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Carbon & the Molecular diversity
of Life
The big picture:
• The subcomponents of biological molecules
and their sequence determine the properties of
that molecule.
• The electron configuration of carbon gives it
covalent compatibility with many different
elements.
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• The atomic number of carbon is 6
• How many valence electrons does it have?
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Carbon atoms
• 4 unpaired electrons in valence shell
• Can form up to 4 single covalent bonds
• Can also form double bonds, most commonly
with:
– Oxygen CO2 O=C=O
– Carbon To create long chains
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Organic compounds
• A compound containing carbon
• Most, but not all, also contain hydrogen
• Most common elements in organic compounds
–
–
–
–
–
–
Carbon (all)
Hydrogen (most)
Oxygen
Nitrogen
Sulfur
Phosphorus
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Figure 3.3
Hydrogen
(valence  1)
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Oxygen
(valence  2)
Nitrogen
(valence  3)
Carbon
(valence  4)
Shapes of Simple Organic
Molecules
• They are 3-dimensional
• When 4 single bonds are formed with a single
carbon atom
– Angles 109.50
– Tetrahedron
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Figure 3.2
Name
Methane
Ethane
Ethene
(ethylene)
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Molecular
Formula
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
• Carbon chains can vary in 4 ways
–
–
–
–
Length
Branching
Double bond position
Presence of rings
• Complexity and diversity of organic molecules
is due to
– Variation in carbon chain structure
– Other elements bonded to the chain
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Figure 3.4
(a) Length
Ethane
(c) Double bond position
Propane
(b) Branching
Butane
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1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
• The simplest carbon chain is made of only
carbon and hydrogen.
• Hydrocarbon=hydrogen +carbon.
• Hydrogen molecules are attached to the carbon
molecules wherever electrons are available for
covalent bonding.
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• Chemical groups can replace one or more of
the hydrogen atoms on the hydrocarbon
skeleton.
• They can contribute to the function of the
organic molecule by– Affecting its shape
– Being directly involved in chemical reactions
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Figure 3.5
Chemical Group
Hydroxyl group (
Compound Name
Examples
OH)
Alcohol
Carbonyl group (
C
O)
Ethanol
Ketone
Aldehyde
Acetone
Carboxyl group (
Propanal
COOH)
Carboxylic acid,
or organic acid
Acetic acid
Amino group (
NH2)
Amine
Glycine
Sulfhydryl group (
SH)
Thiol
Phosphate group (
OPO32–)
Organic
phosphate
Methyl group (
Glycerol
phosphate
CH3)
Methylated
compound
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Cysteine
5-Methyl cytosine
Important terms
• Polymer
– A long molecule consisting of many similar or
identical building blocks linked by covalent bonds.
• Monomer
– The repeating units that serve as the building
blocks of a polymer.
• How are monomers joined together?
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Synthesis and Breakdown of
Polymers
• Dehydration reaction
– Connects monomers
– One provides a hydroxyl group (-OH), the other a
hydrogen (-H)
– Water is lost
• Hydrolysis
– The reverse
– Breakage using water
– Water attaches a hydroxyl to one molecule,
hydrogen to the other
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Figure 3.6a
(a) Dehydration reaction: synthesizing a polymer
Short polymer
Dehydration removes
a water molecule,
forming a new bond.
Longer polymer
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Unlinked monomer
Figure 3.6b
(b) Hydrolysis: breaking down a polymer
Hydrolysis adds
a water molecule,
breaking a bond.
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Macromolecules (+ Lipids)
• 4 classes of large organic molecules shared by
all living things.
–
–
–
–
Carbohydrates
Lipids
Proteins
Nucleic acids
• Some do not consider lipids to be true
“macromolecules” because
– They are not big enough
– They are not true polymers
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As we review each macromolecule
•
•
•
•
•
•
Monomer
Polymer
Type of bond that links the monomers together
Basic structure
Example
Function
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Carbohydrates
• Monomer- simple sugar, monosaccharide
• Disaccharide- 2 simple sugars linked together
• Polysaccharide- many simple sugars linked
