MCB 3020, Spring 2005 1102004

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MCB 3020, Spring 20051-10-2004
Chapter 3 The Building Blocks of Life I
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Chapter 3
I. The chemistry of life II. Macromolecules of
the cell A. polysaccharides B. lipids C.
nucleic acids D. proteins
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The Chemistry of Life
All cells are made of organic molecules.
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I. The Chemistry of Life a review
A. the 6 major bioelements B. charge distribution
in molecules C. attractive forces D. important
functional groups
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A. The 6 Major Bioelements
C Carbon H Hydrogen O Oxygen
N Nitrogen P Phosphorus S Sulfur

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B. Charge distribution in molecules
1. electronegativity 2. hydrophilic (polar) 3.
hydrophobic (nonpolar) 4. amphipathic
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1. Electronegativity
A measure of the degree of attraction of valence
electrons
TB
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2. Polar (hydrophilic)
-

asymmetric charge distribution in a molecule
d
d-
H - O - CH2 CH3
TB
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Polar molecules
Polar molecules result from the bonding of atoms
with very different electronegativities
TB
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3. Nonpolar (hydrophobic)
little charge asymmetry
TB
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Nonpolar molecules
Nonpolar molecules result from the bonding
of atoms with similar electronegativities.
TB
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4. Amphipathic
partly polar, partly nonpolar
phospholipid molecule
negatively charged head
nonpolar hydrocarbon tail
TB
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C. Attractive forces
1. ionic bonds 2. covalent bonds 3. hydrogen
bonds 4. van der Waals forces 5. hydrophobic
interactions 6. comparison of bond strengths
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1. Ionic bonds
attraction between charged particles
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3. Hydrogen bonds (H-bonds)
noncovalent bonds formed between the following
TB
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Hydrogen bonding of water molecules
H-bonding of hydroxyl groups
H
O
R
O
R
H
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H-bonding of amino groups
Keto groups
O
R
H
O
R
H-bonds will form with various combinations of
hydroxyl, amino and keto groups that meet the
H-bonding criteria.
TB
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Hydrogen bonding between amino acids in a protein
H-C-R1 CO N-H
H-C-R2 CO N-H
H-C-R3
R4-C-H H N OC
R5-C-H H N OC
Rc- C-H
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Hydrogen bonding between bases in DNA
cytosine
guanine
Three H-bonds between G and C
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4. van der Waals forces
Attraction between molecules that are very close
together
van der Waals attractions result from
attractions between induced dipoles
TB
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5. Hydrophobic forces (interactions)
Attraction between hydrophobic molecules or
hydrophobic portions of molecules
driven by an increase in entropy
(disorder) due to water exclusion
TB
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Water is the biological solvent of life as we
know it.
cells are 70 to 90 water water is polar
many polar biological molecules dissolve in
water nonpolar (hydrophobic) molecules tend
to aggregate together in water
water can H-bond with polar molecules
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6. Comparison of bond strength
strength (kcal/mol)
type of bond
1. Covalent bonds 2. ionic bonds 3. hydrogen
bonds 4. van der waals forces 5. hydrophobic
forces
-50 to -100 -80 or -1 -3 to -6 -0.5 to -1 -0.5 to
-3
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D. Important functional groups
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Important functional groups (contd.)
pyruvate, citric acid cyle intermediates
keto
lipids of Bacteria and Eukarya
ester
DNA, RNA, ATP
phosphoester
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Important functional groups (contd.)
ether
lipids (archaea)
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What functional groups are present in the amino
acid serine?
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II. Macromolecules of the cell
A. polysaccharides B. lipids C. nucleic acids D.
proteins
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(No Transcript)
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Macromolecules are large molecules made
of repeating units (monomers).
s
s
s
s
DNA a nucleic acid a chain (polymer) of
nucleotides
a protein a polymer of amino acids
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Macromolecules make up 96 of the dry weight of
cells.
polysaccharides
proteins
lipids
nucleic acids
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The 4 major cellular macromolecules
chains (polymers) of repeating units
polymer
monomer
example
covalent bond
(see notes for other examples)
polysaccharide sugars cell wall glycosidic
lipid fatty acids or membranes ester
or ether isoprenoids
nucleic acid nucleotides DNA, RNA
phosphodiester protein amino
acids enzymes peptide
Important recurring theme
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B. Polysaccharides
polymers of sugars linked by glycosidic bonds
starch glycogen cellulose peptidoglycan
1. common sugar monomers 2. glycosidic bonds 3.
cellular polysaccharides
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1. common sugar monomers
a. glucose (ring form)
O
b. fructose (ring form)
HOH2C
CH2OH
HO
OH
HO
TB
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O
HOH2C
c. ribose
OH
HO
HO
O
HOH2C
d. deoxyribose
OH
HO
TB
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CH2OH
O
OH
e. glucosamine
OH
HO
NH2
CH2OH
O
OH
f. muramic acid
HO
NH2
-OOCCHCH3
TB
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2. Glycosidic bonds a. ?-1,4-glycosidic bond?
CH2OH
O
OH
H
H
OH
O

