Compiled Notes

University of the Immaculate Conception
COLLEGE OF MEDICAL AND BIOLOGICAL SCIENCE
Course Code : CHM311

Course Title : Biochemistry for Medical Laboratory Science
Credit units : 3 units
Class Schedule : Monday - Friday
Course Description : This course deals with the study of drugs: history and sources; physical and
chemical properties; biochemical and physiologic effects; mechanism of action; distribution,
metabolism, excretion, pharmacokinetics and indications; side and adverse reactions and drug
interactions. Emphasis of therapeutic drugs and drugs of abuse.
COURSE OUTCOMES :
CO 1. Attribute basic and advance concepts of biochemistry in relation to specific biomolecules suc
as: Water, amino acids, proteins, enzymes, carbohydrates, etc
CO 2. Correlate the basic principles of theoretical and practical applications of the biomolecules discussed.
CO 3. Formulate a working term paper (research paper) in relation to the biomolecules discussed.
COURSE OUTLINE :
TOPICS Page No.
1. Introduction to Biochemistry 2
2. Water: The Solvent of Biochemical Reactions 7
3. Proteins: Amino Acids and Peptides & Three-Dimensional Structure of Protein 10
4. Enzymes: Basic Functions and Clinical Uses 14
5. Energy Changes and Electron Transfer in Metabolism 17
6. Carbohydrates 23
7. Glycolysis 31
8. Storage Mechanism and Control in Carbohydrate Metabolism 41
9. Citric Acid Cycle 46
10. Lipids and Proteins: Structure Functions 51
11. Lipid Metabolism 55
12. Nucleic Acids: How Structure Conveys Information 61
COURSE EVALUATION
∑𝑛𝑖=1 𝐶𝑂𝑖
𝑇𝑒𝑟𝑚𝑖𝑛𝑎𝑙 𝐺𝑟𝑎𝑑𝑒 = 70% ( ) + 30%𝐸𝑥𝑎𝑚
𝑛
𝑘 𝑚
𝐶𝑂𝑖 = 70% ∑ 𝐴𝑇𝑗 + 30% ∑ 𝑇𝐿𝐴𝑧

𝑗=1 𝑧=1
Where
1. AT = Assessment Task
2. CO = Course Outcome
3. TLA = Teaching Learning Activities (e.g. Quiz, Recitation, Laboratory Activity, etc.)
CMBS CHM331: Biochemistry for MLS A.Y. 2020-2021 Page 1 of 70

TOPIC 1
INTRODUCTION TO BIOCHEMISTRY
LEARNING OBJECTIVES:
At the end of the lesson, the student will be able to:
a. Discuss the general concepts of Biochemistry.
b. Discuss the biochemistry connections between biodiversity, organic chemistry, origin of life,
prokaryotes, and eukaryotes.
INTRODUCTION
Biochemistry is the chemistry of living organisms ( (Moore & Langley, 2011). Try to pause and
look around, if we try to see the world beyond our naked eye, millions of chemical reactions are
simultaneously happening right now. Even as you breathe, complex mechanism and systems work
together for this to happen. And yet when we try to recall, one theory (Big Bang Theory) says that this
all originated from one powerful explosion, billions of years ago.
Fast forward in our present day, we already have some understanding to the different systems
and processes of life and our world. From our universe down to a cell and its molecular and chemical
interactions. The fascination of understanding these myriads of phenomenon gave birth to different
disciplines of science.
As a future medical laboratory scientist, understanding the basic principles of biochemistry is vital.
It allows us to understand the different molecular nature of life processes. For example, the
understanding of health and disease at the molecular level leads to more effective treatment of illness
of many kinds. (Campbell & Farell, 2015).
In this topic, we will unravel the different foundations of life, its origin and evolution.
Time allotment/ duration: 5 hours
Core-Related values and Biblical Reflection:
Excellence: Competence
Whoever pursues righteousness and love finds life, prosperity and honor (Proverbs 21:21)
LEARNING CONTENT
Topic Content:
A. Introduction
B. Chemical Foundations of Biochemistry
C. Beginnings of Biology: Origin of Life
D. Prokaryotic and Eukaryotic Cells
A. Introduction
1. BIOCHEMISTRY SPEAKS OF BIODIVERSITY
• Variety of different lifeforms on EARTH, not only in HUMANS
• Diversity: genetic variation, ecosystem variation, species variation.
• INTERRELATED due to the similarity in biomolecules that makes up their entire existence.
> H2O, CH4, CO2, NH3, N2, and H2
2. BIOCHEMISTRY SPEAKS OF DIVERSE BIOCHEMICAL PATHWAYS

• Biochemistry attracts a multitude of disciplines in the scientific community.
• The UNDERSTANDING OF THE MOLECULAR ACTIVITIES and PATHWAYS within the cell
allowed medical practitioners to effectively treat diseases.
• Pathways occurs simultaneously: some molecules have a single role while others have
multiple roles.
3. BIOCHEMISTRY SPEAKS ABOUT STRUCTURE AND ORGANIZATION
B. Chemical Foundations of Biochemistry
BIOCHEMISTRY and ORGANIC CHEMISTRY

ORGANIC CHEMISTRY
- The study of compounds of carbon, especially of carbon and hydrogen and their derivatives.
Side note: it was previously thought that in the 19th century, vital forces (molecules unique to living things cannot
be prepared/made “in vitro”
- Friedrich Wohler in 1828

4. BIOCHEMISTRY and BIOMOLECULES
- Biomolecules are composed of biologically important “FUNCTIONAL GROUPS”
- Formation of ATP is one of the most important biochemical processes in species.
Note: The complete table may be accessed in page 5 of Biochemistry 5 th Ed. by Mary Campbell and Shawn Farrell.
5. BIOCHEMISTRY and The Origin of Life

- We are the only life sustaining planet in the universe.
- The Big Bang Theory
: a tremendous explosion happened. A “primordial fireball” started to expand with great force.
Composed of: Hydrogen, Helium, Lithium
- Proposed formation of the other elements:
1. thermonuclear reactions,
2. in explosion of stars, and
3. action of cosmic rays
6. BIOCHEMISTRY and BIOMOLECULES

- Gases present in the atmosphere of the early earth included NH3, H2S, CO, CO2, CH4, N2,
H2, and H2O
- The formation of biomolecules happened ABIOTICALLY.
- Recent works suggests that RNA, not proteins, as the first genetic molecules.
- The possibility to synthesize nucleotides from simpler molecules using a PRECURSOR THAT
IS NOT A SUGAR NOR A NUCLEOBASE.
Living cells consists of assembly of VERY LARGE MOLECULES:

1. Amino acids → Peptides → Proteins
2. Nucleotides → Nucleic acids
3. Monosaccharides → Polysaccharides
4. Glycerol and three fatty acids → Lipids
MONOMERS – small molecules that may bond to form a polymer

POLYMERS – large molecules/macromolecules that are formed through bonding of smaller units
The formation or polymerization of monomers have a SENSE OF “DIRECTIONALITY” which

comprises a cascade of events.

- The effect of monomer sequence affects the properties of polymers THEREFORE DICTATING ITS
BIOLOGICAL FUNCTION.
- Enzymes increases the rates of chemical reactions →CATALYTIC ACTIVITY
- Catalysis: Depends on the sequence of amino acids.
C. Beginnings of Biology: Origin of Life
EVOLUTION OF REPLICATION
From Molecules to Cells:
➢ Key point: Formation of membranes that separates the cells from their environment.
➢ This membrane makes communication and internal pathway processes more efficient within
the cell.
➢ Double Origin Theory:
1. Rise of aggregates of molecules for catalysis
2. Rise of nucleic acid-based coding system

PROKARYOTES and EUKARYOTES
Closely linked to primitive cells are the “PROKARYOTES”
➢ Greek derivation: “karyon” = kernel, nut, literally means “before the nucleus”
➢ Comprises of two organisms: Bacteria and Cyanobacteria
EUKARYOTES are more modern, complex, that can be multicellular or single-celled (yeasts and
paramecium).
➢ means “true nucleus”
➢ Fact: eukaryotes evolved from eukaryotes about 1.5 billion years ago.
PROKARYOTES
- Has a NUCLEAR REGION: contains the genetic material and has the essentially the same
function as the nucleus in a EUKARYOTIC CELL.
- Nuclear region: single, closed, circular molecule of DNA (ATTACHED to THE CELL
MEMBRANE)
- One copy of the DNA is passed to the two daughter cells
- CYTOSOL: has a slightly granular appearance, due to the presence of ribosomes (ALSO
KNOWN AS RIBONUCLEOPROTEIN PARTICLES.
EUKARYOTES
- Has subcellular organelles; Important: NUCLEUS, MITOCHONDRION,
*CHLOROPLAST
- Chloroplast: found in green plants and green algae, sites of photosynthesis.
Note: MITOCHONDRIA and CHLOROPLASTS contain DNA, have their own transcription
and ability to synthesize proteins.

ORGANELLES
LEARNING EVALUATION
Teaching-Learning Activities
TLA1: Lecture
For Asynchronous learners and Category 2A students, you may access the recorded video
lecture during your available time.
TLA 2: Small Group Discussion and Reflective Writing

Expected Output: Reflection Paper
Discuss the following questions: (Answers per question should written in be 3-4 sentences only.)
1. Why is the development of catalysis important to the development of life?
2. Why was the development of coding system important to the development of life?
3. Did symbiosis play a role in the development of eukaryotes?
Format:
Paper size: Letter Font size: 11
Font style: Arial/Tahoma Margin: Moderate
REFERENCES
Campbell, M. K., & Farell, S. O. (2015). Biochemistry (8th ed.). (R. Lee, Ed.) Singapore:
Cengage Learning Asia.
Moore, J. T., & Langley, R. H. (2011). Biochemistry for Dummies 2nd Edition. Hoboken, NJ:
Wiley Publishing Inc.

TOPIC 2
WATER: The Solvent for Biochemical Reactions
c. Discuss the intermolecular forces that governs the world
d. Compute for the pH, acid and base using the Henderson-Hasselbach equation
INTRODUCTION
Water is one of the most important substances on earth. People swim, bathe, boat, and fish in it. It
carries waste from people’s homes and is used in the generation of electrical power. Humans drink it in
a variety of forms: pure water, soft drinks, tea, coffee, beer, and so on. Water, in one form or another,
moderates the temperature of the earth and of the human body.
In the area of biochemistry, water is also one of the lead actors. The human body is about 70 percent
water. Water plays a role in the transport of material to and from cells. And many, many aqueous
solutions take part in the biochemical reactions in the body.
In this topic, we will examine the water molecule’s structure and properties. We explain how water
behaves as a solvent. We also look at the properties of acids and bases and the equilibria that they may
undergo. Finally, we discuss the pH scale and buffers, including the infamous Henderson-Hasselbalch
equation. So sit back, grab a glass of water (or your favorite water-based beverage), and dive in! (Moore
& Langley, 2011).
LEARNING CONTENT
Topic Content:
E. Water and Polarity
F. Hydrogen Bonds
G. Acids, Bases and pH
A. Water and Polarity

• Water is the principal component of most cells
• The geometry of the water molecule and its properties as a solvent plays a major role in
determining the properties of living systems
• Water is regulated in the body through hypothalamic and pituitary systems
• DIABETES INSIPIDUS: characterized by large amounts of dilute urine and increased thirst
• Neurogenic (Central) DI
• Nephrogenic (renal tubule defect)
ELECTRONEGATIVITY: tendency of an atom to attract electrons to itself in a chemical bond.

