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Water and Carbon
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
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
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.
Water: a molecular view
2H2 + O2 --> 2H2O
Properties of water molecule
• The water molecule is a polar molecule
– Allows formation of hydrogen bonds
– Contributes to the various properties water
exhibits
Properties of water
• Cohesion
• Moderation of temperature
• Expansion upon freezing
• Versatile solvent
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
Versatile solvent
• Polar water molecules interact with:
Ionic compounds
–
Na+
+
–
–
Na+
Cl–
other polar molecules
(like proteins)
+
–
Cl–
+
+ –
–
+
+
–
–
+
+ –
-
Dissolving agent = Solvent
Agent being dissolved = Solute
–
+
Hydrophilic and Hydrophobic Substances
• A hydrophilic substance
– Has an affinity for water
• A hydrophobic substance
– Does not have an affinity for water
Dissociation of water
• Water can dissociate into hydronium ions
(H3O+) and hydroxide ions (OH-)
• H+ is not stable
–
+
H
H
H
H
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
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-)
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+]
The pH scale
0
More Acidic
[H+] > [OH–]
1
2
Battery acid
Digestive (stomach) juice, lemon juice
3
Vinegar, beer, wine, cola
4
Tomato juice
5
Black coffee
Rainwater
6
More Basic
[H+] < [OH–]
Neutral
[H+] = [OH–]
7
8
Pure water
Human blood
Seawater
9
10
11
12
13
14
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Buffers
• Minimize changes in the concentrations of
H3O+ and HO- ions
• Consist of an acid-base pair that reversibly
combines with hydrogen ions
Carbonic acid
H2CO3
HCO3- + H+ (H3O+)
More H+ (H3O+)
More OH-
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
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
Hydrogen
Oxygen
Nitrogen
Carbon
(valence = 1)
(valence = 2)
(valence = 3)
(valence = 4)
H
O
N
C
Isomers
• Isomers: molecules with the same molecular
formula but different structures and properties
Structural
Geometric
Enantiomers
CO2H
H H H H H
H C C C C C
H H H H H
H
H C H
H C H
H
H
H C C C H
H H H
H
X
X
C C
H
H
C
H
C C
X
CO2H
X
H
trans
NH2
CH3
cis
H
L-
C
NH2
C
DH
CH3
C
Enantiomers and Parkinson’s
L-Dopa
D-Dopa
(effective against
Parkinson’s disease)
(biologically
inactive)
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
OH
Carboxyl
O
O
(may be written HO
)
C
C
OH
Amino
Sulfhydryl
H
N
O
SH
(may be written HS
H
Phosphate
)
O P OH
OH
Biological molecules
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
Types of macromolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
Synthesis of Polymers
Monomers form larger molecules by dehydration
reactions
HO
1
3
2
H
HO
H
Unlinked monomer
Short polymer
H 2O
HO
1
2
3
Longer polymer
4
H
Dehydration
removes a water
molecule
Breakdown of Polymers
• Polymers can disassemble by hydrolysis
HO
1
2
3
4
H
H2O
HO
1
2
3
H
HO
H
