Download protein - Hagan Bayley

BIOLOGICAL CHEMISTRY
Prof. J.H.P. Bayley, Dr. R.M. Adlington and Dr. L. Smith
Trinity Term 2007 - 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]
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
Lecture notes are at:
www.chem.ox.ac.uk/bayleygroup/
on weblearn soon
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
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
LIPIDS
3 major classes
phospholipids
glycolipids
cholesterol
amphipathic molecules
about 109 lipid molecules in a small eukaryotic cell
Four representations of a phosphatidylcholine molecule
the kink in the unsaturated fatty acid chain is exaggerated
The four major phospholipids of mammalian membranes
fatty acids 14- 24 carbon atoms
16 carbon and 18 carbon predominate
saturated and unsaturated
Glycolipid molecules
Various representations of cholesterol
The lipids in archaea are distinctive
Ether links- will not hydrolyze
Saturated fatty acid chains- will not be oxidized
Wedge-shaped lipid molecules tend to form micelles, while
cylinder-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 and
hydrogen 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 s
and for 10 µm = 50 s
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
Glycolipids
part of cell coatglycocalyx
cell-cell recognition
toxin receptors
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
PROTEINS continued
No flip-flop
Single orientation arising from biosynthesis in
endoplasmic reticulum (ER)
… the first major class of
membrane protein is the
α helix bundle …
… the second major
class is the β barrel …
porin: 16-stranded β barrel
Prostaglandin synthase
Catalyzes 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 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
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.
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, Ca2+ 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
Plant cells: plastids (e.g. chloroplastphotosynthesis), vacuoles (control hydrostatic
pressure through fluid uptake, storage and
breakdown of molecules), cell wall
Bacterial membranes
Escherichia coli
Staphylococcus aureus
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, 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 stacked
membranes- thylakoids. Endosymbiosis: own DNA and internal ribosomes; replicates but only
semiautonomous (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 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  2CO2/ GTP/ 8e- (as
FADH2 and NADH)
• Used to generate a proton gradient across the inner
mitochondrial membrane- (8e- / 2O2  36 H+
translocated)
• Proton gradient converts ADP + Pi  ATP, using ATP
synthase- 3 H+ translocated per ATP?
???Why does this require compartmentalization?
mitochondrion
mitochondrial inner membrane
ATP synthase
Forms ATP from ADP and Pi by using a transmembrane proton gradient as an energy
source
see you in Week 4