➢ Same electronegativity = equal sharing of electrons
➢ Some atoms still bond even with difference in electronegativity
➢ Difference in electronegativity: electrons are not equally shared
➢ Partial positive (Hydrogen) and partial negative (Oxygen): polar bonds
WATER: SOLVENT PROPERTIES

POLAR NATURE of Water determines its solvent properties.
Types of Interactions:
a. IONIC BONDS: Bonds that holds positive and negative ions together.
b. SALT BRIDGES: Attraction that occurs when oppositely charged molecules are in close proximity.
c. ION-DIPOLE: When ions in solution interact with molecules with dipoles
d. VAN-DER WAALS FORCES: Bonds that do not involve electrostatic interactions
e. DIPOLE-DIPOLE: Forces that occur between molecules with dipoles, one positive and one negative
f. DIPOLE INDUCED-DIPOLE: Weak and generally do not lead to solubility in water
g. INDUCED DIPOLE-INDUCED DIPOLE: Weak and generally do not lead to solubility in water

SOLUBILITY in WATER
Hydrophilic: “water loving”
Hydrophobic: “water hating” or “water fearing”
Micelles: a spherical arrangement of organic molecules in water solution clustered so that polar head
groups are in contact with the water and non-polar parts are protected from contact with water
B. Hydrogen Bonds
Non-covalent association formed between a hydrogen atom covalently bonded to one electronegative
atom and a lone pair of electrons.
HYDROGEN BONDS – BIOLOGICALLY IMPORTANT MOLECULES
NOTE:
- Each water molecule can be involved in 4 hydrogen bonds: 2 as donor, and 2 as acceptor

C. ACIDS, BASES and pH
Biochemical behavior of many important compounds depends on their acid-base properties.
ACID: a molecule that behaves as a proton donor
BASE: a molecule that behaves as a proton acceptor
ACID DISSOCIATION CONSTANT: expression of acid strength
pH: power of HYDROGEN, is a scale used to specify how acidic or basic a water-based solution is.
C. HENDERSON-HASSELBACH EQUATION
LEARNING EVALUATION
TLA1: Lecture
lecture during your available time at the google site.
TLA 2: Illustration
Expected Output: Illustration
Instruction: Illustrate and describe the different types of molecular interactions.

Twist: Aside from illustrating it using scientific models, create an illustration of its analogy to common
relationships you can observe in a day-to-day basis. Be creative.
Format:
Paper size: Letter *** Hand-made and colored
TLA 3: Computation Exercise

Solve the following questions.
1. What is the pH of a solution consisting of 0.85M HC2H3O2 and 0.60M NaC2H3O2?
Ka of HC2H3O2 = 1.8 x 10-5
2. What is the pH of a solution consisting of 0.20M NH4Cl and 2.0 NH3.
Kb of NH3= 1.8 x 10-5
REFERENCES

TOPIC 3
AMINO ACIDS, PEPTIDES and its STRUCTURES
e. Discuss the nature of amino acids;
f. Discuss the different levels of protein structures; and
g. Discuss the different biological functions of each amino acid structure.
INTRODUCTION
Proteins mediate every process that takes place in a cell (Nelson & Cox, 2013). All cell types contain
thousands of proteins and amino acids are the building blocks of protein. The sequential order, number and
chemical identity of the amino acids in the protein determines the protein’s structure and function.
Therefore, to understand the different chemical properties of amino acids is key to understand the behavior
proteins (Moore & Langley, 2011)
In this topic, we will understand and unravel the different properties of amino acids, how it
contributes to its structures and functions and its interaction with other molecules to maintain homeostasis
within YOU!
LEARNING CONTENT
INTRODUCTION
General Properties of Amino Acids

a. They can join to form proteins.
b. They all have both an acid and a base
- Amino Group: “Amino” terminology
- Carboxylic Acid: “Acid” terminology
- Amino and Carboxyl group: adjacent to each other
- Alpha carbon = forms covalent bonds with amino, carboxyl and hydrogen
- R group: dictates the variation in amino acids
c. They all have variations in what part of the structure is protonated, depending on the solution’s pH and
the rest of the molecule’s structure.
d. All CHIRAL in nature except, Glycine (achiral).

ESSENTIAL AMINO ACIDS
(PVT TIM HALL): Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine,
Arginine, Lysine, Leucine
AMINO ACID CLASSIFICATION

HYDROPHOBIC
1. Aliphatic
2. Aromatic
3. Sulfur containing compound
HYDROPHILIC
1. Polar/ Uncharged amino acid
2. Basic/ Acidic
Aliphatic Amino Acid Polar or Uncharged

- Proline - Glycine - Asparagine
- Isoleucine - Valine - Glutamine
- Alanine - Serine
- Phenylalanine - Tryptophan Basic Amino Acid
- Tyrosine Aromatic Amino Acid - Histidine - Lysine
- Arginine
Sulfur containing compound Acidic Amino Acid
- Methionine - Cystine - Aspartate
- Cysteine - Glutamate
Peptide Bonds
- Amino acids are joined linearly by peptide bonds via dehydration
- 1 H2O molecule is produced per peptide bond formed.

STRUCTURE OF PROTEINS
• Biologically active proteins are polymers of amino acids covalently linked by PEPTIDE
BONDS.
• Native conformations: Three-dimensional shape of proteins with biological activity.
• BIOCHEMISTS identified several levels of structural organization of proteins.
a. Primary Structures
- Sequence of amino acids in a polypeptide chain – from the N-terminal end to the C terminal end.
- Any alterations in one amino acid sequence the proteins GREATLY AFFECTS its biological function.
- important for deciding the higher structure of proteins.
- it is simply the amino acid sequence; determines the
b. Secondary Structures
Hydrogen bonded arrangement of backbone of the protein
1. Bond between alpha-carbon and amino nitrogen in residue
2. Bond between the alpha-carbon and carboxyl carbon
residue
Alpha helix
- Rod-like and involves only one polypeptide chain
- Composed of 3.6 amino acids per turn.
- Repeat distance is 5.4A
- Each peptide bond is s-trans and planar
- The C=O of each peptide bond is hydrogen bonded to the
N-H of the fourth amino acid
- These bonds are parallel to the helical axis
Beta-Pleated Sheets
- Polypeptide chains lie adjacent to one another; may be
parallel or anti-parallel
- R groups alternate, first above and then below plane
- Each peptide bond is s-trans and planar
- C=O and N-H groups of each peptide bond are
perpendicular to axis of the sheet
- C=O – H-N hydrogen bonds are between adjacent sheets
and perpendicular to the direction of the sheet
Supersecondary Structures
Described as the combination of alpha and beta-sections
✓ BaB unit: two parallel strands of B-sheet connected
by a stretch of alpha helix
✓ aa unit: two antiparallel alpha helices
✓ B-meander: antiparallel sheet formed by a series of tight reverse turns connecting stretches of a
polypeptide chain
✓ Described as the combination of alpha and beta-sections
✓ Greek key: a repetitive supersecondary structure formed when an antiparallel sheet doubles
back on itself
✓ B-barrel: created when beta-sheets are extensive enough to fold back on themselves
c. Tertiary Structure
- the result of the combination of the primary structure, secondary structure and the interaction between
the different side chains.
- the overall shape of a single protein molecule
- three-dimensional folding pattern of a protein due to side chain interactions.
Fibrous Proteins:
- Polypeptide chains are organized approximately parallel along a single axis
- Plays an important structural role in nature
Globular Proteins:
- Proteins which are folded to a more or less spherical shape
- Nearly all have substantial sections of alpha-helix and Beta sheets.

Tertiary Structures – Forces
d.
Quaternary Structure
- organization of multiple polypeptide chains (subunits) into functional multimeric protein
- results from the interaction of more than one protein molecule, which function as part of the larger
assembly or protein complex.
LEARNING EVALUATION
Meeting No. 1:
TLA 01: Lecture
For Asynchronous learners and Category 2A students, you may access the recorded video lecture during
your available time.
TLA 02: Summary, classifications and illustrations

Expected Output: Summary of amino acid classifications, structures and brief description
List of Amino Acid Classification Amino acid (with Illustration Description and
abbreviations) Functions
Example: Aliphatic Proline (Pro, P) Drawing: Highlight the
sidechain or R-group
Format:
Orientation: Landscape *** Hand-made and colored
Meeting No. 2
TLA 03: Small Group Discussion and Clinical Application Evaluation
4. Discuss the pathophysiology of Sickle Cell Anemia and Prion Diseases.
5. How did the mutation in the amino acid sequence affected the proteins’ structures and functions in Sickle
Cell Anemia and Prion Diseases?
6. Why is understanding the basic understanding of amino acids and protein characteristics and properties
relevant in the diagnosis and management of patients?
7. Discuss 2 diagnostic methods used to detect protein abnormalities.
Name of Method:
Principle:
General Procedure:
Results and Interpretations:
Give its advantages and disadvantages
Format:
NOTE: ALWAYS CITE REFERENCES USING APA FORMAT

REFERENCES
Campbell, M. K., & Farell, S. O. (2015). Biochemistry (8th ed.). (R. Lee, Ed.) Singapore: Cengage
Learning Asia.
Moore, J. T., & Langley, R. H. (2011). Biochemistry for Dummies 2nd Edition. Hoboken, NJ: Wiley
Publishing Inc.
Nelson, D. L., & Cox, M. M. (2013). Lehninger Principles of Biochemistry 6th Edition. 41 Madison Avenue,
New York: W. H. Freeman and Company.

TOPIC 4
ENZYMES
h. Discuss the different classifications and functions of enzymes;
i. Discuss enzymes kinetics and equations used to measure enzyme behavior
j. Discuss the different types of enzyme inhibition and regulation and its application to research and
medicine.
INTRODUCTION
There are two fundamental conditions for life. First, the organism must be able to self-replicate;
second, it must be able to catalyze chemical reactions efficiently and selectively (Nelson & Cox, 2013).
Enzymes are complex biological molecules, primarily or entirely protein, that behave as biological catalysts.
As catalysts, they increase the rate of chemical reactions without being consumed in the reaction (Moore &
Langley, 2011).
In this topic, we will focus our attention to understanding the mechanisms of biological system’s
catalysts, the enzymes.
LEARNING CONTENT
ENZYMES: speeds up the rate of reaction but cannot change the equilibrium constant (free energy
change)
RATE OF REACTION: Depends on FREE ENERGY OF ACTIVATION or ACTIVATION ENERGY
Activation Energy: the amount of energy which must be added to a reaction to allow it to go forward.
Enzyme Substrate Binding
Basic Terms:
a. Substrate
- the substance which is recognized by the enzyme and is transformed into product by the reaction/
b. Product
- the substance formed by the interaction of the substrate and enzyme.
c. Active Site
- binds the specific substrate
- the part of the enzyme which is catalytic
d. Affinity
- attraction between enzyme and substrate
e. Isoenzyme
-enzymes which have different amino acid sequences but catalyzes the same reactions.
f. Holoenzyme
- An enzyme which requires a co-factor to be active.
g. Prosthetic Group
- A co-factor which is permanently complexed with its enzymes.

Classification:
1. Oxidoreductases (LDH, G6PD)
2. Transferases (CK, AST, ALT)
3. Hydrolases (ACP, ALP, LPS)
4. Lyases (Aldolase, glutamate decarboxylase)
5. Isomerases
6. Ligases
Nomenclature:
- an enzyme’s name usually corresponds with its substrate and ends with the suffix -ase
- all enzymes are given numerical designations by the EC of the International Union of
Biochemistry
 EC 3.1.3.1 for Alkaline phosphatase
 EC 1.1.1.27 for Lactate dehydrogenase
 First number – classification
 Second two numbers – subclass & sub-subclass
 Last number – serial number
ENZYME KINETICS
Factors the Influence Enzymatic Reactions

• SUBSTRATE CONCENTRATION
• pH ( 7.0- 8.0)
• TEMPERATURE
• ENZYME CONCENTRATION
• COFACTORS
• INHIBITORS
• Competitive inhibitors
• Noncompetitive inhibitor
• Uncompetitive inhibitor

Michaelis-Menten Curve of Velocity
LEARNING EVALUATION
Meeting No. 1:
TLA 01: Lecture
TLA 02: Summary, classifications and illustrations

Expected Output: Summary of classifications of enzymes.
Enzyme Classification Name of Function Clinical Applications

Enzyme
Example: Oxido-reductases Glucose
dehydrogenase
Meeting No. 2
TLA 03: Illustration
Expected Output: Summary and Illustration
1. Draw/ Illustrate a workflow of the different types of enzyme inhibition.

