented as ΔG°′, which is the
standard free-energy change of a reaction in an aqueous solution at pH= 7, approximating the
conditions inside a cell. The quantity of free energy generated from one mole of ATP
hydrolyzed to ADP in non-proliferating cells is known as phosphorylation potential (G).
Phosphorylation thus describes the extent of the conservation of the capacity to do useful
work.
(c)
Under anaerobic conditions, creatine phosphate or otherwise phosphocreatine may quickly
contribute a phosphate group to ADP creating ATP and creatine. In skeletal muscle, heart,
and the brain, phosphocreatine functions as a highly mobilizable reservoir of high-energy
phosphates for recycling adenosine triphosphate, the energy or fuel of a cell. The high
concentration or levels of phosphocreatine in myocyte allows it to supply ATP continuously
 Biochemistry Assignment 3

and for a longer period (Champe et al., 2008).

(d)
The ability of a chemical species to receive electrons and hence be reduced is measured by
reduction potential also known as oxidation/reduction potential, redox potential, or Eh. Every
chemical species has its inherent capacity for reduction. The more positive the redox
potential, the more the species tend to undergo reduction or the higher the affinity of the
chemical species to gain or receive electrons. The loss of electrons in oxidation is called
oxidation, whereas the gain of electrons is called reduction. Redox reactions take place
simultaneously (Champe et al., 2008). The reducing agent is oxidized while the oxidizing
agent is reduced as electrons move from the reducing agent to the oxidizing agent.  The two
half-reactions of a redox reaction are physically separated to form an electrochemical cell.
Consider the general redox reaction
n+ ¿¿

Anox+¿+B red ⇌ Ared +Box ¿

The free energy of this reaction is given by the equation:

0
∆ G=∆ G + RT ln ⁡¿
According to electrostatics, the work required to transfer n moles of electrons through an
electric potential of ∆ ξ is w el=nF Δ ξ . Using the Nernst equation, ∆ ξ describes
the electromotive force while the quantity Δ ξ0 is the redox potential in the standard state and
is called the standard redox potential. Therefore
0' RT
∆ ξ=∆ ξ + ln ⁡¿
nF
F=Faradays constant , the electrical charge of 1 mole of electron=96,494 J /Vmol .
For example, consider the following redox reaction.
+¿¿

Acetaldehyde+ NADH + H +¿⟶ ethanol +NAD ¿

The half cell reactions

'
0

Acetaldehyde+2 H +¿⟶ ethanol ξ =−0.197 V ¿

'
0
+ ¿+2e⟶ NADH+ H+ ¿ ξ =−0.320 V ¿
¿
+¿+2 H ¿
NAD
'

ξ 0total=−0.197−(−0.320 )=0.123 V
n=2; F=96.5 kJ /V . mol
'

∆ G0 =−nF ∆ ξ 0 =2 ( 96.5 × 0.123 )=−23.7 kJ /mol

 Biochemistry Assignment 4

This is the free energy change when acetaldehyde, ethanol, NADH and NAD+ are 1 molar
and the pH is 7.0. The free energy change be if [Acetaldehyde]=1M, [NADH] = 1M,
[ethanol] = 0.1 M and [NAD+] = 0.1 M

∆ ξ=0.123V − ( 8.3145 ×10−3 × 298

2 × 96.5 )
ln
[ 0.1 M ] [0.1 M ]
[ 1 M ] [1 M ]
∆ ξ=0.123V −( 0.0128 ) −4.6=0.182V
∆ G=−nF ∆ ξ=−2 ( 96.5 ) ( 0.182 )=−35.1 kJ /mol

