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Chapter 3
Molecules of a cell
Molecules
2 types
– Organic
– Inorganic
Organic- generally C based
Inorganic- generally non-C based
** Exceptions include CO2, CO, CN, etc
C-H
H
H
• Hydrocarbons
– Compounds
composed of only C
and H
 Methane, propane,
butane, benzene,
etc
H
C
C
H
H
H
H
H
C
C
C
H
H
H
Ethane
H
Propane
Carbon skeletons vary in length.
H
C
H
H
H
H
H
H
C
C
C
C
H
H
H
H
H
H
H
H
H
C
C
H
H
C
H
H
Butane
Isobutane
Skeletons may be unbranched or branched.
H
H
H
C
C
C
H
H
H
H
C
• Chain, branch or
ring of C
– C skeleton
H
H
H
H
H
H
H
H
C
C
C
C
H
H
H
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
H
H
H
H
C
H
H
H
C
C
C
C
C
H
H
H
C
H
H
C
H
C
H
H
Cyclohexane
C
H
C
C
H
Benzene
Skeletons may be arranged in rings.
H

Isomers
Compounds with the same formula different
structures
– Different shapes = unique properties
Functional Groups
• Determine the
properties of organic
compounds
• Polar
– O and N exert a
“strong pull” on
shared electrons
– Hydrophilic
Functional Groups
•
•
•
•
•
•
Hydroxyl- OH
Carbonyl- C=O
Carboxyl- COOH
Amino- NH2
Phosphate- OPO32Methyl- CH3
Biological Molecules
4 primary classes
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic acids
These molecules are large (dozens to
millions of C) = macromolecules
Polymers & Monomers
Cells make large molecules by joining together
smaller molecules into chains
– Chains are called polymers
– Individual molecules are monomers
• Monomers connect into polymers
***Mono=1
Poly=many
Meros= part
Making Polymers
• Cells link monomers to form polymers
via a dehydration reaction
Dehydration Reaction
• Removes H-O-H
• For each monomer added, 1 molecule
water is removed
• Held via covalent bonds
**2 monomers are contributing to the H20
molecule
One monomer looses an OH and the
other looses a H+
Breaking Polymers
• Cells break polymers into monomers via a
hydrolysis reaction
Hydrolysis Reaction
• Breaks covalent bond between monomers
by adding water
• A OH- joins to one monomer and a H joins
to an adjacent monomer
• For each monomer removed, 1 molecule
water is added
Sugar!
• Carbohydrates
– Monomer is
monosaccharide
– OH & C=O
– Link two sugars
into disaccharide
• Ex: sucrose (table
sugar) and maltose
(brewing sugar)
CH2OH
CH2OH
O
O
H
H
H
H
OH
H
OH
HO
H
H
H
H
H
OH
O
OH
OH
H
Glucose
OH
Glucose
H2O
CH2OH
CH2OH
O
O
H
H
OH
H
HO
H
H
H
O
OH
OH
H
OH
H
Maltose
H
H
OH
•
•
•
•
Monosaccharides- one monomer (glucose)
Disaccharides- two monomers (sucrose)
Oligosaccharides- several monomers
Polysaccharides- hundreds of monomers
Sugar uses
• Starch and glycogen: Nutritional Store
chemical energy
– Starch in plants
– Glycogen in animals
Structural Sugar
• Cellulose: Structural
– Forms the cell walls of plants
– Digestible by some animals, but not humans
• Chitin forms exoskeletons of insects and
crustaceans and cell walls in fungi
Sugar Storage
Glucose
monomer
STARCH
Starch granules in
potato tuber cells
O
O
O
O
O
O
O
Glycogen
granules in
muscle tissue
O
O
O O
GLYCOGEN
O
O
O
O
O
O
O
O
O
O
O
O
Cellulose fibrils in a
plant cell wall
CELLULOSE
O
Cellulose
molecules
O
O
OO
O OH
OO
OO
O
OH
O
OO
OO
Figure 3.7
O O
O
O
O O
O
O
Lipids
• No true monomer
– some are formed via
dehydration reactions
• Fats, Steroids,
Phospholipids
• Energy storage,
membrane function
• Hydrophobic
Fats
• Solid and liquid states
• Consist of glycerol
linked to three fatty
acids
– Termed Triacylglycerol
– Hydrophobic
• Fatty acid has COOH
• Glycerol has OH
group
H
H
H C
C
OH OH
H
C H
OH
Glycerol
HO
C O
H2O
CH2
CH2
CH2
CH2
CH2
Fatty acid
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
H
H
H
H
C
C
C
O
O
O
C
O C
O C
H
O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
CH3
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH3
Figure 3.8C
Figure 3.8B
Fatty Acids
• Simple lipids containing 2 parts
– Long hydrocarbon chain (non-polar,
hydrophobic)
– Carboxylic acid functional group (polar,
hydrophilic)
Saturated & Unsaturated
• Double bonding between C prevents H
from bonding
– Fatty acids with double bonds are unsaturated
– Fatty acids without double bonds are
saturated
• Saturated/unsaturated refers to whether or
not the C chains contain the maximum
number of H possible
Kinky
• Double bonds
kink the structure
• Kinks reduce
packing density
• Lower packing
density
decreases
melting point
Saturation and melting point
• Saturated fatty
acids have melting
points above 25ºC
– Liquid at room
temp
• As number of
double bonds
increases, melting
point decreases
– More likely to be
solid at room temp
Hydrogenation
• Highly unsaturated fats can be very soft
and are hydrogenated (saturated) to make
them more butter-like.
