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Lecture #2
Date ______
•  Chapter 4~
Carbon &
The Molecular
Diversity of Life
•  Chapter 5~
The Structure &
Function of
Large Biological
Molecules
Vitalism vs. Mechanism
–  Vitalism: the idea that organic compounds
arise only within living organisms (Jons Jakob
Berzelius)
–  Mechanism: the thought that all natural
phenomena are governed by physical &
chemical laws
•  Experimental design that supported mechanistic
thought and disproved vitalism…
Stanley Miller Experiment
EXPERIMENT
In 1953, Stanley Miller simulated what were thought to be environmental
conditions on the lifeless, primordial Earth. As shown in this recreation, Miller
used electrical discharges (simulated lightning) to trigger reactions in a
primitive “atmosphere” of H2O, H2, NH3 (ammonia), and CH4 (methane)—
some of the gases released by volcanoes.
http://www.ucsd.tv/miller-urey/
http://chemistry.beloit.edu/Origins/pages/spark.html
RESULTS
A variety of organic compounds that play key roles in living cells were synthesized
in Miller’s apparatus…. 13 of 20 amino acids, nitrogen bases, & adenine (ATP
base) formed, (overall, 10-15% of C in system fixed)
CONCLUSION
Organic compounds may have been synthesized abiotically on the early
Earth, setting the stage for the origin of life. (We will explore this
hypothesis in more detail in Chapter 26.)
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Organic chemistry
•  Organic chemistry is the
study of carbon containing
compounds
•  Why carbon?
(a) Length
H H
H C C H
tetravalence
H H
Ethane
tetrahedron (bond angle)
shape determines function (b) Branching H CH CH CH CH H
H H H H
•  Carbon can form “skeletons”
Butane
H H H H
that allow for variation
(c) Double bonds H
C C C C H
–
–
–
–
length
double bonds
branching
rings
(d) Rings
H H
1-Butene
H
H
H
C
H
C H
H C
H
H
H C C C H
Cyclohexane
H H H
H C C C H
H H H
Propane
H
H C H
H
H
H C C C H
H H H
2-methylpropane
(commonly called isobutane)
H H H H
H C C C C H
H
H
2-Butene
H
H
C C H
C
C
C
Benzene
Nomenclature (Naming)
- Carbons (often) numbered (important later)
•
•
•
•
•
•
•
•
•
•
CH4
C 2H 6
C 3H 8
C4H10
C5H12
C6H14
C7H16
C8H18
C9H20
C10H22
methane
ethane
propane
butane
pentane
hexane
heptane
octane
nonane
decane
- Saturated = all single bonds (suffix –ane)
- General Formula = Cn H2n+2
- Unsaturated (multiple bonds and less H+)
- Double bond between 2 C’s (suffix –ene)
- General Formula = Cn H2n (n>2)
- Triple bond between s C’s (suffix –yne)
- General Formula = Cn H2n-2 (n>2)
- Cycloalkanes have one or more rings of carbons
- Example: cyclohexane also called benzene
Hydrocarbons
•  Only carbon & hydrogen
(petroleum; lipid ‘tails’)
•  Covalent bonding; nonpolar
•  High energy storage
•  Isomers (same molecular
formula, but different structure &
properties)
–  structural~differing covalent
bonding arrangement
–  geometric~differing spatial
1
arrangement
–  enantiomers~mirror images
pharmacological industry
(thalidomide is an example of
Chirality…click to link!)
