Introduction to biochemistry slides.pptx

Intro to biochemistry

1. INTRODUCTION The word “biochemistry” was first proposed in 1903 by a German chemist , Carl Neuberg (1877- 1956) as a combination of two discipline: biology and chemistry. He was an early pioneer in biochemistry, and often referred to as the “Father of Biochemistry”. Biochemistry concern was developed by placing biological phenomena on firm chemical foundations. E.g. chemical oxidation and respiratory process. C + O 2 CO 2 C 6 H 12 O 6 + 6O 2 6H 2 O + 6CO 2

2. Definitions of Biochemistry? It is the study of chemical processes in living organisms. Biochemistry governs all living organisms and living processes Biochemistry is the science concerned with the chemical basis of life (Gk bios “life”). Since the cell is the structural unit of living systems, thus, biochemistry can also be described as the science concerned with the chemical constituents of living cells and with the reactions and processes they undergo. The major objective of biochemistry is to understand and describe all chemical processes associated with living cells at molecular level.

3. Significance of Biochemistry in Medical Sciences Knowledge of Biochemistry is essential to all life sciences, for example: Biochemistry of nucleic acids (RNA & DNA) is the basis of genetics Study of body functions (physiology) completely overlaps with biochemistry Pharmacology and pharmacy rest on a sound knowledge of biochemistry since most drugs are metabolized by enzyme-catalyzed reactions Poisons act on biochemical reactions or processes; this is the subject matter of toxicology. Biochemistry is the basis of pathology (study of diseases), such as inflammation, cell injury, and cancer. Microbiology, zoology, and botany employ biochemical approaches and biochemistry is increasingly becoming their common language Exclusive reliance of other biological science courses on biochemistry is because life as we know it depends on biochemical reactions and processes

4. All disease has a biochemical basis Biochemistry Carbohydrates Lipids Nucleic acids Proteins Diabetes Atherosclerosis Genetic Sickle cell Mellitus diseases anemia Pathology 3/4/21 5

5. The question is: How can we study chemical processes of all living organisms since biology is diverse & complex from extremely small, single cell prokaryotes such as bacteria, to very large multicellular eukaryotes, such as human being like you? 3/4/21 6

6. At the molecular level, living systems look similar. “What is true of E. coli is true of the elephant.”---Jacques Monod This similarity is a reflection of how life evolved. All organisms share a common evolutionary origin Biochemistry simply deals with structures and functions of cellular components otherwise called biological molecules such as proteins, carbohydrates, lipids and nucleic acids. These are all polymers. Protein is formed from amino acids ( monomers) ; Carbohydrates from sugars like monosaccharide, disaccharides, oligosaccharides, and polysaccharides; Lipids from fatty acids and glycerols; Nucleic acids from nucleotides. 3/4/21 7 [email protected]

7. All chemical changes within organisms- either degradation of substances to gain energy or building up of complex molecules of life- are collectively termed metabolism . These chemical changes depend on the action of organic catalysts known as enzymes , and enzymes, in turn, depend for their existence on the genetic apparatus of the cell. Historical Development: Biochemistry concern was placing biological phenomena on firm chemical foundations. Between 1650 – 1780: Robert Boyle: questioned the basis of the chemical theory and taught that proper objective of chemistry was to determine the composition of compounds; John Mayow: observed the fundamental analogy between respiration of animal and oxidation of organic matter in the air; 3/4/21 8 [email protected]

8. Antonie-Lavoiser (Father of modern chemistry): showed quantitatively the similarity between chemical oxidation and respiratory process; In late 18 th century, Joseph priestly et. al : showed that photosynthesis is the reverse of respiration. This was a milestone in the development of biochemical thought; In spite of these early discoveries, rapid progress in biochemistry had to wait upon the development of structural organic chemistry in 19 th century. But in 1840, Justus von Liebig : described the great chemical cycles in nature. He pointed out that animals would disappear from the face of the earth if it were not for the photosynthesizing plants; - In his analysis of fermentation, putrefaction, & infectious disease, he failed to admit that living organisms might function as causative agents; 9 [email protected]