Question 2: Carbohydrate Metabolism

a)
A fruitless cycle or substrate cycle happens when two metabolic processes run in opposing
directions at the same time and have no overall impact other than dissipating heat energy. A
futile cycle is a system that oscillates between two states and is extremely sensitive to slight
changes in the activity of each of the enzymes involved and is significant in regulating
metabolic processes (Dashty, 2013, 1339). The cycle does produce heat, and it may be
employed to maintain thermal homeostasis in the brown adipose tissue of mammals or to
spontaneously produce heat in hibernating animals.
(b)
Glycogen synthase (UDP-glucose-glycogen glucosyltransferase) is an
important enzyme in glycogenesis, which entails the process of converting glucose to
glycogen.  Glycogen synthase regulation is a crucial step in controlling glycogen biosynthesis
and glucose storage. Protein kinase A (PKA), glycogen synthase kinase 3 (GSK-3), casein
kinase 2, and AMPK are all direct regulators of the enzyme (CK2). Each of these protein
kinases causes glycogen synthase inactivation and activation through phosphorylation and
dephosphorylation (Dashty, 2013). Glycogen synthase is inhibited by serine/threonine
kinases such as protein kinase A (PKA), casein kinase-1, and glycogen synthase kinase-3
phosphorylating several serine residues (GSK-3). both dephosphorylated and active GSK-3
phosphorylates inactivates glycogen synthase under fasting conditions, inhibiting hepatic
glycogen production. Increased insulin signalling in the cell stimulates Akt, which in turn
phosphorylates and inactivates GSK-3, resulting in activating glycogen synthase activity
(Dashty, 2013, 1339). Furthermore, increasing glucose 6-phosphate concentrations
allosterically activate this enzyme, enhancing its catalytic activity under feeding conditions.
 Biochemistry Assignment 5

(c)
The deficiency of glucose-6-phosphate dehydrogenase is a genetic condition that affects red
blood cells, which transport oxygen from the lungs to other body organs.  According to
Dashty (2013, 1339), a deficiency in glucose-6-phosphate dehydrogenase enzyme causes red
blood cells to break down early in affected people. The destruction of red blood cells is called
hemolysis. Hemolytic anaemia is the most prevalent medical condition associated with a lack
of glucose-6-phosphate dehydrogenase and occurs when red cells break down faster than the
body can replenish them. Paleness, jaundice (yellowing of the skin and whites of the eyes),
weariness, dark urine, shortness of breath, and a high heart rate are some of the symptoms of
hemolytic anemia. In people having a deficiency of glucose-6-phosphate dehydrogenase, the
condition is triggered by viral or bacterial infections, or certain medications such as some
antibiotics and medications used to treat malaria).
(d)
The catalytic components of the mammalian pyruvate dehydrogenase unit are pyruvate
dehydrogenase (E1), dihydrolipoyl transacetylase (E2), and dihydrolipoyl dehydrogenase
(E3). The pyruvate dehydrogenase complex is formed around an oligomeric E2 core, to
which numerous copies of El and E3 are noncovalently bonded. Higher eukaryotic PDCs
feature a supplementary structural component, dihydrolipoamide dehydrogenase-binding
protein (E3BP), as well as major regulatory enzymes, pyruvate dehydrogenase phosphatase
and pyruvate dehydrogenase kinase, for a total of 11 proteins in PDCh (Dashty, 2013). The
molecular weights of the pyruvate dehydrogenase complexes isolated from bovine kidney
and heart mitochondria are roughly 7 and 8.5 million, respectively.

Figure 1: The Five Reactions Catalyzed by the PDC

 Biochemistry Assignment 6

The oxidative decarboxylation of pyruvate is catalyzed by these three catalytic components,

which produce acetyl-CoA, CO2, and NADH (H+). The E1 is a thiamin diphosphate (ThDP)-
dependent enzyme that catalyzes two steps: First is the decarboxylation of pyruvate to CO2
with the creation of the C2α-hydroxyethylidene-ThDP (enamine) intermediate. Second is
the reductive acetylation of the lipoyl groups covalently bound to the E2. The E2 catalyzes
the formation of acetyl-CoA by transferring an acetyl group to CoA. E3 is responsible for
transferring electrons from the dihydrolipoyl moieties of E2 to FAD and then on to NAD+.
The mammalian complex also contains minute quantities of two regulatory enzymes, a kinase
and a phosphatase, which phosphorylate and dephosphorylate El, respectively, to adjust its
activity.
PDC acts as a regulator in the metabolism of pyruvate in mammals, ensuring glucose
homeostasis in both feeding and fasting states. Under various metabolic settings, the flow via
PDC is closely controlled in tissues (Dashty, 2013, 1339). This is done by using specific
kinases and phosphatases to covalently modify the rate-limiting aspect of the PDC.
Additionally, PDC has also been linked to degenerative neurological disorders, type 2
diabetes, obesity, and a variety of other illnesses.

