BIOLOGICAL CHEMISTRY Prof. J.H.P. Bayley, Dr. R.M. Adlington and Dr. L. Smith Trinity Term First Year. Lecture 2 Hagan Bayley

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1 BIOLOGICAL CHEMISTRY Prof. J.H.P. Bayley, Dr. R.M. Adlington and Dr. L. Smith Trinity Term First Year Lecture 2 Hagan Bayley Introduction to the macromolecules of life and cell structures. Introduction to lipids and cell membranes. Barrier role and structure of membranes. Organelle structure, roles of organelles, role of compartmentalisation, comparison between plant and animal cells. [HB]

2 RECOMMENDED TEXTBOOK Biochemistry 5th edition 2002 JM Berg, JL Tymoczko, L Stryer Freeman We call this book Stryer This week mainly Chapter 12 Figures mainly from Bruce Alberts et al. Molecular Biology of the Cell Also a good text for organelles

3 Lecture notes are at: on weblearn soon

4 Introduction to lipids and cell membranes FUNCTIONS OF MEMBRANES Boundary of cells and organelles concentrate enzymes, metabolites etc. ionic gradients reducing environment ph control etc- i.e. membranes maintain the intracellular environment Import and export- proteins transporters secretion Electrical signals- also proteins channels Organization of enzymes and cytoskeleton Energy storage and utilization Signaling

5 MEMBRANE COMPOSITION Lipids Proteins channels pumps receptors enzymes about 30% of proteins encoded in the genome are membrane proteins Oligosaccharides (attached to lipids or proteins) Lipid: protein ratio myelin 3: 1 plasma membrane 1: 1 mitochondrial inner membrane 1: 3

6 LIPIDS 3 major classes phospholipids glycolipids cholesterol amphipathic molecules about 10 9 lipid molecules in a small eukaryotic cell

7 Four representations of a phosphatidylcholine molecule the kink in the unsaturated fatty acid chain is exaggerated

8 The four major phospholipids of mammalian membranes fatty acids carbon atoms 16 carbon and 18 carbon predominate saturated and unsaturated

9 Glycolipid molecules

10 Various representations of cholesterol

11 The lipids in archaea are distinctive Ether links- will not hydrolyze Saturated fatty acid chains- will not be oxidized

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13 Wedge-shaped lipid molecules tend to form micelles, while cylinder-shaped phospholipids form bilayers

14 Driving forces for bilayer formation Hydrophobic effect- buried side chains Van der Waals interactions between side chains Headgroups interact with water- electrostatics and hydrogen bonding

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16 Electron microscopy of a pure lipid bilayer (liposome)

17 PERMEABILITY COEFFICIENT typical values for P S : Na cm s -1 tryptophan 10-7 cm s -1 water 5 X 10-3 cm s -1

18 LIPID DIFFUSION For a one-dimensional random walk: x rms = (2Dt) 1/2 x = mean distance from a point in time t t = x 2 / 2D lipids D = 10-8 cm 2 s -1 = 1 µm 2 s -1 For 1 µm, t = 0.5 s and for 10 µm = 50 s

19 LIPID FLIP-FLOP Flip-flop by contrast with diffusion confined to one leaflet is very slow: 1 per month per phospholipid This is the basis of lipid asymmetry sphingomyelin/ phosphatidylcholine outside phosphatidylethanolamine/ phosphatidylserine inside cholesterol in both halves These distributions, set up during biosynthesis, cannot change unless catalyzed

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21 Glycolipids part of cell coatglycocalyx cell-cell recognition toxin receptors

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24 PROTEINS in membranes Fluid mosaic model Various topographies Integral- cannot be extracted except with detergents Mostly membrane spanning Peripheral- extractable with salt or base (e.g. proteins of the cytoskeleton) Proteins with lipid anchors- e.g. myristoyl, prenylmost of these act like integral proteins

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28 PROTEINS continued No flip-flop Single orientation arising from biosynthesis in endoplasmic reticulum (ER)

