Transcript Ch. 5 - Macromolecules

+
P
1
The ATP Cycle
http://www.youtube.com/watch?v=Ahuq
XwvFv2E&feature=related
2
The Structure and Hydrolysis of ATP
• ATP (adenosine triphosphate)
– Is the cell’s energy shuttle
– Provides energy for cellular functions
Adenine
N
O
O
-O
O-
O-
Phosphate groups
Figure 8.8
C
HC
O
O
O
O
C
NH2
N
CH2
O-
O
H
CH
N
H
H
H
OH
C
OH
N
Ribose
• Energy is released from ATP
– When the terminal phosphate bond is broken
P
P
P
Adenosine triphosphate (ATP)
H2 O
P
i
+
P
P
Inorganic phosphate
Figure 8.9
Adenosine diphosphate (ADP)
Energy
Chapter 5
The Structure and
Function of
Macromolecules
5
The Molecules of Life
• Overview:
– Another level in the hierarchy
of biological organization is
reached when small organic
molecules are joined together
– Atom ---> molecule ---
compound
6
Macromolecules
– Are large molecules composed of smaller
molecules
– Are complex in their structures
Figure 5.1
7
Macromolecules
•Most macromolecules are polymers,
built from monomers
• Four classes of life’s organic
molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
– Lipids
8
• A polymer
– Is a long molecule consisting of
many similar building blocks called
monomers
– Specific monomers make up each
macromolecule
– E.g. amino acids are the monomers
for proteins
9
The Synthesis and Breakdown of
Polymers
• Monomers form larger molecules by
condensation reactions called dehydration
synthesis HO 1
H
HO
H
3
2
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
1
2
3
H 2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
10
The Synthesis and Breakdown of
Polymers
• Polymers can disassemble by
– Hydrolysis (addition of water molecules)
HO
1
2
3
4
H
Hydrolysis adds a water
molecule, breaking a bond
HO
Figure 5.2B
1
2
3
H
H 2O
HO
H
(b) Hydrolysis of a polymer
11
• 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
12
Carbohydrates
• Serve as fuel and building
material
• Include both sugars and
their polymers (starch,
cellulose, etc.)
13
Sugars
• Monosaccharides
– Are the simplest sugars
– Can be used for fuel
– Can be converted into other
organic molecules
– Can be combined into polymers
14
• Examples of monosaccharides
Triose sugars
(C3H6O3)
H
O
Pentose sugars
(C5H10O5)
H
Aldoses
C
O
Hexose sugars
(C6H12O6)
H
C
H
O
C
C
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
HO
C
H
C
OH
H
H
C
OH
H
Glyceraldehyde
H
Ribose
H
C
OH
H
HO
C
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
H
Glucose
H
H
Ketoses
C
Figure 5.3
Galactose
H
C OH
H
H
C OH
C
O
H
C OH
C
O
O
C OH
H
C OH
HO
H
H
C OH
H
C OH
Dihydroxyacetone
H
C OH
H
C OH
H
H
C OH
H
O
Ribulose
C H
H
Fructose
15
• Monosaccharides
– May be linear
– Can form rings
H
H
HO
H
H
H
O
1C
2
6CH
C
OH
C
H
C
OH
3
4
5
C
6
C
OH
OH
2OH
5C
H
4C
OH 3
H
OH
C
H
6CH
O
H
2C
OH
H
1C
H
O
H
4C
OH
2OH
5C
H
OH
3C
H
CH2OH
O
H
H
1C
2C
OH
OH
6
H
5
4
HO
H
OH
3
H
O
H
1
2
OH
OH
H
Figure 5.4 (a) Linear and ring forms. Chemical equilibrium between the linear and ring
structures greatly favors the formation of rings. To form the glucose ring,
carbon 1 bonds to the oxygen attached to carbon 5.
16
• Disaccharides
– Consist of two
monosaccharides
– Are joined by a glycosidic
linkage
17
(a) Dehydration reaction
in the synthesis of
maltose. The bonding
of two glucose units
H
forms maltose. The
glycosidic link joins
the number 1 carbon
of one glucose to the HO
number 4 carbon of
the second glucose.
Joining the glucose
monomers in a
different way would
result in a different
disaccharide.
H
(b) Dehydration reaction
H
in the synthesis of
O
sucrose. Sucrose is
a disaccharide formed
from glucose and fructose.
Notice that fructose,
though a hexose like
glucose, forms a
five-sided ring.
