B i c o l U n i v e r s i t y Ta b a c o C a m p u s

Ta y h i , Ta b a c o C i t y

Nursing Department

LEARNING MODULE FOR BIOCHEMISTRY

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PART 1
A. Introduction to Biochemistry
A.1 Basic Biochemistry Concepts
• Biomolecules
• Metabolism
A.2 Cell structure and imaging
• Types of Living Cells

Suggested Laboratory Activity:

• Biochemical Processes
• Plant and Animal Cell

A.1 Basic Biochemistry Concepts

Why Biochemistry?
Why not?
Biochemistry is the chemistry of living organisms. Biochemists study the chemical reactions that occur at the
molecular level of organisms. Normally it is listed as a separate field of chemistry. However, in some schools
it is part of biology, and in others it is separate from both chemistry and biology.

The chemical constituents of living cells and of the reactions and processes they undergo.
The key thing to remember is that biochemistry is the chemistry of the living world. Plants, animals, and
single-celled organisms all use the same basic chemical compounds to live their lives. Biochemistry is not
about the cells or the organisms. It's about the smallest parts of those organisms, the molecules. It's also
about the cycles that create those biological compounds.

You can probably guess that biochemical cycles repeat over and
over. Those cycles allow living creatures to survive on Earth. It could
be the constant process of photosynthesis that creates sugars in
plants or building complex proteins in the cells of your body. Also,
cycles rely on enzymes and other proteins to move the atoms and
molecules. Understanding the helper molecules is as important as
learning about the cycles themselves. Every cycle has a place, and
each one is just a small piece that helps an organism survive. In
each cycle, molecules are used as reactants and then transformed
into products. Life is one big network of activity where each piece relies on all of the others.

Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular
level. It emerged as a distinct discipline around the beginning of the 20th century when scientists combined
chemistry, physiology and biology to investigate the chemistry of living systems by:

A. Studying the structure and behavior of the complex molecules found in biological material and
B. the ways these molecules interact to form cells, tissues and whole organism

PRINCIPLES OF BIOCHEMISTRY

Biochemistry really reaches out and combines aspects of all the fields of chemistry. By this definition,
biochemistry
Encompasses large areas of cell biology, molecular biology, and molecular genetics
Cell Theory Molecular Biology and Genetics
1. Every living thing is made up of one or more cells
2. Cell carry out the function to support life
3. Cells are produced by other cells

PRINCIPLES OF BIOCHEMISTRY

1. Cells (basic structural units of living

organisms) are highly organized
Biomolecules include large macromolecules (or polyanions) such as and constant source of energy is
proteins, carbohydrates, lipids, and nucleic acids, as well as small required to maintain the ordered
molecules such as primary metabolites, secondary metabolites, and state.
natural products. A more general name for this class of material is 2. Living processes contains
biological materials. thousands of chemical reactions.
Precise regulation and integration
The four classes of biological molecules of these reactions are required to
1. Lipids maintain life
▪ Saturated, unsaturated, trans fats 3. Certain important reactions (e.g.
▪ Phospholipids Glycolysis is found in almost all
▪ Steroids organisms)
2. Carbohydrates 4. All organisms use the same type of
▪ Monosaccharides molecules: carbohydrates, proteins,
▪ Disaccharides lipids & nucleic acids.
▪ Polysaccharides 5. Instructions for growth,
3. Proteins reproduction and developments for
▪ Amino acids each organism is encoded in their
▪ Primary, secondary, tertiary, quarternary structure DNA
4. Nucleic acids
▪ Nucleotides (DNA and RNA)
 Brain Challenge!
Give the importance and functions
of Nucleic Acids in general aspect.

✓ Just like cells are building blocks of tissues likewise molecules are building blocks of cells.
✓ Animal and plant cells contain approximately 10,000 kinds of molecules (bio-molecules)
✓ Water constitutes 50-95% of cells content by weight.
✓ Ions like Na+, K+ and Ca+ may account for another 1%
✓ Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)
✓ Infinite variety of molecules contain C.
✓ Most bio-molecules considered to be derived from hydrocarbons.
✓ The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-
molecules have more than one.
MOLECULES AND MACROMOLECULES
Atoms – smallest unit of an element

Molecule/Monomer – a group of two or more atoms held

together by covalent bonds.

