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9/14/2012
MACROMOLECULES
MACROMOLECULES
• The four biologically important
macromolecules:
– Carbohydrates
– Proteins
– Lipids
– Nucleic Acids
Carbohydrates
CARBOHYDRATES
• Carbohydrates are composed of C, H, O
carbo - hydr - ate
CH2O
(CH
O)
CC66HH1212OO66
(CH
O)
2 2x x
• Function:
–
–
–
–
fast energy
energy storage
raw materials
structural materials
• Monomer: sugars
• ex: sugars, starches, cellulose
sugar
Sugars
– 6C = hexose (glucose)
– 5C = pentose (ribose)
– 3C = triose (glyceraldehyde)
H
HO
6H
H
Glucose
OH
OH
HO
H
5
OH
sugar
sugar
sugar
sugar
aldehyde
H
O
C
O
H
sugar
carbonyl
CH2OH
O
H
OH
sugar
Functional groups determine function
• Most names for sugars end in -ose
• Classified by number of carbons
CH2OH
sugar
HO
H
Ribose
H
H
C
H
H
C
3
OH
carbonyl
OH
ketone
H
Glyceraldehyde
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Sugar structure
Numbered carbons
5C & 6C sugars form rings in solution
C 6'
5' C
These will become
important!
O
4'C
C 1'
energy stored in C-C bonds
harvested in cellular respiration
Where do
you find solutions
in biology?
In cells!
C 3'
Simple & complex sugars
• Monosaccharides
Building sugars
CH2OH
H
– simple 1 monomer sugars
– glucose
O
H
OH
H
H
OH
HO
• Disaccharides
H
• Dehydration synthesis
OH
monosaccharides
disaccharide
Glucose
– 2 monomers
– sucrose
H2O
|
glucose
• Polysaccharides
|
glucose
– large polymers
– starch
|
maltose
glycosidic linkage
Building sugars
Polysaccharides
• Polymers of sugars
• Dehydration synthesis
monosaccharides
C 2'
Carbons are numbered
disaccharide
– costs little energy to build
– easily reversible = release energy
• Function:
– energy storage
|
glucose
H2O
|
fructose
• starch (plants)
• glycogen (animals)
|
sucrose
(table sugar)
– in liver & muscles
– structure
• cellulose (plants)
• chitin (arthropods & fungi)
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Linear vs. branched polysaccharides
Polysaccharide diversity
• Molecular structure determines function
slow release
in starch
starch
(plant)
in cellulose
energy
storage
glycogen
(animal)


isomers of glucose
structure determines function…
fast release
Digesting starch vs. cellulose
Cellulose
• Most abundant organic
compound on Earth
starch
easy to
digest
enzyme
– herbivores have evolved a mechanism to digest
cellulose
– most carnivores have not
• that’s why they
eat meat to get
their energy &
nutrients
• cellulose = undigestible roughage
cellulose
hard to
digest
But it tastes
like hay!
Who can live
on this stuff?!
enzyme
only bacteria can digest
Helpful bacteria
Cow
can digest cellulose well;
no need to eat other sugars
Gorilla
• How can herbivores digest cellulose so well?
– BACTERIA live in their digestive systems & help
digest cellulose-rich (grass) meals
can’t digest cellulose well;
must add another sugar
source, like fruit to diet
Caprophage
Ruminants
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PROTEINS
Proteins
Multipurpose
molecules
2008-2009
Proteins
Protein Structure
• Most structurally & functionally diverse group
• monomer = amino acids
– 20 different amino acids
• Function: involved in almost everything
–
–
–
–
enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication
• signals (insulin & other hormones)
• receptors
– defense (antibodies)
– movement (actin & myosin)
– storage (bean seed proteins)
• polymer = polypeptide
– protein can be one or more polypeptide
chains folded & bonded together
– large & complex molecules
– complex 3-D shape
hemoglobin
Rubisco
– central carbon
– amino group
– carboxyl group (acid)
– R group (side chain)
• variable group
• different for each amino acid
• confers unique chemical
properties to each amino acid
– like 20 different letters of an
alphabet
– can make many words (proteins)
growth
hormones
Effect of different R groups:
Nonpolar amino acids
Amino acids
• Structure
H2O
O
H
|
H
||
—C— C—OH
—N—
|
H
R
 nonpolar & hydrophobic
Oh, I get it!
amino = NH2
acid = COOH
Why are these nonpolar & hydrophobic?