• Addition of hydrogen to C=C double bond.
• Some of the cis bonds are converted to
trans.
Trans Fats
• Naturally occurring unsaturated fats are cis:
hydrocarbon chain is kinked.
• Trans fats are straight.
Buyer Beware
• Trans fats are straighter than cis fats and the
product is stiffer.
• Trans fats pose a health risk – are not broken
down readily.
Phospholipids
• Significant component of cell membranes
• Contain a glycerol backbone:
– Glycerol with two fatty acids
– Also bonded with P group and another small,
polar group
• Amphipathic properties significant for cell
membranes
– Created water resistant membrane
Phospholipids
Hydrophilic/Hyrdophobic
• Cell membrane is bilayer of
phospholipids
• Hydrophilic “head”
• Hydrophobic “tail”
Waxes
• Long fatty acid tails bonded to long-chain
alcohols or carbon rings
– Tightly packed
– Water-repelling
Steroids
• Rigid backbone of 4 C rings and no fatty
acid tail
– Present in all eukaryote cell membranes
– Often hormones
– Cholesterol is an example
Waxes
• Long fatty acid tails bonded to long-chain
alcohols or carbon rings
– Tightly packed
– Form waterproof coating
Proteins
• Monomer= Amino Acids
• Unique sequence of AA (20 AA in total)
• Link between amino acids in protein is a
peptide bond
• COOH & NH2
functional groups
Amino Acids
• Specific properties based on its structure
H
H
H
O
N
H
C
H
C
CH2
O
N
OH
C
H
O
C
N
OH
H
CH
CH3
H
OH
CH2
CH2
OH
C
OH
Serine (Ser)
Hydrophobic
O
Aspartic acid (Asp)
Hydrophilic
Figure 3.12B
C
H
CH3
Leucine (Leu)
C
Functions of Proteins
Enzymes
Structural
Contractile
Defensive
Signal
Receptor
Transport
Storage
**Significant in the plasma membrane
Form determines function
• One or more polypeptide chains folded
into a unique shape
– Unique shape determines the function
Groove
Groove
Levels of Protein Structure
• Primary
– Unique sequence of AA forming the polypeptide
chain
Levels of Protein Structure
Leu
Met
Asn
Val
Pro
Ala
Val
Ile
Arg
Cys
Gly
Thr
Primary structure
Gly
Val
Lys
Ala
Glu
Phe
His
Val
Ser
Lys
Val
Leu
Asp
Ala
Val
Amino acids
Pro
Arg
Gly
Ser
Levels of Protein Structure
• Secondary
– Conformation of portions of the polypeptide
chain
• Conformation- 3-d arrangement of atoms in a
molecule (spatial organization)
• Alpha helix &Hydrogen
pleated sheets
Amino acids
bond
O H
C
N
C
C
C
N H
C
O
N H
N
O
Secondary structure
C
H
O
C
C
O
H
O
C
N H
C
O
C
N
O
H O
C
N H
C
O
H
CC
O
C
C
N
H
N
R
H
N H
C
O
H
C C
N
N
O
C
CN
H
C
H
C N
CC N
C
H
H
CC
N
O
H
C
C N
H
O
C
O
C
C N
H
C
O
O
O
C R
N
H
N C C
N
H
C
H
CC
O
H
C
C
O
O
H
N
C N C
C
O
CN
C
H
O
C
H
Alpha helix
Figure 3.14B
Pleated sheet
H
C
N
C
O
N
C
Levels of Protein Structure
• Tertiary
– Overall threedimensional
shape of a
polypeptide
– Globular or
fibrous
Tertiary structure
Polypeptide
(single subunit
of transthyretin)
Levels of Protein Structure
• Quaternary structure
– Results from the association of two or more
Polypeptide
chain
polypeptide chains
Quaternary structure
Transthyretin, with
four identical
polypeptide subunits
Collagen
When shape fails
• Denaturation
– Polypeptide chains unravel, unfold and
disorganize
– Results from heat, salt concentration, pH, etc.
• Resulting altered shape causes proteins to
loose their function
Prions
• Prions result from
misfolded proteins
• Infectious proteins
– Can cause other
proteins to misfold
Enzymes
• Catalysts
– Increase rate of chemical reactions in cells
Nucleic Acids
H
• Monomer=
nucleotides
H
N
N
N
H
OH
O
P
N
O
CH2
Nitrogenous
base (A)
O

O
Phosphate
group
H
H
H
H
OH
Sugar
N
H
H
– Storage and
transmission of
genetic
information
– Two types of
nucleic acids
• DNA and RNA
• OPO32• CH3 added to DNA
affects expression
DNA & RNA
• DNA consists of two
polynucleotides twisted
around each other in a
double helix
– Held together by hydrogen
bonding
• RNA typically consists of a
single polynucleotide strand
C
A
C
C
T
G
G
A
T
C
G
A
T
T
A
Base
pair
G
T
A
A
T
A
C
T
DNA & RNA
• Five types of nitrogenous
bases
– Purines and Pyrimidines
– DNA = A,T,G and C
– RNA = A,U,G and C
Videos
•
•
•
•
Protein structure
http://www.youtube.com/watch?v=lijQ3a8yUYQ
Carbs
http://www.youtube.com/watch?v=_qf_r5EVP6U
&feature=related
• http://www.youtube.com/user/greatpacificmedia#
p/u/50/_qf_r5EVP6U
• Phospholipids
• http://www.youtube.com/watch?v=7k2KAfRsZ4Q