BIO 121 – Cell Physiology Lecture Section II A. Biological Membranes B. Protein Structure and...
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BIO 121 – Cell PhysiologyLecture Section II
A. Biological MembranesB. Protein Structure and FunctionC. The Cytoskeletal System and AdhesionD. Cellular MovementsE. The Endomembrane System and Intracellular Trafficking
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1. Review of the Fundamental Structures and Functions of Biological Membranes
All cells have a plasmamembrane, eukaryotes have maximized use of membranes
The membranes and membrane-bound compartments of eukaryotic cells allow for the far greater complexity of structure and function in those cells
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Nucleoid
Plasma membrane
Cell wallBacterialchromosome
Prokaryotes: Cytoplasm bound by plasma membrane, no organelles No nucleus, DNA in an unbound region called the nucleoid
The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell
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Smooth ERRough ER
CYTOSKELETON:
Microfilaments
Intermediatefilaments
Microtubules
MitochondrionLysosome
Golgiapparatus
Plasma membrane
Nuclearenvelope
Typicalanimal
cell
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Fig. 6-9b
Nuclear envelope Rough endoplasmic reticulum
Smooth endoplasmic reticulum
Central vacuole
Microfilaments
Intermediate filamentsMicrotubules
CYTO-SKELETON
Chloroplast
PlasmodesmataWall of adjacent cell
Cell wall
Plasma membrane
Mitochondrion
Golgiapparatus
Plant and animal cells have most of the same organelles
Same for fungiand protists.....
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The Eukaryotic Membrane System
• Components of the membrane system:• Plasma membrane• Nuclear envelope• Endoplasmic reticulum• Golgi apparatus• Mitochondria and Chloroplasts• Lysosomes• Peroxisomes• Vacuoles
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
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b. The main components of membrane structure are ......
» The Amphipathic Lipid Bilayer
» Membrane Proteins and Sugars
» The Cytosolic Submembrane Protein Meshwork
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Fig. 7-2
Hydrophilichead
WATER
Hydrophobictail
WATER
The most fundamental structure of a biological membrane is a double layer of phospholipids
The Amphipathic Lipid Bilayer
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Figure 10-3 Molecular Biology of the Cell (© Garland Science 2008)
There are many types of phospholipids
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Figure 10-18 Molecular Biology of the Cell (© Garland Science 2008)
Glycolipids
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Figure 10-5 Molecular Biology of the Cell (© Garland Science 2008)
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Fig. 7-5b
Fluid
Unsaturated hydrocarbontails with kinks
Viscous
Saturated hydro-carbon tails
•Membranes must be fluid to work properly
• they are usually about as fluid as salad oil
• Membranes rich in unsaturated fatty acids are more fluid that those rich in saturated fatty acids
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Fig. 7-5c
Cholesterol
•The steroid cholesterol has different effects on membrane fluidity at different temperatures
•At warm temperatures (such as 37°C), cholesterol restrains movement of phospholipids
•At cool temperatures, it maintains fluidity by preventing tight packing
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Figure 10-9b Molecular Biology of the Cell (© Garland Science 2008)
Membrane lipids provide hydrophobic to most molecules dissolved in water and allow a select few to diffuse across
-oxygen-carbon dioxide-urea-water
Spontaneousformation and ‘healing’
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The Permeability of the Lipid Bilayer
Hydrophobic (nonpolar) molecules, such as hydrocarbons, can dissolve in the lipid bilayer and pass through the membrane rapidly
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Charged or strongly polar molecules, such as ions,sugars and proteins, do not cross the membrane easily
estradiol testosterone
glucose proteins
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Fig. 7-13
Hypotonic solution
(a) Animal cell
(b) Plant cell
H2O
Lysed
H2O
Turgid (normal)
H2O
H2O
H2O
H2O
Normal
Isotonic solution
Flaccid
H2O
H2O
Shriveled
Plasmolyzed
Hypertonic solution
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Figure 10-19 Molecular Biology of the Cell (© Garland Science 2008)
Transmembrane Proteins 1. single pass 2. multiple pass 3. barrel or channel
Proteins can associate with membranes in a variety of ways:
4. single sheath proteins
Anchored Proteins 5. lipid anchor 6. sugar anchor 7/8 protein anchor
Membrane proteins provide the bulk of specific membrane functions and their variation is a primary determinant of cellular identity
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Protein-lipid ratio varies hugely in different membranes
protein lipid1. myelin sheath 20% 80%2. outer mitochondrial 50% 50%3. inner mitochondrial 80% 20%
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Fig. 7-9ac
(a) Transport (b) Enzymatic activity (c) Signal transduction
ATP
Enzymes
Signal transduction
Signaling molecule
Receptor
Typical functions of membrane proteins
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Fig. 7-9df
(d) Cell-cell recognition
Glyco-protein
(e) Intercellular joining (f) Attachment to the cytoskeleton and extracellular matrix (ECM)
Carbohydrates often play important roles on the plasma membrane. Covalently bonded to lipids (forming glycolipids) or more commonly to proteins (forming glycoproteins)
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N-terminus
C-terminus
HelixCYTOPLASMICSIDE
EXTRACELLULARSIDE
Whattypesofsidechainsare on outsideofthesehelices?