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Effect of different R groups:
Polar amino acids
Ionizing in cellular waters
H+ donors
 polar or charged & hydrophilic
Why are these polar & hydrophillic?
Ionizing in cellular waters
H+ acceptors
Sulfur containing amino acids
• Form disulfide bridges
– covalent cross links betweens sulfhydryls
– stabilizes 3-D structure
H-S – S-H
You wondered
why perms
smell like
rotten eggs?
Building proteins
Building proteins
• Polypeptide chains have direction
• Peptide bonds
– covalent bond between NH2 (amine) of one amino acid
& COOH (carboxyl) of another
– C–N bond
– N-terminus = NH2 end
– C-terminus = COOH end
– repeated sequence (N-C-C) is the polypeptide
backbone
• can only grow in one direction
H2O
dehydration synthesis
peptide
bond
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Protein structure & function
• Function depends on structure
Primary (1°) structure
• Order of amino acids in chain
– 3-D structure
• twisted, folded, coiled into unique shape
– amino acid sequence determined by
gene (DNA)
– slight change in amino acid sequence
can affect protein’s structure & its
function
• even just one amino acid change can make
all the difference!
pepsin
hemoglobin
lysozyme: enzyme in
tears & mucus that kills
bacteria
collagen
Sickle cell anemia
Just 1
out of 146
amino acids!
Secondary (2°) structure
• “Local folding”
– folding along short sections of polypeptide
– interactions between
adjacent amino acids
• H bonds
– weak bonds
between R groups
– forms sections of
3-D structure
I’m
hydrophilic!
But I’m
hydrophobic!
Secondary (2°) structure
• -helix
• -pleated sheet
Tertiary (3°) structure
• “Whole molecule folding”
– interactions between distant amino acids
• hydrophobic interactions
– cytoplasm is
water-based
– nonpolar amino
acids cluster away
from water
• H bonds & ionic bonds
• disulfide bridges
– covalent bonds between
sulfurs in sulfhydryls (S–H)
– anchors 3-D shape
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Quaternary (4°) structure
Protein Structure -- Review
• More than one polypeptide chain bonded together
– only then does polypeptide become
functional protein
R groups
hydrophobic
interactions
disulfide bridges
(H & ionic bonds)
• hydrophobic interactions
3°
multiple
polypeptides
hydrophobic
interactions
1°
amino acid
sequence
peptide bonds
collagen = skin & tendons
hemoglobin
Protein denaturation
• Unfolding a protein
determined
by DNA
4°
2°
R groups
H bonds
Chaperonin proteins
• Guide protein folding
– provide shelter for folding polypeptides
– keep the new protein segregated from cytoplasmic
influences
– conditions that disrupt H bonds,
ionic bonds, disulfide bridges
• temperature
• pH
• salinity
– alter 2° & 3° structure
• alter 3-D shape
– destroys functionality
• some proteins can return to their
functional shape after denaturation, many
cannot
In Biology,
size doesn’t
matter,
SHAPE matters!
Protein models
• Protein structure visualized by
– X-ray crystallography
– extrapolating from amino acid sequence
– computer modelling
LIPIDS
lysozyme
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Lipids
• Lipids are composed of C, H, O
– long hydrocarbon chains (H-C)
LIPIDS
• “Family groups”
a.k.a. – fats, oils, waxes
long term energy storage
concentrated energy
– fats
– phospholipids
– steroids
• Do not form polymers
– big molecules made of
smaller subunits
– not a continuing chain
Building Fats
Fats
• Structure:
• Triacylglycerol
– glycerol (3C alcohol) + fatty acid
• fatty acid =
long HC “tail” with carboxyl (COOH) group “head”
– 3 fatty acids linked to glycerol
– ester linkage = between OH & COOH
hydroxyl
carboxyl
Look at structure… What
makes them hydrophobic?
enzyme
H2O
dehydration synthesis
Dehydration synthesis
Fats store energy
• Long HC chain
– polar or non-polar?
– hydrophilic or hydrophobic?
H2O
dehydration synthesis
Why do humans
like fatty foods?
• Function:
– energy storage
• concentrated
enzyme
H2O
enzyme
H2O
enzyme
– all H-C!
• 2x carbohydrates
– cushion organs
– insulates body
• think whale blubber!
H2O
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Saturated fats
Unsaturated fats
• C=C double bonds in
the fatty acids
• All C bonded to H
• No C=C double bonds
– plant & fish fats
– vegetable oils
– liquid at room temperature
– long, straight chain
– most animal fats
– solid at room temp.
