University of Santo Tomas

Faculty of Pharmacy
An Outcomes-Based Teaching-Learning Program for Chemistry of Biomolecules
2nd Semester, A.Y. 2014-2015

Course Title:

Chemistry of Biomolecules

Course Number:

BIOCHEM 1

Credit Units::

5 units (3 units lecture and 2 units laboratory)

Contact Hours:

3 lecture hours and 6 laboratory hours per week

Course Placement:

2nd year, 2nd sem

Prerequisite:

CHEM 200

Course Facilitator:

GI Bathan, AS Sarile, and PC Torres

Course Description:

The course deals with the structure and function, isolation, purification and characterization of biomolecules:
carbohydrates, proteins, lipids and nucleic acids, transmission and expression of genetic information, and
generation and storage of metabolic energy.

Prepared by:

Prof. Angelita S. Sarile, Ph.D

Reviewed by:

Asst. Prof. Andrea G. Vargas, Chair, Department of Biochemistry

Approved by:

Assoc. Prof. Ma. Elena J. Manansala

Dean, Faculty of Pharmacy

Date of Approval:

05 January 2015

INSTITUTIONAL INTENDED LEARNING OUTCOME

GRADUATE ATTRIBUTE
Academic Excellence
Show expertise in the competencies necessary to the
practice of the profession

Leadership and Teamwork

Demonstrate capacity for leadership and teamwork
including the ability to motivate others, to be
responsible and reliable

Critical Thinking and Problem-Solving Skills

Initiate innovative ideas and methods through
research responsive to the changing needs of the
society
Productivity and Accountability
Develop new knowledge and understanding that will
contribute to nation-building and sustainable
development through the processes of inquiry,
research and innovation
Social and Ethical Responsibilities
Hold Catholic values and moral principles reflective of
the competent, committed and compassionate
Thomasian in the formation of humanely progressive
and healthy society
Communication and Relational Skills

PROGRAM INTENDED LEARNING

OUTCOME
Demonstrate creative application of
concepts and methods geared towards
proficiency in the practice of biochemistry
in the allied health, biological and
environmental sciences
Exemplify cooperative leadership that
promotes good work ethics in the practice
of ones profession

Generate innovative ideas and practical

solutions utilizing logical and systematic
methods in biochemistry to real-life
situations
Apply new and existing knowledge in
biochemistry to the development of
concepts and products beneficial to the
society through research and innovation
Exhibit Catholic values and moral
principles true to the Thomasian ideals as
biochemists contributing to the
improvement of the quality of life

COURSE INTENDED LEARNING OUTCOME

1. Demonstrate ability to analyze
biological processes and functions
based on knowledge of the
molecular structures of the
participating biomolecules.
2. Assume effective leadership roles
in devising strategies to exemplify
the impact of biochemistry in the
allied health, biological and
environmental sciences and in
everyday life.
3. Evaluate the interplay of
biochemical reactions and
pathways based on structurefunction relationship of
biomolecules and xenobiotics
4. Correlate biochemical studies and
principles to a molecular and
detailed understanding of health
and diseases, technology,
nutrition and environment.
5. Exhibit Catholic values and ethical
principles on current biochemical
researches and applications in
recombinant DNA technology,
gene and stem cell therapy.
6. Communicate the application of

Develop effective communication competencies

through interpersonal skills and utilize information
technology responsibly as effective tool in exploring
and expressing ideas

Intended Learning Outcomes

Demonstrate effective competencies in

communication and relational skills
through collaborations utilizing available
information technologies in expressing
concepts and principles in biochemistry

Content

information technology on the

storage, organization and analysis
of data (e.g. gene and protein
sequencing, biomolecular
structural information, data
mining, drug and therapeutic
applications).

Teaching-Learning
Activities

Assessment Tasks

Unit I: Biochemistry and the

Organization of Cells
Recognize biochemistry as a multidisciplined course and explain why it is
central to all life sciences CILO 1

1. Scope of Biochemistry

Correlate function of cell organelles

with the different biochemical systems

2. Cell types, structure, function and

chemical composition

Interactivity or Interactive
Work

Goal Ranking and Matching

Objective Test

Lecture Forum

Analytic assessment

Scientific laboratory
session

Lab practical

CILO 2

2.1 pH and buffers

3. Organelle structure and function

Analyze factors affecting buffer
capacity and buffer solution
preparation CILO 3

Intended Learning Outcomes

Content

Teaching-Learning
Activities

Assessment Tasks

Unit II: Amino Acids and Peptides

Relate protein systems and their
biochemical functions CILO 1
Analyze fundamental structure of
amino acids, classification and
interactions associated with the R
groups CILO 3

