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134 Cards in this Set
- Front
- Back
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The cell
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life's definition
cytoplamic membrane est. the boundary b/w non-cell and cell has size limits |
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central dogma
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DNA to RNA to Protein
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prokaryotes
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no nucleus
small genome: circular no internal organelles |
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eukaryote
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large genomes
usually linear chromosomes internal organelles: mitochondria, chloroplasts, golgi, and endoplasmic reticulum |
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importance of water
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70% of the cell
influences structure metabolic reactions can ionize transiently (hydroxide and hydrogen ion, rare) pH= 7 |
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pH
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tells you how many H+ are around
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importance of pH
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harvesting energy in metabolism
macromolecular functions macromolecular structures solubility transport |
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Macromolecules
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polysaccharides
proteins nucleic acid lipids |
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Monomer: Sugars
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Polymer: Polysaccharides
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Monomer: Fatty acids
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Polymer: Fats, lipids, membranes
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Monomer: amino acids
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Polymer: Proteins
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Monomer: nucleotides
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Polymer: Nucleic acids
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Principles of building polymers
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monomers
lose of water (a condensation/dehydration reaction) directionality energy input |
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Carbohydrates: Monomers: Monosaccharides
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simple sugars:
glucose fructose ribose |
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Carbohydrates: Monomers: Oligosaccharides
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informational
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Carbohydrates: Polymers: Polysaccharides
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long chains
Storage: strach: amylose, amylopectin, glycogen Structure: fiber: cellulose |
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Monosaccharides
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monomers
1. one carbonyl group: aldehyde or ketone (ketose or aldose) 2. each other carbon has one hydroxyl group |
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Monosaccharides differ by
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number of carbons
spatial geometry (stereoisomers, chiral) 5&6 carbon sugars cicularize |
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Stereoisomers differ by
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"L-form" left
"D-form" right |
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Di-, Oligo-, Poly-saccharides
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condensation/dehydration reaction
glycosidc bond: alpha (1->2) |
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Polysaccharides
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millions of monomers
most common, only glucose storage reserves stucture |
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Glycogen
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energy storage in most animals
glucose alpha (1->4) linkage with a alpha (1->6) branches |
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Cellulose
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glucose beta(1->4)
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Polysaccharide paradox
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"polymer effect"
are hydrophilic, but generally insoluble in water |
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Amylose helical coil
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secondary structure
h-bonds to itself |
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Sugar derivatives: 5-carbon deoxyribose
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missing one hydroxyl group
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Sugar derivatives: Glycerol
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3-carbon sugar
w/ 3 hydroxyl groups |
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Sugar derivatives: sugar amines & acids
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have amine or carboxylic acid group in place of -OH
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Chitin
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polymer of N-acetyl glucosamine
beta (1->4) linkage |
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Sugar derivatives: Glycosaminoglycans: chondroitin sulfate
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tensile strength of cartilage, tendons, ligaments, aorta
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Sugar derivatives: Glycosaminoglycans: Keratan sulfate
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cornae, cartilage, bone, heparin
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Sugar derivatives: Glycosaminoglycans: hyaluronic acid
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clear viscous fluid, joints, eyes, extracellular matrix of cartilage, & tendons
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Oligosaccharides
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"few"
informaional "sugar code" billions of combinations possible external surface of plasma membrane |
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Lipids
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hydrophobic character
Fatty acids & glycerol: triglycerides: fats, oils, long term storage phospholipids: membranes Other: steroids: membranes, hormones |
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Fatty acids
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carboxylic acid + a long hydrocarbon chain
polar head + very hydrophobic tail (amphipathic) differ by: chain length, saturation (ex. # of double bonds) |
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Triglycerides
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condensation/dehydration reaction
fatty acids are stored as energy through ester linkage to glycerol to form triacylglycerols insoluble in water |
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Fats vs. Oils
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fats: solid, saturated
oils: liquid, unsaturated and polyunsaturated |
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Phospholipids
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glycerol +2 fatty acids + phosphate
polar head: phospate+ head group nonpolar tail: glycerol + 2 fatty acid tails head hydrophilic, tial hydrophobic |
