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- 1. HBC1011 Biochemistry I Trimester I, 2018/2019 Lecture 1 – Introduction to Biochemistry Ng Chong Han, PhD MNAR1010, 06-2523751 chng@mmu.edu.my
- 2. Overview • History of Biochemistry • Biomolecules • Overview of Cell Structure 2
- 3. What is Biochemistry? • The chemistry that take places within living systems • “The study of life at the molecular level” • “The study of the chemistry of life processes” 2 components: Biology & Chemistry 3
- 4. Biochemistry • What is the important characteristics of life? – Extract energy from molecules (nutrients) – Growth, differentiation & reproduction – Respond to changes in their environments • What is the overall goal of Biochemistry? – To better understand how biochemistry works to describe biological processes. 4
- 5. The overall goal of biochemistry • is to describe life’s processes using the language of molecules, that is, applying the principles and methods of chemistry to determine molecular structure from which it is often possible to explain biological function. 5
- 6. Why should we learn biochemistry? • Lead us to a fundamental understanding of life -How do our bodies work? -What are the biochemical similarities and differences among the many forms of life? -How do organisms store and transfer information necessary to reproduce themselves? -What primary molecules and processes were involved in the origin of life? -How is food digested to provide cellular energy? -How does a brain cell store mathematical and chemical formulas? 6
- 7. Why should we learn biochemistry? • Impact on our understanding of Medicine, Health, Nutrient & the Environment: molecular understanding of diseases ---such as diabetes, sickle-cell anemia. Biotechnology: enzymes are used in the pharmaceutical industry to synthesize complex drugs, manufacturing fuel alcohol, cleaning up oil and other toxic spills. 7
- 8. Early history of Biochemistry • People of early civilizations • The Chinese • The early Greek • Arabic biology • European science 8 Grape harvest and wine production as depicted in an early Egyptian wall painting. Fermentation of carbohydrates in grape juice to ethanol is carried out by yeast. (© George Holton/Photo Researchers.)
- 9. Early history of Biochemistry • The Chinese in the fourth century B.C. believed that humans contained five elements: water, fire, wood, metal, and earth. • When all elements were present in proper balance, good health is resulted. 9
- 11. Biological processes and macromolecules • Even the smallest living cell contains thousands of organic and inorganic chemicals, many of them large molecules called macromolecules. • All biological processes, including vision, thinking, digestion, immunity, motion, and disease conditions result from how molecules act and, sometimes, misbehave. 11
- 13. Structural and functional biochemistry 1. Structural and functional biochemistry focuses initially on discovering the chemical structures and three-dimensional arrangements of biomolecules, those chemicals that are found in living matter. To describe biological processes, one must have a knowledge of the molecular structures of the participating biomolecules, which then often leads to an understanding of the function or purpose of the cellular molecules. 13
- 14. Informational biochemistry 2. Informational biochemistry defines the language(s) for storing biological data and for transmitting that data in cells and organisms. This area includes molecular genetics, which describes the molecular processes in heredity and expression of genetic information and also processes that communicate molecular signals to regulate cellular activities (i.e.,hormone action). 14
- 15. Bioenergetics 3. Bioenergetics describes the flow of energy in living organisms and how it may be transferred from one process to another. (endergonic and exergonic reactions). How organisms use biochemical reactions and biomolecules to transfer energy from exergonic to endergonic events will be pivotal in our understanding of life processes. The transfer of energy usually means the transformation of one type of energy to another. 15
- 16. All living matter contains C, H, O, N, P, and S Of the 100 plus chemical elements, only about 31 (28%) occur naturally in plants and animals. •Elements present in biological material can be divided into 3 categories: 1.Elements found in bulk form and essential for life: Carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur make up about 92% of the dry weight of living things. 2.Elements in trace quantities in most organisms and very likely essential for life, such as calcium, manganese, iron, and iodine. 3. Trace elements that are present in some organisms and may be essential for life, such as arsenic, bromine, molybdenum, and vanadium. 16
- 17. The biochemist’s periodic table. Elements in red: present in bulk form in living cells and are essential for life. Yellow: trace elements, very likely essential. Blue: present in some organisms and may be essential. 17
- 18. How these elements were selected by primitive life-forms during the early stages of evolutionary development? •Two hypotheses to explain the selection: 1. There was a deliberate choice because of an element’s favorable characteristic 2. There was a random selection from the alphabet soup of elements present in the earth’s crust, atmospheres, and universe. So, which one is true?? 18