1. Biochemical functions of protein

systems

Interactive Lecturing

Problem Sets

Work Along Activities

Documented Problem
Solution

Scientific Laboratory
Session, Cookbook
Laboratory Work

Analytic Assessment
Lab Practical
Whats the Principle
Paper Prospective

Gapped Lecture

Summarizing

Lecture Forum

Analytic Assessment

2. Amino acid structure and

classification
2.1 Color reactions
2.2 Chromatography

3. Amino acid interactions

Explain acid-base behavior and IpH of
amino acids CILO 1

4. Acid-base behavior of amino acids

Calculate the charge of amino acids at

different pH conditions CILO 3

5. Definition and calculation of IpH of

amino acids and peptides

Illustrate the structure of small

peptides and explain its stability CILO 3

6. Peptide bond formation, structural

features and stability
Unit III: The Three-Dimensional
Structure of Proteins

Discuss the different interactions that

give rise to the four levels of protein
structure CILO 6

1. 1, 2, 3 and 4 structures

Predict the effects of pH, temperature

and chemical agents on the

2. Denaturation

Assigned Reading

Intended Learning Outcomes

Content

Teaching-Learning
Activities

Assessment Tasks

organization of protein structure CILO 3

Give examples of proteins and relate
their structure to their function CILO 1

3. Protein structure function: collagen

and elastin, hemoglobin and
myoglobin, insulin and glucagon,
immunoglobulins

Explain the molecular basis of some

disease states CILO 1

4. Collagen diseases, malaria, sickle

cell anemia and autoimmune
diseases
Unit IV: Protein Purification and
Characterization Techniques

Apply the appropriate technique for the

purification and characterization of
proteins CILO 4

1. Purification of proteins, column

chromatography and electrophoresis

1.1 Isolation and characterization of

proteins
1.2 Quantitative protein analysis

Predict the primary structure of a

protein based on enzymatic reactions
and chemical hydrolysis CILO 3

Gapped Lecture

Problem Sets

Work Along Exercises

Problem Recognition Tasks

Problem Solving Learning

Cookbook Laboratory Work
Scientific Laboratory
Session

Documented Problem
Solution
Whats the Principle
Paper Prospective
Lab Practical

Gapped Lecture
Lecture Forum
Three-Minute Essay

Focused Listing

2. Sequencing of amino acids in a protein

Unit V: The Behavior of Proteins:

Enzymes
Evaluate enzymes according to the
physico-chemical properties CILO 2

1. Chemical nature/role of enzymes

1.1 Enzyme classification and

Whats the Principle

Intended Learning Outcomes

Content

Teaching-Learning
Activities

Nomenclature

Analytic Assessment
Paper Prospective
Lab Practical

1.2 Isolation and characterization of

enzyme
Compare kinetic and thermodynamic
aspects of catalytic reactions CILO 3

Assessment Tasks

2. Michaelis-Menten kinetic theory;

Lineweaver-Burk Equation
2.1Factors affecting enzyme activity

Distinguish between two models of

enzyme-substrate interaction and
different types of enzyme inhibition CILO3

3. Lock and Key; Induced Fit

* Reversible and Irreversible
Inhibitors

Hypothesize on the role of enzymes in

clinical diagnosis CILO 1

4. Enzymes as markers for disease

Unit VI: The Behavior of Proteins:
Enzymes, Mechanisms, and Control

Illustrate the factors for enzyme

regulation CILO 1

1. Models for the behavior of allosteric

enzymes; Zymogens

Enumerate the different coenzymes

and their vitamin sources CILO 1

2. Coenzymes, their reactions and

their vitamin precursors

Gapped Lecture

Focused Listing

Lecture Forum

Whats the Principle

Three-Minute Essay

Analytic Assessment

Interactive Lecturing

Problem Sets

Work Along Activities

Documented Problem
Solution

Unit VII: Nucleic Acids: How Structure

Conveys Information
Enumerate the functions of nucleic
acids CILO 1

1. Types and their functions

Discuss the nomenclature and

2. Pentose sugar, base and phosphate

Intended Learning Outcomes

components of nucleotides, the
building blocks of nucleic acids CILO 1

Content

Teaching-Learning
Activities

Assessment Tasks

Ribonucleotides/Deoxyribonucleotides

2.1 Isolation and characterization of

nucleic acids
Analyze the structural organizations of
DNA and RNA CILO 3

3. Four levels of structure in nucleic

acids
Unit VIII: Biosynthesis of Nucleic Acids:
Replication

Describe proofs of DNA as the genetic

material CILO 1

1. Experiments done by Avery et al.

Discuss the replication process CILO 1

2. Steps in replication

Explain mutagenesis CILO 3

3. Spontaneous and induced mutation

Physical, chemical and viral
mutagens

Scientific Laboratory
Session, Cookbook
Laboratory Work

Whats the Principle

Analytic Assessment
Paper Prospective
Lab Practical

Gapped Lecture

Summarizing

Lecture Forum

Analytic Assessment

Assigned Reading

Discuss the different protective systems

and repair mechanisms in the cell CILO 3
Associate gene mutations to tumor,
cancer and genetic disorders CILO 5

Workshop

4. Antimutagens, mismatch repair,

base and nucleotide excision repair
5. Hot topics in cell and molecular
biology
Unit IX: Transcription of the Genetic
Code: The Biosynthesis of RNA

Discuss the transcription process CILO 1

1. General features of RNA synthesis

Gapped Lecture

Summarizing

Justify posttranscriptional modification

2. Enzymatic modifications of tRNA,

Lecture Forum

Analytic Assessment

Intended Learning Outcomes

of RNA in eukaryotes CILO 3

Content

Teaching-Learning
Activities

Assessment Tasks

rRNAand mRNA
Assigned Reading

Describe RNA as an enzyme CILO 1

3. Ribozymes

Unit X: Protein Synthesis: Translation

of the Genetic Message
Describe the important features of the
genetic code CILO 1
Discuss the translation process CILO 1

1. Genetic code

Gapped Lecture

Focused Listing

Lecture Forum

Whats the Principle

Three-Minute Essay

Analytic Assessment

Lecture Forum

Summarizing

1. Monosaccharides, oligosaccharides
and polysaccharides

Gapped Lecture
Lecture Forum
Assigned Reading

Summarizing
Analytic Assessment

1.1 Isolation and characterization

1.2 Qualitative and Quantitative
Analysis

Scientific Laboratory
Session, Cookbook
Laboratory Work

Paper Prospective
Whats the Principle
Lab Practical

2. Steps in protein biosynthesis

Unit XI: Nucleic Acid Biotechnology
Techniques

Explain the general steps in

recombinant DNA technology CILO 3

1. Recombinant DNA technology and

Polymerase Chain Reaction

Critique issues relevant to recombinant

DNA technology CILO 5
Unit XII: Carbohydrates
Evaluate carbohydrates based on
structure and function CILO 3

Intended Learning Outcomes

Content

Illustrate the different structural

representations of sugars and glycosidic
linkages CILO 1

2. Fischer projection formulas,

Haworth projections,
conformational formulas

Discuss different carbohydrate

derivatives CILO 1

3. Phosphate esters, amino sugars,

deoxy sugars, sugar acids and sugar
alcohols

Discuss biological functions of some

oligo- and polysaccharides CILO 3

4. Starch, glycogen, cellulose, chitin

Explain some important glycoproteins

including ABO blood group antigens CILO6

5. O- and N-linked glycoproteins,

Glycosaminoglycans

Teaching-Learning
Activities

Assessment Tasks

Unit XIII: Lipids

Evaluate lipid structure, classification
and functions CILO 2

1. Fatty acids, phospholipids, sphingolipids, eicosanoids, steroids,

lipoproteins
1.1 Isolation and characterization

Explain molecular basis of some disease

states CILO 6

2. Lipoprotein profile with

hypercholesterolemia

Gapped Lecture
Lecture Forum
Assigned Reading

Focused Listing
Summarizing

Scientific Laboratory
Session
Cookbook Laboratory Work

Whats the Principle

Lab Practical
Paper Prospective

Intended Learning Outcomes

Content

Teaching-Learning
Activities

Assessment Tasks

Unit XIV: Glycolysis

Examine some general principles of
thermodynamics as applied to
biochemical systems and give an
overview of intermediary metabolism

1. Overview of intermediary metabolism

Empty Outlines

Lecture Forum

Analytic Assessment

Assigned Reading

CILO 1

Discuss the different reactions that lead

to the formation of ATP CILO 3

Gapped Lecture

2. Glycolytic pathway
* Substrate level phosphorylations
Oxidation Reduction reactions
Unit XV: Storage Mechanisms and
Control in Carbohydrate Metabolism