together
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• Monosaccharides
– Contain a carbonyl group (C=O) and multiple
hydroxyl groups (-OH)
– Vary in the length of the carbon skeleton and
position of the carbonyl group
– All have chemical formulas that are multiples of
CH2O, ex. Glucose is C6H12O6
– Names end in “ose”
– Used as fuel
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Figure 3.7
Triose: 3-carbon sugar (C3H6O3)
Pentose: 5-carbon sugar (C5H10O5)
Glyceraldehyde
An initial breakdown
product of glucose in cells
Ribose
A component of RNA
Hexoses: 6-carbon sugars (C6H12O6)
Glucose
Fructose
Energy sources for organisms
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• Sugars can exist in both a linear and ring form
• Equilibrium favors the ring form.
• Notice the convention for naming the carbon
atoms.
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Figure 3.8
(a) Linear and ring forms
(b) Abbreviated ring structure
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• Two monosaccharides are linked by a covalent
bond through a dehydration reaction.
• The resulting linkage is called a glycosidic
linkage.
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Figure 3.9-1
Glucose
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Fructose
Figure 3.9-2
Glucose
Fructose
1–2
glycosidic
linkage
Sucrose
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Polysaccharides
• 2 functions
– Storage- sugars for later use
– Structural- building material
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Storage
• Plants
– Starch
• Polymer of glucose
• Mostly unbranched
• Most animals also have enzymes to break it down so it
can be a food source
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Figure 3.10a
Starch granules
in a potato tuber cell
Starch (amylose)
Glucose
monomer
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• Animals
– Glycogen
•
•
•
•
Also a polymer of glucose
Extensive branching
Stored in liver and muscles
Stores for only 1 day
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Figure 3.10b
Glycogen granules
in muscle
tissue
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Glycogen
Figure 3.10
Starch granules
in a potato tuber cell
Starch (amylose)
Glucose
monomer
Glycogen granules
in muscle
tissue
Cellulose microfibrils
in a plant cell wall
Cellulose
molecules
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Glycogen
Cellulose
Hydrogen bonds
between —OH groups
(not shown) attached to
carbons 3 and 6
Structural
• Cellulose
– Plant cell walls
– Never branched
– Different from starch because of presence of 2 ring
forms of glucose
• Cellulose α glucose
• Starch β glucose
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Figure 3.11
(a)  and  glucose
ring structures
 Glucose
 Glucose
(b) Starch: 1–4 linkage of  glucose monomers
(c) Cellulose: 1–4 linkage of  glucose monomers
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• Cellulose polymers lie parallel and can form
hydrogen bonds with neighboring polymers
• Creates cable-like microfibrils
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Figure 3.10c
Cellulose microfibrils
in a plant cell wall
Cellulose
molecules
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Cellulose
Hydrogen bonds
between —OH
groups on
carbons 3 and 6
Figure 3.10ca
Cellulose
microfibrils
in a plant
cell wall
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Lipids
• No true monomers
• Not big enough to be considered “macro”
• Share one important trait
– They are all hydrophobic (due to hydrocarbons)
• 3 biologically important lipids
– Fats
– Phospholipids
– Steroids
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Fats
• Composed of
– Glycerol (1)
– Fatty acids (3)
• Linkage is called an “ester bond” and it is a
covalent bond between a hydroxyl group and a
carboxyl group
• What kind of reaction is used in the synthesis
of a fat?
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Figure 3.12
Fatty acid
(in this case, palmitic acid)
Glycerol
(a) One of three dehydration reactions in the synthesis of a fat
Ester linkage
(b) Fat molecule (triacylglycerol)
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Saturated vs. Unsaturated
• Are there any carbon double bonds within the
hydrocarbon chains of the fatty acids?
– Yes- unsaturated
– No- saturated
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Figure 3.13
(a) Saturated fat
Structural
formula of a
saturated fat
molecule
Space-filling
model of
stearic acid,
a saturated
fatty acid
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(b) Unsaturated fat
Structural
formula
of an
unsaturated
fat molecule
Space-filling
