Che 214 lecture 01


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  • This image shows the primary structure of glycophorin A , a glycoprotein that spans the plasma membrane ("Lipid bilayer") of human red blood cells. Each RBC has some 500,000 copies of the molecule embedded in its plasma membrane. Fifteen carbohydrate chains are "O-linked" to serine (Ser) and threonine (Thr) residues. One carbohydrate chain is "N-linked" to the asparagine (Asn) at position 26. Two polymorphic versions of glycophorin A, which differ only at residues 1 and 5, occur in humans. These give rise to the MN blood groups The M allele encodes Ser at position 1 (Ser-1) and Gly at position 5 (Gly-5) The N allele encodes Leu-1 and Glu-5 Genotype to Phenotype Individuals who inherit two N alleles have blood group N. Individuals who are homozygous for the M allele have blood group M. Heterozygous individuals produce both proteins and have blood group MN . Glycophorin A is the most important attachment site by which the parasite Plasmodium falciparum invades human red blood cells.
  • Che 214 lecture 01

    1. 1. CHE 214: BiochemistryLecture oneTODAYS TOPICS •INTRODUCTION AND COURSE OUTLINE •CARBOHYDRATES •LIPIDSLecturer: Dr. G. Kattam MaiyohFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 1
    2. 2. CHE 214: BIOCHEMISTRYContact informationDr. Geoffrey Kattam MaiyohE-mail: / Tel: 0713-592879Website: Recommended Textbooks/ Lecture Notes •L. Stryer, Biochemistry •Lehninger, Principles of Biochemistry •Any other textbook of Biochemistry •Power point lecture notes will be available after class (Class representatives to collect on flash discs).February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 2
    3. 3. Examination –CAT s – 20% –Practical – 10% –Final Exam – 70% –Everyone is required to be present during CATs and Exams •Examination / CATs Format •CAT Questions – Both CATs will comprise 30 questions each. There will be 3sections in each CAT paper (Multiple choice, Structured i.e. “Filling in the blank spaces”and True/False sections) • Examination Questions – All Exam questions will be in essay form •Attendance –Exams will mostly be based on the material presented during classes. –It is in your best interest to attend each lecture.February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 3
    4. 4. TOPICS Title DNA 1. Biological Molecules: Structure, Chemistry and Function of Carbohydrates and Lipids 2. Biological Molecules: Structure, Chemistry and Function of Proteins and Nucleic acids 3. Bioenergetics: Pathways of Glucose, Fat and Amino acid metabolism CAT ONE 4. Biomembrane Chemistry 5. Introduction to Enzymology 6. Biochemistry Techniques: Preparation of buffers and PH measurement 7. Biochemistry Techniques: Chromatography, Column, Paper, Gas-Liquid Chromatography PROTEIN CAT TWO 8. Biochemistry Techniques: Electrophoresis, Precipitation, Colorimetry, Spectrophotometry, Flame Photometry EXAMINATIONSFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 4
    5. 5. Cells as chemical reactors • Living organisms obey the laws of chemistry and physics – Can think of cells as complex chemical reactors in which many different chemical reactions are proceeding at the same time • All cells are more similar than different if looked at on the inside! – Strip away the exterior and we see that all cells need to accomplish similar tasks and in a broad sense they use the same mechanisms (chemical reactions) – This MAY reflects a singular origin of all living things!February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 5
    6. 6. LUCA (Last Universal Common Ancestor)February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 6
    7. 7. Some key similarities among all types of cells • All cells use nucleic acids (DNA) to store information – RNA viruses, but not true cells (incapable of autonomous replication) – All cells use nucleic acids (RNA) to access stored information • All cells use proteins as catalysts (enzymes) for chemical reactions – A few examples of RNA based enzymes, which may reflect primordial use of RNA • All cells use lipids for membrane components – Different types of lipids in different types of cells • All cells use carbohydrates for cell walls (if present), recognition, and energy generation February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 7
    8. 8. • Biologically important macromolecules are “polymers” of smaller subunits • Created through condensation reactions Macromolecule Subunit Carbohydrates : simple sugars Lipids : CH2 units Proteins : amino acids Nucleic acids : nucleotides (Base, Sugar and Phosahate)February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 8