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
Monosaccharides
H
O
C
H C OH
H C OH
H C OH
O
C
H C OH
O
C
HO C H
H
H
HO C H
H
HO C H
H C OH
H C OH
H C OH
C O
H C OH
H
H C OH
H
HO C H
Glucose
Galactose
H C OH
H C OH
H C OH
H
H C OH
H
Glyceraldehyde
Fructose
Triose: C3H6O3
Hexose: C3H12O6
Monosaccharides are linear or form rings
H
H
HO
H
H
H
O
1C
2
C
3
C
4
C
5
C
6
C
H
6CH OH
2
OH
H
OH
H
4C
OH
5C
H
OH
OH
3C
OH
H
H
O
H
H
1C
2C
OH
H
6CH OH
2
5C
O
4C
O
OH 3
H
OH
C
H
H
H
1C
2C
OH
OH
Disaccharides are formed by dehydration
H
Glucose
Glucose
CH2OH
CH2OH
O
H
OH
H
OH
HO
H
H
H
HO
O
H
OH
H
H
OH
Maltose
CH2OH
H
OH
OH
O
H
H
OH
CH2OH
H
HO
O
H
OH
H
H
OH
O
H
OH
H
4
H
1
H
OH
OH
H2O
CH2OH
H
O
H
OH
H
HO
H
CH2OH
H
OH
HO
CH2OH
O
H
H
O
H
H
OH
HO
CH2OH
OH
OH
H
H
CH2OH
O
H
1
2
H
Fructose
HO
O
HO
H
OH
CH2OH
OH
H2O
Glucose
H
Sucrose
H
Polysaccharides functions
• Storage polysaccharides
Glycogen
Starch
CH2OH
O
HO
4
1
OH
O
OH
CH2OH
CH2OH
CH2OH
O
O
O
1
OH
O
OH
4
1
OH
OH
O
4
1
OH
O
OH
Polysaccharides functions
• Structural polysaccharides: cellulose
CH2OH
O
HO
OH
1
OH
CH2OH
O
OH
O
4 OH
O
CH2O
H
O
OH
O
OH
OH
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH
OH
O
O O
O O
OH CH2OH
OH CH2OH
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH O
OH
O
O
O
O
OH CH2OH
OH CH2OH
CH2OH
OH
OH CH2OH
O
O O
OH O
OH
OH
OH O
O
O O
O
OH CH2OH
OH CH2OH
OH
O
CH2O
H
O
Lipids
• Are not polymers
• Classes:
– Fats
– Phospholipids
– Steroids
Fats
• Formed from glycerol + Fatty acid
H
C
H
H
O
OH
C
C
HO
H
C
H
OH
H
C
H
H
C
H
H
C
H
C
H
C
H
H
H
H
C
H
C
H
H
H
C
H
C
H
H
H
C
H
C
H
H
H
C
H
C
H
C
H
H
Fatty acid
H
C
(palmitic acid)
OH
H
Glycerol
H
H
C
dehydration
O
O
C
H
C
H
O
H
H
C
C
H
Ester
O
O
C
O
C
H
C
H
H
C
H
C
H
H
H
C
H
C
H
H
H
C
H
C
H
C
H
C
H
H
H
H
H
C
H
C
H
C
H
C
H
H
C
H
H
H
C
H
H
H
C
H
H
C
H
C
H
C
H
C
H
C
H
H
H
H
H
H
C
H
C
H
C
H
C
H
C
H
H
H
H
H
H
H
H
C
H
C
H
C
H
H
C
H
C
H
C
H
H
H
C
H
H
H
H
H
H
C
C
H
H
C
H
H
C
H
C
H
H
C
H
C
H
H
C
H
H
H
H
C
H
C
H
C
H
H
H
H
H
H
H
H
Saturated and Unsaturated fats
•Saturated fatty acids
– Max single bonds
– Contain double bonds
– Solid at room temp
– Liquid at room temp
O
HO
•Unsaturated fatty acids
H
C
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
O
H
HO
H
C
C
H
H
H
C
C
H
C
H
H
C
H
H
C
H
H
Phospholipids
• Have only two fatty acids and a Phosphate group
• Hydrophilic head (phosphate), hydrophobic tail
(hydrocarbon)
+
CH2
N(CH3)3
Choline
CH2
O
O
P
O–
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Fatty acids
Phospholipid
symbol
Phospholipids are major component of cell
membranes
Hydrophilic
heads
WATER
WATER
Hydrophobic
tails
Steroids
• Contain a carbon skeleton consisting of four sixmembered rings
• Cholesterol is a prime example
– Essential for cell membrane fluidity
– Precursor for some hormones
H3C
CH3
CH3
HO
CH3
CH3
Proteins: the cell’s workhorse
• Have many roles inside the cell
Structural
proteins
Storage
proteins
Enzymes
Motor
proteins
Transport
proteins
Receptor
proteins
Defense
proteins
Hormonal
proteins
Enzymes
• Proteins that accelerate chemical reactions