(add a brief description 3-4 sentences)
2. Cite an example of a research or clinical application in each mechanism where it is applied or used.
Format:
Paper size: Letter Font size: 11 Illustrations should be hand-made ****

REFERENCES
Learning Asia.
Publishing Inc.

TOPIC 5
ENERGY CHANGES AND ELECTRON TRANSFER IN METABOLISM
k. Discuss the principles of bioenergetics and thermodynamics;
l. Discuss the standards states for free energy changes and its application metabolism
INTRODUCTION
Living cells and organisms must perform work to stay alive, to grow and to reproduce. The ability
to harness energy and to channel it into biological work is a fundamental property of all living organisms.
Modern organisms carry out a remarkable variety of energy transduction, conversions of one form of energy
to another. They use the chemical energy of fuels into the concentration gradients, into motion and heat,
and in a few organisms such as fireflies and deep-sea fish, into light. Photosynthetic organisms transduce
light energy into all these other forms of energy (Nelson & Cox, 2013).
In this topic, we will discuss the laws of thermodynamics and the quantitative relationships among
free energy, enthalpy, and entropy. After, we will discuss the common types of biochemical reactions that
occur in the living cells, particularly to reactions that has special roles in biological energy exchanges like
those involving ATP.
LEARNING CONTENT
Bioenergetics
- A quantitative study of energy transduction (i.e. changes of one form of energy into another)
Biological Energy Transformations Obey the Laws

of Thermodynamics
LAWS OF THERMODYNAMICS
1. Principle of the Conservation of Energy
- for any physical or chemical change, the total
energy in the universe remains constant; energy
may change form or maybe transported from one
region to another but it CANNOT BE created or
destroyed.
2. The Universe always tends toward increasing

disorder (entropy)
- in all natural processes, the entropy of the universe
increases.
Note: it does not require that the entropy increase
take place in the reacting system itself.
Gibbs Free Energy, (G)

- expresses the amount of an energy capable of doing
work during a reaction at constant temperature and
pressure
Enthalpy, (H)
- heat content of the reacting system
- reflects the number and kinds of chemical bonds in the
reactants and products
Entropy, (S)
- quantitative expression for randomness or disorder in a
system; increase disorder, increase entropy

Standard Energy Change is Directly Related to the Equilibrium Constant.
- The composition of the reacting system tends to continue changing until equilibrium is reached.
General Reaction: aA +bB ↔ cC + dD
; where a, b, c and d are the number of molecules of A, B C and D.
Equilibrium constant:
Note:
- Standard free energy change ( G’˚) is the difference between the free energy content of the
products and free-energy content of the reactant under standard conditions
- When (▲G’˚) is negative, the products contain less free energy than the reactants and the
reaction will process spontaneously under standard conditions.
- When (▲G’˚) is positive, the products in the reaction contain more free energy than the
reactants and this reaction will tend to go in the reverse direction
▲G = free energy change

▲ H = enthalpy; (its value is negative for a reaction that releases heat)
▲ S = entropy; (its value is positive for a reaction that increases the system’s randomness
Note:
- The process tends to occur spontaneously if ▲G is negative (i.e. energy is released in the
process)
- However, cell function depends largely on molecules, such as proteins and nucleic acids, for
which energy formation is positive
- To carry-out thermodynamically unfavorable, energy-requiring (endergonic) reactions, cells
couple them to reactions that liberate free energy (exergonic reaction). Thus, the overall process
is exergonic, and the sum of free-energy changes is negative.

Nature of Metabolism
Metabolism
- the sum of all biochemical reactions that take place in an organism
a. Catabolism – the breakdown of nutrients to provide energy
- an oxidative process that releases energy
b. Anabolism – the synthesis of biomolecules from simpler compounds
- a reductive process that requires energy
Oxidation: the loss of electrons

Reduction: the gain of electrons
Reducing Agent: a substance that gives up electrons to other substances

Oxidizing Agent: a substance that accepts electrons from other substances
Mnemonic: LEORA (Loss of Electron, Oxidation, Reducing Agent)

GEROA (Gain of Electron, Reduction, Oxidizing Agent)
Coenzymes in Biologically Important Oxidation-Reduction Reactions

Coupling of Production and Use of Energy
- The formation of ATP is intimately linked with the
release of energy from oxidation of nutrients. The
coupling of energy-producing reactions and energy-
requiring reactions is the central feature in the
metabolism of all organisms.
- The phosphorylation of ADP to produce ATP requires
energy, which can be supplied by the oxidation of
nutrients. Conversely, the hydrolysis of ATP to ADP
releases energy.
Increase in entropy on hydrolysis of phosphoenolpyruvate.

When phosphoenolpyruvate is hydrolyzed to pyruvate and
phosphate, it results in an increase in entropy. Both the
information of the keto form of pyruvate and the resonance
structures of phosphate lead to the increase in entropy.

LEARNING EVALUATION
Meeting No. 1:
TLA 01: Lecture
TLA 02: Small Group Discussion and Summary

Expected Output: Summary and Essay
Read this article:

Guide Questions:
1. Briefly discuss entropy based on the following cases:
a. Case 1
b. Case 2
c. Case 3
2. Based on the article, every reaction leads to increase entropy. How do living organisms follow the
laws of thermodynamics?

REFERENCES
Learning Asia.
Publishing Inc.

TOPIC 6
CARBOHYDRATES
a. Define what are Carbohydrates
b. Differentiate between simple and complex sugars
c. Explain the structure formation of sugars
INTRODUCTION
Carbohydrates are a third major group of biomolecules. This diverse group is commonly described
as sugars, or saccharides, from the Greek word for sugar. The simplest carbohydrates are called
monosaccharides, or simple sugars. An example is glucose. Monosaccharides can be joined to make larger
molecules. Disaccharides contain two monosaccharides. Sucrose is a disaccharide, containing both fructose
and glucose. Polysaccharides are chains of many sugar subunits. Examples include glycogen and cellulose,
both of which are polymers of glucose but with different configurations. Carbohydrates are literally
“hydrates of carbon.” This designation derives from the generalized formula of simple monosaccharides.
Not all sugars have this formula, however. Deoxyribose, the sugar found in every nucleotide in a DNA
molecule lacks one oxygen and thus has a different formula. (Aherm, 2019)
Carbohydrates are important in cells as energy sources (glucose, glycogen, amylose), as markers of
cellular identity (oligosaccharides on the surface of cells of multicellular organisms), as structural
components (cellulose in plants), and as constituents of nucleotides (ribose in RNA, deoxyribose in DNA).
(Aherm, 2019). A big chunk of our diet are sources of carbohydrates such as rice and bread. In this topic
it will present not just the definition of carbohydrates but also the structure of different sugars, its function
and uses.

Excellence: Discipline
Proverbs 25:28 “A man without self-control is like a city broken into and left without walls”tgfr
LEARNING CONTENT
Topic Content:
A. Sugars: Their structures and Stereochemistry
B. Reactions of Monosaccharides
C. Some Important Oligosaccharides
D. Structures and Functions of Polysaccharides
Watch the following videos https://youtu.be/jQi84TnstI4 & https://youtu.be/JxK5rZxbyQY and or read

Chapter 16 of Biochemistry 8th Ed. By Mary K. Campbell & Shawn O. Farrell
A. Sugars: Their structures and Stereochemistry

When the word carbohydrates was coined, it originally referred to compounds of the general
formulas Cn(H2O)n. However, only the simple sugars, or monosaccharides, fit this formula exactly.
The other types of carbohydrates, oligosaccharides and polysaccharides, are based on the
monosaccharide units and have slightly different formulas. Oligosaccharides are formed when a
few monosaccharides are linked; Polysaccharides are formed when many monosaccharides are
bonded together. The reaction that adds monosaccharide units to a growing carbohydrate
molecule involves the loss of some H2O for each new link formed accounting for the difference in
the general formula.
Many common encountered carbohydrates are polysaccharides, including glycogen, which is
found in animals, and starch and cellulose, which occur in plants. Carbohydrates play a number of
important roles in biochemistry.
1st -Major source of energy
2nd- oligosaccharides play a key role in processes that take place on the surface of the cells,
particularly in cell-cell interactions and immune recognition
3rd- polysaccharides are essential structural components of several classes of organism
• Carbohydrate- a polyhydroxyaldehyde or polyhydroxyketone, or a substance that gives

these compounds on hydrolysis

• Monosaccharide-
o a carbohydrate that cannot be hydrolyzed to a simpler carbohydrate
o Building blocks of all carbohydrates
o They have the general formula CnH2nOn, where n varies from 3 to 8
o Aldose: a monosaccharide containing an aldehyde group
o Ketose: a monosaccharide containing a ketone group
Structure of Monosaccharide
• Monosaccharides are classified by their number of carbon atoms
• Trioses are simplest carbohydrate monosaccharides
• Glyceraldehyde contains a stereocenter and exists as a pair of enantiomers
• Mirror-images stereoisomers are called enantiomers
Fischer Projections
• Fischer projection: bonds are written in a two dimensional representation showing the
configuration of tetrahedral stereocenters
• horizontal lines represent bonds projecting forward
• vertical lines represent bonds projecting to the rear
• the carbon atom at the intersection of the horizontal and vertical lines is not shown
D,L Monosaccharides
According to the conventions proposed by Fischer:

• D-monosaccharide: a monosaccharide that, when written as a Fischer projection, has the
-OH on its penultimate carbon on the right
• L-monosaccharide: a monosaccharide that, when written as a Fischer projection, has the -
OH on its penultimate carbon on the left
Aldotetroses
• Enantiomers: stereoisomers that are mirror images
o example: D-erythrose and L-erythrose are enantiomers
• Diastereomers: stereoisomers that are not mirror images
o example: D-erythrose and D-threose are diastereomers

What Happens if a Sugar Forms a Cyclic Molecule?
• Cyclization of sugars takes place due to interaction between functional groups on distant
carbons, C1 to C5, to make a cyclic hemiacetal
• Cyclization using C2 to C5 results in hemiketal formation.
• In both cases, the carbonyl carbon is new chiral center and becomes an anomeric carbon
Cyclic Structure
• Monosaccharides have -OH and C=O groups in the same molecule and exist almost entirely
as five- and six-membered cyclic hemiacetals
• anomeric carbon: the new stereocenter resulting from cyclic hemiacetal formation
• anomers: carbohydrates that differ in configuration only at their anomeric carbons
THE THREE FORMS OF GLUCOSE
HAWORTH PROJECTIONS
• five- and six-membered hemiacetals are represented as planar pentagons or hexagons, as
the case may be, viewed through the edge
• most commonly written with the anomeric carbon on the right and the hemiacetal oxygen
to the back right
• the designation β- means that -OH on the anomeric carbon is cis to the terminal -CH2OH;
α- means that it is trans
• A six-membered hemiacetal ring is shown by the infix -pyran- (pyranose)
• A five-membered hemiacetal ring is shown by the infix -furan- (furanose)

• Five-membered rings are so close to being planar that Haworth projections are adequate
to represent furanoses
• For pyranoses, the six-membered ring is more accurately represented as a strain-free chair
conformation
COMPARISON OF FISCHER AND HAWORTH PROJECTION
B. Reactions of Monosaccharides
✓ Reducing sugar: one that reduces an oxidizing agent

o Oxidation of a cyclic hemiacetal form gives a lactone
o When the oxidizing agent is Tollens solution, silver precipitates as a silver mirror
✓ If anomeric carbons are involved in glycosidic linkage, there will be a negative Tollens
reagent test
✓ If another anomeric carbon is not bonded and is free, there will be a positive Tollens
reagent test
✓ The carbonyl group of a monosaccharide can be reduced to an hydroxyl group by a variety

of reducing agents, such as NaBH4
o reduction of the C=O group of a monosaccharide gives a polyhydroxy compound
called an alditol