    9. 9. Where do the subunits come from? • All cells need a source of the atomic components of the subunits – (C, O, H, N, P, and a few other trace elements ) There are several possibilities to acquire them. They include; i. Some cells can synthesize all of the subunits given these atomic components and an energy source ii. Some cells can obtain these subunits from external sources iii. Some cells can convert other compounds into these subunits • We will discuss further in section on BioenergeticsFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 9
    10. 10. Carbohydrates• All have general formula CnH2nOn (hydrates (H2O) of carbon)• A variety of functions in the cell – Large cross-linked carbohydrates make up the rigid cell wall of plants, bacteria, and insects – In animal cells, carbohydrates on the exterior surface of the cell serve a recognition and identification function – A central function is energy storage and energy production !February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 10
    11. 11. Carbohydrates – Cell structure: – Cellulose, LPS, chitin Chitin in exoskeletonCellulose in plant cell walls Lipopolysaccharides (LPS) in bacterial cell wall February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 11
    12. 12. Carbohydrate Structure Monosaccharides may also form part of other biologically important moleculesFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 12
    13. 13. Carbohydrate Structure• Complex carbohydrates are built from simple sugars – Most often five (pentose) or six (hexose) carbon sugars – Numerous –OH (hydroxyl) groups can form many types of “cross links” – Can result in very complex and highly cross linked structures ( cellulose, chitin, starch, etc.)February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 13
    14. 14. Carbohydrate Structure A Few Examples• Triose (3 carbon) – Glyceraldehyde• Pentose (5 carbon) – RiboseFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 14
    15. 15. Carbohydrate StructureExample of two hexoses – Glucose Galactose – What’s the difference? Both are C6H12O6 • They are isomers of one another! • Same molecular formula, but different structure (3D- shape).February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 15
    16. 16. Carbohydrate Structure• Monosacharides can be joined to one another to form disaccharides, trisaccharides, ……..polysaccharides – Saccharide is a term derived from the Latin for sugar (origin = "sweet sand")• Carbohydrates classified according to the number of saccharide units they contain. – A monosaccharide contains a single carbohydrate, over 200 different monosaccharides are known. – A disaccharide gives two carbohydrate units on hydrolysis. – An oligosaccharide gives a "few" carbohydrate units on hydrolysis, usually 3 to 10. – A polysaccharide gives many carbohydrates on hydrolysis, examples are starch and cellulose.February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 16
    17. 17. Carbohydrate Structure Pentoses and hexoses are capable of forming ring (cyclic) structures. An equilibrium exists between the ring and open form. Linear form Ring (cyclic) form Fructose GlucoseThe carbonyl group reacts with the –OH group on the second to the last carbonFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 17
    18. 18. Condensation reaction Two simple sugars can polymerize to form a disaccharide. For example, galactose reacts with glucose to form lactose, which is the sugar found in milk. Lactose on the other hand can be hydrolyzed to form the two monosaccharodes the enzyme by lactase February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 18
    19. 19. Glycosidic bond •The type of chemical linkage between the monosaccharide units of disaccharides, oligosaccharides, and polysaccharides, which is formed by the removal of a molecule of water (i.e. a condensation reaction). •The bond is normally formed between the carbon-1 on one sugar and the carbon-4 on the other. •An α-glycosidic bond is formed when the –OH group on carbon-1 is below the plane of the glucose ring and a β- glycosidic bond is formed when it is above the plane. •Cellulose is formed of glucose molecules linked by 1-4 β- glycosidic bonds, whereas starch is composed of 1-4 α- glycosidic bonds. February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 19
    20. 20. Carbohydrate Structure They are a special type of isomers of one another. Called anomers α-isomer β-isomerFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 20
    21. 21. Two common small carbohydrates Glyceraldehyde RiboseFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 21
    22. 22. Complex Carbohydrates • Cellulose Most abundant carbohydrate on the planet! – Component of plant cell walls – Indigestible by animals • β 1-4 bonds • Starch – Energy storage molecule in plants – Can be digested by animals • α 1-4 bondsFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 22
