Intermolecular Forces. Bonding Ionic Covalent Polar covalent.
Water and Carbon. BONDS IONIC: between two ions – not as strong – comes apart easily, e.g....
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Transcript of Water and Carbon. BONDS IONIC: between two ions – not as strong – comes apart easily, e.g....
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Water and CarbonWater and Carbon
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BONDS
•IONIC: between two ions
– not as strong
– comes apart easily, e.g. soluble in water
•COVALENT: shared electrons
– very strong
–most common in biological matter
– can be POLAR or NON POLAR
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Polar vs. Nonpolar Bonds
• Polar — charged surface– electrons are shared unevenly– Prefer other polar molecules– Soluble in water, which is also polar
• Nonpolar — no residual charge– electrons are shared evenly– Prefer other nonpolar molecules – Soluble in oils
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Molecular Rules of Attraction
• Charged molecules have ionic or polar covalent bonds.
• e.g.: water, salt
• Uncharged molecules have non polar covalent bonds.
• e.g.: oils
CHARGED MOLECULES ARE ATTRACTED TO CHARGED MOLECULES.
• specifically: + charges/polarity is attracted to - charges/polarity
UNCHARGED MOLECULES ARE ATTRACTED TO UNCHARGED MOLECULES.
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Water: a molecular view
2H2 + O2 --> 2H2O
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Properties of water molecule
• The water molecule is a polar molecule
– Allows formation of hydrogen bonds
– Contributes to the various properties water exhibits
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Properties of water
• Cohesion
• Moderation of temperature
• Expansion upon freezing
• Versatile solvent
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Frozen water, a.k.a. Ice
• The hydrogen bonds in ice are more “ordered” than in liquid water, making ice less dense and able to float
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Versatile solvent
• Polar water molecules interact with:
Ionic compounds other polar molecules
(like proteins)+
+
+
+Cl–
–
-
–
–
Na+
++
+
+
–
––
––
–Na+
Cl–
Dissolving agent = SolventAgent being dissolved = Solute +
–
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Hydrophilic and Hydrophobic Substances
• A hydrophilic substance
– Has an affinity for water
• A hydrophobic substance
– Does not have an affinity for water
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Dissociation of water
• Water can dissociate into hydronium ions (H3O+) and hydroxide ions (OH-)
• H+ is not stable
H
Hydroniumion (H3O+)
H
Hydroxideion (OH–)
H
H
H
H
H
H
+ –
+
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Acids and Bases
• An acid
– Increases the hydrogen ion concentration of a solution (more H3O+)
• A base
– Reduces the hydrogen ion concentration of a solution (more OH-)
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The pH Scale• The pH of a solution
– Is determined by the relative concentration of hydrogen ions
– Is low in an acid
– Is high in a base
• pH paper
pH = -log10[H+]
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The pH scale
More
Acid
ic[H
+]
> [
OH
– ]M
ore
Basic
[H+]
< [
OH
– ]
Neutral[H+] = [OH–]
Oven cleaner
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Battery acidDigestive (stomach) juice, lemon juice
Vinegar, beer, wine, cola
Tomato juice
Black coffeeRainwater
Pure waterHuman blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
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Buffers
• Minimize changes in the concentrations of H3O+ and HO- ions
• Consist of an acid-base pair that reversibly combines with hydrogen ions
H2CO3 HCO3- + H+ (H3O+)
More OH-
More H+ (H3O+)
Carbonic acid
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Carbon
• The Backbone of Biological Molecules
• All living organisms are made up of chemicals based mostly on the element carbon
• Organic chemistry is the study of carbon compounds