Question 3: Amino Acid Metabolism

(a)
Carbamoyl-phosphate synthetase, which is found in the mitochondrial matrix, converts one
nitrogen derived from ammonia into carbamoyl phosphate. The second nitrogen comes from
aspartate, which is converted to argininosuccinate by the cytoplasmic enzyme
argininosuccinate synthetase.
(b)
Aminotransferases catalyzes the transamination reaction of amino acid with an α-keto acid,
moving the alpha-amino group to the alpha-ketoglutarate to obtain glutamate. The
ammonium ion is formed when glutamate is oxidatively deaminated. The reversible
interconversion of glutamate to α-ketoglutarate and ammonia is catalyzed by glutamate
dehydrogenase (GDH).
(c)
The urea cycle is a metabolic mechanism that transforms highly hazardous ammonia into less
toxic urea for elimination from the body. The urea cycle is intrinsically associated with the
citric acid cycle, since one of its nitrogens is obtained by transamination of oxaloacetate to
generate asparate, whilst fumarate is returned to the citric acid cycle. In the cycle, fumarate is
 Biochemistry Assignment 7

generated, which is then utilized to make NADH molecules from the TCA cycle (Wu, 2021).
Therefore, to create energy, NADH is supplied to the oxidative phosphate pathway.
(d)
The fundamental purpose of the liver is to convert harmful and toxic compounds to harmless
in the body. These compounds can either be produced by the body such as ammonia or taken
in as medications. Notably, hepatic encephalopathy is a nervous system disorder caused by
severe liver damage. When the liver is affected, these toxic substances can build up and enter
various systems such as the blood circulatory system and the nervous system (Wu, 2021).
High blood ammonia levels can also cause major health concerns, such as brain damage,
coma, and even death.  
(e)
Transamination is a chemical process in which an amino group is transferred from an amino
acid to a ketoacid, resulting in the formation of new amino acids. Transferring an amino
group to the α-keto acids pyruvate, oxaloacetate, and a-ketoglutarate, respectively, produces
alanine, aspartate, and glutamate, since their respective alpha-keto acids are generated during
the metabolism of fuels (Wu, 2021). Lysine, threonine, and proline, are the three amino acids
that do not necessarily undergo transamination but instead employ their respective
dehydrogenases, despite being a significant degradative amino acid mechanism.

(f)
Urea production is increased when protein is consumed, whereas it is decreased when
carbohydrates are consumed. However, glucose inhibits urea production through a hepatic
mechanism that is unrelated to the drop-in blood amino acid content. The effects of
increasing dietary protein consumption as well as the distinct effects of glucose, glucagon,
and insulin on functional hepatic nitrogen clearance in normal people and patients with
cirrhosis of the liver give further insights.  Increased dietary protein consumption enhances
hepatic nitrogen clearance in both healthy persons and patients with cirrhosis (Bender, 2012).
Protein consumption, in addition to the substrate impact, boosts urea production through a
liver effect, most likely due to enzyme formation.
The effect might be significant for maintaining blood amino acid concentrations on a high-
protein diet, and it could help explain why individuals with cirrhosis can tolerate protein
hyperalimentation without experiencing hepatic encephalopathy. Hepatic nitrogen clearance
is reduced by glucose in response to hyperglycemia, and this is done by the combined effects
of a direct hormone-independent effect of glucose and indirect inhibition of glucagon.
 Biochemistry Assignment 8

Although insulin does not directly affect hepatic nitrogen clearance, its decreasing effects on
blood amino acid concentrations make it a key regulator of urea production (Wu, 2021).