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Functional Groups, I
•  Attachments that replace
one or more of the
hydrogens bonded to the
carbon skeleton of the
hydrocarbon
•  Each has a unique property
from one organic to another
OH
CH3
Estradiol
HO
Female lion
OH
CH3
–  Give organic molecules
distinctive chemical properties
•  An alkane that has lost a H
so it can bond to a carbon is
called an alkyl (group)
CH3
O
Testosterone
Male lion
Functional Groups, I continued
•  Hydroxyl Group
HYDROXYL
–  H bonded to O
–  Name of Compounds: Alcohols
–  polar (oxygen)
OH
–  soluble in water
•  Carbonyl Group
–  C double bonded to O
–  Name of Compounds:
(may be written HO
CARBONYL
H
H
O
•  Ketone if carbonyl group is
w/in carbon skeleton
•  Aldehyde if carbonyl group is at
the end of a carbon skeleton
)
O
C
H
C
H
H
C
C
H
Acetone, the simplest ketone
H H
O
H C C C
H
H H
Propanal, an aldehyde
Functional Groups, II
•  Carboxyl Group (COOH group)
- C double bonded to O and single
bonded to a hydroxyl group
- Name of Compounds: Carboxylic Acids
- covalent bond between O and H
- polar
- undergo dissociation, losses H+ ion
(in other words, they form organic acids)
-Found in body (cells) in an ionic form
•  Amino Group (NH2 group)
- N bonded to 2 H atoms and C skeleton
- Name of Compounds: Amines
- acts as a base (absorbs H+ ions)
CARBOXYL
H
O
C
OH
H
C
H
O
C
OH
Acetic acid, which gives vinegar
its sour tatste
AMINO
H
N
H
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Functional Groups, II continued
•
Sulfhydral Group
SULFHYDRYL
- sulfur bonded to H
- Name of Compounds: Thiols
SH
- two sulfhydryl groups interact
in proteins to stabilize the
structure
•
Phosphate Group
- phosphate ion covalently attached
by 1 of its O to the C skeleton
- Name of Compounds: Organic
Phosphates
- makes molecule to which it is
attached an anion (negatively
charged ion)
- critical role in energy exchange for
living organisms
PHOSPHATE
O
O P O(H)
O(H)
Practice: Molecular Models
Polymers
•  Covalent monomers
•  Condensation reaction
(dehydration reaction):
One monomer provides a
hydroxyl group while the other
provides a hydrogen to form a
water molecule and a polymer
•  Hydrolysis: bonds between
individual monomers of a
polymer are broken by adding
water (digestion)
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Classification & Diversity
•  The four classes of life’s organic molecules
–  Carbohydrates
–  Proteins
–  Nucleic acids
–  Lipids (not a true polymer)
•  Although organisms share the same limited
number of monomer types, each organism is
unique based on the arrangement of
monomers into polymers
•  An immense variety of polymers can be built
from a small set of monomers
Carbohydrates, I
•  Monosaccharides
√ CH2O formula;
√ multiple hydroxyl (-OH) groups
and 1 carbonyl (C=O) group:
- aldehyde (aldoses) sugar
- ketone sugar
√ glucose product of photosynthesis
√ cellular respiration
√ raw material for amino acids
and fatty acids
Carbohydrates, II
•  Disaccharide
√ glycosidic linkage (covalent
bond) between 2
monosaccharides
√ covalent bond formed by
dehydration reaction
•  Sucrose (table sugar)
√ most common disaccharide
√ disaccharide consisting of a
single glucose and
fructose monomer
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Disaccharides
Carbohydrates, III
Polysaccharides: long chains of glucose
molecules (differ due to orientation
of individual glucose monomers)
Storage
Structural
•  Starch in plants (stored in
•  Cellulose~ most abundant
plastids)
organic compound, found in
•  Glycogen in animals (stored in
plants
liver & muscles)
•  Chitin~exoskeletons, cell
walls of fungi, & surgical thread
Polysaccharides
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Lipids
•
•
•
•
•
•
•
•
No polymers; glycerol and fatty acid
Fats, phospholipids, steroids
Hydrophobic; H bonds in water exclude fats
Carboxyl group = fatty acid
Non-polar C-H bonds in fatty acid ‘tails’
Ester linkage: 3 fatty acids to 1 glycerol
(dehydration formation)
Triacyglycerol (triglyceride)
Saturated vs. unsaturated fats; single vs. double
bonds
Lipids, II
Phospholipids
•  2 fatty acids instead of
3 (phosphate group)
•  ‘Tails’ hydrophobic;
‘heads’ hydrophilic
•  Micelle (phospholipid
droplet in water)
•  Bilayer (double layer);
cell membranes
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Steroids
•  Lipids with 4 fused carbon
rings
•  Ex: cholesterol
–  gives cell membranes
pliability
–  precursor for other steroids
(sex hormones)
–  produced naturally in the
body
–  excess in body contributes
to formation of
atherosclerosis
Putting it All Together: How Our Bodies
Use the Energy of Carbs & Fats
•  Importance
Proteins
–  instrumental in nearly everything organisms do
–  50% dry weight of cells
–  most structurally sophisticated molecules known
•  Monomer: amino acids (there are 20)
–
–
–
–
carboxyl (-COOH) group
amino group (NH2)
H atom
variable group (R)….