• Organic compounds range from simple molecules to colossal ones
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Carbon can covalently bond with four atoms
• Carbon has four valence electrons
• This allows it to form four covalent bonds with a variety of atoms
• Carbon can single, double and triple bond
H O N C
Hydrogen(valence = 1)
Oxygen(valence = 2)
Nitrogen(valence = 3)
Carbon(valence = 4)
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Isomers
• Isomers: molecules with the same molecular formula but different structures and properties
Structural Geometric Enantiomers
HHH
HH
H
H
H
HHH
CC
C C CH
H H
X XC C
H H H H HH
H H H H HHC C C C C
H
HX
XC C
H
CO2H
CH3
NH2
C
C
C
CO2H
H
CH3
NH2
C
cis
trans
L-
D-
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Enantiomers and Parkinson’s
L-Dopa
(effective against Parkinson’s
disease)
D-Dopa
(biologically inactive)
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Functional groups• Functional groups are the parts of molecules
involved in chemical reactions
• Six functional groups are important in the chemistry of life
Hydroxyl Carbonyl Carboxyl
Amino Sulfhydryl Phosphate
(may be written HO )
OH
C
O O
C
OH
NH
H(may be written HS )
SHO P
O
OH
OH
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Biological moleculesBiological molecules
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Macromolecules
• Large molecules composed of smaller molecules
• Most macromolecules are polymers
• A polymer is a long molecule consisting of many similar building blocks called monomers
monomers polymers
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Types of macromolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
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Synthesis of Polymers
Monomers form larger molecules by dehydration reactions
HO H1 2 3 HO
HO H1 2 3 4
H
H2O
Short polymer Unlinked monomer
Longer polymer
Dehydration removes a water molecule
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Breakdown of Polymers
• Polymers can disassemble by hydrolysis
HO 1 2 3 H
HO H1 2 3 4
H2O
HHO
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Carbohydrates
• Carbohydrates =
sugars (Monosaccharides or Disaccharides
sugar polymers (Polysaccharides)
• Monosaccharides can be used for fuel
• Polysaccharides
– Are polymers of sugars
– Serve many roles in organisms
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Monosaccharides
H C OH
H C OH
H
H
C
O
Glucose
H C OH
H C OH
H C OH
H C OH
H
HO C H
H
C
O
C O
H C OH
H C OH
H C OHH
HO C H
H C OH
H
Glyceraldehyde
HO C H
H C OH
H C OH
H
H
C
O
HO C H
H C OH
Galactose
Fructose
Triose: C3H6O3Hexose: C3H12O6
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Monosaccharides are linear or form rings
H
HO C H
H C OH
OC
H
12
3
4
5
6
H
OH
4C
6CH2OH 6CH2OH
5C
HOH
C
H OH
H2 C
1CH
O
H
OH
4C
5C
3 C
H
HOH
OH
H2C
1 C
OH
H
3
O H O
H C OH
H C OH
H C OH
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Disaccharides are formed by dehydration
H
HO
H
HOH H
OH
O H
OH
CH2OH
H
HO
H
HOH H
OH
O H
OH
CH2OH
H
O
H
HOH H
OH
O H
OH
CH2OH
H
H2O
H2O
H
H
O
H
HOH
OH
O H
CH2OH
CH2OH HO
OHH
CH2OH
HOH H
H
HO
OHH
CH2OH
HOH H
O
O H
OHH
CH2OH
HOH H
O
HOH
CH2OH
H HO
O
CH2OH
H
H
OH
O
O
1 2
1 4
Glucose
Glucose Glucose
Fructose
Maltose
Sucrose
OH
H
H
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Polysaccharides functions
• Storage polysaccharides
Glycogen Starch
CH2OH
O
OH
OH
HO41
O
CH2OH
O
OH
OH
O
CH2OH
O
OH
OH
CH2OH
O
OH
OH
O O1 4 41 1
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Polysaccharides functions
• Structural polysaccharides: cellulose
CH2OH
CH2OH
OH
OHO
OOHO
CH2OHO
OOH
OCH2OH OH
OH OHO
O
CH2OH
OO
OH
CH2OH
OO
OHO
O
CH2OHOH
CH2OHOHOOH OH OH OH
O
OH OH
CH2OH
CH2OH
OHO
OH CH2OH
OO
OH CH2OH
OH
O
O
O
O
O
O
OH
OH
O
OOH
4
CH2OH
OOH
OH
HO
O1
OH
OOH
CH2OH
O
CH2OH
OOH
OH
OOH
O
CH2OH
O
OH
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Lipids
• Are not polymers
• Classes:
– Fats
– Phospholipids
– Steroids
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Fats
• Formed from glycerol + Fatty acidH H
H HHH
H HH
H H HH
HH
HOH O HC
C
C
H
H OH
OH
H
HH
HH