model of oleic
acid, an
unsaturated
fatty acid
Double bond
causes bending.
Phospholipids
• Differ from fats in that there are only 2 fatty
acids
• The third hydroxyl group of the glycerol
molecule bonds to a phosphate
• The phosphate is negatively charged AND
other small polar molecules can be attached to
the phosphate. Both of these things make the
phosphate end. . . Hydrophilic!
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Hydrophobic tails
Hydrophilic head
Figure 3.14ab
Choline
Phosphate
Glycerol
Fatty acids
(a) Structural formula
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(b) Space-filling model
• Where in a cell might you find phospholipids?
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Hydrophobic tails
Hydrophilic head
Figure 3.14
Choline
Phosphate
Glycerol
Fatty acids
(a) Structural formula
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Hydrophilic
head
Hydrophobic
tails
(b) Space-filling model
(c) Phospholipid
symbol
(d) Phospholipid
bilayer
Steroids
• Carbon skeleton of 4 fused carbon rings
• Distinguished by the attached chemical groups
• Cholesterol is an example
– Common component of animal cell membranes
– Other important steroids are synthesized from it
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Figure 3.15
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Proteins
• Proeios- “first” or “primary”
• Play a roll in almost everything a cell does
• 50% of dry mass of most cells
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Protein functions include:
–
–
–
–
–
–
–
Speeding up chemical reactions (enzymes)
Defense
Storage
Transport
Cellular communication
Movement
Structural support
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Figure 3.16a
Enzymatic proteins
Defensive proteins
Function: Selective acceleration of
chemical reactions
Function: Protection against disease
Example: Digestive enzymes catalyze the
hydrolysis of bonds in food molecules.
Example: Antibodies inactivate and help
destroy viruses and bacteria.
Antibodies
Enzyme
Virus
Bacterium
Storage proteins
Transport proteins
Function: Storage of amino acids
Function: Transport of substances
Examples: Casein, the protein of milk, is
the major source of amino acids for baby
mammals. Plants have storage proteins
in their seeds. Ovalbumin is the protein
of egg white, used as an amino acid
source for the developing embryo.
Examples: Hemoglobin, the iron-containing
protein of vertebrate blood, transports
oxygen from the lungs to other parts of the
body. Other proteins transport molecules
across cell membranes.
Transport
protein
Ovalbumin
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Amino acids
for embryo
Cell membrane
Figure 3.16b
Hormonal proteins
Receptor proteins
Function: Coordination of an organism’s
activities
Function: Response of cell to chemical
stimuli
Example: Insulin, a hormone secreted by
the pancreas, causes other tissues to
take up glucose, thus regulating blood
sugar concentration.
Example: Receptors built into the
membrane of a nerve cell detect signaling
molecules released by other nerve cells.
Receptor
protein
High
blood sugar
Insulin
secreted
Signaling molecules
Normal
blood sugar
Contractile and motor proteins
Function: Movement
Examples: Motor proteins are responsible
for the undulations of cilia and flagella.
Actin and myosin proteins are
responsible for the contraction of
muscles.
Actin
Structural proteins
Function: Support
Examples: Keratin is the protein of hair,
horns, feathers, and other skin appendages.
Insects and spiders use silk fibers to make
their cocoons and webs, respectively.
Collagen and elastin proteins provide a
fibrous framework in animal connective
tissues.
Myosin
Collagen
Muscle tissue
30 m
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Connective tissue 60 m
• Monomer- amino acid
• Polymer- polypeptide (unbranched)
• Linkage- peptide bond, a covalent bond
between an amino group and a carboxyl group
(What kind of reaction?)
• Protein definition=
– A biologically functional molecule that consists of
one or more polypeptides folded and coiled into a
specific 3-dimensional structure.
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Amino acids
• 20 amino acids
• All have a common structure
– α carbon in the center
– 4 partners
•
•
•
•
Hydrogen
Amino group
Carboxyl group
R group (Think “R” = “the rest”)
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Figure 3.UN04
Side chain (R group)
 carbon
Amino
group
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Carboxyl
group
R Groups
• Unique to each amino acid
• Often ionized at the pH found in cells (=7.2)
• Chemical and physical properties determine