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Phospholipid Bilayer
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boundaries
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Steroids
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membranes, hormones
cortisol, estradiol, testosterone, cholesterol |
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Polyisoprenoids
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long-chain polymers of isoprene
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Nucleotides
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phosphate + sugar+ base (nitrogenous group)
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Nucleotide: bases
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purines & pyrimidines
bases help accept protons |
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Nucleotide: 5 bases
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DNA: adenine, cytosine, guanine, thymine
RNA: adenine, cytosine, guanine, uracil N= anybase R= purine Y= pyrimidine |
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Nucleotide is a Base plus a Sugar
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For RNA the sugar is ribose
For DNA the sugar is 2-deoxyribose Both are 5-carbon sugars The positions in the sugar ring have to be renumbered using a prime (') designation to distinguish them from the positions in the bases |
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Tautomerize
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fluctuates between keto and enol
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Other nucleotide roles
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energy carries (ATP, GTP)
reducing power (NADH, NADPH) carrir of intermediates (CoA) Signaling molecules (cyclic AMP & GMP) |
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Proteins roles
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motility
structural role regulate many cellular processes enzymes: biological catalysts signals |
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Important bond in proteins
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S-S bond
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Peptide bonds
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condensation/dehydration reaction
amide linkage |
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Proteins levels of organization
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primary: sequence of amino acid residue
secondary: local folding of backbone tertiary: overall 3d folding quaternary: greater to or equal to 2 polypeptides folding |
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Secondary structure
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stabilized by h-bands to other peptide bonds
local folding alpha helix beta sheet unorganized: hinges, turns, loops linus pualing |
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Alpha helix
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backbone: hydrogen bonds
one side all hydrophilic, the other hydrophobic |
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Beta sheet
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hydrogen bonds between adjacent backbone segments
either parallel or anti-parallel |
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Unorganized structure
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hinges, turns, loops, random coils
very flexible |
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Surfaces of R-groups
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fuzzy can: tube structure
shag carpet: folded like a fan |
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Tertiary structure
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interactions of r-groups
overall 3d structure conformation |
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What governs tertiary structure?
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hydrogen bonds
ionic/electrostatic bonds van der waals forces hydrophobic interactions |
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Hydrophobic interactions
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cytochrome C: hydrophilic residue outside nonpolar residue tucked inside
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Chris Anfinsen
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self assembly primary to tertiary
ribonuclease with help from molecular chaperones/ chaperonins |
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Prion
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protein misfolding
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Quaternary Structures
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proteins with greater than 1 polypeptide chain
stabilized by r-group interactions one protein |
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Protein domains
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evolutionary shuffle
spatially distinct molecules |
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SH-2 domain
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Src homology
Peyton Rous 1911 oncoprotein Rous sarcoma virus signaling cascades Phosphotyrosine peptides |
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alpha helices...
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can formed coiled-coils
ex. alpha keratin |
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Motor proteins
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Generate force to produce large movements Muscle contraction Organelles Chromosomes Enzymes along DNA
Conformational changes ATP hydrolysis unidirectional |
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Extracellular matrix proteins
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Elastin: Skin, lungs, arteries
Triple helix collagen |
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Protein families: serine proteases
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elastase sm neutral –A,G,S,V Chymotrypsin –bulky hydrophobic – Phe,Trp,Tyr Trypsin –(+) charge – Lys, arg
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ENZYMES
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biological CATALYSTS
specific small amount - reusable promotes a favorable reaction |
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Enzyme class: Oxido-reductase
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one molecule is oxidized while the other is reduced
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Uncatalyzed reactions
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most collisions are not productive
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Catalyze reactions
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reaction rates greatly enhanced
lowering the activation energy |
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How do enzymes lower activation energy
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Enzymes have BINDING AFFINITY for reactants=Substrates: stabilize Interactions: specificity
series of small steps Enzymes ORIENT Substrates Enzymes cause BOND STRAIN |
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BOND STRAIN
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chemical strain: substrate acquires charged region
physical strain: substrate stressed: "nutcracker effect" |
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Lysozyme
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causes physical bond strain
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How are proteins regulated?