• Names always end in “-ase”
• Chemical reactions occur in the active site
Active site
Substrate
(sucrose)
Enzyme
(sucrase)
Glucose
OH
Fructose
H O
H2O
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
R
H3N C COOH
H
Amino acids
CH
O–
OH
3
CH
2
H3C CH
O
H3N
C C
+
O–
H
Isoleucine (Ile)
SH
H3N+
CH2
O
CH2
C C
H3N+
O–
C C
H
Cysteine
(Cys)
H2
C
H2
N
CH2
CH
O
2
C
H
C
O–
Proline (Pro)
H
Tyrosine
(Tyr)
C
CH2
CH2
CH2
CH2
O
H3N
+
O–
NH3+
O
C C
H
CH2
O
O–
CH2
H3N
+
C C
H
Glutamic acid
(Glu)
O
O–
Lysine (Lys)
Amino Acid are linked by peptide bonds
• Peptide bonds
peptide
bond
OH
CH2
H
N
H
OH
SH
CH2
H
C C
H O
CH2
H
N C C OH H N C
H O
H
DESMOSOMES
C OH
O
OH
OH
CH2
H2O
H
H N C C
H O
amino end
(N-terminus)
____ SH
CH2 ___ CH2
H
H
N C C
H O
N C C OH
H O
carboxy end
(C-terminus)
Side
chains
Backbone
Protein Conformation and Function
• A protein’s specific structure determines how it
functions
Ribbon model
Space-filling model
Four Levels of Protein Structure
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure
+H N
3
Amino end
Amino acid
subunits
helix
1˚
2˚
3˚
4˚
Primary Structure
Is the unique sequence of amino acids in a
polypeptide
Cys
Met
Ala
Thr
Thr
Gly
Thr
Ala
Thr
amino terminus
(NH3+)
Trp
Ala
Thr
Ala
Cys Trp
Trp
Thr
Leu
Thr
Gly
Leu
Met
Thr
Trp
carboxy terminus
(CO2-)
Secondary structure
• Is the folding or coiling of the polypeptide into a
repeating configuration
• Includes the alpha helix and the Beta sheet
Beta sheet
O H H
C C N
Amino acid
subunits
C N
H
R
R
O H H
C C N
CC N
O H H
R
R
O H H
C C N
C C N
OH H
R
R
O
O
C
H
H
C
H
H
C N HC N
C N HC N
C
H
H
C
O
C
O C
R
R
O
R
C
N H
O C
N H
O C
O
H
H C R
C
R
N H O C
O C
N H
C
R H
H
N H
R
C
H
O C
N H
C
H C RH C R
N H
O C
O C
N H
C
H
R
Alpha helix
R
R
O H H
R
C C N
N
C C
R C C
H
OH
O
R
O
C
H
H
C
H
NH C N
C N HC N
H
H O C
O C
R
Tertiary structure
• The overall three-dimensional shape of a
polypeptide
• Results from interactions between amino acids
and R groups
Hydrophobic bonds
Hydrogen
bond
CH22
CH
O
H
O
CH
H3C
CH3
H3C
CH3
CH
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
O
disulfide bridge
CH2 NH3+ -O C CH2
ionic
bond
Quaternary structure
• Aggregation of two or more polypeptide
subunits for overall structure
Polypeptide
chain
 Chains
Iron
Heme
 Chains
Collagen
Hemoglobin
Sickle-Cell Disease: results from a single
amino acid change
• Glutamate to Valine change in hemoglobin
ß subunit
Protein folding in the cell
• Chaperones assist in the proper folding of
other proteins
Polypeptide
Hollow cylinder
Cap
Correctly
folded
protein
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
The Structure of Nucleic Acids
• Nucleic acids exist as polymers = polynucleotides
5’ end
5’C
O
3’C
Nitrogenous
Base
O
O
O

O
P O
5’C
CH2
O

O
5’C
Phosphate
group
O
3’C
_________
sugar
3’C
OH
3’ end
Monomer = nucleotide
Structural difference between DNA and RNA
Nucleoside
Base
O

O
P O
5’C
CH2
O

O
Phosphate
group
3’C
Pentose
sugar
Pentose sugars
5”
HOCH2 O OH
HOCH2 O OH
4’ H H 1’
4’ H H 1’
H
H
H
H
3’ 2’
3’ 2’