CH2OH
CH2OH
O
H
OH H
H
H
H
OH
HO
H
OH
H 2O
H
O
H
Glucose
CH2OH
H
O
H
HO
H 2O
O
H
H
OHOH
H
HO
H
O
H
H
OH
O
H
CH2OH
H
1–4
1 glycosidic
linkage
HO
OH
H
Fructose
H
O
H
H
O
H
H
OH
OH
Maltose
H
H
4
O
CH2OH
O
H
OH
Glucose
Glucose
CH2O
H
O
H
O
H
H
H
OH
CH2OH
CH2OH
H
HO
H
O
H
O
H
OH
H
1–2
H
glycosidic
1
linkage
O
CH2OH
O
2
H HO
H
CH2OH
OH H
Sucrose
Figure 5.5
18
Polysaccharides
• Polysaccharides
– Are polymers of sugars
– Serve many roles in organisms
19
Storage Polysaccharides
Chloroplast
Starch
• Starch
– Is a polymer
consisting
entirely of
glucose
monomers
– Is the major
storage form of
glucose in plants
1 m
Amylose
Amylopectin
Figure 5.6 (a) Starch: a plant polysaccharide
20
• Glycogen
– Consists of glucose monomers
– Is the major storage form of glucose in
animals
Mitochondria Glycogen
granules
0.5 m
Glycogen
Figure 5.6(b) Glycogen: an animal polysaccharide
21
Structural Polysaccharides
• Cellulose
– Is a polymer of glucose
22
– Has different glycosidic linkages than
starch
H
CH2OH
H
4
HO
H
OH
H
O
H
O
C
H
OH
OH
 glucose
H
C
OH
H
HO
C
H
4
H
C
OH
H
C
OH
H
C
OH
CH2OH
H
OH
HO
H
O
OH
H
1
H
OH
 glucose
(a)  and  glucose ring structures
CH2OH
CH2OH
O
HO
O
1
OH
O
4
O
4
1
OH
OH
OH
O
O
1
OH
CH2OH
CH2OH
O
4
1
OH
O
OH
OH
(b) Starch: 1– 4 linkage of  glucose monomers
CH2OH
O
HO
OH
1
O
4
OH
O
OH
Figure 5.7 A–C
OH
CH2OH
CH2OH
O
O
OH
OH
O
OH
O
OH
(c) Cellulose: 1– 4 linkage of  glucose monomers
CH2OH
OH
23
– Is a major component of the tough walls
that enclose plant cells
Cell walls
Cellulose microfibrils
in a plant cell wall
Microfibril
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
0.5 m
Plant cells
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
Figure 5.8
OH CH2OH
OH
CH2OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH2OH
2
H
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH
2
2OH
H
CH2OH
OH
OH CH2OH
O O
O O
OH
OH
OH O
O OH
O O
O
O CH OH
OH CH2OH
2
H
 Glucose
monomer
Cellulose
molecules
A cellulose molecule
is an unbranched 
glucose polymer.
24
• Cellulose is difficult to digest
– Cows have microbes in their stomachs to
facilitate this process
Figure 5.9
25
• Chitin, another important structural
polysaccharide
– Is found in the exoskeleton of arthropods
– Can be used as surgical thread
CH2O
H
O OH
H
H
OH H
OH
H
H
NH
C
O
CH3
(a) The structure of the
chitin monomer.
Figure 5.10 A–C
(b) Chitin forms the exoskeleton
of arthropods. This cicada
is molting, shedding its old
exoskeleton and emerging
in adult form.
(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.
26
Lipids
• Lipids are a diverse group of
hydrophobic molecules
• Lipids
– Are the one class of large biological
molecules that do not consist of
polymers
– Share the common trait of being
hydrophobic
27
Fats
– Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty
acids
– Vary in the length and number and locations of
double bonds they contain
28
Fats
• Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty
acids
29
• Saturated fatty acids
– Have the maximum number of
hydrogen atoms possible
– Have no double bonds
Stearic acid
Figure 5.12
(a) Saturated fat and fatty acid
30
• Unsaturated fatty acids
– Have one or more double bonds
Oleic acid
Figure 5.12 (b) Unsaturated fat and fatty acid
cis double bond
causes bending
31
Fig. 4-7b
cis isomer: The two Xs are
on the same side.
(b) Geometric isomers
trans isomer: The two Xs are
on opposite sides.
• The FDA has determined that partially
hydrogenated oils (which contain trans fats)
are not "recognized as safe", which is
expected to lead to a ban on trans fats from
the American diet. Alternatives are saturated
fats such as lard, palm oil or completely
hydrogenated fats. Hydrogenated oil is not a
synonym for trans fat: complete
hydrogenation removes all unsaturated,
both cis and trans, fats.