OH
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b. ?-1,4-glycosidic bond?
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3. cellular polysaccharides
a. starch
a-1,4 glycosidic bonds
large polymer of glucose
mostly a-1,4 glycosidic bonds
glucose storage molecule of plants
TB
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b. glycogen
a-1,6
a-1,6
a-1,6 glycosidic bonds produce branching
glucose storage molecule of animals and
some microorganisms
TB
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c. cellulose
large glucose polymer
major structural polysaccharide of plants
mostly b-1,4 glycosidic bonds
only microbes can break the b-1,4 bond
TB
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d. peptidoglycan
large polymer of N-acetyl glucosamine and
N-acetyl muramic acid
the main structural component of most
Bacterial cell walls ?-1,4-glycosidic bonds
Penicillin inhibits Bacterial cell wall
synthesis by inhibiting the formation of
peptidoglycan.
TB
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Study objectives
1. Memorize the 6 major bioelements. 2.
Understand the terms electronegativity,
hydrophilic, hydrophobic, polar, nonpolar,
amphipathic. Know how these properties are
important in chemical bonds and
interactions. 3. Very important recurring theme
Understand the attractive forces (ionic,
covalent, hydrogen bonds, van der Waals forces,
and hydrophobic interactions), the examples
presented in class, where they might occur.
Which are strong bonds? Which are weaker? 4.
Understand the role of water as the solvent of
life. 5. Know the functional groups. Be able to
recognize their structures. Know their
biological importance and where they occur in
cellular molecules. 6. Recurring theme Know
the four important cellular macromolecules
(polymers), the monomers that comprise them, the
bonds that connect the monomers, and the
specific example presented in class. These
macromolecules are the building blocks of
cells. 7. In what parts of cells are the four
macromolecules found?
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Study objectives
8. Describe the structure and functions of
the four cellular macromolecules, the
monomers, connecting bonds. Memorize the
specific examples of monomers, polymers,
and bonds presented in class. 9. Be able to
recognize the structures of glucose, ribose, and
deoxyribose. 10. Know the difference between
?-1,4 glycosidic bonds and ?-1,4-glycosidic
bonds and where they can be found. Know the
features of the cellular polysaccharides
presented. How does penicillin inhibit microbial
growth? 8.
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MCB 3020, Spring 20041-14-2004
Chapter 2 The Building Blocks of Life II
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Chapter 2 (contd.)
II. Macromolecules of the cell A.
polysaccharides B. lipids C. nucleic
acids D. proteins
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B. Lipids 1. fatty acids (glycerol) 2.
membrane lipids a. bacterial and eukaryal
b. archaeal
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B. Lipids
glycerol bonded to fatty acids (or
isoprenoid units) and other groups by ester
or ether linkages
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1. Fatty acids
a. common fatty acids
palmitic (C16)
COO-
stearic (C18)
COO-
TB
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b. saturated and unsaturated fatty acids
saturated no double bonds
COO-
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Unsaturated fatty acids can make the membrane
more fluid.
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2. Membrane lipids
glycerol phosphate bonded to fatty acids and
other groups by ester or ether bonds
Membrane lipids are amphipathic.
hydrophobic tail
polar head
"chemical definition"
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In aqueous solution lipids associate spontaneously
to form bilayers that are the basis of
biological membranes
The polar heads are in contact with water the
nonpolar tails group with one another.
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a. bacterial and eukaryal membrane lipids
fatty acids connected to glycerol phosphate
through ester bonds
phosphatidic acid phosphatidyl ethanolamine phosph
atidyl serine
TB
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phosphatidic acid
ester bond
o
-o-
o
-o-
o-
o
o
fatty acid
P
o-
TB
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phosphatidyl ethanolamine
fatty acid
o-
o
o
P
o-
CH2CH2NH3
ethanolamine
TB
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b. archaeal lipids isoprenoid units connected to
glycerol phosphate through ether bonds
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C. Nucleic acids (DNA, RNA)
polymer of nucleotides covalently linked by
phosphodiester bonds
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1. Nucleotides Base sugar
phosphate(s) (up to 3)
a.
thymine (T) (DNA only) cytosine (C) uracil (U)
(RNA only)
pyrimidines
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Detailed picture of a nucleotide (ATP)
NH2
5' phosphate end
N
N
O -O -P - O-
O O - P O -
O O - P O -
5'
N
O-CH2
N
O
adenosine triphosphate (ATP)
OH
OH
3' hydroxyl
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b. phosphodiester bonds
between the 3' carbon of one sugar and the 5'
carbon of the adjacent one
5'
5' phosphate
OCH2
O
base
5'
3'
O
H
3'
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c. Nitrogen bases
purines adenine guanine
pyrimidines cytosine thymine uracil
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Purines
guanine
adenine
O
N
NH
N
NH2
N
H
TB
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Pyrimidines
H
H
TB
in RNA
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2. DNA structure
a. double-stranded helix b. sugar-phosphate
backbone sugar deoxyribose c.
nucleotide bases pair through hydrogen bonds
between the helical strands d. the sequence
of the bases is the "primary structure"
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c. nucleotide base pairing
The most stable complementary DNA base pairing
pattern is called "Watson-Crick base pairing"
where AT and G?C
H
N
H
N
N
N
N
H
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c. nucleotide base pairing
cytosine
guanine
Three H-bonds between G and C
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d. DNA sequence (primary structure)
DNA carries genetic information in the sequence
of the bases.
AAA ? UUU
DNA ? mRNA ? protein
transcription
translation
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3. RNA structure
RNA is usually single stranded (ssRNA) ribose
instead of deoxyribose uracil instead of thymine
primary structure the base sequence
secondary structure complementary base
pairing in a single RNA molecule G ? C A
U
ssRNA
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RNA secondary structure
A-G-A-C-A-A-A-C-C-G-U-C-A
e.g. tRNA stem loops
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DNA
Functions of the major RNAs
1. messenger RNAs (mRNA) contain genetic
information to encode a protein
mRNA
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D. Proteins 1. general structure 2. the 21
amino acids 3. peptide bonds 4. levels of
protein structure 5. stereoisomers
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average 300 aa long
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1. General structure of L-amino acids
O C OH H2N C H R
carboxylic acid
amino group
O C O- H3N C H
R
?-carbon

