SIM Biochemistry ULO1

College of Health Sciences Education
3rd Floor, DPT Building

Matina Campus, Davao City
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Phone No.: (082)300-5456/300-0647 Local 117
Big Picture
Week 1-9: Unit Learning Outcomes (ULO): At the end of the unit, you are expected to:
1. Demonstrate knowledge on the concepts of biochemistry, biochemical systems, and

biochemical methods.
2. Demonstrate knowledge on carbohydrates’ structure, functions, classification,
physicochemical properties, and its clinical significance.
3. Demonstrate understanding of carbohydrate metabolic pathways and its intermediate
compounds.
4. Demonstrate knowledge on lipids’ structure, functions, classification, physicochemical
properties, and its clinical significance.
5. Demonstrate understanding of lipid metabolic pathways and its intermediate
compounds.
6. Demonstrate knowledge on proteins’ structure, functions, synthesis, processes, levels
of organization, and its clinical significance.
7. Demonstrate understanding of protein metabolic pathways and its intermediate
compounds.
8. Demonstrate knowledge on structures, functions, synthesis, and clinical significance of
enzymes and vitamins.
9. Demonstrate knowledge on structures, functions, synthesis, and levels of organization
of nucleic acids; as well as understanding of the central dogma in the transfer of genetic
information and mutations.
Big Picture in Focus: ULO1. Demonstrate knowledge on the

concepts of biochemistry, biochemical systems, and
biochemical methods.
Essential Knowledge
Biochemistry – An Overview
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Reference textbook: Stoker, H. S. (2017). Biochemistry 3rd Edition. C & E Publishing Inc. Quezon City.
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Phone No.: (082)300-5456/300-0647 Local 117
Part I. The Study of Living Things

• Biochemistry is the systematic study of the chemical substances found in living organisms, their
organization & chemical interactions with each other, and the principles of their participation in the
processes of life.
• Its importance is due to the increasing recognition that underlying each and every biological function is a
chemical reaction.
• Hundreds/thousands of chemical reactions are taking place in our cells every minute of our lives.
• Biochemical investigations have been directed towards the study of the chemical composition of cells
and the chemical processes in which they participate.
• A biochemical substance is a chemical substance found within a living organism.
• Two types of biochemical substances:
• Bioinorganic substances : water and inorganic salts.
• Bioorganic substances : carbohydrates, lipids, proteins, and nucleic acids
Biochemical Substances
• As isolated compounds, bioinorganic and bioorganic substances have no life in and of themselves.
• Yet when these substances are gathered together in a cell, their chemical interactions are able to sustain
life.
• A cell in particular, and a whole organism in general, has three basic needs: materials, information, and
energy.
• Without the daily satisfaction of these, human life would be severely constrained.
Main Classes of Foodstuffs - Materials

• The bioorganic materials of life will be considered, starting with the three main classes of foodstuffs –
carbohydrates, lipids, and proteins.
• Humans use these molecules to build and run their bodies and to try to stay in some state of repair.
• Plants rely heavily on carbohydrate for cell walls, and animals obtain considerable energy from
carbohydrates made by plants.
• Lipids serve many purposes. They are used, both by plants and animals, as materials to make cell
membranes and as sources of chemical energy.
• Proteins are particularly important in both the structures and functions of cells.
• Because of the catalytic role of proteins in regulating chemical events in cells, the study of proteins will
be immediately followed with an examination of enzymes, which make up a particular family of proteins.
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Information system
• Every cell has an information system – enzymes, hormones, and neurotransmitters are components of
the intricate information system in the body.
• Without information, the materials and energy delivered to the body could produce only rubbish.
• Although enzymes are major players in the cells’ information system, they do not originate the cellular
script.
• They only help to carry out directions that are encoded in the molecular structures of the nucleic acids,
which are compounds that are able to direct the synthesis of enzymes.
• Thus the study of the enzyme makers, the nucleic acids, is included in any study of the molecular basis of
life.
• Hormones & neurotransmitters, two other components of cellular information, depend on the presence
of right enzymes not only for their existence but for their functions.
Biochemical Substances
• To supply materials for any use – parts, information, or energy – each organism has basic nutritional
needs.
• These include not just bioorganic materials, including vitamins, but also bioinorganic materials including
minerals, water, and oxygen.
• Thus, together with learning about the bioorganic materials of life and how they are processed and
used, the need for vitamins, minerals, water, and oxygen will also be considered.
Part II. The Study of Living Things – The CELL STRUCTURE