    23. 23. February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 23
    24. 24. Complex Carbohydrates• Glycogen – Branched chain polymer of glucose – Animal energy reserve – Found primarily in liver and muscle • α 1-4 & α 1-6 bonds February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 24
    25. 25. • GlycogenFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 25
    26. 26. Cellulose• Cellulose is a linear polysaccharide in which some 1500 glucose rings link together. It is the chief constituent of cell walls in plants.• Human digestion cannot break down cellulose for use as a food, animals such as cattle and termites rely on the energy content of cellulose.• They have protozoa and bacteria with the necessary enzymes in their digestive systems. February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 26
    27. 27. Starches• Starches are carbohydrates in which 300 to 1000 glucose units join together. It is a polysaccharide used to store energy for later use.• Starch forms in grains with an insoluble outer layer which remain in the cell where it is stored until the energy is needed. Then it can be broken down into soluble glucose units.• Starches are smaller than cellulose units, and can be more readily used for energy. In animals, the equivalent of starch is glycogen, which can be stored in the muscles or in the liver for later use. Has α-1,6 bonds glycosidic linkages February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 27
    28. 28. polysaccharides can be linked to other molecules to form glyco-proteins and glyco-lipidsFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 28
    29. 29. GlycoproteinsSome examples • Polysaccharide component of antibodies has major effect on antibody function • Polysaccharides attached to proteins on surface of red blood cells (RBC) determine blood type (A,B,O) .  See next slide – Polysaccharides are attached to proteins in the Golgi apparatus through a process of post-translational modification • Different types of cells do different post-tranlational modificationsMarch 21, 2013 GKM/BMLS/SEM2/LEC 02/2012 29
    30. 30. GlycoproteinsMediate CellRecognitionYour ABO bloodtype isdetermined by what sugarsyou have in a particularoligosaccharide side chainon one of the proteins thatlies on the surface of yourred blood cells March 21, 2013 GKM/BMLS/SEM2/LEC 02/2012 30
    31. 31. Other Functions Of Glycoproteins Contact Inhibition Cells stop growing when they contact neighbors This function is disrupted in some cancers Protein Turnover Many glycoproteins have sialic acid residues at the end of the carbohydrate chain. Loss of these sialic acid residues indicates the protein is old and ready to be turned over. Antifreeze Some fish that live in cold water produce glycoproteins that lower the freezing point of their body’s water, thereby enabling them to survive the cold water Hiding Viruses Some viruses can modify their cell surface proteins to mimic the native glycoproteins, thereby hiding from the host’s immune systemMarch 21, 2013 GKM/BMLS/SEM2/LEC 02/2012 31
    32. 32. Glycolipids• Polysaccharides can be attached to lipid molecules •An outer-membrane constituent of gram negative bacteria, LPS, which includes O-antigen, a core polysaccharide and a Lipid A, coats the cell surface and works to exclude large hydrophobic compounds such as bile salts and antibiotics from invading the cell. •O-antigen are long hydrophilic carbohydrate chains (up to 50 sugars long) that extend out from the outer membrane •While Lipid A (and fatty acids) anchors the LPS to the outer membrane. February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 32
    33. 33. Lipids• Lipids include the following; – Fatty acids (Polymers of CH2 units) – Glycerol – Triglycerides – Other subunits (phosphate, choline, etc) may be attached to yield “phospholipids” • Charged phosphate groups will create a polar molecule with a hydrophobic (nonpolar) end and a hydrophillic (polar) endFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 33
    34. 34. February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 34
    35. 35. LipidsFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 35
    36. 36. PhospholipidsFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 36
    37. 37. Function – Energy Storage • Triglycerides – Cell membranes and cell compartments – Bi-layer structure • Outer or plasma membrane • Nuclear membrane • Internal structures – ER, Golgi, Vesicles, etc.February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 37
    38. 38. Phospholipid bilayer Hydrophillic heads Hydrophobic tailsFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 38
    39. 39. SteroidsFebruary 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 39