HH
HH
HH
HH
HH
H
HCCCC
CC
CCC
CC
CC
CC C
Glycerol
Fatty acid(palmitic acid)
HO
HH
H
H
H H HH
HH
HH
HH
H HH
HH H
HHHHHHHHHHHHHHHH
H
HH H H H H H H H H H H H H H
H
HHHHHHHHHHHHHH
H H H H H H H H H H H H H H HH
HHHHHHHHHHHHHHH
OO
O
OC
C
C C C C C C C C C C C C C C C C C
C
CCCCCCCCCCCCCCCC
C C C C C C C C C C C C C C CO
O
dehydration
Ester
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Saturated and Unsaturated fats
•Saturated fatty acids
– Max single bonds
– Solid at room temp
•Unsaturated fatty acids
– Contain double bonds
– Liquid at room temp
HH H
HHHO
H H H H H H
CC
CC
CC
CHO H
HH H
HHO
H H H H H
CC
CC
CC
CHO H
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Phospholipids• Have only two fatty acids and a Phosphate
group
• Hydrophilic head (phosphate), hydrophobic tail (hydrocarbon)
Phospholipid symbol
CH2
O
PO O
O
CH2CHCH2
OO
C O C O
Phosphate
Glycerol
Fatty acids
–
CH2 Choline+N(CH3)3
Hyd
rop
hi lic
h
ead
Hyd
rop
hob
ic t
ai ls
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Phospholipids are major component of cell membranes
Hydrophilicheads
WATER
WATERHydrophobictails
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Steroids• Contain a carbon skeleton consisting of four
six-membered rings
• Cholesterol is a prime example– Essential for cell membrane fluidity
– Precursor for some hormones
HO
CH3
CH3
H3C CH3
CH3
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Proteins: the cell’s workhorse
• Have many roles inside the cell
Structuralproteins
Storageprotein
s
Transportproteins
Hormonalproteins
Motorproteins
Enzymes
Defenseproteins
Receptorproteins
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Enzymes• Proteins that accelerate chemical
reactions• Names always end in “-ase”• Chemical reactions occur in the active
site Substrate(sucrose)
Enzyme (sucrase)
Glucose
OH
H O
H2O
Fructose
Active site
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Polypeptides and amino acids
• Proteins consist of one or more polypeptides
• Polypeptides = polymers of amino acids
• Amino acids
– Contain an amino group and a carboxyl group (acid)
– Have 20 different side chains (R groups); 20 amino acids make up proteins
C
H
R
COOHH3N
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Amino acids
O
O–
CH3CH2
CH
C
H
H3N+
C
CH2H2
CH2
NC
CH2
H
C
Isoleucine (Ile)
Proline (Pro)
H3C O
O–
SH
CH2
C
H
H3N+
CO
O–
H3N+
C C
CH2
OH
H
O
O–
Cysteine (Cys)
Tyrosine(Tyr)
O– OCCH
2
C CH3N
+
H
O
O–
CH2
CH2CH2
CH2
NH3+
CH2
C CH3N
+
H
O
O–
Glutamic acid (Glu)
Lysine (Lys)
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Amino Acid are linked by peptide bonds
• Peptide bonds
DESMOSOMES
OH
OH
CH2
C
N
H
C
H O
H OH OH
peptidebond
H H
HH
HN N
SH
OO
CH2 CH2
C CC C
OH
OH
OHH
H
H
H
H H
H
NN N
SHSide
chains
O O O
CH2 CH2 CH2
C C C C C C
_______
amino end(N-terminus)
Backbone
carboxy end(C-terminus)
H2O
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Protein Conformation and Function
• A protein’s specific structure determines how it functions
Ribbon model Space-filling model
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Four Levels of Protein Structure
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure+H3N
Amino end
Amino acidsubunits
helix
1˚ 2˚ 3˚ 4˚
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Primary Structure
Is the unique sequence of amino acids in a polypeptide
TrpGly
Thr
LeuMet
MetTrp
Trp
Trp
Ala
Ala
Ala
AlaCys Cys
Gly Thr
Leu
Thr
ThrThr
ThrThr
Thr
amino terminus(NH3
+) carboxy terminus(CO2
-)
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Secondary structure• Is the folding or coiling of the polypeptide
into a repeating configuration
• Includes the alpha helix and the Beta sheet
R R
O C Alpha helix
Beta sheet
Amino acidsubunits NC
H
C
O
C N
H
CO H
R
C NH
C
O H
C
RN
HH
R C
O
R
CH
NH
C
O H
NCO
R
CH
NH
H
C
R
C
O
C
O
C
NH
H
R
CC
ON
HH
C
R
C
O
NH
R
CH C
ON
H H
C
R
C
O
NH
R
CH C
ON
H H
C
R
C
O
N H
H C RN H
O
O C N
C
CH O
CHR
N HO C
RC
H
N H
O CH C R
N H
CC
N H
O C
H C R
N H
O C
RC
H
H
C
RN
H
CO
C
NH
R
CH C
ON
H
C
H H
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Tertiary structure
