introduction to the macromolecules of life and cell...

Introduction to the macromolecules of lifeand cell structures. Introduction to lipids andcell membranes. Barrier role and structure ofmembranes. Organelle structure, roles oforganelles, role of compartmentalisation,comparison between plant and animal cells. [HB]

BIOLOGICAL CHEMISTRYProf. J.H.P. Bayley, Dr. R.M. Adlington and Dr. L. Smith

Trinity Term 2007 - First Year

Lecture 2Hagan Bayley

RECOMMENDED TEXTBOOK

“Biochemistry” 5th edition 2002JM 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

Lecture notes are at:

www.chem.ox.ac.uk/bayleygroup/

on weblearn soon

Introduction to lipids and cell membranesFUNCTIONS OF MEMBRANES

Boundary of cells and organellesconcentrate enzymes, metabolites etc.ionic gradientsreducing environmentpH controletc- i.e. membranes maintain the intracellular environment

Import and export- proteinstransporterssecretion

Electrical signals- also proteinschannels

Organization of enzymes and cytoskeleton

Energy storage and utilization

Signaling

MEMBRANE COMPOSITION

Lipids

Proteinschannelspumpsreceptorsenzymes

Oligosaccharides (attached to lipids or proteins)

Lipid: protein ratiomyelin 3: 1plasma membrane 1: 1mitochondrial inner membrane 1: 3

about 30% ofproteinsencoded in thegenome aremembraneproteins

LIPIDS

3 major classesphospholipidsglycolipidscholesterol

amphipathic molecules

about 109 lipid molecules in a small eukaryotic cell

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

The four major phospholipids of mammalian membranesfatty acids 14- 24 carbon atoms16 carbon and 18 carbon predominatesaturated and unsaturated

Glycolipid molecules

Various representations of cholesterol

The lipids in archaea are distinctive

Ether links- will not hydrolyzeSaturated fatty acid chains- will not be oxidized

Wedge-shaped lipid molecules tend to form micelles, whilecylinder-shaped phospholipids form bilayers

Driving forces for bilayer formation

Hydrophobic effect- buried side chains

Van der Waals interactions between side chains

Headgroups interact with water- electrostatics andhydrogen bonding

Electron microscopy of a pure lipid bilayer (liposome)

PERMEABILITY COEFFICIENT

typical values for PS:

Na+ 10-12 cm s-1

tryptophan 10-7 cm s-1

water 5 X 10-3 cm s-1

LIPID DIFFUSION

For a one-dimensional random walk:

xrms = (2Dt)1/2

x = mean distance from a point in time t

t = x2/ 2D

lipids D = 10-8 cm2 s-1 = 1 µm2 s-1

For 1 µm, t = 0.5 sand for 10 µm = 50 s

LIPID FLIP-FLOP

Flip-flop by contrast with diffusion confined to one leaflet is veryslow:

1 per month per phospholipid

This is the basis of lipid asymmetrysphingomyelin/ phosphatidylcholine outsidephosphatidylethanolamine/ phosphatidylserine insidecholesterol in both halves

These distributions, set up during biosynthesis, cannot changeunless catalyzed

Glycolipids

part of cell coat-glycocalyx

cell-cell recognition

toxin receptors

PROTEINS in membranes

Fluid mosaic model

Various topographiesIntegral- cannot be extracted except with detergentsMostly membrane spanning

Peripheral- extractable with salt or base (e.g.proteins of the cytoskeleton)

Proteins with lipid anchors- e.g. myristoyl, prenyl-most of these act like integral proteins

PROTEINS continued

No flip-flop

Single orientation arising from biosynthesis inendoplasmic reticulum (ER)

… the first major class ofmembrane protein is theα helix bundle …

porin: 16-stranded β barrel

… the second majorclass is the β barrel …

Prostaglandin synthaseCatalyzes the conversion of arachidonic acid to prostaglandin PGG2 and then to PGH2

Cytoskeleton- example of peripheral membrane proteins

Electron microscopy of red cell cytoskeleton

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

COMPARTMENTALIZATION

Boundary of cells and organellesconcentrate enzymes, metabolites etc.ionic gradientsreducing environmentpH controletc- i.e. membranes maintain the intracellular environment

Import and exporttransporterssecretion

Electrical signalspumps and channels

Organization of enzymes and cytoskeleton

Energy storage and utilization

Signaling

Focus on organelles

Introduction to the macromolecules of lifeand cell structures. Introduction to lipids andcell membranes. Barrier role and structure ofmembranes. Organelle structure, roles oforganelles, role of compartmentalisation,comparison between plant and animal cells.

The major organelles of a eukaryotic cellare:NUCLEUS – contains the chromosomes, which consist of DNAand histones. Gene replication. mRNA synthesis. Ribosomeproduction.

MITOCHONDRIA – principal function is the production of ATP

ENDOPLASMIC RETICULUM:ROUGH – studded with ribosomes- sites of protein synthesis formembrane and secreted proteinsSMOOTH –steroid hormone biosynthesis, Ca2+ storage

LYSOSOMES - contain hydrolytic enzymesPEROXISOMES - contain oxidative enzymesThe lysosomes and peroxisomes degrade foreign substances thathave been brought into the cell (simplification)

GOLGI COMPLEXES –newly biosynthesised proteins areprocessed here (post-translational modification), e.g. glycosylated

Plant cells: plastids (e.g. chloroplast-photosynthesis), vacuoles (control hydrostaticpressure through fluid uptake, storage andbreakdown of molecules), cell wall

Bacterial membranes

Escherichia coli

Staphylococcus aureus

Major organelles- membrane structure and originMitochondrion- Double membrane cf certain bacteria. Endosymbiosis: own DNA andinternal ribosomes; replicate but only semiautonomous (cannot exist outside the eukaryotic cell)

Nucleus- Double membrane through which nuclear pores penetrate, directly connected to therough endoplasmic reticulum (ER)

Endoplasmic reticulum- Single membrane. Rough ER is site of secreted andmembrane 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 recentresults suggest peroxisomes are derived from the ER: Cell 122, 85-95 (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 stackedmembranes- thylakoids. Endosymbiosis: own DNA and internal ribosomes; replicates but onlysemiautonomous (cannot exist outside the plant cell)

Origin of organelles other than mitochondria

nucleus

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

Mitochondria (singular: mitochondrion)Mitochondria generate ATP- the energy “currency” of thecell. They are semiautonomous. They encode some butnot all of their own proteins. They have exchangedgenes with the nucleus-- in turn the host cell nowrequires their ATP.

Glycolysis (anaerobic, in the cytoplasm) generates someATP and also pyruvate.

In the mitochondrion:• pyruvate acetylCoA• In the Krebs cycle: acetate 2CO2/ GTP/ 8e- (asFADH2 and NADH)• Used to generate a proton gradient across the innermitochondrial membrane- (8e- / 2O2 36 H+

translocated)• Proton gradient converts ADP + Pi ATP, using ATPsynthase- 3 H+ translocated per ATP?

???Why does this require compartmentalization?

mitochondrion

mitochondrial inner membrane

ATP synthaseForms ATP from ADP and Pi by using a transmembrane proton gradient as an energysource

see you in Week 4