- 19. A comparison of the elemental composition of the earth’s crust and the universe with that of living matter shown in Figure 1.4 refutes the second hypothesis. Elemental composition of the universe (blue), the earth’s crust (pink), and the human body (purple). 19
- 20. Hypothesis 1 • We must conclude that elements were selected according to their abilities to perform certain structural functions or to provide specific reactivity. • Example 1: Carbon forms multiple covalent bonds with other C atoms as well as with other elements such as N, H, O or S. This feature allows the construction of long carbon chains and rings with the presence of reactive functional groups containing N, O and S as in proteins, nucleic acids, lipids, and carbohydrates. • Example 2: Iron was selected by evolutionary forces because it is able to bind the oxygen molecule in a reversible fashion. 20
- 21. Chemical Bonds In Biochemistry • Biochemistry: chemistry that takes place within living systems. • The strongest bonds in biochemicals: covalent bonds, eg C-C, sharing of a pair of electrons between adjacent atoms. Because this energy is relatively high, considerable energy must be expended to break covalent bonds. More than one electron pair can be shared between two atoms to form a multiple covalent bond. For example, carbon–oxygen (C:O) double bonds. These bonds are even stronger than C–C single bonds. 21
- 22. Reversible Interactions of Biomolecules Are Mediated by Three Kinds of Noncovalent Bonds • Electrostatic interactions: An electrostatic interaction depends on the electric charges on atoms. • Hydrogen bonds: relatively weak interactions, which are crucial for biological macromolecules such as DNA and proteins. • van der Waals interactions: the distribution of electronic charge around an atom changes with time. 22
- 23. Combining elements into compounds 23 • The combination of chemical elements into biomolecules great variety in chemical structure & reactivity • Nature’s molecules: cations, anions, covalent compounds, ionic compounds, metal ions, coordination complexes, & polymers.
- 24. Combining elements into compounds 24 • Organic & organometallic chemicals: amino acids, carbohydrates, lipids, vitamins • Prominent among the natural organometallic compounds: Heme & chlorophyll consist of a substituted porphyrin ring coordinated with metal ion.
- 25. (a) Heme: containing a porphyrin ring & iron. b) chlorophyll: containing a porphyrin ring and Mg 25
- 26. Important Functional Groups in Biochemistry 26
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- 28. Biological Macromolecules • 3 major classes of natural polymeric macromolecule: – Nucleic acids, proteins, & polysaccharides 28 (Lipids are also considered a major class of biomolecules, but because they are not polymeric macromolecules, they are not described in this section)
- 29. Macromolecules 29 Types of natural polymers. (a) Cellulose, a homopolymer formed by joining many identical glucose units. (b) Starch, a homopolymer formed by joining many identical glucose molecules. Note that different types of bonding are used in starch and in cellulose. (c) Protein, a heteropolymer formed by linking together amino acids. (d) Nucleic acid, a heteropolymer formed by combining different nucleotides, A, G, C, and T or U.
- 30. Cellular reactions This represents the chemistry for combining amino acids to make proteins. 30 Chemical reaction that connects monomer units is called condensation and results in the loss of a small molecule (water). The reverse process is called cleavage or hydrolysis (if water is used).
- 31. Organelles, Cells, & Organisms • Supermolecular assemblies (organized clusters of macromolecules) • i.e.: cell membranes, chromatin, ribosomes, cytoskeleton. 31 Molecules that are complementary diffuse together to form a complex that displays some biological activity. The molecules are held together by weak and reversible chemical forces.
- 32. Tree of life • Cell = fundamental unit of life • 2 basics classification of organisms based on morphological cell structure & anatomy: eukaryotes & prokaryotes • Classification based on genetic analysis: Bacteria, Archaea, & Eukarya 32 The tree of life Nature Microbiology vol1: 16048 (2016)
- 33. Prokaryotic cells • Most abundant & widespread of organisms • Characteristics: – Size range from 1-10μm in diameter – Cellular components are encapsulated within a cell membrane & rigid cell wall. – Interior of the cell: cytoplasm; ribosomes – chromosome 33
- 34. Schematic diagram of a typical prokaryotic cell 34
- 35. Eukaryotic Cells • Class of eukaryotes: plants, animals, fungi, protozoan, yeast, and some algae • Characteristics: – 10-100 μm – Surrounded by plasma membrane – organelles 35
- 36. Typical eukaryotic cells showing a schematic drawing (above) and an electron micrograph (below): (a) An animal cell. (© Biophoto Associates/Photo Researchers (b, on opposite page), A plant cell. © Alfred Pasiceka/Science Photo Library/Photo Source: Based on Wolfe, 1993.) 36
- 37. Prokaryotic vs Eukaryotic cells 37
- 38. Storage & Transfer of Biological Information • How biological information is transferred from 1 generation to another? • The flow of info can be described using the basic principles of chemistry. • DNA, RNA, proteins are information-rich molecules that carry instructions for cellular processes. 38