• The overall three-dimensional shape of a polypeptide
• Results from interactions between amino acids and R groups
CH2CH
OH
O
CHO
CH2
CH2 NH3+ C-O CH2
O
CH2SSCH2
CH
CH3
CH3
H3C
H3C
Hydrophobic bonds
Polypeptide
backbone
Hydrogen bond
ionic bond
CH2
disulfide bridge
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Quaternary structure
• Aggregation of two or more polypeptide subunits for overall structure
Polypeptidechain
Collagen
Chains
Chains
Hemoglobin
IronHeme
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Sickle-Cell Disease: results from a single amino acid change
• Glutamate to Valine change in hemoglobin
ß subunit
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Protein folding in the cell
• Chaperones assist in the proper folding of other proteins
Hollo
w
cylin
der
Cap
Correctlyfoldedprotein
Polypeptide
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Nucleic acids• Deoxyribonucleic acid (DNA) Hydrogen at 2’
C
– Stores information (blueprint)
– Directs DNA synthesis and protein synthesis through RNA
• Ribonucleic acid (RNA) OH at 2’ C
– Working copy
– Used directly in protein synthesis
• The Central Dogma
DNA RNA protein
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The Structure of Nucleic Acids
• Nucleic acids exist as polymers = polynucleotides
3’C
5’ end
5’C
3’C
5’C
3’ endOH
O
O
O
O
NitrogenousBase
O
O
O
O P CH2
5’C
3’CPhosphate
group_________
sugar
O
Monomer = nucleotide
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Structural difference between DNA and RNA
Ribose (in RNA)
OHOCH2
H
H H
OH
H
OHOCH2
HH H
OH
H
Pentose sugars
Deoxyribose (in DNA)Ribose (in RNA)OHOH
4’
5”
3’OH H
2’
1’
5”
4’
3’2’
1’Base
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
O
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The nitrogenous bases
O H
N
N
O
H
SugarUracil (U)
________
N HN
N
N
N
Sugar
Adenine (A)
N
N
N
N
Sugar
O H N
NH
N OH
H
N
Sugar
Guanine (G) Cytosine (C)
H
O CH3
N
N
O
H
SugarThymine (T)
H__________
________
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Forming the DNA double helix
3’C
5’ end
5’C
3’C
5’C
3’ endOH
O
O
O
O
3’ end
5’ end
OH
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Base-pairing of nitrogenous bases
O H
N
N
O
H
SugarUracil (U)
N HN
N
N
N
Sugar
Adenine (A)
N
N
N
N
Sugar
O H N
NH
N OH
H
N
Sugar
Guanine (G) Cytosine (C)
H
O CH3
N
N
O
H
SugarThymine (T)
H
A TG CA U
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The DNA double helix
Base pair
3’ end
Phosphatebackbone
3’ end5’ end
3’ end
5’ end
5’ end
Base pair
3’ end
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Cell membranes
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Cell Theory
All living things are composed of one or more cells.
All cells come from preexisting cells
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Animal Cells
- Boundaries:- Boundaries: membranesmembranes
- Movement: - Movement: cytoskeletoncytoskeleton
- Energy:- Energy: mitochondriamitochondria
- Protein synthesis and transport:- Protein synthesis and transport: nucleus, ribosomes, ER, Golgi, vesiclesnucleus, ribosomes, ER, Golgi, vesicles
- Waste:- Waste: lysosomeslysosomes
- Communication:- Communication: junctionsjunctions
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CellsCellsCellsCells
NucleusNucleusNucleusNucleus
Plasma membranePlasma membranePlasma membranePlasma membrane
CytoplasmCytoplasmCytoplasmCytoplasm
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Lipid bilayers
Phospholipids form membranes as lipid bilayers.
HydrophobicHydrophobicHydrophilicHydrophilic OUTOUT
ININ
HydrophobicHydrophobicHydrophilicHydrophilic OUTOUT
ININ
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Plasma Membrane (aka Cell Membrane)
OUTSIDEOUTSIDE
INSIDEINSIDE
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OligosaccharidesOligosaccharides Membrane ProteinsMembrane Proteins
CholesterolCholesterol
OuterOuterSurfaceSurface
Fluid Mosaic Modelof Membrane Structure
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Membranes
How do substances get across membranes?Diffusion
How does diffusion work?