9. In 1860s, Louis Pasteur : proved that various yeasts and bacteria are responsible “ferments”, substances that caused fermentation and, in some cases, disease; In 1878, Pasteur’s ferments were designated as enzymes by a German physiologist, Wilhelm kuhne ; viii. In 1897, German chemist, Eduard. Buchner : showed that fermentation could occur in a press juice of yeast, devoid of living cells; - Thus, a life process of cells was reduced by analysis to a nonliving system of enzymes; - He named the enzyme that brought the fermentation of sucrose zymase; - In 1907, he received Nobel prize in chemistry for this; - Following Buchner’s example, enzymes are usually named according to the reaction they carry out ; Typically the suffix –ase is added to the name of the substrate e.g. lactase is the enzyme that cleaves lactose, OR the type of reaction e.g. DNA polymerase forms DNA polymers. 3/4/21 10 [email protected]

10. Having shown that enzymes could function outside a living cell, what next? This is to determine their biochemical nature. Nobel laureate Richard Willstatter argued that protein were merely carriers for the true enzymes and that proteins per se were incapable of true catalysis. i.e. all enzymes are proteins & not all proteins are enzymes In 1926, James B. Summer : isolated the first pure crystalline enzyme urease ; - He did likewise for the enzyme catalase in 1937. Though the conclusion that pure proteins can be enzymes was proved by Northrop and Stanley who worked on the digestive enzyme pepsin and chymotrypsin in 1930. These 3 scientists were awarded the 1946 Nobel prize in chemistry. This discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. xi. This was first done for lysozyme , an enzyme found in tears, saliva and egg whites by David Chilton Philips in 1965. 3/4/21 11 [email protected]

11. What are your expectations in Biochemistry as students of Health sciences? Apply your knowledge of general and organic chemistry to predict the structures and interactions of biological molecules from their elemental compositions and structures; Develop and understanding of how the chemical structures and physical properties of biological molecules relate to their functions; Develop an understanding of how biological molecules interact with one another to produce complex, self-regulating systems, and how chemical energy is utilized to drive and sustain these processes. 3/4/21 12 [email protected]

12. Cell A cell is the smallest/basic unit of living thing that is capable of performing life functions. Cells are highly organized to form a simple or complex organism The nature and form of any organisms is structurally and chemically determined by cells [email protected] 3/4/21 13

13. Review of Cell Theory Contributing Scientists Anton Von Leuwenhoek : invented the microscope & observed tiny things in water Robert Hooke : coined the term “cell” after observing that cork consisted of tiny chambers Francesco Redi : proved that living things can not be produced from non living matter Louis Pasteur & Rudolf Virchow : discovered that cells come only from other living cells [email protected] 3/4/21 14

14. Showing Robert Hooke’s drawing of cork cells [email protected] 3/4/21 15

15. Cell Theory Principles All living things are made up of cells Cells are the basic units of structure and function in an organism Cells come only from the replication of existing cells Cells contain the hereditary information necessary for regulating cell functions and transmitting information to the next generation of cells. [email protected] 3/4/21 16

16. Examples of Cells Amoeba Proteus Plant Stem Red Blood Cell Nerve Cell Bacteria [email protected] 3/4/21 17

17. Cell Diversity Not all cells are alike Even cells within the same organism show enormous diversity in: size, shape, and internal organization [email protected] 3/4/21 18

18. Cell size A few types of cells are large enough to be seen by the unaided eye E.g. human egg (ovum) is the largest cell in the body Most cells are small for 2 main reasons : The cell’s nucleus can only control a certain volume of active cytoplasm Cells are limited in size by their surface area to volume ratio A group of small cells has a relatively larger surface area than a single large cell of the same volume This is important because the nutrients, oxygen, and other materials a cell requires must enter through it surface As a cell grows larger at some point its surface area becomes too small to allow these materials to enter the cell quickly enough to meet the cell's need [email protected] 3/4/21 19