Macromolecules/Polymer – a long molecules made of

monomer bonded together to form a polymer

Polymerization Reactions
The chemical reaction in which high
molecular mass molecules are formed from
monomers is known as polymerization. There
STRUCTURE OF MONOMER AND POLYMER are two basic types of polymerization, chain-
reaction (or addition) and step-reaction (or
condensation) polymerization.

Chain-Reaction Polymerization

This type of polymerization is a three step

process involving two chemical entities. The
first, known simply as a monomer, can be
regarded as one link in a polymer chain. It
initially exists as simple units. In nearly all
cases, the monomers have at least one
carbon-carbon double bond.
Step-Reaction Polymerization
This polymerization method typically
produces polymers of lower molecular weight
 CREATING AND BREAKING DOWN POLYMERS

DEHYDRATION/ CONDENSATION REACTION HYDROLYSIS

- two monomers bond together through the loss - two bonded monomers split apart using a water
of a water molecule molecule

Metabolism
Metabolism is a general term that encompasses all chemical
changes occurring in living organism. The term metabolic pathway
describes a series of chemical reactions that either break down a
large compound into smaller units (catabolism) or build more
complex molecules from smaller ones (anabolism). Metabolism
begins with the ingestion of food that is foreign to the organism
(containing a varying amount of smaller and larger compounds),
which is broken down in the digestive tract to smaller molecules by
hydrolysis
The Cell is the Metabolic Processing Center
- Cells are the “work centers” of metabolism. Although our
bodies are made up of different types of cells (liver cells,
brain kidney cells muscle cells), most have a similar
structure. Mitochondria, the power plants within the cells,
contain many of the breakdown pathways that produce
energy.

Key Energy Terms

ATP : Adenosine triphosphate
NAD+ : Nicotinamide adenine dinucleotide (oxidized)
NADH : Nicotinamide adenine dinucleotide (reduced)
NADP+ : Nicotinamide adenine dinucleotide phosphate
(oxidized)
NADPH : Nicotinamide adenine dinucleotide phosphate
(reduced)
FAD+ : Flavin adenine dinucleotide (oxidized)
FADH2 : Flavin adenine dinucleotide (reduced)
 Energy: Fuel for Work

All cells require energy to sustain life. Even during sleep, your body uses
energy for breathing, pumping blood, maintaining body temperature,
delivering oxygen to tissues, removing waste products, synthesizing new
tissue for growth, and repairing damaged or worn-out tissues. When awake,
you need additional energy for physical movement (such as standing,
walking, and talking) and for the digestion and absorption of foods.

Biological systems use heat, mechanical, electrical, and chemical forms of

energy. Our cells get their energy from chemical energy held in the molecular
bonds of carbohydrates, fats, and protein—the energy macronutrients—as
well as alcohol. The chemical energy in foods and beverages originates as
light energy from the sun. Green plants use light energy to make
carbohydrate in a process called photosynthesis. In photosynthesis, carbon
dioxide (CO2) from the air combines with water (H2O) from the earth to form
a carbohydrate, usually glucose (C6H12O6), and oxygen (O2). Plants store
glucose as starch and release oxygen into the atmosphere. Plants such as
corn, peas, squash, turnips, potatoes, and rice store especially high amounts
of starch in their edible parts. In the glucose molecule, the chemical bonds
between the carbon (C) and hydrogen (H) atoms hold energy from the sun.
When our bodies extract energy from food and convert it to a form that our
cells can use, we lose more than half of the total food energy as heat

Transferring Food Energy to Cellular Energy

Although burning food releases energy as heat, we cannot use heat

to power the many cellular functions that maintain life. Rather than
using combustion, we transfer energy from food to a form that our
cells can use.