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Activity coordinated
Regulated at many levels: Amount, Location, Conformational change (Interactions with other proteins Post-translational modifications) |
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Feedback inhibition
Biosynthetic pathways |
negative regulation
a form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway |
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Allosteric regulation
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conformational change
can activate or inactivate an enzyme |
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Protein phosphorylation
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the covalent addition of a phosphate group to a side chain of a protein catalyzed by a protein kinase
either activates or inhibits alters protein activity or properties in some way |
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GTP binding: Molecular switches
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Conformational change
protein or protein complex that operates in an intracellular signaling pathway and can reversibly switch b/w an active and inactive site |
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GTP binding: protein synthesis
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Conformational change
translation from RNA to protein |
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Membranes define...
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spaces with distinctive character and function
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Membrane Functions
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receiving information
import and export of molecules capacity for movement and expansion scaffold for specialized functions selectively permeable boundary |
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Lipid bilayer
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basis of membrane structure
proteins: carry out most functions no free edges: self-sealing |
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Singer & Nicholson
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Fluid Mosaic Model and the dynamic nature of membranes
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Membrane lipids...
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are amphipathic
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Membrane major components
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Lipids – structural backbone & barrier
Proteins- specific functions Lipid/protein ratio varies Carbohydrates: Usually attached to lipid or protein |
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Lipid bilayer is..
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dynamic
Eukaryotes – interconnected networks Flexible Vesicles for delivery |
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Fluidity of Lipid Bilayer
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Lateral exchanges: 1x107 times/sec. moves several microm/sec
Flip-flop – rare <1 time/month “flippases” Rotation - ~30,000 rpm flexation |
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Lipids: critical role in maintaining
membrane fluidity Shorter chains |
Saturated fatty acids stack nicely
Unsaturated fatty acids –more fluid; double bond causes kinks Stack poorly Lipids: critical role in maintaining membrane fluidity Shorter chains – stack poorly; More movement than longer chains Length & saturation of hydrocarbon tails affect packing & membrane fluidity |
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Importance of lipid fluidity
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Protein conformational changes Distribution of new proteins & lipids
Membrane fusion Cell division |
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Cholesterol modulates fluidity in animal cells
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Paradox:
a)↓ fluidity at high temp. b)↑ fluidity at low temp. |
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lipid bilayer is asymmetrical
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Glycolipids, PC, sphingomyelin
PE, PI,PS |
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Van Deenen
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Evidence for lipid asymmetry
Intact red blood cells Broken red blood cells Phospholipase |
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Lipids are made
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Phospholipids are made in the ER Glycolipids get sugar Groups in the Golgi
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Roles of membrane proteins
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Transport
Links to structural proteins Receptors Enzymes Electron carriers |
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Association with membrane
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cross membrane
alpha helix amphipathic ~30% of all proteins outside noncovalent attachment structure signaling signaling integral or peripheral |
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How does a protein cross a membrane
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Typically protein crosses membrane as α helix
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Β Barrel
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porins
wide channels mitochondria & bacteria |
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Plasma membrane is supported...
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by a cell cortex
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Evidence for membrane protein fluidity
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Cell fusion: 1970 D.L. Frye & M. Edidin 26
“FRAP”: fluorescence recovery after photobleaching |
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Patterns of movement of integral membrane proteins
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Random (10-8 to 10-9 cm2/sec)
Immobile -cytoskeleton Motor protein - directed D. restricted Fenced by cytoskeleton Tethered by extracellular matrix Not all proteins are free to drift around in a “sea” of lipids |
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Restriction of protein movement
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cortex
linked to extracellular matrix cell adhesion tight junctions |
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Glycocalyx: “sugar coat"
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protects from mechanical & chemical damage
cell adhesion cell-cell recognition |
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“typical” mammalian cell …….