• Based on their cell structures, organisms are divided into two main groups:
• Prokaryote: Greek - meaning “before the nucleus”; single- celled organisms
• Eukaryote: Greek - meaning “true nucleus”
o contain a well-defined nucleus surrounded by a nuclear membrane
o can be single celled, such as yeasts and Paramecium, or multicellular, such as animals and plants
 Five kingdoms:
1. Monera - prokaryotic organisms; includes bacteria and cyanobacteria
2. Protista - unicellular eukaryotes: yeast, Euglena, Volvox, Amoeba, and Paramecium
3. Fungi - molds and mushrooms
4. Plantae
5. Animalia
 Fungi, plants, and animals are multicellular eukaryotes (with few unicellular eukaryotes)
• The main difference between prokaryotic and eukaryotic cells is the existence of organelles, especially the
nucleus, in eukaryotes.
• An organelle is a part of the cell that has a distinct function; it is surrounded by its own membrane within
the cell.
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Prokaryote vs Eukaryote
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Animal Cell
Plant Cell
The CELL STRUCTURE – Functions of the Organelles
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The Cell Membrane

• A semi-permeable membrane surrounding the cell separating its internal environment from the external
environment.
• Permits and/or enhances the absorption of essential nutrients into the cell while preventing the diffusion
of needed metabolites.
• A lipid bilayer that mechanically holds cell together
• Component biomolecules:
– Lipids: phospholipids, cholesterol
– Proteins
– Carbohydrates
 Lipids provide the basic structure of biological membranes.
 Proteins are embedded in the membranes and provide channels/carriers for the transport of ions and
nutrients.
The Cytoplasm
• Structureless and highly viscous.
• The aqueous phase of the cell in which many particulate constituents like mitochondria, ribosomes, etc.
are suspended.
• Contains a wide variety of solutes including proteins, enzymes, nucleic acids (RNA), a number of
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electrolytes, metabolites for cellular utilization (e.g., glucose), and waste products of cellular activity
(e.g., urea, creatinine, uric acid, etc.).
The Nucleus
• The “information center” of the cell; enclosed by a nuclear membrane and contains the cell’s genetic
information and the machinery for converting that information into protein molecules.
• Site of DNA and RNA synthesis.
• Contains a comparatively large amount of nucleoprotein (50% DNA and 50% proteins, histones and
prolamines located in the chromosomes, and a small amount of RNA; >95% of nucleic acids of the cell is
in the nucleus.
• Nucleolus - small, round dense body present within the nucleus; not surrounded by a membrane;
essentially a cluster of looped chromosomal segments; contains 10-20% of the total RNA of the cell,
chiefly mRNA.
• Serve as a storehouse for mRNA prior to its movement into the cytoplasm by way of the nuclear pores.
The Mitochondria
• The second largest organelle.
• The powerhouse of the cell where carbohydrates, lipids, and amino acids are oxidized to CO 2 and H2O by
molecular O2 and the energy set free is converted into the energy of ATP.
• Has a double-membrane structure, an outer membrane and an inner membrane.
• Site for cellular respiration.
• The inner membrane, in which the enzymes of electron transport and energy conversion are located, is
convoluted to form shelves termed cristae.
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The Endoplasmic Reticulum