Phosphoric Esters
✓ Phosphoric esters are particularly important in the metabolism of sugars to provide

energy
o phosphoric esters are frequently formed by transfer of a phosphate group from
ATP
Glycosidic Bond Formation
✓ Glycoside: a carbohydrate in which the -OH of the anomeric carbon is replaced by -OR
o those derived from furanoses are furanosides; those derived from pyranoses are
pyranosides
o glycosidic bond: the bond from the anomeric carbon to the -OR group
o This is the basis for the formation polysaccharides/oligosaccharides
Two Different Disaccharides of α-D-Glucose
✓ Glycosidic linkages can take various

forms; the anomeric carbon of one
sugar to any of the -OH groups of
another sugar to forma an α- or
β-glycosidic linkage
Amino Sugars
✓ Are interesting class of
compounds related to the
monosaccharides.
✓ In sugars of this type,
an amino group (-NH2) or
one of its derivatives is
substituted for the hydroxyl
group of the parent sugar.
✓ In N-acetyl amino sugars,
the amino group itself
carriers an acetyl group
(CH3-CO-) as a substitute
NOTE:
➢ Sugars can and undergo oxidation reactions, as well as, forming esters
➢ Glycosidic linkages are responsible for the bonding of monosaccharides to form
oligosaccharides and polysaccharides

C. Some Important Oligosaccharides
✓ Sucrose
o Table sugar; obtained from the juice of sugar cane and sugar beet
o One unit of D-glucose and one unit of D-fructose joined by an α-1,2-glycosidic
bond
o Another artificial sweetener is a derivative of sucrose
✓ Lactose
o Made up of D-galactose and one unit of D-glucose joined by a β-1,4-glycosidic
bond
o Galactose is a C-4 epimer of glucose
✓ Maltose
o Two units of D-glucose joined by an α-1,4-glycosidic bond
o Formed from the hydrolysis of starch
o Differs from cellobiose by the conformation of the glycosidic linkage
NOTE:
➢ The disaccharide sucrose is a common table sugar. It consists of glucose and fructose
linked by a glycosidic bond
➢ Lactose, found in milk, and maltose, obtained from starch, are two other common
disaccharides
D. Structures and Functions of Polysaccharides
✓ Polysaccharide- When many monosaccharides are linked together

✓ Cellulose: the major structural component of plants, especially wood and plant fibers
o a linear polymer of approximately 2800 D-glucose units per molecule joined by β-1,4-
glycosidic bonds
o fully extended conformation with alternating 180° flips of glucose units
o extensive intra- and intermolecular hydrogen bonding between chains

Polysaccharide
✓ Starch is used for energy storage in plants a polymers of α-D-glucose units

✓ amylose: continuous, unbranched chains of up to 4000 α-D-glucose units joined by α-1,4-
glycosidic bonds
✓ amylopectin: a highly branched polymer consisting of 24-30 units of D-glucose joined by
α-1,4-glycosidic bonds and branches created by α-1,6-glycosidic bonds
✓ amylases catalyze hydrolysis of α-1,4-glycosidic bonds
✓ β-amylase is an exoglycosidase and cleaves from the nonreducing end of the polymer
✓ α-amylase is an endoglycosidase and hydrolyzes glycosidic linkages anywhere along the
chain to produce glucose and maltose
✓ debranching enzymes catalyze the hydrolysis of α-1,6-glycosidic bonds
AMYLOSE AND AMYLOPECTIN
✓ Chitin: the major structural component of the exoskeletons of invertebrates, such as

insects and crustaceans; also occurs in cell walls of algae, fungi, and yeasts
o composed of units of N-acetyl-β-D-glucosamine joined by β-1,4-glycosidic bonds
✓ Bacterial cell walls: prokaryotic cell walls are constructed on the framework of the
repeating unit NAM-NAG joined by β-1,4-glycosidic bonds
✓ Glycosaminoglycans: polysaccharides based on a repeating disaccharide where one of
the monomers is an amino sugar and the other has a negative charge due to a sulfate or
carboxylate group
o Heparin: natural anticoagulant
o Hyaluronic acid: a component of the vitreous humor of the eye and the lubricating
fluid of joints
o Chondroitin sulfate and keratan sulfate: components of connective tissue
NOTE:
➢ Polysaccharides are formed by linking monomeric sugars through glycosidic linkages

➢ Starch and glycogen are energy-storage polymers or sugars
➢ Cellulose and chitin are structural polymers
➢ Polysaccharides are important components of cell walls in bacteria and plants

LEARNING EVALUATION
TLA : Carbohydrates Worksheet (50points)

Expected Output: Answered Worksheet
Instructions: Answer the worksheet found in your google classroom.
ASSESSMENTS
AT . (30 points)
Instructions: Answer the assessment found in your google classroom.
ASSIGNMENTS
Assignment for the next meeting:
Instruction: Advance reading on Glycolysis and answer the following questions:
1. What is Glycolysis?
2.What are the steps of glycolysis?
3.How important is glycolysis?
RUBRICS FOR GRADING
A. Activities & Quizzes: Use the numeric scores
REFERENCES
Campbell, M.K., & Farrel, S.O. (2015). Biochemisty 8th Edition. Singapore; Cengage Learning Asia Pte Ltd.
Gonzales, C. (n.d.). Carbohydrates and the Energy Mystery. Retrieved July 18, 2020, from
https://www.cpalms.org/Public/PreviewResourceLesson/Preview/129047
Libretexts. (2020, July 14). 2.7: Structure and Function- Carbohydrates. Retrieved July 18, 2020, from
https://bio.libretexts.org/Bookshelves/Biochemistry/Book:_Biochemistry_Free_For_All_(Ahern,_Raja
gopal,_and_Tan)/02:_Structure_and_Function/2.07:_Structure_and_Function-_Carbohydrates

TOPIC 7
GLYCOLYSIS
a. Define what is Glycolysis
b. Explain the different reactions involved in Glycolysis
c. Explain the Control points of Glycolysis
INTRODUCTION
In the previous topic, Carbohydrates were presented. As we all know Carbohydrate is the source
of energy but how are these sources converted to energy will be the main discussion in the succeeding
topics. The first stage of glucose metabolism in organisms is called Glycolysis. Glycolysis according to
Merriam is defined as the enzymatic breakdown of a carbohydrates such as glucose by way of phosphate
derivatives with the production of pyruvic or lactic acid and energy is stored in high-energy phosphate
bonds of ATP. In glycolysis, one molecule of glucose is converted to fructose-1,6-bisphosphate, which
eventually gives rise to two molecules of pyruvate. The glycolytic pathway involves many steps, including
the reactions in which metabolites of glucose are oxidized. (Campbell & Farrell, 2015)
Glycolysis is the principle route for carbohydrate metabolism. The ability of glycolysis to provide
ATP in the absence of oxygen is especially important, because this allows skeletal muscle to perform at
very high levels of work output when oxygen supply is insufficient, and it allows tissue to survive anoxic
episodes. (Bender, 2015)

Faith: Competence
Psalm 139:14 “I praise you, for I am fearfully and wonderfully made. Wonderful are Your
works; my soul know it very well.”
LEARNING CONTENT
Topic Content:
A. The Overall Pathway of Glycolysis
B. Conversion of Six-Carbon Glucose to Three-Carbon Glyceraldehyde-3-Phosphate
C. Glyceraldehyde-3-Phosphate is converted to Pyruvate
D. Anaerobic Metabolism of Pyruvate
E. Energy Production in Glycolysis
F. Control of Glycolysis
Watch the following videos https://youtu.be/8qij1m7XUhk & https://youtu.be/A1nJRoPGkRs ; or

read Chapter 17 of Biochemistry 8th Ed. By Mary K. Cambell & Shawn O. Farrell
✓ The Overall Pathway of Glycolysis
Each reaction in the pathway is catalyzed by an enzyme specific for that reaction. In each of two
reactions in the pathway, one molecule of ATP is hydrolyzed for each molecule of glucose
metabolized; the energy released in the hydrolysis of these two ATP molecules makes coupled
endergonic reactions possible. In each of two other reactions, two molecules of ATP are
produced by phosphorylation of ADP for each molecule of glucose, giving a total of four ATP
molecules produced. A comparison of the number of ATP molecules used by hydrolysis (two)
and the number produced (four) shows that there is a net gain of two ATP molecules for each
molecule of glucose processed in glycolysis. Glycolysis plays a key role in the way organisms
extract energy from nutrients.

What are the possible fates of pyruvate in glycolysis?
When pyruvate is formed, it can have one of several fates (Figure 17.1). In aerobic
metabolism (in the presence of oxygen), pyruvate loses carbon dioxide. The remaining two
carbon atoms become linked to coenzyme A (Section 15-7) as an acetyl group to form acetyl-
CoA, which then enters the citric acid cycle (Chapter 19). There are two fates for pyruvate
in anaerobic metabolism (in the absence of oxygen). In organisms capable of alcoholic
fermentation, pyruvate loses carbon dioxide, this time producing acetaldehyde, which, in
turn, is reduced to produce ethanol (Section 17-4). The more common fate of pyruvate in
anaerobic metabolism is reduction to lactate, called anaerobic glycolysis to distinguish it
from conversion of glucose to pyruvate, which is simply called glycolysis. Anaerobic
metabolism is the only energy source in mammalian red blood cells, as well as in several
species of bacteria, such as Lactobacillus in sour milk and Clostridium botulinum in tainted
canned food.

THE REACTION OF GLYCOLYSIS
1. Phosphorylation of glucose to give glucose-6-phosphate

In the first step of glycolysis, the glucose ring is phosphorylated. Phosphorylation is the process
of adding a phosphate group to a molecule derived from ATP. As a result, at this point in
glycolysis, 1 molecule of ATP has been consumed
The reaction occurs with the help of the enzyme hexokinase, an enzyme that catalyzes the
phosphorylation of many six-membered glucose-like ring structures. A kinase is the name given
to an enzyme that phosphorylates other molecules. Atomic magnesium (Mg) is also involved to
help shield the negative charges from the phosphate groups on the ATP molecule. The result of
this phosphorylation is a molecule called glucose-6-phosphate (G6P), thusly called because the
6' carbon of the glucose acquires the phosphate group
2. Isomerization of glucose-6-phosphate to give fructose-6-phosphate

The second step of glycolysis involves the conversion of glucose-6-phosphate to fructose-6-
phosphate (F6P). This reaction occurs with the help of the enzyme phosphoglucose isomerase
(PI). As the name of the enzyme suggests, this reaction involves an isomerization reaction
The reaction involves the rearrangement of the carbon-oxygen bond to transform the six-
membered ring into a five-membered ring. To rearrangement takes place when the six-
membered ring opens and then closes in such a way that the first carbon becomes now external
to the ring.