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distribution of ions inside vs out
maintained by transport proteins & membrane permeability |
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Lipid bilayers are selectively permeable
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Rate of diffusion Size – polarity - charged
small hydrophobic molecules>small uncharged polar molecules>large uncharged polar molecules>ions |
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Diffusion
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HIGH to low concentration
"Spontaneous” – energetically favorable Solutes – dissolved ions and small organic molecules |
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Simple diffusion
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DIRECTLY thru bilayer
Oxygen crossing red blood cell membrane Driving force: concentration gradient HIGH -> low |
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Membrane transport proteins:
Transporters & channels Size |
transporter: Specific binding site & conformational change
channel protein: Size & charge |
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What controls the direction of transport?
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1.Concentration gradient
2.HIGH to low – favorable direction 3.If passageway exists 4.Passive transport (facilitated diffusion) |
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What if we want to move solute from low to HIGH concentration?
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If passageway exists
Need to add energy Active transport – “pumps” |
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Passive transport: Glucose transporter
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Liver cell – transporter crosses 12 time
High external conc – glucose moves in Low external conc- glycogen breakdown, glucose moves out |
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electrochemical gradient
passive |
concentration + charge
membrane potential net driving force for CHARGED solutes (ions) |
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Active transport
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Transporter protein moves solute AGAINST its gradient
Na+/K+ ATPase “pump” |
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Na+/K+ ATPase “pump”
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3 Na+out;2 K+ in
“bilge pump” Creates an electrochemical gradient Drives ion movement in one direction |
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Osmosis
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hypotonic solution: net water gain, cell swells
hypertonic solution: net water loss, cell shrinks isotonic solution: no net loss or gain |
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Na+K+ pump helps to maintain osmotic balance
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Movement of water from low to high [solute]
water moves into cell by osmosis, swelling the cell |
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Coping with osmotic stress
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animal cell: pumps ions out
plant cell: cell wall protozoan: water out, discharging contractile vacuole |
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Ca++ pumps maintain low intracellular [Ca++]
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Ca++ - cell signaling muscle contraction
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Uniport: active transport
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one molecule transported
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Symport: active transport
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two molecules transports in the same direction
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Antiport: active transport
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two molecules being transported in opposite directions
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Example of indirect (secondary) active transport
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Na+ gradient drives other transport
Na+ glucose co-transporter Glucose + ATP->(hexokinase)glucose-6-phosphate + ADP symport |
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Directional Transport
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Glucose IN via active transport
Glucose OUT via passive facilitated diffusion |
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Bacteriorhodopsin: Halobacterium halobium
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Light energy H+ gradient
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3 kinds of transmembrane protein channels
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Porins – larger, less specific
ß-barrel Aquaporins – rapid water movement Peter Agre 1992 Ion channels – tiny pores highly selective |
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Ion channels
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selective & gated
passive transport rapid transport |
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Stress-gated channels
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auditory response
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Gates
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Ligand-gated ion channel
“Wastebasket model” – step on pedal & lid opens “Key” - acetylcholine |
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Cystic fibrosis: when gates go wrong
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1989 Collins, Tsui, Riordan CFTR*
ABC transporter family Cystic fibrosis transmembrane conductance regulator defect in a ligand-gated Cl- channel Not responsive to ligand cAMP Infections? Cl-,H2O Bacteria binding HCO3 –pH change Gene therapy – adenovirus or liposomes |
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Voltage-gated channels
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Ex. Eukaryotic K+ channel
channels are passive transport systems |
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Simple diffusion
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Directly thru bilayer OR aqueous channel
HIGH to low conc favorable |
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Facilitated diffusion
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Facilitated diffusion
transporter protein Conformational change HIGH to low conc favorable |
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Active transport
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transporter protein
Conformational change low to HIGH conc Unfavorable Add energy |