• the kinks made by double
bonded C prevent the
molecules from packing
tightly together
• contributes to
cardiovascular disease
(atherosclerosis)
= plaque deposits
mono-unsaturated?
poly-unsaturated?
Saturated vs. unsaturated
saturated
unsaturated

Phospholipids
• Hydrophobic or hydrophilic?
Phospholipids
• Structure:
– glycerol + 2 fatty acids + PO4
• PO4 = negatively charged
Phospholipids in water
• Hydrophilic heads “attracted” to H2O
• Hydrophobic tails “hide” from H2O
– fatty acid tails = hydrophobic
– PO4 head = hydrophillic
– split “personality”
– can self-assemble into “bubbles”
“attracted to water”
• bubble = “micelle”
• can also form a phospholipid bilayer
• early evolutionary stage of cell?
water
bilayer
interaction with H2O is
complex & very important!
“repelled by water”
water
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Why is this important?
• Phospholipids create a barrier in water
– define outside vs. inside
– they make cell membranes!
Phospholipids & cells
• Phospholipids of cell membrane
– double layer = bilayer
– hydrophilic heads on outside
• in contact with aqueous solution outside of cell and inside
of cell
– hydrophobic tails on inside
• form core
– forms barrier between cell
& external environment
Steroids
• Structure:
– 4 fused C rings + FG
• different steroids created by attaching different functional
groups to rings
• different structure creates different function
– examples: cholesterol, sex hormones
cholesterol
Cholesterol
• Important cell
component
– animal cell membranes
• Helps to keep cell
membrane fluid and
flexible
– precursor of all other
steroids
• including vertebrate sex
hormones
– high levels in blood
may contribute to
cardiovascular disease
From Cholesterol  Sex Hormones
• What a big difference a few atoms can make!
NUCLEIC ACIDS
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Nucleic Acids
• Function:
– genetic material
• stores information
– genes
– blueprint for building proteins
» DNA  RNA  proteins
Nucleic Acids
Information
storage & transmission
• transfers information
DNA
– blueprint for new cells
– blueprint for next generation
proteins
Nucleic Acids
• Examples:
– RNA (ribonucleic acid)
• single helix
– DNA (deoxyribonucleic acid)
• double helix
• Structure:
T
G
C
T
A
A
C
– monomers = nucleotides
A
A
C
G
G
DNA
T
Types of nucleotides
Nucleotides
• 2 types of nucleotides
• 3 parts
– nitrogen base (C-N ring)
– pentose sugar (5C)
• ribose in RNA
• deoxyribose in DNA
– phosphate (PO4) group
Are nucleic acids
charged molecules?
RNA
Nitrogen base
I’m the
A,T,C,G or U
part!
– different nitrogen bases
– purines
• double ring N base
• adenine (A)
• guanine (G)
Purin
Pure
– pyrimidines
•
•
•
•
single ring N base
cytosine (C)
thymine (T)
uracil (U)
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Nucleic polymer
• Backbone
– sugar to PO4 bond
– phosphodiester bond
• new base added to sugar of previous base
• polymer grows in one direction
– N bases hang off the
sugar-phosphate backbone
Pairing of nucleotides
• Nucleotides bond between
DNA strands
– H bonds
– purine :: pyrimidine
– A :: T
• 2 H bonds
– G ::: C
• 3 H bonds
Matching bases?
Why is this important?
DNA molecule
• Double helix
– H bonds between bases
join the 2 strands
Copying DNA
• Replication
– 2 strands of DNA helix are
complementary
• have one, can build other
• have one, can rebuild the whole
• A :: T
• C :: G
H bonds?
Why is this important?
When does a cell copy DNA?
• When in the life of a cell does DNA have to be
copied?
– cell reproduction
• mitosis
DNA replication
“It has not escaped our notice that the
specific pairing we have postulated
immediately suggests a possible copying
mechanism for the genetic material.”
James Watson
Francis Crick
1953
– gamete production
• meiosis
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1953 | 1962
Watson and Crick … and others…
1953 | 1962
Maurice Wilkins… and…
Interesting note…
Rosalind Franklin (1920-1958)
• Ratio of A-T::G-C
affects stability
of DNA molecule
– 2 H bonds vs. 3 H bonds
– biotech procedures
• more G-C =
need higher T° to
separate strands
– high T° organisms
• many G-C
– parasites
• many A-T (don’t know why)
Another interesting note…
• ATP
Adenosine triphosphate

modified nucleotide
 adenine (AMP) + Pi + Pi
+
+
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