1. An Introduction to Biochemistry
Principles of Biochemistry (BCH 3000)
An Introduction to Biochemistry
Dr. Syahida Ahmad
Department of Biochemistry
Faculty of Biotechnology & Biomolecular Sciences
UPM

2. Online References GARRETT & GRISHAM (BOOK ONLINE)
RODNEY BOYER (INTERACTIVE NOTES)

3. You Study Biochemistry?
Why Should
You Study Biochemistry?

4. What is Biochemistry?
Scientific discipline – explain life at the molecular level
What are we made of?
How do we work?
Underlie other advances field:
Genetics
Cell biology
Immunology
Treatment of diseases eg. Cancer & Diabetes
Improves the efficiency of industries
Wastewater treatment
Synthesis of pesticides & drugs
Understand how molecules cooperate & combine to form larger functional units & ultimately the intact organism

5. The nature of biochemistry

6. This course will explain…
What are living organisms made of?
How do organisms acquire and use energy?
How does an organism maintain its identity across generations?

7. Chemical Elements in Biological molecules (Biomolecules)
Elements found in bulk form and essential for life (92%):
C, H, O, N, P and S
Elements in trace quantities in most organisms and very likely essential for life
Ca, Mn, Fe and I
Trace elements that are present in some organisms and may be essential for life
As, Br, Mo and V

9. Combining Elements into Compounds Combining Elements into Compounds
Biomolecules contain functional groups that are common in organic chemistry
In living cells, compounds are present in all three states of matter
Gases, Liquids and Solids
Nature’s molecules include
Cations, anions, covalent compounds, ionic compounds, metal ions, coordination complexes and polymers

10. Important Functional Groups in Biochemistry

12. Example of organic and organometallic chemicals
Amino Acids
Building blocks for protein structure
Carbohydrates
As nutrients in energy metabolism, cell structure and molecular recognition
Lipids
Display low water solubility, primary functions as energy molecules in metabolism, components for construction of cell membranes and hormones
Vitamins
Ensure proper growth and development
Heme and Chlorophyll (Natural organometallic compounds)
Both consist a substituted porphyrin ring coordinated with a metal ion
Function?

14. Cellular Reactions Condensation or Polymerization
Reaction process that connects monomer units
Results in the loss of water
starch or cellulose (homopolymer)
Protein or Nucleic acid (heteropolymer)
Cleavage or Hydrolysis
The reverse process and water was used

17. Organelles, Cells and Organisms
Supramolecular assemblies
Organized clusters of macromolecules
Cell membranes
Complexes of proteins and lipids
Chromatin
Complexes of DNA and proteins
Ribosomes
Complexes of RNA and proteins
Virus
Consist of a single DNA or RNA molecule wrapped in a protein package

22. HUMAN ORGANS – WHAT ARE THEIR FUNCTIONS?

23. TISSUES MADE UP THE ORGANS
TISSUES COMPOSED OF CELLS
CELLS - ORGANNELLES
BIOMOLECULES
ELEMENTS

24. Living Cells Cells The fundamental unit of life Eukaryotes
Plants and animals
Cells have distinct membrane-enclosed nucleus and well defined internal compartmentation
Prokaryotes
Simple, unicellular organisms, mainly bacteria and blue-green algae
With neither a distinct cell nucleus nor an internal cellular compartmentation

25. Archaebacteria or Archaea
Ancient bacteria
Different from prokaryotes and eukaryotes
Able to thrive in an environment of high acidity, high salt, high temperature and absence of oxygen
Abundance in the hot springs of Yellowstone National Park or in volcanic areas on land and sea
But, according to morphological observation – more closely resemble the prokaryotes

27. Prokaryotic Cells
Least developed, but are the most abundant and widespread organisms
Size range 1-10 m in diameter
3 basic shapes
Spheroidal (cocci), rodlike (bacilli) and helically coiled (spirilla)
Cellular components are encapsulated within cell membrane and rigid cell wall
Mesosomes – membrane may infold to form multilayered structures
Flagella – outside surface, appendages for locomotion
Pili – for the transfer of DNA during sexual conjunction and for attachment to surfaces
Cytoplasm
Interior of the cell, a gel-like, heterogenous suspension of biomolecules (ribosomes)
Chromosome
A single copy of DNA (Each cell has one chromosome)

33. Eukaryotic Cells
Plants, animals, fungi, protozoans, yeasts and some algae
Size range m in diameter
Surrounded by a plasma membrane made of protein and lipid
Chemical barrier through which all molecules that enter or exit the cell must pass
Organelles
Membrane-enclosed packages of organized macromolecules that perform a specialized function for the cell
Nucleus, endoplasmic reticulum (contains ribosomes), Golgi apparatus and mitochondria
Animal Cells
Lysosomes and peroxisomes
Plant cells
Chloroplasts, glyoxysomes and rigid cell wall (polysaccharide cellulose)
Vacuoles
Presents in both plant (more prominent) and animal cells

41. Storage and Transfer of Biological information
For cells to grow and divide, For species to remain viable, Secure and faithful processes, For storage and transfer of genetic information
Genome
Total genetic information content of each cell
Resides in the long, coiled, macromolecules of DNA
Human genome project (HGP)
To map and sequence the estimated 3 billion nucleotide base pairs of the human genome
High impact on medicine – gene therapy to treat defective diseases
Proteomics
Name given to the broad field investigating the thousands of proteins products made from the genome
Bioinformatics
Apply computers to organizing the mass of nucleic acid sequence data and studying relationships between protein sequence and structure

43. Water – The Medium of Life
It is the major chemical component of the earth’s surface.
It is the only liquid that most organisms encounter.
Organisms can live away from water but carries 70 – 90% water internally.

44. Behave very differently when compared with similar sized molecules e.g. ammonia, hydrogen flouride and hydrogen sulphide.
Has higher boiling point, melting point, heat of vaporization and surface tension compared to these molecules
These properties suggest that intermolecular forces of attraction between water molecules are high.

45. The ability to form hydrogen bonds is the crucial fact in understanding its properties.
The bent structure of water molecule allows it to exhibit polarity.

47. Dipole moments - due to non-uniform distributions of positive and negative charges on the various atoms.
Dipole moment the product of magnitude of charge & distance of separation between the charges
dipole moments are measured in units named debye
A molecule with a permanent dipole moment is called a polar molecule.
Water is a polar molecule