33
• Phospholipids
– Have only two fatty acids
– Have a phosphate group instead of a
third fatty acid
34
• Phospholipid structure
– Consists of a hydrophilic “head” and
hydrophobic “tails”
CH2
CH2
O
O
P
O–
+
N(CH3)3
Choline
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Figure 5.13
(a) Structural formula
(b) Space-filling model
(c) Phospholipid
symbol
35
• The structure of phospholipids
– Results in a bilayer arrangement found in
cell membranes
WATER
Hydrophilic
heads
Hydrophobic
tails
WATER
Figure 5.14
36
Steroids
• Steroids
– Are lipids characterized by a carbon
skeleton consisting of four fused rings
37
• One steroid, cholesterol
– Is found in cell membranes
– Is a precursor for some hormones
H 3C
CH3
CH3
CH3
CH3
Figure 5.15
HO
38
Proteins
• Proteins have many structures,
resulting in a wide range of
functions
• Proteins do most of the work in
cells and act as enzymes
• Proteins are made of monomers
called amino acids
39
• An overview of protein functions
40
• Enzymes
– Are a type of protein that acts as a
catalyst, speeding up chemical reactions
1
Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H 2O
Fructose
H O
4 Products are released.
Figure 5.16
3 Substrate is converted
to products.
41
Polypeptides
• Polypeptides
– Are polymers (chains) of amino acids
• A protein
– Consists of one or more polypeptides
42
• Amino acids
– Are organic molecules possessing both
carboxyl and amino groups
– Differ in their properties due to
differing side chains, called R groups
43
Twenty Amino Acids
• 20 different amino acids make up
proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N
C
H
+
O–
C
CH2
O
H 3N
C
H
Valine (Val)
Alanine (Ala)
CH
CH3
CH3
O
CH3
CH3
C
+
O–
CH2
O
C
H
Leucine (Leu)
H3C
H3N
+
O–
CH
C
O
C
H
Isoleucine (Ile)
O–
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
H3N+
C
O–
Methionine (Met)
Figure 5.17
CH2
O
C
H
CH2
O
C
O–
Phenylalanine (Phe)
H3N+
C
H
O
C
H2C
CH2
H2
N
C
O
C
H
O–
Tryptophan (Trp)
Proline (Pro)
44
O–
OH
OH
Polar
H3N
+
CH2
C
O
C
H
CH
H3N
O–
Serine (Ser)
C
+
O
C
H3N
O–
H
+
CH2
C
H
O
C
CH2
H3N
O–
C
+
O
C
H
Electrically
charged
H3N
+
C
+
O–
O–
O
NH3+
NH2
C
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
H
O–
H3N
+
CH2
C
O
C
H
O–
H3N
+
CH2
C
H
Aspartic acid
(Asp)
O–
+
CH2
C
O
C
H
O–
Glutamine
(Gln)
Asparagine
(Asn)
C
C
C
H3N
Basic
O
C
CH2
O
H
Acidic
–O
CH2
H3N
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
Glutamic acid
(Glu)
O–
Lysine (Lys)
NH2+
H3N
+
CH2
O
C
NH+
H3N
+
CH2
C
H
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
45
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
46
Protein Conformation and
Function
• A protein’s specific conformation
(shape) determines how it functions
47
Four Levels of Protein Structure
• Primary structure
+H
– Is the unique
sequence of amino
acids in a polypeptide
3N
Amino
end
Amino
acid
subunits
Gly ProThrGly
Thr
Gly
Glu
Cys LysSeu
LeuPro
Met
Val
Lys
Val
Leu
Asp
AlaVal ArgGly
Ser
Pro
Ala
Glu Lle
Leu Ala
Gly
Asp
Thr
Lys
Ser
Lys TrpTyr
lle
Ser
Pro Phe
His Glu
AlaThrPhe Val
Asn
His
Ala
Glu
Val
Thr
Asp
Tyr
Arg
Ser
Arg
Gly Pro
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Tyr
Ser
Thr
Thr
Ala
Val
Val
Glu
Thr Pro Lys
Asn
Figure 5.20
c
o
o–
Carboxyl end
48
• Secondary structure
– Is the folding or coiling of the polypeptide
into a repeating configuration
– Includes the  helix and the  pleated
sheet
 pleated sheet
Amino acid
subunits
O H H
C C N
C N
H
R
R
C C N
O H H
C
C
R
N H
C
H
R
O C
O C
N H
N H
N H
O C
O C
H C R H C R
H C R H C
R
N H O C
N H
O C
O C
H
C
O
N H
N
C
C
H
R
R H
Figure 5.20
C
R
R
O H H
C C N
C C N
OH H
R
R
R
O
O H H
C C N
O
H
O H H
C C N
C C N
OH H
R
O
C
H
H
N HC N H C N H C N
C
H
H
C
O
C
O
R
R
C
R
O
C
H
H
NH C N
C
H
O C
R
R
C C
O
R
H
C
N HC N
H
O C
H
 helix
49
• Tertiary structure
– Is the overall three-dimensional shape of
a polypeptide
– Results from interactions between amino
acids and R groups
Hyrdogen
bond
CH22
CH
O
H
O
H 3C
CH
CH3
H 3C
CH3
CH
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+-O C CH2
Ionic bond
50
• Quaternary structure
– Is the overall protein structure that
results from the aggregation of two or
more polypeptide subunits
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
51
Review of Protein Structure
+H
3N
Amino end
Amino acid
subunits
helix
52
Sickle-Cell Disease: A Simple Change
in Primary Structure
• Sickle-cell disease
– Results from a single amino acid
substitution in the protein
hemoglobin
53
Primary
structure
Normal hemoglobin
Val
His Leu
Figure 5.21
Glul
Glu
. . . Primary
Val
His
Leu Thr


Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Pro
Val
Glu
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Red blood
cell shape
Pro
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Function
Thr
Sickle-cell hemoglobin
Quaternary
structure




10 m
Red blood
cell shape
Exposed
hydrophobic
region
 subunit
Function
10 m
...