19. Cell Shape Cells come in a variety of shapes – depending on their function The neurons from your toes to your head are long and thin Blood cells are rounded disks, so that they can flow smoothly [email protected] 3/4/21 20

20. Internal Organization Cells contain a variety of internal structures called organelles An organelle is a cell component that performs a specific function in that cell Just as the organs of a multicellular organism carry out the organism's life functions, the organelles of a cell maintain the life of the cell Examples: Nucleus, Mitochondria, Golgi apparatus, Ribosome, Endoplasmic reticulum, Lysosomes, Vacuoles, Chloroplasts [email protected] 3/4/21 21

21. Two Types of Cells: Prokaryotes Vs Eukaryotes "Karyose" comes from a Greek word which means "kernel," as in a kernel of grain In biology, we use this word root to refer to the nucleus of a cell "Pro" means "before," and "eu" means "true," or "good.“ "Prokaryotic" means "before a nucleus ” (cells, like bacteria, have no 'nucleus) “Eukaryotic” means "possessing a true nucleus ” (like those of the human body) [email protected] 3/4/21 22

22. Prokaryotes are organisms whose cells lack a nucleus and have no membrane-bound organelles are the simplest cellular organisms E.g. bacteria and archaea (archaebacteria) A Prokaryotic cell (bacterium) [email protected] 3/4/21 23

23. Eukaryotes are organisms whose cells normally contain a nucleus Eukaryotic cells contain a membrane-bound nucleus and numerous membrane-enclosed organelles E.g. animals, plants, fungi, and protists A Eukaryotic cell (plant) [email protected] 3/4/21 24

24. Similarities They perform most of the same kinds of functions, and in the same ways. Both are enclosed by plasma membranes, filled with cytoplasm, and The cytoplasm of both cells types are loaded with small structures called ribosomes. Both have DNA which carries the archived instructions for operating the cell [email protected] 3/4/21 25

25. Differences: size and complexity Eukaryotic cells are much larger and much more complex than prokaryotic cells Eukaryotic cells have a true nucleus, bound by a double membrane. Prokaryotic cells have no nucleus Eukaryotic DNA is linear; prokaryotic DNA is circular (it has no ends) Eukaryotic DNA is complexed with proteins called "histones," and is organized into chromosomes; prokaryotic DNA is "naked," meaning that it has no histones associated with it, and it is not formed into chromosomes A eukaryotic cell contains a number of chromosomes; a prokaryotic cell contains only one circular DNA molecule and a varied assortment of much smaller circlets of DNA called "plasmids“ A eukaryotic ribosome is composed of five kinds of rRNA and about eighty kinds of proteins. Prokaryotic ribosomes are composed of only three kinds of rRNA and about fifty kinds of protein Cell division is by binary fission in prokaryotes while is by mitosis and meiosis in eukaryotes [email protected] 3/4/21 26

26. Typical Animal Cell [email protected] 3/4/21 27

27. Typical Plant Cell [email protected] 3/4/21 28

28. Cell Parts [email protected]

29. Surrounding the Cell [email protected]

30. Cell Membrane Outer membrane of cell that controls movement in and out of the cell Double layer i.e. a phospholipid bilayer In a plant cell, it lies beneath the cell wall In animal cells, it is the outer boundary Provides cell with Protection Control of movement of materials in/out of cell Support Maintains condition of cell It’s like the border of a city! [email protected] 3/4/21 31

31. Cell Wall Supports & protects cells Only found surrounding plant, fungal and bacterial cells Made of cellulose Is rigid, strong and stiff It’s like the wall that surrounds a medieval city! [email protected] 3/4/21 32

32. Inside the Cell [email protected]

33. Nucleus Identified in 1833 by Robert Brown Found in both plant and animal cells Large, oval shape Centrally located in cell Directs cell activities Separated from cytoplasm by nuclear membrane Contains genetic material – DNA It’s like the Governor’s Office in a State! [email protected] 3/4/21 34

34. Nuclear Membrane Surrounds nucleus Made of two layers Openings allow material to enter and leave nucleus [email protected] 3/4/21 35