Biochemical structure depends on surroundings
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Fig. 7-17Passive transport
Diffusion Facilitated diffusion
Active transport
ATP
Nutrient uptakeWaste eliminationpH and osmolarity maintenanceElectrical gradient maintenance
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Figure 11-12 Molecular Biology of the Cell (© Garland Science 2008)
We have pumps for glucose, amino acids, calcium, and many other molecules
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Figure 10-28b Molecular Biology of the Cell (© Garland Science 2008)
Sugars are found on the non-cytosolic face of membranes
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Figure 10-41a Molecular Biology of the Cell (© Garland Science 2008)
Review of Membrane Structure
The third component: submembrane protein meshwork
Always on the cytosolic face
Allows membrane to communicate with the rest of the cell
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Figure 10-42 Molecular Biology of the Cell (© Garland Science 2008)
A major role of the meshwork is to segregate and establish functional domains in the membrane
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Some Structures that Live in the Submembrane Meshwork:
- Membrane identification proteins
- Anchor proteins for cadherins and integrins
- 2nd messengers for signaling pathways
- Ribosome docking proteins
- Chaperonin docking proteins
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What are the Principle Functions of Cell Membranes?
• Compartmentilization of Cell Functions
• Defense and Integrity of Cellular or Compartmental Contents
• Selective Permeability in Two Directions
• Regulation of Internal Cellular or Compartmental Activities
• Attachment and Movement of the cell or Compartment
• Response to Signals from Outside of the Cell or Compartment
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Table 12-2 Molecular Biology of the Cell (© Garland Science 2008)
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Key Functions of the Nucleus and Endoplasmic Reticulum
• Store, protect and transcribe the DNA• Deliver RNAs for translation• Lipid biosynthesis and protein translation• Integration of membrane lipid and protein• Detoxification of dangerous materials• Calcium sequestration
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Figure 12-8 Molecular Biology of the Cell (© Garland Science 2008)
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rRNA Production
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mRNA Production
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Figure 12-9a Molecular Biology of the Cell (© Garland Science 2008)
Nuclear Pore Complex
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Translation and Lipid Synthesis
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Key Functions of the Golgi Apparatus (GA)
1. Post-translational modification of membrane lipid and protein constituents.
a. Sulfation, glycosylation, adenylation, phosphorylation, etc.
2. Membrane Targeting. Control of the cellular
destinations of prepared membrane and protein vesicles.
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Figure 13-28 Molecular Biology of the Cell (© Garland Science 2008)
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Functions of Mitochondria and Chloroplasts
1. Captive energy plants for the cell 2. Store, protect, express their own DNA
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Figure 13-42a Molecular Biology of the Cell (© Garland Science 2008)
Key Functions of the Endosomal System
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Figure 13-53 Molecular Biology of the Cell (© Garland Science 2008)
Recycling of membranecomponents
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Key Functions of the Peroxisome
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Key Functions of the Vacuole
Control of water and ion exchange is organisms dependent on a variable external environment
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B. Protein Structure and Function
Protein biochemistry dictates their functional activities
Regulation of protein structure and function is one of the most fundamental means by which cells control their own activities
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Figure 3-1 (part 2 of 2) Molecular Biology of the Cell (© Garland Science 2008)
a. Final amino acid position results from the conformation that gives the lowest free energy
most of this is driven by the polar aqueous and non-polar membrane phases
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Figure 3-5 Molecular Biology of the Cell (© Garland Science 2008)
In the aqueous phase polar side chains face out, in the membrane they are hidden
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Figure 3-4 Molecular Biology of the Cell (© Garland Science 2008)
Many forces help maintain the final shape
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Figure 3-22 Molecular Biology of the Cell (© Garland Science 2008)
Self- and regulated- assembly of large structures
hemoglobin is made up of 2 alpha and 2 beta subunits
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Figure 3-27a Molecular Biology of the Cell (© Garland Science 2008)
Collagen fibrils are made up of many collagen proteins, each of which are made of 3 collagen subunit peptides
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Figure 3-12 Molecular Biology of the Cell (© Garland Science 2008)
Because of gene duplication and exon duplication modularity of structure is common: Protein families and domains
Two serine protease genes give nearly exact binding site structure
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Final Structure = Final Function
Active amino acids widely distributed Folding places them into
active distribution
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Fig. 7-16-1
EXTRACELLULAR FLUID [Na+] high [K+] low Na+
Na+
Na+ [Na+] low[K+] high
CYTOPLASM
Cytoplasmic Na+ binds
1
Example:The sodium-potassium pump
Binding changes protein conformation,change in conformation alters activity
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Na+ binding stimulates phosphorylation by ATP.