•  Variable group characteristics
–  polar (hydrophilic) or nonpolar (hydrophobic)
–  acid or base
•  Three-dimensional shape (conformation)
•  Polypeptides (dehydration reaction):
–  peptide bonds~ covalent bond
–  carboxyl group to amino group (polar)
•  Nearly limitless combinations
–  Ex: A protein 50 amino acids long = 2050 = 1.13 X 1065 different combinations!
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20 Different Amino Acids in Proteins
H 3N +
CH3
O
H 3N +
C
C
H
Glycine (Gly)
O–
C
O
C
H 3N +
C
O–
H
Alanine (Ala)
CH
CH3
CH3
CH2
CH2
O
H 3N +
C
H
Valine (Val)
CH3
CH3
CH3
CH3
H
O–
C
H 3C
O
C
H
Leucine (Leu)
C
H 3N +
O–
CH
O
C
H
Isoleucine (Ile)
O–
Nonpolar
CH3
CH2
S
CH2
C
H 2N
CH2
H 3N +
H 2C
NH
CH2
CH2
O
C
H 3N +
C
C
O–
H
CH2
O
C
H 3N +
H
O
C
H
O–
C
O–
H
Phenylalanine (Phe)
Methionine (Met)
C
O–
O
Proline (Pro)
Tryptophan (Trp)
Amino Acids continued…
OH
OH
Polar
CH2
H 3N +
C
CH
O
H 3N +
C
O–
H
Serine (Ser)
C
CH2
O
H 3N +
C
O–
H
NH2 O
C
CH2
O
C
H
O–
C
H 3N +
CH2
O
H 3N +
C
H
Electrically
charged
H 3N +
Asparagine
(Asn)
NH3+
O
C
CH2
C
CH2
CH2
CH2
CH2
C
O
CH2
C
O–
H 3N +
C
CH2
O
O
C
O–
Glutamine
(Gln)
O–
H 3N +
C
H
Glutamic acid
(Glu)
NH+
NH2+
CH2
CH2
C
H
Aspartic acid
(Asp)
C
H
NH2
C
H
CH2
H 3N +
O–
Basic
O–
O
CH2
O
C
H
Acidic
–O
C
O–
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
O–
Lysine (Lys)
H 3N +
CH2
O
C
CH2
H 3N +
C
H
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
An Overview of Protein Functions
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Protein Structure
Primary Structure
•  Conformation:
- Linear structure
•  Molecular Biology:
- each type of protein has a
unique primary
structure of
amino acids
•  Amino acid substitution:
- hemoglobin
- sickle-cell anemia
Secondary Structure
•  Conformation:
- coils & folds (hydrogen bonds)
•  Alpha Helix (α helix):
- coiling
- ex. Keratin (hair)
•  Beta Pleated Sheet (β pleated sheet):
- parallel regions cause byfolding
- ex. silk
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Secondary Protein Structure
Tertiary Structure
•  Conformation:
- irregular contortions created
by R group bonding
√hydrophobic
√disulfide bridges
√hydrogen bonds
√ionic bonds
Tertiary Protein Structure
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Quaternary Structure
•  Conformation:
-2 or more polypeptide chains
aggregated into 1 macromolecule
√collagen (connective tissue)
√hemoglobin
Quaternary Protein Structure
Nucleic Acids, I
•
•
•
•
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA → RNA → protein
Polymers of nucleotides
(polynucleotide):
nitrogenous base
pentose sugar
phosphate group
•  Nitrogenous bases:
pyrimidines~cytosine, thymine, uracil
purines~adenine, guanine
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Nucleic Acids, II
•  Pentoses:
√ribose (RNA)
√deoxyribose (DNA)
√nucleoside (base + sugar)
•  Polynucleotide:
√phosphodiester linkages
(covalent) between phosphate +
sugar of nucleic acid backbone
Nucleic Acids, III
•  Inheritance based on DNA
replication
•  Double helix
- Watson & Crick - 1953
- H bonds: between paired bases
- van der Waals: between stacked
bases
•  A to T; C to G pairing
•  Complementary
Macromolecule
Monomer
Polymer
Bond Type
Carbs
Monosaccharids
Disaccharides/
Polysaccharides
Glycosidic
Linkages
(ά and β)
Proteins
Amino Acids
Polypeptide
(protein)
Peptide
(H-bonds, ionic,
Disulfide
bridges)
Lipids
Fatty Acids
Chains
(sat v. unsat)
(Not a true
polymer)
Phospholipids
Triglycerides
Steriods
Ester linkages
Nucleic
Acids
Nucleotide
DNA or RNA
Phosphodiester
linkages
(also H-bonds,
Van der Walls)
Examples
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