the characteristics of the amino acid and its
role in a polypeptide
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R groups (also called side chains)
can be:
• Nonpolar: hydrophobic
• Polar: hydrophilic
• Electrically charged: hydrophilic
– Acidic
– Basic
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Figure 3.17a
Nonpolar side chains; hydrophobic
Side chain
(R group)
Glycine
(Gly or G)
Methionine
(Met or M)
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Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(le or )
Proline
(Pro or P)
Figure 3.17b
Polar side chains; hydrophilic
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Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Figure 3.17c
Electrically charged side chains; hydrophilic
Basic (positively charged)
Acidic (negatively charged)
Aspartic acid Glutamic acid
(Asp or D)
(Glu or E)
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Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Polypeptides
• Amino acids linked in a non-branching
polymer by peptide bonds through a
dehydration reaction.
• N-terminus: the amino end of a polypeptide
• C-terminus: the carboxyl end of a polypeptide
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Figure 3.18
Peptide bond
New peptide
bond forming
Side
chains
Backbone
Amino end
(N-terminus)
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Peptide
bond
Carboxyl end
(C-terminus)
To be clear . . .
• A polypeptide is NOT a protein
• A protein is one or more polypeptides
precisely twisted, coiled and folded into a
unique shape.
• The sequence of amino acids determines this
shape
• The shape determines how it functions
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• Function depends on the protein’s ability to
recognize and bind with other molecules.
• The binding requires an exact match between
the protein and the other molecule.
• Like puzzle pieces or a lock and key.
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Figure 3.20
Antibody protein
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Protein from flu virus
4 Levels of Protein Structure
•
•
•
•
Primary
Secondary
Tertiary
Quaternary
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Primary
• The sequence of amino acids
• The primary structure then controls the
secondary and tertiary structures .
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Figure 3.21a
Primary structure
Amino
acids
1
10
5
Amino end
30
35
15
20
25
45
40
50
Primary structure of transthyretin
65
70
55
60
75
80
90
85
95
115
120
110
105
100
125
Carboxyl end
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Secondary
• Coiled or folded patterns that result from
hydrogen bonds between parts of the
polypeptide backbone NOT the R-groups.
• 2 types
– α helix
– Β pleated sheet
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Figure 3.21ba
Secondary structure
 helix
 pleated sheet
Hydrogen bond
 strand
Hydrogen
bond
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Tertiary
• The overall shape of the polypeptide resulting
from interactions between the side chains (Rgroups)
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Interactions contributing to tertiary
structure
– Hydrophobic interactions
• Amino acids with nonpolar (hydrophobic) side chains
get moved to the inner core away from water, then van
der Waals interactions hold them together.
– Hydrogen bonds
• Between polar side chains
– Ionic bonds
• Between positively and negatively charged side chains
– Disulfide bridges
• Covalent bond between the sulfur of 2 cysteine
monomers
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Figure 3.21d
Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
Ionic bond
Polypeptide
backbone
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Figure 3.21bb
Tertiary structure
Transthyretin
polypeptide
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Quaternary
• The overall protein structure that results from
the aggregation of polypeptide subunits.
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Figure 3.21bc
Quaternary structure
Transthyretin
protein
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Figure 3.21b
Secondary
structure
Tertiary
structure
Quaternary
structure
Transthyretin
polypeptide
Transthyretin
protein
 helix
 pleated sheet
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Figure 3.21f
Heme
Iron
 subunit
 subunit
 subunit
 subunit
Hemoglobin
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Figure 3.22a
Normal
Primary
Structure
1
2
3
4
5
6
7
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Secondary
and Tertiary
Structures
Quaternary
Structure
Normal
hemoglobin
 subunit