Stage 1: Digestion, absorption, and transportation. Digestion

breaks food down into small subunits—simple sugars, fatty acids,
monoglycerides, glycerol, and amino acids—that the small intestine
can absorb. The circulatory system then transports these nutrients
to tissues throughout the body.
Stage 2: Breakdown of many small molecules to a few key
metabolites. Inside individual cells, chemical reactions convert
simple sugars, fatty acids, glycerol, and amino acids into a few key
metabolites (products of metabolic reactions). This process
liberates a small amount of usable energy.
Stage 3: Transfer of energy to a form that cells can use. The
complete breakdown of metabolites to carbon dioxide and water
liberates large amounts of energy. The reactions during this stage
are responsible for converting more than 90 percent of the available
food energy to a form that our bodies can use.
 Key Energy Players

Certain compounds have recurring roles in metabolic activities.

Adenosine triphosphate (ATP) is the fundamental energy molecule used
to power cellular functions, so it is known as the universal energy. Two
other molecules, NADH and FADH2, are important couriers that carry
energy for the synthesis of ATP. A similar energy carrier, NADPH,
delivers energy for biosynthesis.

ATP: The Body’s Energy Currency

To power its needs, your body must convert the energy in food to a
readily usable form—ATP. This universal energy currency kick-starts
many energy releasing processes, such as the breakdown of glucose
and fatty acids, and powers energy-consuming processes, such as
building glucose from other compounds. Remember that making large
molecules from smaller ones, like constructing a building from bricks,
requires energy.
Production of ATP is the fundamental goal of metabolism’s energy-producing pathways. The body’s energy-
producing pathways lead to ATP production.
The ATP molecule has three phosphate groups attached to adenosine, which is an organic compound.
Because breaking the bonds between the phosphate groups releases a tremendous amount of energy, ATP
is an energy rich molecule. Cells can use this energy to power biological work. When a metabolic reaction
breaks the first phosphate bond, it breaks down ATP to adenosine diphosphate (ADP) and pyrophosphate
(Pi). Breaking the remaining phosphate bond releases an equal amount of energy and breaks down ADP to
adenosine monophosphate (AMP) and Pi.

ATP, ADP, and AMP. Your body can The ADP–ATP cycle. When extracting
readily use the energy in high-energy energy from nutrients, the formation of
phosphate bonds. During metabolic ATP from ADP + Pi captures energy.
reactions, phosphate bonds form or break Breaking a phosphate bond in ATP to form
to capture or release energy. ADP + Pi releases energy for biosynthesis
and work
Because the reaction can proceed in either direction, ATP and ADP
are interconvertible. When extracting energy from carbohydrate,
protein, and fat, ADP binds Pi, forming a phosphate bond and
capturing energy in a new ATP molecule. When the reaction flows in
the opposite direction, ATP releases Pi, breaking a phosphate bond
and liberating energy while re-forming ADP. This liberated energy can
power biological activities such as motion, active transport across cell
membranes, biosynthesis, and signal amplification.

The molecule guanosine triphosphate (GTP) is similar to ATP and

holds the same amount of available energy. Like ATP, GTP has high-
energy phosphate bonds and three phosphate groups, but they are
linked to guanosine rather than to adenosine. Energy-rich GTP
molecules are crucial for vision and supply part of the power needed
to synthesize protein and glucose. GTP readily converts to ATP

NADH and FADH2: the body’s energy shuttles

When breaking down nutrients, metabolic reactions release high-energy electrons. Further reactions transfer
energy from these electrons to ATP. (See Figure 7.7.) To reach the site of ATP production, high-energy
electrons hitch a ride on special molecular carriers. One major electron acceptor is nicotinamide adenine
dinucleotide (NAD+), a derivative of the B vitamin niacin. The metabolic
pathways have several energy-transfer points where an NAD+ accepts
two high-energy electrons and two hydrogen ions (two protons [2H +])
to form NADH + H+. For simplicity, the “+ H+” is often dropped when
talking about NADH. The other major electron acceptor is flavin
adenine dinucleotide (FAD), a derivative of the B vitamin riboflavin.
When FAD accepts two high-energy electrons, it picks up two protons
(2H+) and forms FADH2
 NADPH: An Energy Shuttle for Biosynthesis

Energy powers the assembly of building blocks into complex

molecules of carbohydrate, fat, and protein. NADPH, an energy-
carrying molecule similar to NADH, delivers much of the energy these
biosynthetic reactions require. The only structural difference between
NADPH and NADH is the presence or absence of a phosphate group.
Although both molecules are energy carriers, their metabolic roles are
vastly different. Whereas the energy carried by NADH primarily
produces ATP, nearly all the energy carried by NADPH drives
biosynthesis. When a reaction transforms NADPH into NADP+
(nicotinamide adenine dinucleotide phosphate), NADPH releases its
cargo of two energetic electrons.