3. Phosphorylation of fructose-6-phosphate to yield fructose-1,6-bisphosphate
In the third step of glycolysis, fructose-6-phosphate is converted to fructose- 1,6-bisphosphate
(FBP). Similar to the reaction that occurs in step 1 of glycolysis, a second molecule of ATP
provides the phosphate group that is added on to the F6P molecule.
The enzyme that catalyzes this reaction is phosphofructokinase (PFK). As in step 1, a magnesium
atom is involved to help shield negative charges
4. Cleavage of fructose-1,6,-bisphosphate to give glyceraldehyde-3-phosphate and

dihyroxyacetone phosphate
The final step of the first stage of glycolysis utilizes the enzyme aldolase, which catalyzes the
cleavage of FBP to yield two 3-carbon molecules. One of these molecules is called
glyceraldehyde-3-phosphate (GAP) and the other is called dihydroxyacetone phosphate (DHAP).
GAP is the only molecule that continues in the glycolytic pathway. As a result, all of the DHAP
molecules produced are further acted on by the enzyme triphoshpate isomerase (TIM), which
reorganizes the DHAP into GAP so it can continue in glycolysis. At this point in the glycolytic
pathway, we have two 3-carbon molecules, but have not yet fully converted glucose into
pyruvate

5. Isomerization of dihyroxyacetone phosphate to give glyceraldehyde-3-phosphate
The enzyme that catalyzes this reaction is triosephosphate isomerase. (Both dihydroxyacetone
and glyceraldehyde are trioses.) One molecule of glyceraldehyde-3-phosphate has already been
produced by the aldolase reaction; we now have a second molecule of glyceraldehyde-3-
phosphate, produced by the triosephosphate isomerase reaction. The original molecule of
glucose, which contains six carbon atoms, has now been converted to two molecules of
glyceraldehyde-3-phosphate, each of which contains three carbon atoms. The DG value for this
reaction under physiological conditions is slightly positive (12.41 kJ mol21 or 10.58 kcal mol21).
It might be tempting to think that the reaction would not occur and that glycolysis would be
halted at this step. We must remember that just as coupled reactions involving ATP hydrolysis
add their DG values together for the overall reaction, glycolysis is composed of many reactions
that have very negative DG values that can drive the reaction to completion. A few reactions in
glycolysis have small, positive DG values, but four reactions have very large, negative values, so
that the DG for the whole process is negative.
6. Oxidation of glyceraldehyde-3-phosphate to give 1,3-bisphosphoglycerate

In this step, two main events take place: 1) glyceraldehyde-3-phosphate is oxidized by the
coenzyme nicotinamide adenine dinucleotide (NAD); 2) the molecule is phosphorylated by the
addition of a free phosphate group. The enzyme that catalyzes this reaction is glyceraldehyde-
3-phosphate dehydrogenase (GAPDH).
The chemistry that takes place in this reaction is more complex than that of the previous
reactions we've discussed. Knowledge of organic chemistry is needed to understand the specific
mechanisms of the conversion. Generally, the enzyme GAPDH contains appropriate structures
and holds the molecule in a conformation such that it allows the NAD molecule to pull a hydrogen
off the GAP, converting the NAD to NADH. The phosphate group then attacks the GAP molecule
and releases it from the enzyme to yield 1,3 bisphoglycerate, NADH, and a hydrogen atom. We
will come back to the role of this NAD/NADH molecule in the next section.
7. Transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP to give 3-

phosphoglycerate
In this step, 1,3 bisphoglycerate is converted to 3-phosphoglycerate by the enzyme
phosphoglycerate kinase (PGK). This reaction involves the loss of a phosphate group from the
starting material. The phosphate is transferred to a molecule of ADP that yields our first molecule
of ATP. Since we actually have two molecules of 1,3 bisphoglycerate (because there were two
3-carbon products from stage 1 of glycolysis), we actually synthesize two molecules of ATP at
this step. With this synthesis of ATP, we have cancelled the first two molecules of ATP that we
used, leaving us with a net of 0 ATP molecules up to this stage of glycolysis.
Again, we see that an atom of magnesium is involved to shield the negative charges on the
phosphate groups of the ATP molecule.

8. Isomerization of 3-phosphoglycerate to give 2-phosphoglycerate
This step involves a simple rearrangement of the position of the phosphate group on the 3
phosphoglycerate molecule, making it 2 phosphoglycerate. The molecule responsible for
catalyzing this reaction is called phosphoglycerate mutase (PGM). A mutase is an enzyme that
catalyzes the transfer of a functional group from one position on a molecule to another.
The reaction mechanism proceeds by first adding an additional phosphate group to the 2'
position of the 3 phosphoglycerate. The enzyme then removes the phosphate from the 3'
position leaving just the 2' phosphate, and thus yielding 2 phosphoglycerate. In this way, the
enzyme is also restored to its original, phosphorylated state.
9. Dehydration of 2-phosphoglycerate to give phosphoenolpyruvate

The ninth step involves the conversion of 2 phosphoglycerate to phosphoenolpyruvate
(PEP). The reaction is catalyzed by the enzyme enolase. Enolase works by removing a
water group, or dehydrating the 2 phosphoglycerate. The specificity of the enzyme
pocket allows for the reaction to occur through a series of steps too complicated to
cover here.
10. Transfer of a phosphate group from phosphoenolpyruvate to ADP to give pyruvate

The final step of glycolysis converts phosphoenolpyruvate into pyruvate with the help of the
enzyme pyruvate kinase. As the enzyme's name suggests, this reaction involves the transfer of
a phosphate group. The phosphate group attached to the 2' carbon of the PEP is transferred to
a molecule of ADP, yielding ATP. Again, since there are two molecules of PEP, here we actually
generate 2 ATP molecules.
We have now completed our discussion of the steps of glycolysis. If we go back and take count
of our ATP usage and generation, we find that we have consumed two molecules of ATP and
generate four to leave a net gain of two ATP molecules from the glycolytic pathway. We have
gone from our starting product, glucose, to our final product, pyruvate.

✓ Conversion of Six-Carbon Glucose to Three-Carbon Glyceraldehyde-3-
Phosphate
The first steps of the glycolytic pathway prepare for the electron transfer and the eventual
phosphorylation of ADP; these reactions make use of the free energy of hydrolysis of ATP;
Which is also called the “Preparation Step”
The First phase of Glycolysis involves Steps 1, 2, 3, 4 & 5.
• In Step 1, The reaction is endergonic, as it is driven by the free energy of

hydrolysis of ATP
✓ Glyceraldehyde-3-Phosphate is converted to Pyruvate
At this point, a molecule of glucose (a six-carbon compound) that enters the pathway has
been converted to two molecules of glyceraldehyde-3-phosphate. We have not seen any
oxidation reactions yet, but now we shall encounter them. Keep in mind that in the rest of the
pathway two molecules of each of the three carbon compounds take part in every reaction for
each original glucose molecule.
The second phase of Glycolysis involves Steps 6, 7, 8, 9 & 10
NOTE:
• In the final stages of glycolysis, two molecules of pyruvate are produced for each
molecule of glucose that entered the pathway
• These reactions involve electron transfer, and the net production of two ATP for
each glucose
• There are three control points in the glycolytic pathway
✓ Anaerobic Metabolism of Pyruvate

o Under anaerobic conditions, the most important pathway for the regeneration of
NAD+ is reduction of pyruvate to lactate
o Lactate dehydrogenase (LDH) is a tetrameric isoenzyme consisting of H and M
subunits; H4 predominates in heart muscle, and M4 in skeletal muscle
NAD+ Needs to be Recycled to Prevent Decrease in Oxidation Reactions

Alcoholic Fermentation
✓ Two reactions lead to the production of ethanol:
o Decarboxylation of pyruvate to acetaldehyde
o Reduction of acetaldehyde to ethanol
✓ Pyruvate decarboxylase is the enzyme that catalyzes the first reaction
✓ This enzyme require Mg2+ and the cofactor, thiamine pyrophosphate (TPP)
✓ Alcohol dehydrogenase catalyzes the conversion of acetaldehyde to ethanol
NOTE:
✓ Pyruvate is converted to lactate in anaerobic tissues, such as actively metabolizing muscle.
NAD+ is recycled in the process
✓ In some organisms, pyruvate is converted to ethanol in a process requiring thiamine
pyrophosphate as a coenzyme
E. Energy Production in Glycolysis

✓ Glycolysis is exergonic, and releases ~73.4 kJ/mole glucose converted to 2 moles of
pyruvate.
✓ Phosphorylation is also involved as 2 moles of ADP are converted to ATP.

F. Control of Glycolysis
One of the most important questions that we can ask about any metabolic pathway is, at which
points is control exercised? Pathways can be “shut down” if an organism has no immediate need
for their products, which saves energy for the organism. In glycolysis, three reactions are control
points. The first is the reaction of glucose to glucose-6-phosphate, catalyzed by hexokinase; the
second, which is the production of fructose-1,6-bisphosphate, is catalyzed by
phosphofructokinase; and the last is the reaction of PEP to pyruvate, catalyzed by pyruvate
kinas. It is frequently observed that control is exercised near the start and end of a pathway, as
well as at points involving key intermediates such as fructose-1,6-bisphosphate. When we have
learned more about the metabolism of carbohydrates, we can return to the role of
phosphofructokinase and efructose-1,6-bisphosphate in the regulation of several pathways of
carbohydrate metabolism.
Three reactions exhibit particularly large decreases in free energy; the enzymes that catalyze
these reactions are sites of allosteric control
• Hexokinase
• Phosphofructokinase
• Pyruvate kinase
✓ What roles do the first and last steps of glycolysis play in control of carbohydrate
metabolism?
Hexokinase and pyruvate kinase, the enzymes that catalyze the first and last steps,
respectively, are also important control points. They have the effect of slowing down the
pathway when energy is not needed and speeding it up when there is a need.
Control of liver pyruvate kinase

by phosphorylation. When blood
glucose is low, phosphorylation of
pyruvate kinase is favored.
The phosphorylated form is less
active, thereby slowing glycolysis
and allowing pyruvate to produce
glucose by gluconeogenesis.

LEARNING EVALUATION
TLA : Glycolysis Worksheet (45 points)

Expected Output: Answered Worksheet
Instructions: Answer the worksheet found in your google classroom
ASSESSMENTS
AT . (30 points)
Instructions: Answer the assessment found in your google classroom.
ASSIGNMENTS
Assignment for the next meeting:
Instruction: Advance reading on Storage Mechanisms and Control in Carbohydrate Metabolism.
RUBRICS FOR GRADING
A. Activities & Quizzes: Use the numeric scores
REFERENCES
Campbell, M.K., & Farrel, S.O. (2015). Biochemisty 8th Edition. Singapore; Cengage Learning Asia Pte
Ltd.
Rodwell, V.W., et al (2015). Harper’s Illustrated Biochemistry 30th Edition. United States: McGraw-Hill
Education
Fundamentals of Biology retrieved on July 18, 2020 from https://ocw.mit.edu/courses/biology/7-01sc-

fundamentals-of-biology-fall-2011/biochemistry/respiration-and-
fermentation/MIT7_01SCF11_1.6prob.pdf
Glycolysis Exercise retrieved on July 18, 2020 from

http://oregonstate.edu/instruct/bb450/450material/Recitations/week10/glycolysisexercise.pdf
Spark Notes Authors. (2005). Glycolysis. Retrieved July 18, 2020, from
https://www.sparknotes.com/biology/cellrespiration/glycolysis/section2/

TOPIC 8
STORAGE MECHANISM AND CONTROL IN CARBOHYDRATE METABOLISM
d. Describe why carbohydrate is a preferred energy source during exercise and why
carbohydrate metabolism is necessary for fat metabolism.
e. Demonstrate how glycogen is produced and degraded and how gluconeogenesis produce
glucose from pyruvate.
f. Discuss how glucose is diverted through the Pentose Phosphate Pathway
INTRODUCTION
When we digest a meal high in carbohydrates, we have a supply of glucose that exceeds
our immediate needs. We store glucose as a polymer, glycogen that is similar to the starches found
in plants; glycogen differs from starch only in the degree of chain branching. In fact, glycogen is
sometimes called “animal starch” because of this similarity.
A look at the metabolism of glycogen will give us some insights into how glucose can be
stored in this form and made available on demand. In the degradation of glycogen, several glucose
residues can be released simultaneously, one from each end of a branch, rather than one at a time
as would be the case in a linear polymer (Campbell & Farell, 2015).