Discuss the different pathways that

lead to the storage of metabolic fuel

1. Glycogen metabolism
*Gluconeogenesis

Gapped Lecture

Empty Outlines

Lecture Forum

Analytic Assessment

CILO 1

Assigned Reading
Unit XVI: The Citric Acid Cycle
Analyze the reactions of the citric
acid cycle CILO 3

1. Individual steps of the citric acid

cycle

Lecture Forum

Summarizing

Gapped Lecture

Problem Sets

Work Along Exercises

Problem Recognition Tasks

Problem Solving Learning

Documented Problem

Unit XVII: Electron Transport and

Oxidative Phosphorylation
Relate electron transport chain with
oxidative phosphorylation CILO 3

1. Electron Transport Chain

Compare the shuttle mechanisms CILO 3

2. Malate-aspartate and Glycerolphosphate

Intended Learning Outcomes

Content

Teaching-Learning
Activities

Assessment Tasks
Solution

Compute for the ATP yield from

complete oxidation of glucose CILO 3

3. Net gain of ATP molecules

Unit XVIII: Lipid Metabolism

Illustrate the pathways involved in the
metabolism of lipids CILO 1

1. -oxidation of fatty acids;

ketogenesis

Compute for the energy yield from the

oxidation of fatty acids CILO 3

2. Balance sheet from oxidation of fatty

acids

Appraise the strategy of metabolism by

showing the interplay of pathways in
terms of the flow of metabolites at
three crossroads: glucose 6-phosphate,
pyruvate and acetyl CoA CILO 3
REFERENCES:

3. Important aspects of intermediary

metabolism

Gapped Lecture

Problem Sets

Work Along Exercises

Problem Recognition Tasks

Problem Solving Learning

Documented Problem
Solution
Reflective Exercises

Campbell, M.K. and S.O. Farrell. (2012). Biochemistry. 7th ed. BROOKS/COLE CENGAGE Learning
Berg, J., J. Tymoczko and L. Stryer. (2012). Biochemistry. 7th ed. New York: W.H. Freeman and Co.
Devlin, T.M. (2010). Textbook of Biochemistry with Clinical Correlations. 7th ed. New York: Wiley-Liss.
Mathews, C.K., K.E. van Holde and K.G. Ahern. (2013). Biochemistry. 4th ed. San Francisco: Addison Wesley Longman, Inc.
Pratt, C.W. and Cornely K. (2013). Essential Biochemistry 3rd ed. New Jersey: John Wiley & Sons
Sylianco, C.L. and L. Sylianco-Wu. Biochemistry 4th ed. Quezon City: Aurum Technical Books
Voet, D., Voet, J.G., Pratt C.W. (2013). Principles of Biochemistry 4th ed. Singapore Pte. Ltd.: John Wiley & Sons
http://www.academic.cengage.com
http://www.wiley.com

GRADING SYSTEM:
The final grade is computed as 30% monthly, 35 % preliminary and 35% finals. The grade is composed of 60% lecture and 40% laboratory per
grading period. The lecture and laboratory grades are computed as follows:

Departmental Examination

Quizzes
Class Standing (Attendance/ Performance/Conduct)
Formal Reports
Pre-Lab Assignment
Data Sheet
Post-Lab Assignment
Total

Course Policy: 80% Attendance; 75% Passing Rate

Lecture (%)
50
40
10
------------------------100

Laboratory (%)
30
30
10
15
5
5
5
100

TENTATIVE COURSE CALENDAR:

WEEK
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

CONTENT
Biochemistry and the Organization of Cells
Amino Acids and Proteins
Protein Isolation, Purification, and Characterization Techniques
Enzymes: Structure and Function
Enzymes: Mechanism and Control
MONTHLY
Nucleic Acids: How Structure Conveys Information
Replication: Biosynthesis of Nucleic Acids
Transcription of the Genetic Code: The Biosynthesis of RNA
Protein Synthesis: Translation of the Genetic Message
Mutation and Repair Mechanisms
PRELIMS
Nucleic Acid Biotechnology Techniques
Carbohydrates: Nomenclature, Classification and Function
Lipids: Nomenclature, Classification and Function
Glycolysis; Storage Mechanisms and Control in Carbohydrate Metabolism; The Citric Acid Cycle
Electron Transport and Oxidative Phosphorylation; Lipid Metabolism
FINALS