35. Chromosomes In nucleus Made of DNA Contain instructions for traits & characteristics [email protected] 3/4/21 36

36. Nucleolus Inside nucleus Contains RNA to build proteins [email protected] 3/4/21 37

37. Cytoplasm Found in both plant and animal cells Clear, thick, jelly-like material Located beneath cell membrane Supports and protects cell organelles Contains hereditary material It’s like the sidewalks that are found throughout a city! [email protected] 3/4/21 38

38. Endoplasmic Reticulum Found in both plant and animal cells Network of tubes Transports materials throughout the cell Two types Smooth (no ribosomes) Rough (covered with ribosomes) It’s like a city’s highway system! [email protected] 3/4/21 39

39. Ribosomes Found in both plant and animal cells Each cell contains thousands Make proteins Can be attached to the Endoplasmic Membrane or floating free in the cytoplasm The smallest organelles It’s like the brick yard that supplies a city with what it’s made of! [email protected] 3/4/21 40

40. Mitochondria Found in both plant and animal cells Looks like a jelly bean Breaks down sugar molecules to release usable energy Has inner foldings (Cristae) that increase the internal surface area It’s like a city’s power plant! [email protected] 3/4/21 41

41. Golgi Bodies/Apparatus Discovered in 1898 by Camillo Golgi Found in both plant and animal cells Looks like a flattened stack of membranes (or pancakes!) Processes and packages molecules, like lipids and proteins, that were made by the cell It’s like a city’s Post Office or UPS center! Move materials within the cell Move materials out of the cell [email protected] 3/4/21 42

42. Lysosome Found in animal cells only Small and round in shape Breaks down larger food molecules into smaller ones Digests old cell parts Digestive 'plant/machine' for proteins, fats, and carbohydrates Transports undigested material to cell membrane for removal Cell breaks down if lysosome explodes It’s like a city’s Recycling Center! [email protected] 3/4/21 43

43. Vacuoles Found in both plant and animal cells In plant cells: very few and very large In animal cells: many little ones Fluid-filled sacs Store food and water, and remove waste It’s like a city’s warehouses, water towers and garbage dumps! [email protected] 3/4/21 44

44. Chloroplast Found in plant cells only Oval-shaped Green in color due to chlorophyll Uses energy from the sun to make food for the plant It’s like the solar panels on a city’s buildings! [email protected] 3/4/21 45

45. Levels of cell Organization in Living Things [email protected] 3/4/21 46

46. Cell organization: How organisms FUNCTION and survive in continually changing environments 5 Levels of Organization: Chemical Level: i ncludes all chemical substances necessary for life e.g. heme group of hemoglobin molecule, inorganic ions like sodium, sugars like glucose, amino acids, nucleic acids, fatty acids etc. Together form the next higher level [email protected] 3/4/21 47

47. Cellular Level: Cellular arrangement is of two types; the Prokaryotic cells and Eukaryotic cells, & there are many different types of cells Tissue Level: A tissue is a group of cells that perform a specific function and the basic types of tissues in the human body include epithelial, muscle, nervous, and connective tissues Organ Level: An organ consists of 2 or more tissues that perform a particular function (e.g., heart, liver, stomach etc) System Level: An association of organs that have a common function; the major systems in the human body include digestive, nervous, endocrine, circulatory, respiratory, urinary, and reproductive [email protected] 3/4/21 48

48. Arrangement of cell forming tissue, organ and system levels [email protected] 3/4/21 49

49. Chemical Elements and Molecules of Life There are 81 stable elements in nature. Fifteen of these are present in all living things, and a further 8–10 are only found in particular organisms. More than 99% of the atoms in animals’ bodies are accounted for by just four elements: Hydrogen (H): 63.5%, Oxygen (O): 25.6% Carbon (C) : 9.1% Nitrogen (N): 1.06% Total= 99.3% Hydrogen and oxygen are the constituents of water, which alone makes <80% of cell mass Together with carbon and nitrogen, hydrogen and oxygen are also the major constituents of the organic compounds on which most living processes depend.

