An Introduction to Biochemistry

1. 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) http://www.web.virginia.edu/Heidi/home.htm RODNEY BOYER (INTERACTIVE NOTES) http://www.wiley.com/legacy/college/boyer/0470003790/chapter/chapter.htm

3. 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? http://www.pubquizreference.co.uk/trivref/humanbody/organs/organs.html

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 10-100 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