I will commit whatever I do to the Lord and my plans will succeed. (Proverbs 16:3)
LEARNING CONTENT
Topic Content:
A. Production and Degradation of Glycogen
B. Gluconeogenesis
C. Control of Carbohydrate Metabolism
D. Pentose Phosphate Pathway
A. Production and Degradation of Glycogen

• The breakdown of glycogen takes place
• The Biochemical Connections Exercise Physiology – Why do athletes go in for glycogen
loading?
• Formation of glycogen to glucose – not the exact reversal of the breakdown of
glycogen to glucose.
➢ requires energy which is provided by the hydrolysis of a nucleoside
triphosphate, UTP.
• How is glycogen metabolism controlled?
➢ A major controlling factor lies in the behavior of glycogen phosphorylase
B. Gluconeogenesis
- gluconeogenesis the pathway of synthesis of glucose from lactate
- not the exact reversal of glycolysis
• Gluconeogenesis Produces Glucose from Pyruvate
➢ Glycolysis involves three irreversible steps, and the differences between glycolysis
and gluconeogenesis are found in these three reactions
1. The production of pyruvate (ATP) from phosphoenolpyruvate
2. The production of fructose-1,6-bisphosphate from fructose-6 phosphate
3. The production of glucose-6-phosphate from glucose
• Oxaloacetate an intermediate in gluconeogenesis
- The reaction of pyruvate and CO2 to give oxaloacetate – requires energy,
available from the hydrolysis of ATP

- Pyruvate carboxylase – the enzyme that catalyzes this reaction; an allosteric
enzyme found in mitochondria
- Acetyl-CoA is an allosteric effector that activate pyruvate carboxylase
- Biotin is a carrier of CO2; it has a specific site for covalent attachment of CO2

C. Control of Carbohydrate Metabolism
- The two sets of opposing pathways- glycolysis and gluconeogenesis, and the breakdown
and synthesis of glycogen – are reciprocally regulated
• The role of hormones in regulation of glycogen synthesis and breakdown

➢ The three important hormones – insulin, glucagon, and epinephrine – play a
significant role in regulation of carbohydrate metabolism
1. Insulin – secreted by the beta cells of the islets of Langerhans in the pancreas
– in response to increased blood glucose level
2. Glucagon – is a peptide hormone secreted by the alpha cells of the islets of
Langerhans; plays an important role when blood glucose level decreases
3. Epinephrine – is important on the very short time scale of the “fight of
flight” response
• Main categories of Metabolic Control

➢ Substrate cycling – refers to the fact that opposing reactions can be catalyzed
by different enzymes

• Different organs share Carbohydrate Metabolism
- an organism can set up a division of labor among tissues and organs to
maintain control of glucose metabolism.
➢ Cori cycle – cycling of glucose to glycolysis in muscle and gluconeogenesis in
➢ liver. It is named for Gerty and Carl Cori, who first described it.
D. Pentose Phosphate Pathway

- an alternative to glycolysis and differs from it in several ways.
- the production of ATP is not the crux of the matter compare to glycolysis.
- the important facet is the production of nicotinamide adenine dinucleotide
phosphate (NADPH)
➢ glucose-6-phosphate dehydrogenase – the enzyme that catalyzes the
reaction. Note that NADPH is produced by the reaction

LEARNING EVALUATION
TLA1: Lecture
For Asynchronous learners and Category 2A students, you may access the recorded
video lecture during your available time.

1. Why is it essential that the mechanisms that activate glycogen synthesis
also deactivate glycogen phosphorylase?
2. What is the role of biotin in gluconeogenesis?
3. Name two forms of control enzymatic action. Which of the two is
important in control of glycogen breakdown?
Format:
REFERENCES

TOPIC 9
THE CITRIC ACID CYCLE
g. Describe the function of the citric acid cycle during aerobic respiration and indicate the
reactants and products
h. Memorize the Citric Acid Cycle
i. Correlate certain metabolic processes that involves the conversion of non-glucose sources
into energy (Gluconeogenesis)
j. Articulate its biological connections with the spectrum of disease states that are associated
with it.
INTRODUCTION
The name we all primarily use here, the citric acid cycle, refers to the first molecule that
forms during the cycle's reactions—citrate, or, in its protonated form, citric acid. However, you may
also hear this series of reactions called the tricarboxylic acid (TCA) cycle, for the three carboxyl
groups on its first two intermediates, or the Krebs cycle, after its discoverer, Hans Krebs (Berg,
Tymoczko & Stryer, 2007).
The evolution of aerobic metabolism, by which nutrients are oxidized to carbon dioxide
and water, was an important step in the history of life on the Earth. Organisms can obtain far more
energy from nutrients by aerobic oxidation than by anaerobic oxidation. (Even yeast—which is
usually thought of in terms of the anaerobic reactions of alcoholic fermentation and is responsible
for producing bread, beer, and wine—uses the citric acid cycle and aerobically degrades glucose to
carbon dioxide and water.) (Campbell & Farell, 2015).
In my knowledge of God, I have everything I need for life and godliness. (2 Peter 1:3)
LEARNING CONTENT
Topic Content:
E. Central Role of the Citric Acid Cycle in Metabolism
F. Overall Pathway of the Citric Acid Cycle
G. Conversion of Pyruvate to Acetyl-CoA
H. Individual Reactions of the Citric Acid Cycle
I. The Glyoxylate Cycle: A Related Pathway
J. The Citric Acid Cycle in Catabolism and Anabolism
A. Central Role of the Citric Acid Cycle in Metabolism

• Citric Acid Cycle – a central metabolic pathway; part of aerobic metabolism
- amphibolic, it plays a role in both catabolism and anabolism
- two other common names:
1. Krebs cycle, after Sir Hans Krebs who first investigated the pathway
(Nobel Prize in 1953).
2. Ticarboxylic acid cycle (TCA cycle), some of the molecules involved
are acidswith three carboxylic groups.
• Three processes play roles in aerobic metabolism:
1. Citric acid cycle
2. Electron transport
3. Oxidative phosphorylation
B. Overall Pathway of the Citric Acid Cycle

1. Where does the citric acid cycle takes place in the cell
• Mitochondrion
➢ Mitochondrial matrix – inner membrane; the reaction of citric acid takes place
➢ Intermembrane space – exists between the inner and outer membranes

2. Key Features of the Citric Acid Cycle
C. Conversion of Pyruvate to Acetyl-CoA

• Five enzymes make up the pyruvate dehydrogenase complex in mammals
➢ Pyruvate dehydrogenase (PDH)
➢ Dihydrolipoyl transacetylase
➢ Dihydrolipoyl dehydrogenase
➢ Pyruvate dehydrogenase kinase
➢ Pyruvate dehydrogenase phosphatase

• The first three are involved in the conversion of pyruvate to Acetyl-CoA
• The kinase and phosphatase are enzymes used in the control of PDH and present
on a single polypeptide
• Lipoic acid – a compound that has a disulfide group in its oxidized form and two
sulfhydryl groups in its reduced form; act as an oxidizing agent
D. Individual Reactions of the Citric Acid Cycle
E. The Glyoxylate Cycle: A Related Pathway

• Glyoxylate Cycle – a pathway in plants that is an alternative to the citric acid cycle and that
bypasses several citric acid cycle reactions; result in the net conversion of two acetyl-CoA to
oxaloacetate
• Glyoxysomes – specialized organelles in plants; the sites of the glyoxylate cycle. It also
occurs in bacteria.

F. The Citric Acid Cycle
• In Catabolism
- the catabolic reactions occur in the cytosol; the citric acid cycle takes place in
mitochondria
- notice that sugars, fatty acids, and amino acids are all included in the overall catabolic
scheme. Just as “all roads lead to Rome” all pathways lead to citric acid cycle.
• In Anabolism
➢ Anaplerotic reaction – a reaction that replenishes a citric acid cycle intermediate
➢ In some organisms, acetyl-CoA can be converted to oxaloacetate and other
intermediates by the glyoxylate cycle, but mammals cannot do this
➢ In mammals, oxaloacetate is produced from pyruvate by the enzyme pyruvate
carboxylase

LEARNING EVALUATION
TLA1: Lecture
For Asynchronous learners and Category 2A students, you may access the recorded
video lecture during your available time.

1. Which pathways are involved in the anaerobic metabolism and aerobic
metabolism of glucose?
2. What are the unique reactions of the glyoxylate cycle?
3. Describe the various purposes of the citric acid cycle.
Format:
REFERENCES
Berg, J. M., J. A. Tymoczko, and L. Stryer. "The Citric Acid Cycle." In Biochemistry. 6th ed.
(New York, NY: W.H. Freeman and Company, 2007), 485.

TOPIC 10
LIPIDS AND PROTEINS: STRUCTURE FUNCTIONS
k. Know the structure of lipids and how it is metabolized
l. Articulate its biological connections with the spectrum of disease states that are associated
with it
INTRODUCTION
Lipids are compounds that occur frequently in nature. They are found in places as diverse as egg
yolks and the human nervous system and are an important component of plant, animal, and microbial
membranes. The definition of a lipid is based on solubility. Lipids are marginally soluble (at best) in water
but readily soluble in organic solvents, such as chloroform or acetone (Campbell & Farell, 2015).

I can do all things through Christ who strengthens me. (Philippians 4:13)
LEARNING CONTENT
Topic Content:
K. Introduction
L. The Chemical Natures of the Lipid Types
M. Biological Membranes
N. Kinds of Membrane Proteins
O. Function of Membranes
P. Lipid-Soluble Vitamins and Their Functions
A. Introduction
1. The Definition of Lipids
• Lipids – compounds thet occur frequently in nature; soluble (at best) in water but readily
soluble in organic solvents, such as chloroform or acetone
- Also known as FATS
- Considered as the “Petroleum Industry”
- Transported by lipoproteins
- Essential for STEROIDGENESIS
-
➢ Main Types of Lipids:
1. Triglycerides - contains three fatty acid molecules attached to one molecule of
glycerol; water insoluble
2. Cholesterol - can exist in an esterified form (cholesterol ester); cannot be utilized as
energy; can be converted to Vitamin D3.
2. Lipoproteins and Apolipoproteins

• Lipoproteins
➢ Low Density Lipoproteins (LDL)
- Apo B and Apo E
- Promotes ATHEROSCLEROSIS
- If taken up by the macrophages – FOAM CELLS
- Marker of coronary heart risk
- BAD CHOLESTEROL
➢ High Density Lipoproteins (HDL)

- Smallest and Most Dense
Two shapes:
1. Disc - contain two molecules of Apo A1; most active form
2. Spherical - forms a Core Region (Lipid, cholesterol esters TAG)
➢ Very Low-Density Lipoproteins (VLDL)

- Contains Apo B100, Apo E, and Apo C
- Carries ENDOGENOUS TRIGLYCERIDES
- Causes TURBIDITY ON ULTRACENTRIFUGATION

➢ Chylomicrons
- Contains Apo B48, Apo A, Apo C3
- Largest and LEAST DENSE
- Carries EXOGENOUS TRIGLYCERIDES
➢ Lpa
- LDL like particles
- If increased = may lead to CORONARY HEART DISEASE
- Competes with PLASMINOGEN
- GLYCOPROTEIN A binds to Apo B
• Apolipoproteins
- located on the surface of lipoproteins
Functions:
1. Receptors for inhibitors and activators that alter the lipoprotein structure.
2. Structural integrity to emulsified macromolecules.
3. Facilitates movement of lipids inside and outside the cell.
➢ Apolipoprotein B
➢ Apolipoprotein A
➢ Apolipoprotein C
➢ Apolipoprotein E
B. The Chemical Natures of the Lipid Types

• Fatty Acids – has a carboxyl group at the polar end and hydrocarbon chain at the nonpolar
tail; amphipathic
➢ Unsaturated – there are carbon – carbon double bonds
➢ Saturated – only single bond

• Triacylglycerols – when all three of the alcohol groups form ester linkages with fatty acids
- triglyceride, older name
• Phosphoacylglycerol – a phosphorous-containing portion esterified to glycerol
• Waxes – mixtures of esters of long-chain carboxylic acids and long-chain alcohols
• Sphingolipids – does not contain glycerol; contain long-chain amino alcohol sphingosine
• Glycolipids – a lipid to which a sugar moiety is boned
• Steroids – lipids with a characteristic fused-ring structure
C. Biological Membranes
• Lipid bilayer – an aggregate of a lipid molecule in which the polar head groups are in contact
with water and the hydrophobic parts are not.
D. Kinds of Membrane Proteins