How do substances get across membranes?Diffusion
How does diffusion work?
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Properties of the Lipid Bilayer
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Types of PASSIVE Transport Across a Membrane
1. Simple diffusion• down the concentration gradient• no extra energy
2. Facilitated diffusion• down the concentration gradient• no extra energy• uses Channel proteins.
3. Osmosis•Water down the concentration gradient•no extra energy•special membrane, such as plasma
membrane: lets only water go across
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Diffusion
1111 2222
3333The direction of movement is
from high concentration to low.
The direction of movement is
from high concentration to low.
DOWN gradientDOWN gradientDOWN gradientDOWN gradient
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Diffusion across a membrane
1. SIMPLE DIFFUSION1. SIMPLE DIFFUSION1. SIMPLE DIFFUSION1. SIMPLE DIFFUSION
- no extra energy required- no extra energy required- no extra energy required- no extra energy required
Plasma membranePlasma membranePlasma membranePlasma membrane
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Diffusion across a membrane
2. FACILITATED DIFFUSION2. FACILITATED DIFFUSION2. FACILITATED DIFFUSION2. FACILITATED DIFFUSION
- no extra energy- no extra energy- no extra energy- no extra energy
-channel proteins shuttle molecules down the channel proteins shuttle molecules down the -channel proteins shuttle molecules down the channel proteins shuttle molecules down the concentration gradientconcentration gradientconcentration gradientconcentration gradient
Plasma membranePlasma membranePlasma membranePlasma membrane
channelchannelchannelchannel
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Diffusion
Molecules are always vibrating
Molecules in gas and liquid move randomly.
If there is a concentration gradient to start with, over time it will become uniform.
Molecules move from [HIGH] to [LOW].
Doesn’t require extra energy
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Water across a membraneOSMOSIS: Movement of water
across a membranelipid-soluble molecules
(O2, CO2, H2O)
(extracellular fluid)
(cytoplasm)
Simple diffusion
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HYPHYPERERTONICTONICHYPHYPERERTONICTONIC ISOISOTONICTONICISOISOTONICTONIC HYPHYPOOTONICTONICHYPHYPOOTONICTONIC
OSMOSIS – movement of water across a membrane
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OSMOSIS: Results
HYPHYPERERTONICTONICHYPHYPERERTONICTONIC ISOISOTONICTONICISOISOTONICTONIC HYPHYPOOTONICTONICHYPHYPOOTONICTONIC
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Normal RBCs
Isotonic SolutionIsotonic Solution
Osmosis
Equal movement of waterinto and out of cells
Net movement ofwater out of cells Net movement of
water into cells
Shriveled RBCs
Swollen RBCs
Hypertonic SolutionHypertonic Solution Hypotonic SolutionHypotonic SolutionResult: Into Result: Into Hypertonic Hypertonic solution?solution?
Result: Into Result: Into Hypertonic Hypertonic solution?solution?
Result: Into Result: Into Hypotonic Hypotonic solution?solution?
Result: Into Result: Into Hypotonic Hypotonic solution?solution?
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Common theme: REQUIRES NO
EXTRA INPUT OF ENERGY
Common theme: REQUIRES NO
EXTRA INPUT OF ENERGY
PASSIVE Transport Across a Membrane
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Transport through the Plasma Membrane
Passive: DOWN gradient Passive: DOWN gradient Passive: DOWN gradient Passive: DOWN gradient
Acitve: UP gradient Acitve: UP gradient Acitve: UP gradient Acitve: UP gradient
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Active Transport
UP a concentration gradient
Requires energy (ATP)
Protein PUMPS
Movement
from low concentration to high reauires ENERGY!
Movement
from low concentration to high reauires ENERGY!
UP gradientUP gradientUP gradientUP gradient
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Key concepts and words
Plasma membrane includes:Lipid bilayer made of phospholipids (which have hydrophobic and hydrophilic parts)
Integral and peripheral membrane proteinsCholesterol (wedges!)
Transport across a membrane:Passive: simple or facilitated diffusion (channels), down a concentration gradient, no energy.
Active transport (pumps), up a concentration gradient, requires energy.
Osmosis: hypotonic, isotonic, hypertonic