R-group or side chain
at pH 7
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2. The 21 amino acids encoded by DNA
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Hydrophobic amino acids tend to be associated
with hydrophobic environments membranes
inside of proteins
Hydrophilic amino acids are often in contact with
water
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a. Acidic amino acids net negative charge
at pH 7
aspartate (asp) glutamate (glu)
TB
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b. Basic amino acids
net positive charge at pH 7
lysine (lys) arginine (arg) histidine
(his)
TB
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c. Polar but neutral
CH2
CH2
CH2
CH- CH3
SH
OH
OH
OH
Ser (S)
Thr (T)
Tyr (Y)
Cys (C)
TB
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c. Polar but neutral (contd.)
CH2
CH2
CH2
CH2
C
C
SeH
O
NH2
O
NH2
Asn (N)
Gln (Q)
Sec (U)
TB
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d. Nonpolar (hydrophobic)
Gly(G)
Ala (A)
Val (V)
Leu (L)
Ile (I)
TB
Note glycine is sometimes classified as polar.
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d. Nonpolar (hydrophobic)
O
C
OH
CH
HN
CH2
CH2
CH2
Pro (P)
Trp (W)
Phe (F)
Met (M)
TB
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Disulfide bridge
covalent bond between two sulfhydryl groups (eg.
of cysteines)


disulfide bridges
antibody
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selenocysteine the 21st amino acid

found in some microbial enzymes like
hydrogenase
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3. Peptide bonds join L-amino acids in
proteins
dehydration
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4. Levels of protein structure
a. Primary (1) structure amino acid sequence
met leu his val glu asn asp cys
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b. Secondary (2) structure
Patterns of folding due to hydrogen bonds between
groups of the peptide backbone
?-sheet
?-helix
right-handed coil
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1. alpha helix (coil)
O
C
N
CH
H
R
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2. beta sheet
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c. Tertiary (3) structure
Native 3-D structure of a protein
ribonuclease
Stabilized by H-bonds, hydrophobic interactions,
van der Waals forces,covalent disulfide bridges,
and some ionic bonds
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d. Quaternary (4) structure
association of two or more polypeptides
?-chains
hemoglobin
RasMol?
?-chains
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5. Stereoisomers
Mirror-image compounds with the same molecular
formula
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Why is this important?
In biology, D-sugars predominate L-amino
acids are found in proteins D-amino acids
are less common, but are found in
bacterial cell walls and antibiotics
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The 4 major cellular macromolecules
chains (polymers) of repeating units
polymer
monomer
example
covalent bond
(see notes for other examples)
polysaccharide sugars cell wall glycosidic
lipid fatty acids or membranes ester
or ether isoprenoids
nucleic acid nucleotides DNA, RNA
phosphodiester protein amino
acids enzymes peptide
Important recurring theme
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Study objectives
1. Contrast saturated and unsaturated fatty
acids. Understand how and why they
influence membrane fluidity. Know the general
structure of membrane lipids. Know the
names of the fatty acids and lipids presented in
class. You do NOT need to memorize the
structure of the individual fatty acids,
ethanolamine, or serine. 2. Compare and
contrast bacterial,eukaryal, and archaeal lipids,
especially the molecular components and the
bonds. More details later. 3. What are nucleic
acids? Understand that nucleotides are composed
of a nitrogenous base (purine or
pyrimidine), a sugar (ribose or deoxyribose),
and one to three phosphates. Know the
structure of the phosphodiester bond.
What parts of the nucleotides are connected by
the phosphate of the phosphodiester bond?
What is meant by the 5' and 3' ends of DNA and
RNA? 4. Memorize the structure of the
nucleotide ATP. This is a very important
molecule and we will discuss it in great detail
throughout the semester. 5. Know the purines
and pyrimidines. Know the number of rings in
each. What is the structural difference
between thymine (T) and uracil (U)?