• Peripheral proteins – on the surface of the membrane; bound to the charged head groups
of the lipid bilayer by polar interactions, electrostatic interaction or both.
• Integral proteins – within the lipid bilayer
➢ Removing integral proteins from membranes is much more difficult. Harsh conditions,
such as treatment with detergents or extensive sonication (exposure to ultrasonic
vibrations), are usually required.
• Transport proteins – components of membrane that mediate the entry of specific substance
into a cell
• Receptor proteins – proteins on a cell membrane with specific binding sites for extracellular
substances

➢ Fluid-Mosaic Model of Membrane Structure – most widely accepted description
of biological membranes.
- Mosaic implies that two components exist side by side without forming some
other substance of intermediate nature
- The term fluid mosaic implies that the same sort of lateral motion that we
- have already seen in lipid bilayers also occur in membranes.
E. Function of Membranes
1. Passive transport – a substance moves from a region of higher concentration to one of lower
concentration; the movement of the substance is in the same direction as a concentration
gradient, and the cell does not expend energy.
➢ Simple diffusion - molecule move directly through the membrane without interacting
with another molecule.
➢ Facilitated diffusion – the process of moving a molecule passively through a
membrane using a carrier protein.
2. Active transport – a substance moves from a region of lower concentration to one of higher
concentration (against a concentration gradient), requires the cell to expend energy.
➢ Sodium-potassium ion pump – moving potassium ions into a cell and
simultaneously moving sodium ions out of the cell.
F. Lipid-Soluble Vitamins and Their Functions
LEARNING EVALUATION
TLA1: Lecture

Discuss the following questions:

1. Proteins, nucleic acids, and carbohydrates are grouped by common structural features
found within their group. What is the basis for grouping substances as lipids?
2. Which is more hydrophilic, cholesterol or phospholipids? Defend your answer.
3. Why can some vitamin-K antagonists act as anticoagulant?
Format:
REFERENCES
Learning Asia.

TOPIC 11
LIPID METABOLISM
m. Articulate its uses in a biological standpoint
n. Articulate its biological connections with the spectrum of disease states that are associated
with it
INTRODUCTION
Lipids have many important biological roles, including being highly concentrated energy sources,
membrane components, and molecular signals. Along with cholesterol, lipids tend to have a bad
reputation in today’s world, even though they are absolutely necessary to good health. The lipids are an
exceedingly diverse group of biologically important materials that are distinguished by solubility (Moore
& Langley, 2011).
In this topic, we shall see how the metabolic oxidation of lipids releases large quantities of
energy through production of acetyl-CoA, NADH, and FADH2 and how lipids represent an even more
efficient way of storing chemical energy (Campbell & Farell, 2015).

I can ask God for wisdom and He will supply it. (James 1:5)
LEARNING CONTENT
Topic Content:
Q. Lipid Metabolism
R. Catabolism of Lipids
S. Fatty Acid Oxidation
T. The Energy Yield from the Oxidation of Fatty Acids
U. Catabolism of Unsaturated Fatty Acids and Odd Carbon Fatty Acids
V. Ketone Bodies
W. Cholesterol Biosynthesis
X. Mode of Action Fatty Acid Synthase
A. Lipid Metabolism
• Lipids Metabolism
➢ is the process that most of the fat ingested by the body is emulsified into small
particles by bile and then the lipase secreted by the pancreas and small intestine
hydrolyzes the fatty acids in the fat into free fatty acids and monoglycerides.
➢ Endogenous Pathway
➢ Exogenous Pathway
➢ Reverse Cholesterol Pathway
B. Catabolism of Lipids
• Triaglycerol fatty acid oxidation is the principal storage form of energy for most biological
beings.
• Phosphoacylglycerols which are important components of biological membranes, also
contains fatty acids in their structure.
• Pancreatic lipase and phospholipases: released to hydrolyze the bonds between the fatty
acids.
• Phospholipase A2: hydrolyzes the surface of miscelles
• Phospholipase D: occurs in venoms; causes tissue damage.
➢ Spider venom contains phospholipase D that can cause severe tissue damage.
➢ Snake venom also contains phospholipases (usually in low toxin concentrations).

➢ Products of the hydrolysis of lipids due to phospholipases
• Fatty acid release from the adipocyte is hormone mediated: EPINEPHRINE

o Upregulation of Lipid downstream pathway due to epinephrine
1. Epinephrine binds to the receptor on the plasma membranes.
2. Adenylate cyclase is activated.
3. Active protein kinase A is produced.
4. Protein kinase phosphorylates triacylglycerol lipase.
5. Fatty acids are cleaved from the glycerol backbone.
• Other actions of epinephrine.

- Epinephrine inhibits the release of insulin from the islets of Langerhans (beta).
- Epinephrine release must occur in a specified period of time.

C. Fatty Acid Oxidation
o FATTY ACID OXIDATION (BETA-OXIDATION)

• When fatty acids with an even number of carbon atoms (ones normally found in
nature) undergoes successive rounds of Beta-oxidation cycle Acetyl CoA
• The number of molecules of acetyl-CoA produced is equal to half the number of
carbon atoms in the original fatty acid.
Example: STEARIC ACID (18 carbon atoms) 9 molecules of acetyl-CoA
D. The Energy Yield from the Oxidation of Fatty Acids

• The energy released by the oxidation of acetyl-CoA formed by Beta-oxidation of FA can be
used to produce ATP.
➢ TWO SOURCES OF ATP:

• REOXIDATION of NADH and FADH2 produced by the fatty acid to acetyl-CoA.
• Processing of the acetyl-CoA through the citric acid cycle and oxidative phosphorylation
o STEARIC ACID (contains 18 carbon atoms): it takes eight (8) cycles of Beta-
oxidation to convert one mole of stearic acid nine (9) moles of acetyl-CoA
o Eight moles of FAD are reduced to FADH2, and eight moles of NAD are reduced to
NADH.

• 9 moles of acetyl-CoA produced from each mole of stearic acid enter the citric acid cycle.
• One mole of FADH2 and three moles of NADH are produced for each mole of acetyl-CoA
enter the citric acid cycle
• Simultaneously: One mole of GDP is phosphorylated to produce GTP for each turn of the citric
acid cycle.
• FADH2 and NADH products of Beta-oxidation and Citric Acid Cycle enter the electron transport
chain.
• 17 moles for FADH2 (8 beta oxidation, and 9 from citric acid cycle).
• 35 moles for NADH (8 beta oxidation, and 27 from citric acid cycle).
• 2.5 moles of ATP for each mole of NADH and 1.5 moles of ATP result from each mole of
FADH2.
• Overall yield = Beta-oxidation, citric acid cycle, and oxidative phosphorylation.
• Take note: GDP = ADP, and GTP = ATP
• Nine (9) ATP must be added to those produced in the reoxidation of FADH2 and NADH.
• ATP equivalent to the 9 GTP (Citric acid cycle), 25.5 ATP from the reoxidation of
FADH2, and 87.5 ATP from the reoxidation of NADH.
E. Catabolism of Unsaturated Fatty Acids and Odd Carbon Fatty Acids

• Fatty acids with ODD NUMBERS of CARBON ATOMS also undergoes BETA-OXIDATION
➢ UNSATURATED VS SATURATED FATTY ACIDS OXIDATION (MONOSATURATED)

➢ UNSATURATED VS SATURATED FATTY ACIDS OXIDATION (POLYUNSATURATED)
F. Ketone Bodies
• ACETONE related substances are called KETONES results if increased acetyl CoA arises
from beta-oxidation.
• Oxaloacetate is not readily available to react with Acetyl-CoA.
• OXALOACETATE arises from the glycolytic pathway.
➢ Diabetes: The inability to produce or inefficient use of insulin.

➢ Type 1: Insulin Dependent Diabetes Mellitus (JUVENILE): Destruction of the beta cells
of the Islets of Langerhans No or little insulin production.
➢ Prone to Diabetic Ketoacidosis
➢ Type 2: Non-Insulin Dependent Diabetes Mellitus: Adequate amounts of insulin

produced but cells are resistant to it (Insulin resistance/Desensitization)
➢ Not prone Diabetic Ketoacidosis
G. Cholesterol Biosynthesis
- The ultimate precursor of all the carbon atoms in cholesterol and in the other steroids that
are derived from cholesterol is the acetyl group of acetyl-CoA.

• Lipoproteins and Apolipoproteins
o Lipoproteins
➢ Low Density Lipoproteins (LDL)
- Apo B and Apo E
- Promotes ATHEROSCLEROSIS
- If taken up by the macrophages – FOAM CELLS
- Marker of coronary heart risk
- BAD CHOLESTEROL
➢ High Density Lipoproteins (HDL)

- Smallest and Most Dense
Two shapes:
3. Disc - contain two molecules of Apo A1; most active form
4. Spherical - forms a Core Region (Lipid, cholesterol esters TAG)
➢ Very Low-Density Lipoproteins (VLDL)

- Contains Apo B100, Apo E, and Apo C
- Carries ENDOGENOUS TRIGLYCERIDES
- Causes TURBIDITY ON ULTRACENTRIFUGATION
➢ Chylomicrons
- Contains Apo B48, Apo A, Apo C3
- Largest and LEAST DENSE
- Carries EXOGENOUS TRIGLYCERIDES
➢ Lpa
- LDL like particles
- If increased = may lead to CORONARY HEART DISEASE
- Competes with PLASMINOGEN
- GLYCOPROTEIN A binds to Apo B
• Apolipoproteins
- located on the surface of lipoproteins
Functions:
4. Receptors for inhibitors and activators that alter the lipoprotein structure.
5. Structural integrity to emulsified macromolecules.
6. Facilitates movement of lipids inside and outside the cell.
➢ Apolipoprotein B
➢ Apolipoprotein A
➢ Apolipoprotein C
➢ Apolipoprotein E

H. Mode of Action Fatty Acid Synthase
• Addition of two carbon units to the growing fatty acid chain
• This process/reaction involves a multienzyme complex (FATTY ACID SYNTHASE).

• Fat anabolism of anabolism is palmitate
• Before the transfer of 2 carbon units to the fatty acid chain there is a PRIMING STEP.
• Note: 1 molecule of acetyl CoA is required for each molecule of palmitate
• Malonyl group is transferred from thioester linkage with CoA-SH forming a thioester bond with
ACP.
• Condensation reaction occurs.
• Two of the four carbons come from the primary acetyl group – other two comes from malonyl
• Two reductions and 1 dehydration to form butyryl-ACP.
• Beta keto group is reduced to alcohol.
➢ ACYLGLYCEROL and COMPOUND LIPIDS SYNTHESIS; TRIACYLGLYCEROLS and

PHOSPHOACYLGLYCEROLS
LEARNING EVALUATION
TLA1: Lecture

1. Under what conditions are ketone bodies produced?
2. What is the purpose of having ACP as a distinct activating group for fatty-acid synthesis?
3. What is the role of citrate in the transport of acetyl groups from the mitochondrion to the
cytosol?
Format:
REFERENCES
Campbell, M. K., & Farell, S. O. (2015). Biochemistry (8th ed.). (R. Lee, Ed.)
Singapore: Cengage Learning Asia.
Moore, J. T., & Langley, R. H. (2011). Biochemistry for Dummies 2nd Edition.
Hoboken, NJ: Wiley Publishing Inc.