29 the first major class of membrane protein is the α helix bundle

30 porin: 16-stranded β barrel the second major class is the β barrel

31 Prostaglandin synthase Catalyzes the conversion of arachidonic acid to prostaglandin PGG 2 and then to PGH 2

32 Cytoskeleton- example of peripheral membrane proteins

33 Electron microscopy of red cell cytoskeleton

34 Summary of membrane properties Thin sheet-like structures based on the lipid bilayer Contain proteins that provide function Non-covalent assemblies Asymmetric Fluid Transmembrane potential

35 COMPARTMENTALIZATION Boundary of cells and organelles concentrate enzymes, metabolites etc. ionic gradients reducing environment ph control etc- i.e. membranes maintain the intracellular environment Import and export transporters secretion Electrical signals pumps and channels Organization of enzymes and cytoskeleton Energy storage and utilization Signaling

36 Focus on organelles Introduction to the macromolecules of life and cell structures. Introduction to lipids and cell membranes. Barrier role and structure of membranes. Organelle structure, roles of organelles, role of compartmentalisation, comparison between plant and animal cells.

37 The major organelles of a eukaryotic cell are: NUCLEUS contains the chromosomes, which consist of DNA and histones. Gene replication. mrna synthesis. Ribosome production. MITOCHONDRIA principal function is the production of ATP ENDOPLASMIC RETICULUM: ROUGH studded with ribosomes- sites of protein synthesis for membrane and secreted proteins SMOOTH steroid hormone biosynthesis, Ca 2+ storage LYSOSOMES - contain hydrolytic enzymes PEROXISOMES - contain oxidative enzymes The lysosomes and peroxisomes degrade foreign substances that have been brought into the cell (simplification) GOLGI COMPLEXES newly biosynthesised proteins are processed here (post-translational modification), e.g. glycosylated

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39 Plant cells: plastids (e.g. chloroplastphotosynthesis), vacuoles (control hydrostatic pressure through fluid uptake, storage and breakdown of molecules), cell wall

40 Bacterial membranes Escherichia coli Staphylococcus aureus

41 Major organelles- membrane structure and origin Mitochondrion- Double membrane cf certain bacteria. Endosymbiosis: own DNA and internal ribosomes; replicate but only semiautonomous (cannot exist outside the eukaryotic cell) Nucleus- Double membrane through which nuclear pores penetrate, directly connected to the rough endoplasmic reticulum (ER) Endoplasmic reticulum- Single membrane. Rough ER is site of secreted and membrane protein synthesis on external membrane-bound ribosomes Golgi- Single membrane. No DNA or internal ribosomes Endosomes- Single membrane. No DNA or internal ribosomes Lysosomes- Single membrane. No DNA or internal ribosomes Peroxisomes- Single membrane. Thought to divide by enlargement and division, but recent results suggest peroxisomes are derived from the ER: Cell 122, (2005); Current Biology 15, R774-R776 (2005). No DNA or internal ribosomes Plants (cell wall) Vacuole- Single membrane. No DNA or internal ribosomes Chloroplast- Double membrane cf certain bacteria. Contains pinched off stacked membranes- thylakoids. Endosymbiosis: own DNA and internal ribosomes; replicates but only semiautonomous (cannot exist outside the plant cell)

42 Origin of organelles other than mitochondria nucleus

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44 Endosomes: import into cells (good e.g. lipoproteins, bad e.g. some viruses, toxins)

45 Mitochondria (singular: mitochondrion) Mitochondria generate ATP- the energy currency of the cell. They are semiautonomous. They encode some but not all of their own proteins. They have exchanged genes with the nucleus-- in turn the host cell now requires their ATP. Glycolysis (anaerobic, in the cytoplasm) generates some ATP and also pyruvate. In the mitochondrion: pyruvate acetylcoa In the Krebs cycle: acetate 2CO 2 / GTP/ 8e - (as FADH 2 and NADH) Used to generate a proton gradient across the inner mitochondrial membrane- (8e - / 2O 2 36 H + translocated) Proton gradient converts ADP + P i ATP, using ATP synthase- 3 H + translocated per ATP????Why does this require compartmentalization?

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47 mitochondrial inner membrane

48 ATP synthase Forms ATP from ADP and P i by using a transmembrane proton gradient as an energy source see you in Week 4