• Appears to be a system of interconnected tubules or canaliculi extending throughout the cell cytoplasm
and is continuous with the outer nuclear membrane.
• Two types: rough and smooth ER
• Rough ER is lined with a number of small, spheric, electron-dense particles called ribosomes
– primarily involved in synthesis of membrane proteins and proteins for export from the cell
• Smooth ER lacks ribosomes
– appears to be involved in the biosynthesis of steroids, phospholipids, and complex
polysaccharides
– functions also include biotransformation, a process in which water- soluble organic molecules
are prepared for excretion.
The Ribosomes
• Consist of 50% RNA (rRNA) and 50% protein.
• Involved in protein synthesis in the cell and are sometimes referred to as the “workbench” for protein
synthesis.
• Complex structures containing two irregularly shaped subunits of unequal size.
• They come together to form whole ribosomes when protein synthesis is initiated.
• When not in use, the ribosomal subunits separate.
The Golgi Apparatus / Golgi Complex

• Structures composed of flattened sacs with vesicles, located near the nucleus, probably continuous with
ER
• The organelles to which synthesized proteins are transported and temporarily stored before release from
the cell.
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• The “packaging stations” of the cell.

• The primary site for packaging and distribution of cell products to internal and external compartments.
• There is a continuous flow of substances through the Golgi apparatus.
• Responsible for sorting and packaging several types of proteins, small molecules, and new membrane
components.
The Lysosomes
• Membrane-bound organelles containing a variety of hydrolytic and degradative enzymes and having an
optimum pH of 5.0.
• Has regulatory and defense function.
• Function in the digestion of materials brought into the cell by phagocytosis and pinocytosis.
• Also serve to digest cell components after cell death.
• The “suicide bags” of the cell.
• Upon death of the cell or its exposure to environmental conditions, the lysosomal membrane
disintegrates, releasing its contents, which cause the self-digestion or autolysis of the cell constituents.
The Peroxisomes
• Contains oxidative enzymes that oxidize amino acids, uric acid, and various 2-hydroxyamino acids using
O2 with the formation of H2O2.
• H2O2 is then converted to H2O and O2 by the enzyme catalase also present in the peroxisomes.
• Thus the cell protects itself from the toxicity of H 2O2.
Water in the Cell

• The solvent
– The agency that enables water-soluble, water-miscible, or emulsifiable substances to be
transferred in the body not only in the blood but also intercellularly and intracellularly.
• In Biochemical Reactions
– Ionization is a prerequisite to many biochemical reactions and ionization takes place in water.
• In Physiologic Regulation of Body Temperature
– high specific heat (amount of heat required to raise the temperature of 1g of H 2O 1oC) enables
the body to store heat effectively without greatly raising its temperature
– high heat conductivity permits heat to be transferred readily from the interior of the body to the
surface
– high latent heat of evaporation causes a great deal of heat to be used in its evaporation and thus
cools the surface of the body
Characteristics of Biochemical Reactions

 Chemical reactions occurring in vivo have the following properties:
• Speed
– Glucose, for instance, is oxidized in the body with surprising speed, while in vitro, the same
reaction is quite a long and tedious process.
– This is due to the presence of enzymes, without which life as we know it would not be possible.
• Mildness
– Energy is taken up and released in a gentle way, not violently as those occurring in vitro (because
of high specific heat of water which makes up a large proportion of the protoplasm).
• Orderliness
– A high degree of orderliness is due to the existence of cell specialization within the different
organs of the body.
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Phone No.: (082)300-5456/300-0647 Local 117
-END-
GOOD JOB!
Keywords Index
Biochemistry Biochemical substances Bioorganic substances Materials

Plant cell Carbohydrates Bioinorganic substances Information system
Animal cell Proteins Water Prokaryotes
Nucleic acids Lipids Energy Eukaryotes
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College of Health Sciences Education

3rd Floor, DPT Building

1. Demonstrate knowledge on the concepts of biochemistry, biochemical systems, and

Big Picture in Focus: ULO1. Demonstrate knowledge on the

Part I. The Study of Living Things

Main Classes of Foodstuffs - Materials

Part II. The Study of Living Things – The CELL STRUCTURE

The CELL STRUCTURE – Functions of the Organelles

The Cell Membrane

The Endoplasmic Reticulum

The Golgi Apparatus / Golgi Complex

• The “packaging stations” of the cell.

Water in the Cell

Characteristics of Biochemical Reactions

Biochemistry Biochemical substances Bioorganic substances Materials

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