TOPIC 12
Nucleic Acids: INFORMATION MOLECULES
o. Discuss the difference between the level of structures is nucleic acids
p. Discuss and illustrate the structure of DNA and its denaturation
q. Discuss the principal types of RNA and its functions
INTRODUCTION
Nucleotides have a variety of roles in cellular metabolism. They are the energy currency in metabolic
transactions, the essential chemical links in the response of cells to hormones and other extracellular stimuli,
and the structural components of an array of enzyme cofactors and metabolic intermediates. And, last but
certainly not least, they are the constituents of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA), the molecular repositories of genetic information.
The structure of every protein, and ultimately of every biomolecule and cellular component,
is a product of information programmed into the nucleotide sequence of a cell’s nucleic acids. The ability to
store and transmit genetic information from one generation to the next is a fundamental condition for life.
In this topic, we will discuss the overview of the chemical nature of the nucleotides and nucleic
acids found in cells.
LEARNING CONTENT
BASIC and FUNDAMENTALS
LEVELS OF STRUCTURE:
o Primary structure: order of bases in the
polynucleotide sequence
o Secondary structure: three dimensional
conformation of the backbone
o Tertiary structure: supercoiling of the molecule
PRINCIPAL TYPES of NUCLEIC ACIDS

DNA: Deoxyribonucleic Acids
RNA: Ribonucleic Acids
They differ in secondary and tertiary structures
o Covalent structure of polynucleotides:

o Polymers can be broken down into smaller units
(monomers).
o The monomers of nucleic acids are called NUCLEOTIDES

NUCLEIC ACIDS BASES (NUCLEOBASES)
Pyrimidines (single ring aromatic) and Purines (double ring aromatic)
Base: refers to a one or two-ring nitrogenous aromatic compound.
COMPONENTS AND STRUCTURES OF NUCLEOTIDES

NUCLEOSIDE
Base and sugar covalently linked together.
Base forms a glycosidic linkage with the sugar.
B-D-ribose = ribonucleoside
B-D-deoxyribose = Deoxyribonucleoside
When PHOSPHORIC ACID is esterified to one of the hydroxyl

groups of the sugar portion of a NUCLEOSIDE →
NUCLEOTIDE
o Naming: named after the parent nucleoside with the
suffix monophosphate
o Remember: 5’ nucleotides are most commonly

encountered in nature
o With the addition of phosphate groups form
anhydride linkages to the first phosphate ---- >
forming DIPHOSPHATES and TRIPHOSPHATE

NUCLEIC ACID FORMATION
o NUCLEIC ACID POLYMERIZATION results to the formation of nucleic acids
o Link between monomers in nucleic acids is mediated by two ester bonds of phosphoric
acid.
o NOTE: hydroxyl groups in the esterification of phosphoric acid are 3’ and 5’.
o 3’(carries free hydroxyl group) 5’ (carries phosphate group) phosphodiester
o Remember: MOST IMPORTANT features are the identities of the BASES.

o Single letters are used to convey the sequence of information
o Position of the sugar moieties to which the individual bases are attached.
o Represents the PHOSPHODIESTER BOND
o More common way of annotation is to use single letters to show the order of the bases.
o when “p” is written to the left it represents a 5’ nucleotide
o when “p” is written to the left it represents a 3’ nucleotide
o OLIGONUCLEOTIDE SEQUENCE can be written in two ways.
o DNA vs RNA: in DNA the sugar is 2’ deoxyribose instead of ribose

o Sometimes a “d” is added to indicate deoxyribonucleotide residue.
o However the addition of “d” is not necessary because it is understood that it is DNA because of
the presence of:

THE STRUCTURE OF DNA
o The double helix was introduced by James Watson and Francis Crick in 1953
o X-ray patterns + chemical analyses → A = T, G = C (Chargaff’s rule)
o Led to the conclusion that DNA consists of two polynucleotide chains are around each to
form a helix.
o Hydrogen bonds → determines the alignment of the helix
o Sugar-phosphate backbone → outer part of the helix.
o Antiparallel directions → 3’ to 5’’ and 5’ and 3’
o DNA structures exhibit complementary base pairing (A and T, G and C) → COMPLEMENTARY
STRANDS

o Atoms that make up the polynucleotide does not fill up the double helix → empty spaces known
as GROOVES.
o Two types of grooves: MAJOR GROOVE and MINOR GROOVE
o Note: Neutral pH → phosphate group of the backbone carries a negative charge (can be the
site of neutralization by positively charged ions: Na and Mg)
o B – DNA: principal form that occurs in nature.

o A – DNA: 11 base pairs for each turn of the helix, base pairs are not perpendicular to the axis,
with an angle of 20°.
Formed from artifacts of DNA preparation.

o B-DNA and A-DNA: are right handed helices.
o DNA and RNA hybrids can adopt the A formation (Also RNA:RNA hybrids)
o Z-DNA: left handed, occurs in nature, sequence of alternating purine and pyrimidine nucleotides,
dCpGpCpGpCpG
Cytoside methylated at the number 5 position of the pyrimidine ring.
Derivative of the B-DNA (flipping one side of the backbone 180°
Take note of the zigzag look of phosphodiester.
o BASE STACKING: hydrophobic interactions and van der Waals forces of pi cloud electrons.
o In B-DNA: each base pair is rotated 32°.
o Edge bases are exposed to the minor groove.
o Propeller twist: characteristic twisting of the base pairs
Remember:
o DNA molecule has a length considerably greater than its diameter
o DNA is not completely stiff and can fold back to itself (to become tertiary structures)
o Relaxed DNA (without other twists other than the helical twists) are far much easier to
understand than DNA with SUPERCOILS.

PROKARYOTIC SUPERCOILS
TWO TYPES OF SUPERCOILS:

NEGATIVE (UNDERWOUND): circular DNA, fewer than the normal number of turns of the helix,
POSITIVE (OVERWOUND): circular DNA, more than the number of turns of the helix,
o Take note: Naturally occurring circular DNA are negatively supercoiled.

o Supercoils are affected by enzymes:
TOPOISOMERASES:
o Class I: cuts the phosphodiester backbone of one strand of DNA, pass the end, reseal the
backbone
o Class II: cuts both DNA strands, pass remaining DNA helix between the cut ends, reseal.
o DNA GYRASE: Class II topoisomerase, synthesized by the bacterial cell.

o NOTE: Ultracentrifugation can be used to detect supercoiled DNA

EUKARYOTIC SUPERCOILS
o Follows a more complicated path.

o The DNA is complexed with proteins
(positive side chains at neutral pH). →
thru electrostatic attraction with the
negative charged phosphates in DNA
o CHROMATIN → contains histones
o Electron microscope → beads on a string
o Nucleosome: DNA wrapped around a
histone core
o The protein core is an octamer:
o (H2A)2(H2B)2(H3)2(H4)2
o Spacer regions
o Histone modification: acetylation,
methylation, phosphorylation, and
ubiquititnylation
DNA DENATURATION
o Stabilization energy: must be disrupted to
disturb the stacking interactions through
breaking of the hydrogen bonds.
o A.K.A melting: monitored by UV absorption
(260 nm)
o Hyperchromicity effect
o Results to the unstacking of the base
pairs
o Change is absorbance

RNA TYPES AND STRUCTURES
o Six kinds of RNA – tRNA, rRNA, mRNA, snRNA, miRNA, and siRNA.
o Participates in the synthesis of proteins.
o REMEMBER: the base sequences of all types of RNA are determined by that of DNA.
o RIBOSOMES: site for assembly of the growing polypeptide chain in protein synthesis. (rRNA)

PROKARYOTIC and EUKARYOTIC RNA
o Prokaryotes → NO NUCLEAR MEMBRANE: mRNA direct the synthesis of proteins while it is
still being transcribed.
o Eukaryotes → undergoes a tedious process → splicing out INTRONS → EXONS will be
expressed.
o Small nuclear RNAs: found only in the nucleus of eukaryotic cells
o SiRNAs: Main players in RNA interference (RNAi),
o MicroRNAs: evolutionary relationship between bacteria and bacteriophages
ROLE of tRNA in PROTEIN SYNTHESIS

o There are several tRNA for each amino acid.
o Intrachain hydrogen bonding occurs forming A-
U and G-C base pairs.
o forms duplexes of the A-helical form
o Cloverleaf structure: SECONDARY
STRUCTURE of tRNA
o Hydrogen portions are called stems
o Protein Synthesis: Both tRNA and mRNA are
bound to the ribosome.
o L shaped form: allows the tRNA to interact
with the enzyme that attaches amino acid to
the 2’ and 3’ end.
o tRNA nucleotidyltransferase adds CCA to the 3’
end.

LEARNING EVALUATION
Meeting No. 1:
TLA 01: Lecture
TLA 02: Summary and illustrations

Expected Output: Illustrations with description
Instruction:
1. Draw the structures of the common nucleobases (classify to whether it is found in DNA and/or
RNA).
2. Draw the structure of DNA and identify its parts and functions
Meeting No. 2
TLA 03: Illustration and Summary
Expected Output: Summary and Illustration
3. Draw/ Illustrate a workflow of the DNA denaturation process.

4. Identify 2 methods which evaluates DNA and/or RNAs. Give the following details:
Name of Method:
Principle:
Significance:
Results and Interpretations:
Format:
Paper size: Letter Font size: 11 Illustrations should be hand-made ****

REFERENCES
Learning Asia.
Publishing Inc.

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University of the Immaculate Conception

COLLEGE OF MEDICAL AND BIOLOGICAL SCIENCE

Course Code : CHM311

𝐶𝑂𝑖 = 70% ∑ 𝐴𝑇𝑗 + 30% ∑ 𝑇𝐿𝐴𝑧

CMBS CHM331: Biochemistry for MLS A.Y. 2020-2021 Page 1 of 70

2. BIOCHEMISTRY SPEAKS OF DIVERSE BIOCHEMICAL PATHWAYS

3. BIOCHEMISTRY SPEAKS ABOUT STRUCTURE AND ORGANIZATION

B. Chemical Foundations of Biochemistry

BIOCHEMISTRY and ORGANIC CHEMISTRY

CMBS CHM331: Biochemistry for MLS A.Y. 2020-2021 Page 2 of 70

5. BIOCHEMISTRY and The Origin of Life

6. BIOCHEMISTRY and BIOMOLECULES

Living cells consists of assembly of VERY LARGE MOLECULES:

MONOMERS – small molecules that may bond to form a polymer

The formation or polymerization of monomers have a SENSE OF “DIRECTIONALITY” which

CMBS CHM331: Biochemistry for MLS A.Y. 2020-2021 Page 3 of 70

C. Beginnings of Biology: Origin of Life

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TLA 2: Small Group Discussion and Reflective Writing

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A. Water and Polarity

ELECTRONEGATIVITY: tendency of an atom to attract electrons to itself in a chemical bond.

WATER: SOLVENT PROPERTIES

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HYDROGEN BONDS – BIOLOGICALLY IMPORTANT MOLECULES

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ACID DISSOCIATION CONSTANT: expression of acid strength

Instruction: Illustrate and describe the different types of molecular interactions.

TLA 3: Computation Exercise

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General Properties of Amino Acids

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AMINO ACID CLASSIFICATION

Aliphatic Amino Acid Polar or Uncharged

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TLA 02: Summary, classifications and illustrations

NOTE: ALWAYS CITE REFERENCES USING APA FORMAT

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RATE OF REACTION: Depends on FREE ENERGY OF ACTIVATION or ACTIVATION ENERGY

Enzyme Substrate Binding

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Factors the Influence Enzymatic Reactions

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TLA 02: Summary, classifications and illustrations

Enzyme Classification Name of Function Clinical Applications

1. Draw/ Illustrate a workflow of the different types of enzyme inhibition.

NOTE: ALWAYS CITE REFERENCES USING APA FORMAT

CMBS CHM331: Biochemistry for MLS A.Y. 2020-2021 Page 16 of 70

Biological Energy Transformations Obey the Laws

2. The Universe always tends toward increasing

Gibbs Free Energy, (G)

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▲G = free energy change

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Oxidation: the loss of electrons

Reducing Agent: a substance that gives up electrons to other substances

Mnemonic: LEORA (Loss of Electron, Oxidation, Reducing Agent)

Coenzymes in Biologically Important Oxidation-Reduction Reactions