50. Many biomolecules also contain sulfur ( 0.04%) or phosphorus ( 0.18%) These macroelements are essential for all organisms A second biologically important group of elements, which together represent only about 0.5% of the body mass, are present almost exclusively in the form of inorganic ions This group includes the alkali metals sodium ( 0.07% ) and potassium( 0.06% ), and the alkaline earth Metals magnesium (0.01%) and calcium (0.25%) Th e halogen chlorine (0.05%) is also always ionized in the cell All other elements important for life are present in such small quantities that they are referred to as trace elements

51. These trace elements include: Transition metals such as iron ( 0.0006% ), zinc ( 0.0002% ), copper ( 0.000 06% ), cobalt (0.0000003 % ) and manganese ( 0.000 06% ) A few nonmetals, such as iodine (0.00000075%) and selenium (0.000000045%), can also be classed as essential trace elements

52. Biomolecules Most biomolecules are derivatives of simple compounds of carbon (C), oxygen (O), hydrogen (H), nitrogen (N), sulfur (S), and phosphorus (P) The biochemically important oxygen, nitrogen, and sulfur compounds can be formally derived from their compounds with hydrogen (i. e., H 2 O, NH 3 , and H 2 S) In biological systems, phosphorus is found almost exclusively in derivatives of phosphoric acid, H 3 PO 4 If one or more of the hydrogen atoms of a non-metal hydride are replaced formally with another group, R—e. g., alkyl residues—then derived compounds of the type R-XH n–1 , R-XH n–2 -R, etc., are obtained In this way, alcohols (R-OH) and ethers (R-O-R) are derived from water (H 2 O)

53. Primary amines (RNH 2 ), secondary amines (R-NH-R) and tertiary amines (R-N-R’R") amines are obtained from ammonia (NH 3 ) Thiols (R-SH) and thioethers (R-S-R’) arise from hydrogen sulfide (H 2 S) Since such groups are much more reactive than the (R) to which they are attached, they are referred to as functional groups The ‘R’ group is hydrocarbon which consists of hydrogen and carbon The chemistry of living organisms is organized around carbon All molecules that contain carbon are called organic (except for CO2).

54. To these carbon skeletons are added groups of other atoms, called functional groups, which confer specific chemical properties on the molecule Molecules differ in structure and function, in part, because of different functional groups. Most biomolecules can be regarded as derivatives of hydrocarbons, with hydrogen atoms replaced by a variety of functional groups to yield different families of organic compounds. Examples of these organic compounds are: alcohols, which have one or more hydroxyl groups; amines, with amino groups; aldehydes and ketones, with carbonyl groups; carboxylic acids, with carboxyl groups

55. Examples of Functional Groups of Biomolecules

56. Major Macromolecules of Life Large biological molecules are called macromolecules. There are 4 major biological molecules in life: Carbohydrates Lipid Proteins and Nucleic acids Macromolecules are built by combining smaller building blocks into polymers. Polysaccharides (large carbohydrates) are polymers of monosaccharides Fats are built from fatty acids and glycerol

57. Polysaccharides (large carbohydrates) are polymers of monosaccharides Fats are built from fatty acids and glycerol

58. Proteins are polypeptides - polymers of amino acids. Nucleic acids are polymers of nucleotides. When there is problem with metabolism of these 4 major macromolecules, it results in a disease condition

59. All disease has a biochemical basis Biochemistry Carbohydrates Lipids Nucleic acids Proteins Diabetes Atherosclerosis Genetic Sickle cell Mellitus diseases anemia Pathology 63

60. REFERENCES AND FURTHER READING http://library.thinkquest.org/12413/structures.html http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/text_images/ Molecular Biology of the Cell. 4th edition. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.section.1864 Harper’s Illustrated Biochemistry. Twenty-sixth edition. Chapter 1 Colour Atlas of Biochemistry. Second Edition. Pages 10-13. Lehninger Principles of Biochemistry. Fourth Edition. Chapter 1