UNIVERSITY OF SOUTH AFRICA (UNISA)
Department of Life and Consumer Sciences
⋄
BMI2601 ASSIGNMENT 02
Clinical Biochemistry II – Semester 1, 2026
⋄
Module Code: BMI2601
Module Name: Clinical Biochemistry II
Student Name: [Your Full Name]
Student Number: [Your Student Number]
Assignment No.: 02
Due Date: 21 April 2026
Semester: Semester 1, 2026
Unique Number: 258158
Submitted in partial fulfilment of the requirements for BMI2601
at the University of South Africa.
,UNISA | BMI2601 Clinical Biochemistry II – Assignment 02
Contents
1 Question 1: Water Chemistry, pH, and Buffer Systems 3
1.1 1.1 Hydrogen Bonding in Water: High Boiling Point, Cohesion, and Biological Roles 3
1.2 1.2 pH and Enzyme Activity; Strong Versus Weak Bases . . . . . . . . . . . . . . 4
1.2.1 pH and Enzyme Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2.2 Strong Versus Weak Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 1.3 Physiological Buffer Systems: Function, Mechanism, and Optimal Conditions 5
1.3.1 Definition and Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.2 Mechanism of Buffer Action . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3.3 Conditions for Optimal Buffering . . . . . . . . . . . . . . . . . . . . . . . . 7
2 Question 2: Amino Acids, Proteins, and Purification 8
2.1 2.1 How Amino Acid Sequence Determines Protein Three-Dimensional Confor-
mation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2 2.2 Full Structure of the Tripeptide Gly-Leu-His at Physiological pH . . . . . . . 8
2.3 2.3 Three Posttranslational Modifications Involved in Regulating Protein Func-
tion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.4 2.4 Four Chromatographic Techniques for Protein Purification and Analysis . . 11
3 Question 3: Electrophoresis, Transcription, and Enzyme Inhibition 13
3.1 3.1 Gel Electrophoresis Methods for Characterising a Novel Transcription Factor 13
3.2 3.2 Five Differences Between Transcription in Prokaryotic and Eukaryotic Cells 14
3.3 3.3 Lock-and-Key and Induced Fit Models in the Design of Enzyme Inhibitors . . 15
4 Question 4: Sphingolipids and Mitochondrial Dysfunction 18
4.1 4.1 General Structure and Biological Role of Sphingolipids . . . . . . . . . . . . . 18
Page 1 of 22
,UNISA | BMI2601 Clinical Biochemistry II – Assignment 02
4.2 4.2 Mitochondrial Dysfunction, Elevated Lactate, and Acidosis . . . . . . . . . . 19
4.2.1 Background: The TCA Cycle and Oxidative Phosphorylation . . . . . . . . 19
4.2.2 How TCA Cycle Inhibition Leads to Elevated Lactate . . . . . . . . . . . . 19
4.2.3 Clinical Reasoning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Reference List 22
Page 2 of 22
, UNISA | BMI2601 Clinical Biochemistry II – Assignment 02
Question 1: Water Chemistry, pH, and Buffer Systems
1.1 Hydrogen Bonding in Water: High Boiling Point, Cohesion, and Biological Roles
Water is the fundamental solvent of all living systems, and its remarkable physical and bio-
logical properties arise directly from its capacity to form hydrogen bonds (Berg et al., 2019;
Lehninger et al., 2017). Each water molecule consists of one oxygen atom covalently bonded
to two hydrogen atoms. Because oxygen is strongly electronegative, it draws shared elec-
trons toward itself, creating a partial negative charge (δ − ) on the oxygen and partial posi-
tive charges (δ + ) on each hydrogen. This polarity allows neighbouring water molecules to
form hydrogen bonds between the oxygen of one molecule and a hydrogen of an adjacent
molecule, with each water molecule capable of forming up to four such bonds simultaneously
(Alberts et al., 2019).
High boiling point. Hydrogen bonds, though individually weak (approximately 20 kJ/mol), are
collectively extremely strong in liquid water because there are so many of them. To convert
water from a liquid to a gas, a large amount of energy is required to break this extensive net-
work of hydrogen bonds. This is why water has a boiling point of 100°C, far higher than would
be predicted from its molecular weight alone. Comparable molecules of similar size but lack-
ing hydrogen bonds (such as hydrogen sulfide, H2 S) boil at much lower temperatures. For bi-
ological systems, this means that water remains liquid across the temperature range in which
most biochemical reactions occur, which is essential for life on Earth (Berg et al., 2019).
Cohesion. Cohesion refers to the tendency of water molecules to cling to each other because
of hydrogen bonding. In liquid water, individual hydrogen bonds break and reform extremely
rapidly, but the collective network is always maintained. Cohesion is responsible for phenom-
ena such as surface tension, the ability of water to form droplets, and the capillary action that
draws water upward through plant xylem against gravity. In human physiology, cohesion con-
tributes to the integrity of fluid compartments and the behaviour of biofluids in narrow ves-
sels (Lehninger et al., 2017).