Key Concepts ATP is the energy currency of the body. Your body extracts
energy from food to produce ATP. NADH and FADH 2 are hydrogen and
electron carriers that shuttle energy to ATP production sites. NADPH is also a
hydrogen and electron carrier, but it shuttles energy for anabolic process

A.2 Cell Structure and Imaging

The Cells
Organisms are composed of one or more cells, the basic units of life. One of
the basic principles of biology is that cells only arise from other cells. There
are about 200 different kinds of cells in the human body, and each adult
human contains about 1013 cells all working together. Different types of
cells display a wide variety of shapes and sizes. That is why our bodies
contain reserves of stem cells, flexible precursor cells that can
irreversibly change into many different types of specialized cells. For
example, all the different blood cell types (red cells and the various types
of white cells) are replaced regularly, arising from a single type of stem cell
in the bone marrow.

Cell Theory
Cells are the building blocks of life. Some plants and animals are so small and simple that they are made up
of only one cell (unicellular). Most of the plants and animals we are familiar with are made up of many cells
(multicellular). Cell theory is the basis of modern biology. There are three main points to the cell theory:
• The cell is the basic unit of life.
• All living things are composed of one or more cells.
• All cells come from pre-existing cells. Brain Challenge!
Discuss all the characteristics of a
An organism may comprise just a single cell (unicellular), a collection of living organisms.
cells that are not morphologically or functionally differentiated (colonial),
or several distinct cell types with specialised functions (multicellular). Among microorganisms, all bacteria
and protozoans are unicellular; fungi may be unicellular or multicellular, while algae may exist in all three
forms. There is, however, one way that organisms can be differentiated from each other that is even more
fundamental than whether they are uni- or multicellular.

Cells may be Prokaryotic or Eukaryotic

Cell Parts Prokaryotic Eukaryotic
Cell size 0.2-2 um in diameter 10-100 um in diameter
Nucleus Absent Present
Organelles Absent Present
Cell Wall Chemically Complex When present, simple
Ribosomes Smaller (70S) Larger (80S) in cell; 70 S
in organelles
DNA Singular circular Multiple linear
chromosomes chromosomes (histones)
Cell Division Binary fission Mitosis

From Prokaryotes to Eukaryotes

• It is thought that all organisms living now on Earth are derived from a single cell born 3,500 millions of years (my)
ago.
• This primordial cell was defined by an outer\membrane, one of the crucial events leading to the establishment of
life on Earth
• Simple organic molecules are likely to have been produced in the conditions that existed on the Earth in its infant
state (approximately during its first billion years)

By understanding how cells work in healthy and diseased states, gained knowledge through working in animal, plant
and medical sciences is a huge help in developing new vaccines, more effective medicines, plants with improved
qualities and through increased knowledge a better understanding of how all living things live. Hence, Biochemistry
really reaches out and combines aspects of all the fields of chemistry and encompasses large areas of cell biology,
molecular biology, and molecular genetics. Its principles revolves in:

1. Cells (basic structural units of living organisms) are highly organized and constant source of energy is
required to maintain the ordered state.
2. Living processes contains thousands of chemical reactions. Precise regulation and integration of these
reactions are required to maintain life
3. Certain important reactions (e.g. Glycolysis is found in almost all organisms)
4. All organisms use the same type of molecules: CHO, proteins, lipids & nucleic acids.
5. Instructions for growth, reproduction and developments for each organism is encoded in their DNA
PART 2

Online Study Site

https://aklectures.com/subject/biochemistry