Function
Molecules do not
associate with one
another; each carries
oxygen.
Figure 3.22aa
5 m
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Figure 3.22b
Sickle-cell
Primary
Structure
1
2
3
4
5
6
7
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Secondary
and Tertiary
Structures
Quaternary
Structure
Exposed hydrophobic region
Sickle-cell
hemoglobin

 subunit

Function


Molecules crystallized
into a fiber; capacity to
carry oxygen is reduced.
Figure 3.22ba
5 m
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Figure 3.22
Sickle-cell
Normal
Primary
Structure
1
2
3
4
5
6
7
1
2
3
4
5
6
7
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Secondary
and Tertiary
Structures
Quaternary
Structure
Function
Normal
hemoglobin
 subunit

Molecules do not
associate with one
another; each carries
oxygen.


5 m

Exposed hydrophobic region
Sickle-cell
hemoglobin

 subunit

Red Blood Cell
Shape
Molecules crystallized
into a fiber; capacity to
carry oxygen is reduced.


5 m
Protein structure depends on:
•
•
•
•
•
•
Primary sequence of amino acids
AND
pH
Salt concentration
Temperature
Other environmental factors
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Denaturation
• When environmental conditions are changed,
the chemical bonds and interactions are
destroyed .
• The protein unravels.
• Without its native shape, it is no longer
functional.
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Figure 3.23-2
Normal protein
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Denatured protein
Nucleic Acids
• Two types
– DNA (deoxyribonucleic acid)
– RNA (ribonucleic acid)
• Function: Store, transmit, and help express
hereditary information.
• Monomer: nucleotide
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Terms to know
• Chromosome: a single long DNA molecule
• Gene: A specific nucleotide sequence of DNA
that codes for a specific amino acid sequence
• A chromosome may be composed of >100
genes.
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Structure of Nucleic Acids
• Monomer: nucleotide
• Polymer: poly nucleotide
• Nucleotide = nucleoside (nitrogenous base + 5
carbon sugar) + 1 or more phosphates
• Nitrogenous (nitrogen-containing) as in “acid
vs. base” not as in “foundation”. The N tends
to take up H+ from solution acting as a base.
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Figure 3.26b
Nucleoside
Nitrogenous
base
Phosphate
group
(b) Nucleotide
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Sugar
(pentose)
2 types of nitrogenous bases
• Pyrimidine- One 6-member ring of C and N
– Cytosine
– Thymine (only in DNA)
– Uracil (only in RNA)
• Purine- 6-member ring fused to a 5-member
ring
– Adenine
– Guanine
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Figure 3.26c
Nitrogenous bases
Pyrimidines
Cytosine (C)
Thymine
(T, in DNA)
Uracil
(U, in RNA)
Purines
Adenine (A)
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Guanine (G)
Sugars
• Deoxyribose-DNA
• Ribose- RNA
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Figure 3.26d
Sugars
Deoxyribose (in DNA)
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Ribose (in RNA)
• Then a phosphate is added at the 5´ carbon of
the sugar.
• Note: The “prime” symbol ´ distinguishes the
sugar carbon from the nitrogenous base
carbon.
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Figure 3.26b
Nucleoside
Nitrogenous
base
Phosphate
group
(b) Nucleotide
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Sugar
(pentose)
Polynucleotide
• Nucleotides joined by phosphodiester linkage
• The sugars of the nucleotides are linked into a
sugar phosphate backbone.
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Figure 3.26a
5 end
Sugar-phosphate backbone
(on blue background)
5C
3C
Nucleoside
Nitrogenous
base
5C
Phosphate
group
3C
(b) Nucleotide
3 end
(a) Polynucleotide, or nucleic acid
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Sugar
(pentose)
• Note: polynucleotides have directionality
much like proteins
• Each end is different
– 5´end-phosphate attached to 5´C
– 3´end- OH attached to 3´C
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Figure 3.26
5 end
Sugar-phosphate backbone
(on blue background)
Nitrogenous bases
Pyrimidines
5C
3C
Nucleoside
Nitrogenous
base
Cytosine (C)
Thymine
(T, in DNA)
Uracil
(U, in RNA)
Purines
5C
Phosphate
group
3C
Sugar
(pentose)
Adenine (A)
Guanine (G)
(b) Nucleotide
3 end
Sugars
(a) Polynucleotide, or nucleic acid
Deoxyribose (in DNA)
(c) Nucleoside components
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Ribose (in RNA)
DNA
• 2 polynucleotide strands that run antiparallel
• Think of a two way street
– One strand 5´to 3´
– One strand 3´to 5´
• The 2 strands are held together by hydrogen
bonds.
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Figure 3.27a
5
3
3
5
(a) DNA
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Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen bonding
•
•
•
•
•
Only certain bases will bond together
A-T
G-C
This allows 2 identical strands to be made
Form follows function
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RNA
• Only a single strand, but it can fold on itself
• No thymine so. . .
• A-U
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Figure 3.27b
Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen
bonding
(b) Transfer RNA
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Figure 3.27
5
3
Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen
bonding
3
5
(a) DNA
Base pair joined
by hydrogen bonding
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(b) Transfer RNA
Evidence for common ancestry
• More common DNA sequences= more closely
related
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For Monday’s Quiz
Macromolecules plus lipids
To know:
• Monomers
• Polymers
• Linkages
• Basic structure
• Function
• Examples
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Figure 3.UN06
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Figure 3.UN06a
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Figure 3.UN06b
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