Biological roles. Hydrogen bonding in water has several direct consequences for biology. Wa-
ter acts as a universal solvent: it readily dissolves ionic compounds and other polar molecules
by forming hydration shells around them, stabilising them in solution. It participates directly
in biochemical reactions as a reactant in hydrolysis. It stabilises the secondary and tertiary
structures of proteins through the hydrophobic effect, which itself arises from the tendency
Page 3 of 22
Department of Life and Consumer Sciences
⋄
BMI2601 ASSIGNMENT 02
Clinical Biochemistry II – Semester 1, 2026
⋄
Module Code: BMI2601
Module Name: Clinical Biochemistry II
Student Name: [Your Full Name]
Student Number: [Your Student Number]
Assignment No.: 02
Due Date: 21 April 2026
Semester: Semester 1, 2026
Unique Number: 258158
Submitted in partial fulfilment of the requirements for BMI2601
at the University of South Africa.
,UNISA | BMI2601 Clinical Biochemistry II – Assignment 02
Contents
1 Question 1: Water Chemistry, pH, and Buffer Systems 3
1.1 1.1 Hydrogen Bonding in Water: High Boiling Point, Cohesion, and Biological Roles 3
1.2 1.2 pH and Enzyme Activity; Strong Versus Weak Bases . . . . . . . . . . . . . . 4
1.2.1 pH and Enzyme Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2.2 Strong Versus Weak Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 1.3 Physiological Buffer Systems: Function, Mechanism, and Optimal Conditions 5
1.3.1 Definition and Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.2 Mechanism of Buffer Action . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3.3 Conditions for Optimal Buffering . . . . . . . . . . . . . . . . . . . . . . . . 7
2 Question 2: Amino Acids, Proteins, and Purification 8
2.1 2.1 How Amino Acid Sequence Determines Protein Three-Dimensional Confor-
mation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2 2.2 Full Structure of the Tripeptide Gly-Leu-His at Physiological pH . . . . . . . 8
2.3 2.3 Three Posttranslational Modifications Involved in Regulating Protein Func-
tion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.4 2.4 Four Chromatographic Techniques for Protein Purification and Analysis . . 11
3 Question 3: Electrophoresis, Transcription, and Enzyme Inhibition 13
3.1 3.1 Gel Electrophoresis Methods for Characterising a Novel Transcription Factor 13
3.2 3.2 Five Differences Between Transcription in Prokaryotic and Eukaryotic Cells 14
3.3 3.3 Lock-and-Key and Induced Fit Models in the Design of Enzyme Inhibitors . . 15
4 Question 4: Sphingolipids and Mitochondrial Dysfunction 18
4.1 4.1 General Structure and Biological Role of Sphingolipids . . . . . . . . . . . . . 18
Page 1 of 22
,UNISA | BMI2601 Clinical Biochemistry II – Assignment 02
4.2 4.2 Mitochondrial Dysfunction, Elevated Lactate, and Acidosis . . . . . . . . . . 19
4.2.1 Background: The TCA Cycle and Oxidative Phosphorylation . . . . . . . . 19
4.2.2 How TCA Cycle Inhibition Leads to Elevated Lactate . . . . . . . . . . . . 19
4.2.3 Clinical Reasoning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Reference List 22
Page 2 of 22
, UNISA | BMI2601 Clinical Biochemistry II – Assignment 02
Question 1: Water Chemistry, pH, and Buffer Systems
1.1 Hydrogen Bonding in Water: High Boiling Point, Cohesion, and Biological Roles
Water is the fundamental solvent of all living systems, and its remarkable physical and bio-
logical properties arise directly from its capacity to form hydrogen bonds (Berg et al., 2019;
Lehninger et al., 2017). Each water molecule consists of one oxygen atom covalently bonded
to two hydrogen atoms. Because oxygen is strongly electronegative, it draws shared elec-
trons toward itself, creating a partial negative charge (δ − ) on the oxygen and partial posi-
tive charges (δ + ) on each hydrogen. This polarity allows neighbouring water molecules to
form hydrogen bonds between the oxygen of one molecule and a hydrogen of an adjacent
molecule, with each water molecule capable of forming up to four such bonds simultaneously
(Alberts et al., 2019).
High boiling point. Hydrogen bonds, though individually weak (approximately 20 kJ/mol), are
collectively extremely strong in liquid water because there are so many of them. To convert
water from a liquid to a gas, a large amount of energy is required to break this extensive net-
work of hydrogen bonds. This is why water has a boiling point of 100°C, far higher than would
be predicted from its molecular weight alone. Comparable molecules of similar size but lack-
ing hydrogen bonds (such as hydrogen sulfide, H2 S) boil at much lower temperatures. For bi-
ological systems, this means that water remains liquid across the temperature range in which
most biochemical reactions occur, which is essential for life on Earth (Berg et al., 2019).
Cohesion. Cohesion refers to the tendency of water molecules to cling to each other because
of hydrogen bonding. In liquid water, individual hydrogen bonds break and reform extremely
rapidly, but the collective network is always maintained. Cohesion is responsible for phenom-
ena such as surface tension, the ability of water to form droplets, and the capillary action that
draws water upward through plant xylem against gravity. In human physiology, cohesion con-
tributes to the integrity of fluid compartments and the behaviour of biofluids in narrow ves-
sels (Lehninger et al., 2017).
Biological roles. Hydrogen bonding in water has several direct consequences for biology. Wa-
ter acts as a universal solvent: it readily dissolves ionic compounds and other polar molecules
by forming hydration shells around them, stabilising them in solution. It participates directly
in biochemical reactions as a reactant in hydrolysis. It stabilises the secondary and tertiary
structures of proteins through the hydrophobic effect, which itself arises from the tendency
Page 3 of 22