Fig. 7-16-2
Na+
Na+
Na+
ATP P ADP
2
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Fig. 7-16-3
Phosphorylation causes the protein to change its shape. Na+ is expelled to the outside.
Na+
P
Na+ Na+
3
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Fig. 7-16-4
K+ binds on theextracellular side andtriggers release of thephosphate group.
P P
K+
K+
4
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Fig. 7-16-5
Loss of the phosphaterestores the protein’s originalshape.
K+
K+
5
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Fig. 7-16-6
K+ is released, and thecycle repeats.
K+
K+
6
Why do we want Na+ outside of the cell and K+ inside?
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Cells can control protein activity directly by mechanisms that target the protein itself
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Figure 3-58 Molecular Biology of the Cell (© Garland Science 2008)
Definition: “Allosteric”. Proteins with two or more binding sites, wherein activity away from the active site will regulate activity at the active site
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Figure 3-59 Molecular Biology of the Cell (© Garland Science 2008)
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Figure 3-64 Molecular Biology of the Cell (© Garland Science 2008)
1. Cells can start and stop a protein’s activity by changing its structure through the addition of a covalent subgroup
phosphorylation-dephosphorylation
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Figure 12-51 Molecular Biology of the Cell (© Garland Science 2008)
glycosylation
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Figure 10-20 Molecular Biology of the Cell (© Garland Science 2008)
Addition of covalently linked lipids allows a proteinto have a tight association with the membrane
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Figure 3-81a Molecular Biology of the Cell (© Garland Science 2008)
Complex Covalent Regulation of the p53 Transcription Factor
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Figure 3-81c Molecular Biology of the Cell (© Garland Science 2008)
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Figure 3-35 Molecular Biology of the Cell (© Garland Science 2008)
2. Cells can start and stop a protein’s activity by proteolytic cleavage
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Figure 18-5a Molecular Biology of the Cell (© Garland Science 2008)
The clotting cascade is the same
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Figure 3-69 (part 1 of 3) Molecular Biology of the Cell (© Garland Science 2008)
3. Some regulatory mechanisms involve multiple strategies such as activation of Src protein
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Figure 3-69 (part 2 of 3) Molecular Biology of the Cell (© Garland Science 2008)
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Figure 3-69 (part 3 of 3) Molecular Biology of the Cell (© Garland Science 2008)
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Cells can control protein activity indirectly by altering the other molecules that share its environment
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Figure 15-53a Molecular Biology of the Cell (© Garland Science 2008)
1. Cells can start and stop a protein’s activity by regulating the presence of a critical binding partner
a. Ligand interaction activates receptor
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Figure 11-12 Molecular Biology of the Cell (© Garland Science 2008)
2. Sequestration of effector molecules linked to controlled release
eg. Hide all of the calcium until you want to change actin-myosin activity
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c. Cooperative/Coupled binding - Substrate binding in one site effects binding of substrate in second site by changing affinity
Hemoglobin binds oxygenwith greater affinity whenthere is lots of oxygen – thisensures flow of oxygen to the tissues and not away.
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Figure 16-78a Molecular Biology of the Cell (© Garland Science 2008)
2. Cells can start and stop a protein’s activity by blocking its binding site
Tropomyosin blocking the myosin-binding site on actin
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Figure 17-49a Molecular Biology of the Cell (© Garland Science 2008)
3. Cells can start and stop a protein’s activity by regulating the processes that make active polymers from inactive subunits
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Figure 3-79 Molecular Biology of the Cell (© Garland Science 2008)
4. Cells can start and stop a protein’s activity by regulating the scaffolded interaction of the subunits of protein machines
Ubiquitinligasecomplex
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Figure 19-21 Molecular Biology of the Cell (© Garland Science 2008)
Synapticscaffold
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Figure 15-21a Molecular Biology of the Cell (© Garland Science 2008)
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Figure 15-61 Molecular Biology of the Cell (© Garland Science 2008)
Sometimes the scaffold protein is even part of the signaling cascade!