Question 4: Lipid Metabolism

(a)
The primary cause of stroke and heart attack is atherosclerosis. Cholesterol as a course
of atherosclerosis arose from early discoveries that cholesterol is a fundamental component of
arterial plaques. High levels of low-density lipoprotein (LDL) cholesterol and apolipoprotein
B (apoB) 100, the major structural protein of LDL, have been linked to an increased risk of
atherosclerotic cardiovascular events. All apolipoprotein-B (apoB)-containing lipoproteins
such as LDL, VLDL, smaller triglyceride-rich lipoproteins, and their residual particles are
small and can pass through the endothelial membrane and into the intimal layer of the arterial
wall. Lipid-laden foam cells are formed when accumulated lipoproteins are absorbed by
vascular smooth muscle cells and macrophages (Wakil., 2012). The process is aided by non-
oxidative alteration, glycooxidation or glycosylation of the LDL particle. Moreover, oxidised
LDL stimulate atherosclerosis through endothelial disruption due to impaired discharge of
nitric oxide and enhanced endothelial generation of oxygen free radicals, thromboxane
discharge and higher platelet aggregation, and elevated apoptosis of myocytes and endothelial
cells. 
On the other hand, High-density lipoprotein (HDL) is involved in reverse cholesterol
transport (RCT), which involves removing surplus cholesterol from peripheral vessels and
transporting it back to the liver for elimination. Therefore, atherogenesis is inhibited,
prevented, or disrupted by HDL through various processes. These include acting as an
antioxidant, anti-inflammatory of endothelial/vasodilatory, cytoprotective and antithrombotic
(Goldberg et al., 2012, 805). More precisely, HDL may shield LDL in vivo from oxidative
damage caused by free radicals in the artery intima, resulting in a reduction in the production
of proinflammatory oxidized lipids such as lipid hydroperoxides and short-chain oxidized
phospholipids.
(b)
The process of fatty acid synthesis begins with the transport of acetyl coenzyme A into the
cytoplasm of the cell. An acyl transport protein will also be required for the procedure and
this procedure makes use of NADPH. The rate of fatty acid synthesis is determined by the
amount of malonyl-CoA, whereas the rate of fatty acid oxidation is determined by the activity
of carnitine acyltransferase. Since carnitine acyltransferase is inhibited by malonyl CoA, a
 Biochemistry Assignment 9

high rate of fatty acid synthesis leads to a reduced degree of fatty acid oxidation, and vice
versa.

Figure 2: Mechanism for the reciprocal regulation of fatty acid biosynthesis

In catabolism, fatty acids are oxidized to provide energy, mostly in the form of adenosine
triphosphate, through beta-oxidation and the citric acid cycle (ATP) (Goldberg et al., 2012,
805. Fatty acyl-CoA, like palmitoyl CoA, is created during the production of fatty acids. The
presence of an oversupply of fatty acyl-CoA in the cytoplasm allows this molecule to attach
to an enzyme's allosteric site. This enzyme is identified as the acyl CoA carboxylase enzyme.
The synthesis will come to a halt as a result of the binding and the molecule degrades when
the cell demands more energy. Malonyl CoA is the compound that acts as a substrate for the
production of fatty acids. This molecule will occupy the allosteric location of the carnitine
palmitoyl-transferase enzyme and the binding prevents the fatty acids from being transported
to the mitochondria for breakdown (Goldberg et al., 2012, 805. As a result, fatty acyl-CoA
and malonyl CoA govern the fatty acid synthesis and breakdown processes.
(c)
Linoleic acid, like stearic acid, contains 18 carbons, but it has 2 double bonds in its structure.
As a result, two fewer FADH2 is created, leaving 9 acetyl-CoA, 6 FADH2, and 8 NADH as
the end products. The ATP yield can then be calculated as shown below;
Activation energy −2 ATP
Oxidation of acetyl-CoA 9 ×10=90 ATP
Oxidation of FADH2 6 x 1.5=9 ATP
Oxidation of NADH 8 ×2.5=20 ATP
 Biochemistry Assignment 10

Net ATP gain= (−2+90+ 9+20 ¿=117 ATP

 Biochemistry Assignment 11

References
Bender, D.A., 2012. Amino acid metabolism. John Wiley & Sons.
Champe, P.C., Harvey, R.A. and Ferrier, D.R., 2008. Bioenergetics and oxidative
phosphorylation. Lippincott's illustrated reviews: Biochemistry.
Dashty, M., 2013. A quick look at biochemistry: carbohydrate metabolism. Clinical
biochemistry, 46(15), pp.1339-1352.
Goldberg, I.J., Trent, C.M. and Schulze, P.C., 2012. Lipid metabolism and toxicity in the
heart. Cell metabolism, 15(6), pp.805-812.
Wakil, S. ed., 2012. Lipid metabolism. Elsevier.
Wu, G., 2021. Amino acids: biochemistry and nutrition. CRC Press.