OH H
OH OH
Deoxyribose (in DNA) Ribose (in RNA)
5”
The nitrogenous bases
H
N
N
O
H
CH3
________
N
N
Sugar
H
N
N
N
O
Sugar
Thymine (T)
Adenine (A)
H
__________
H
H
N
N
O
N
N
Sugar
O
N
H
H
N
O
Sugar
Uracil (U)
________
N
N
N
N
H
Guanine (G)
H
O
Sugar
Cytosine (C)
Forming the DNA double helix
5’ end
5’C
OH
3’ end
O
3’C
O
O
5’C
O
3’C
OH
3’ end
5’ end
Base-pairing of nitrogenous bases
H
N
N
N
N
Sugar
O
H
H
O
CH3
N
H
N
N
N
O
Sugar
Thymine (T)
Adenine (A)
H
N
O
Sugar
Uracil (U)
H
O
N
N
Sugar
N
H
H
N
N
N
N
N
H
Guanine (G)
H
O
Sugar
Cytosine (C)
A T
G C
A U
The DNA double helix
5’ end
Phosphate
backbone
3’ end
Base
pair
Base pair
3’ end
5’ end
3’ end
5’ end
3’ end
Cell membranes
Cell Theory
All living things are composed
of one or more cells.
All cells come from preexisting
cells
Animal Cells
- Boundaries: membranes
- Movement: cytoskeleton
- Energy: mitochondria
- Protein synthesis and transport:
nucleus, ribosomes, ER, Golgi, vesicles
- Waste: lysosomes
- Communication: junctions
Cells
Plasma membrane
Cytoplasm
Nucleus
Lipid bilayers
Hydrophilic OUT
Hydrophobic IN
Hydrophobic IN
Hydrophilic OUT
Phospholipids form membranes as
lipid bilayers.
Plasma Membrane (aka Cell
Membrane)
OUTSIDE
INSIDE
Fluid Mosaic Model
of Membrane Structure
Oligosaccharides
Membrane Proteins
Outer
Surface
Cholesterol
Membranes
How do substances get across
membranes?
Diffusion
How does diffusion work?
Properties of the Lipid Bilayer
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
Diffusion
1
3
2
The direction of movement is
from
high concentration to low.
DOWN gradient
Diffusion across a membrane
Plasma membrane
1. SIMPLE DIFFUSION
- no extra energy required
Diffusion across a membrane
channel
Plasma membrane
2. FACILITATED DIFFUSION
-channel proteins shuttle molecules down the
concentration gradient
- no extra energy
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
Water across a membrane
OSMOSIS: Movement of water
across a membrane
Simple diffusion
(extracellular fluid)
lipid-soluble molecules
(O2, CO2, H2O)
(cytoplasm)
OSMOSIS –
movement of water across a
membrane
HYPERTONIC
ISOTONIC HYPOTONIC
OSMOSIS:
Results
HYPERTONIC
ISOTONIC HYPOTONIC
Osmosis
Shriveled RBCs
Normal RBCs
Swollen RBCs
Result: Into
Hypertonic
Solution
Isotonic Solution
Net movement of
water out of cells
Equal movement of water
into and out of cells
Hypertonic
solution?
Result:
Into
Hypotonic
Solution
Hypotonic
solution?
Net movement of
water into cells
PASSIVE Transport Across a Membrane
Common theme:
REQUIRES NO
EXTRA INPUT OF
ENERGY
Transport through the Plasma
Membrane
Passive: DOWN gradient
Acitve: UP grad
Active Transport
UP a concentration
gradient
Movement
from low concentration to high
reauires ENERGY!
Requires energy
(ATP)
Protein PUMPS
UP gradient
Key concepts and words
Plasma membrane includes:
Lipid bilayer made of phospholipids (which have
hydrophobic and hydrophilic parts)
Integral and peripheral membrane proteins
Cholesterol (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