- 39. Biological information • The total genetic info content of each cell (genome) resides in the long, coiled, macromolecules of DNA. • 2 ways to express/process informational message: – Exact duplication of the DNA – Expression of info to RNA and then manufacture proteins 39
- 40. The storage and replication of biological information in DNA and its transfer via RNA to synthesize proteins that direct cellular structure and function. 40
- 41. DNA molecules 41 • Long chain, unbranched heteropolymer, constructed from 4 types of monomeric nucleotide units. • Each monomeric unit: – An organic base containing N – A carbohydrate – A phosphate
- 42. Storage and transfer of Biological information DNA DNA •Self-directed process •Replication catalyzed by DNA polymerase •Used as a template to produce a new complementary partner strand DNA RNA •Transcription catalyzed by RNA polymerase •Similar to DNA replication except that: – Ribonucleotides (Deoxyribonucleotides) •Result of the transcription: rRNA, mRNA, tRNA 42
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- 44. Storage and transfer of Biological information RNA Protein 44 • Ultimate product: proteins • Proteome: full array of proteins made from the genomic DNA of an organism • mRNA: intermediate carrier of the info • DNA: A, T, G, C • mRNA: A, U, G, C Translation • Protein: amino acids
- 45. Synthesis of proteins on ribosomes. Each copy of mRNA may have several ribosomes moving along its length, each synthesizing a molecule of the protein. 45
- 46. Molecular organization of the cells 46
- 47. Lecture plan 47 Components Mark Distribution Quizzes (2) 10% Tests (2) 20% Practical 10% Assignments 10% Final Exam 50% Subjected to modification Quiz 2 quizzes (5%, total 10%) •Quiz 1 – week 4 – Lecture 1-5 •Quiz 2 – week 11 – Lecture 14-20 Test 2 tests (10%, total 20%) •Test 1 – week 7 – Lecture 1-13 •Test 2 – week 13 – Lecture 14-25 Tutorial: Tut1(Lec1-5,Week3), Tut2(Lec6-13,Week6), Tut3(Lec14- 20,week10), Tut4(Lec21-26,week13) Assignment (10%): will be announced later. Final exam (50%): Short answer questions (5 questions)
Editor's Notes
- #11: 1833 Robert Brown reported cell contain nucleus 1837 Cell theory by Theodor Schwann "All living things are composed of cells and cell products".[3] This became cell theory or cell doctrine 1933 Electron microscope invented Cyclins are a family of proteins that control the progression of cells through the cell cycle by activating cyclin-dependent kinase (Cdk) enzymes.[1] 2003 Nobel prize in chemistry awarded jointly to Peter Agre for discovery of aquaporins Aquaporins are integral membrane proteins from a larger family of major intrinsic proteins (MIP) that form pores in the membrane of biological cells.[1] Olfactory receptors – odorant receptor – detection of odor molecules
- #13: Bioenergetics-the study of the transformation of energy in living organisms. Bioenergetics is the part of biochemistry concerned with the energy involved in making and breaking of chemical bonds in the molecules found in biological organisms. It can also be defined as the study of energy relationships and energy transformations in living organisms. Life is dependent on energy transformations; living organisms survive because of exchange of energy within and without. Living organisms produce ATP from energy sources via oxidative phosphorylation In photosynthesis, autotrophs can produce ATP using light energy.
- #16: Endergonic - anabolic Exergonic- catabolic
- #29: polymers are made up of monomers, which lipids do not contain. the basic units of lips are fatty acids and glycerol molecules that do not form repetitive chains. Instead, they form triglycerides from three fatty acids and one glycerol molecule.
- #30: The main difference between cellulose and starch is, Cellulose is the polymeric form of glucose which has glucose units linked by glycoside linkage (beta 1, 4 linkages). Starch is a polymeric form of glucose which is linked by alpha 1,4 linkage
- #32: Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. Chromosome, highly condensed DNA during metaphase Cytoskeleton - complex network of interlinking filaments and tubules that extend throughout the cytoplasm, from the nucleus to the plasma membrane -it gives the cell shape and mechanical resistance to deformation -actively contract, thereby deforming the cell and the cell's environment and allowing cells to migrate -uptake of extracellular material -intracellular transport template for the construction of a cell wall.[3] Furthermore, it forms specialized structures, such as flagella, cilia, lamellipodia and podosomes.
- #33: Halophiles- high salt Methanococcus- mesophile (moderate temperature) -methanogens that produce methane (CH4) Microsporidiae-fungi Slime molds were formerly classified as fungi but are no longer considered part of that kingdom.[1] Although not related to one another, they are still sometimes grouped for convenience within the paraphyletic group referred to as kingdom Protista. -found in forest, eat decaying things
- #35: Pili (pilus) for bacterial conjugation) Shorter pili called fimbriae help bacteria attach to surfaces. Flagella - Flagella are long, whip-like protrusion that aids in cellular locomotion. Definition of mesosome. : an organelle of bacteria that appears as an invagination of the plasma membrane and functions either in DNA replication and cell division or excretion of exoenzymes.