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of
abnormal
hemoglobin
deform cell into
sickle shape.
54
What Determines Protein
Conformation?
• Protein conformation Depends
on the physical and chemical
conditions of the protein’s
environment
• Temperature, pH, etc. affect
protein structure
55
•Denaturation is when a protein
unravels and loses its native
conformation
(shape)
Denaturation
Normal protein
Figure 5.22
Denatured protein
Renaturation
56
The Protein-Folding Problem
• Most proteins
– Probably go through several
intermediate states on their way to a
stable conformation
– Denatured proteins no longer work in
their unfolded condition
– Proteins may be denatured by
extreme changes in pH or
temperature
57
• Chaperonins
– Are protein molecules that assist in the
proper folding of other proteins
Cap
Polypeptide
Correctly
folded
protein
Hollow
cylinder
Steps of Chaperonin
Chaperonin
(fully assembled) Action:
An unfolded poly1
peptide enters the
cylinder from one
Figure 5.23
end.
2
The cap attaches, causing
the cylinder to change shape
in such a way that it creates
a hydrophilic environment
for the folding of the
polypeptide.
3
The cap comes
off, and the
properly
folded protein is
released.
58
• X-ray crystallography
– Is used to determine a protein’s threedimensional structure
X-ray
Photographic
film
Diffracted Xrays
diffraction
pattern
X-ray
source
X-ray
beam
Nucleic acid Protein
Crystal
Figure 5.24
(a) X-ray diffraction pattern
(b) 3D computer model
59
Nucleic Acids
• Nucleic acids store and transmit
hereditary information
• Genes
– Are the units of inheritance
– determine the amino acid sequence
of polypeptides
– Are made of nucleotide sequences
on DNA
60
The Roles of Nucleic Acids
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
61
Deoxyribonucleic Acid
• DNA
– Stores information for the synthesis
of specific proteins
– Found in the nucleus of cells
62
DNA Functions
– Directs RNA synthesis (transcription)
– Directs protein synthesis through RNA
DNA
(translation)
1 Synthesis of
mRNA in the nucleus
NUCLEUS
2 Movement of
mRNA into cytoplasm
via nuclear pore
mRNA
CYTOPLASM
mRNA
Ribosome
3 Synthesis
of protein
Figure 5.25
Polypeptide
Amino
acids
63
64
The Structure of Nucleic
Acids
5’ end
• Nucleic acids
– Exist as polymers of
nucleotides
5’C
O
3’C
O
O
5’C
(a) Polynucleotide,
or nucleic acid
Figure 5.26
O
3’C
OH
3’ end
65
• Each nucleotide
– Consists of sugar + phosphate + nitrogen
base
Nucleoside
Nitrogenous
base
O

O
P
5’C
O
CH2
O
O
Phosphate
group
Figure 5.26
3’C
Pentose
sugar
(b) Nucleotide
66
Nucleotide Monomers
• Nucleotide monomers
Nitrogenous bases
Pyrimidines
NH2
O
O
C
C
CH
C
3
N
CH
C
CH HN
HN
CH
C
CH
C
C
CH
N
N
O
N
O
O
H
H
H
Cytosine Thymine (in DNA)Uracil
(in RNA)
RNA)
Uracil (in
U
C
U
T
– Are made up of
nucleosides (sugar +
base) and phosphate
groups
Purines
O
NH2
N C C
N C C
NH
N
HC
HC
C
CH
N C
N
NH2
N
N
H
H
Adenine
Guanine
A
G
5”
Pentose sugars
HOCH2 O
4’
OH
H H
1’
5”
HOCH2 O OH
4’
H H
1’
H
H
H 3’ 2’ H
3’ 2’
OH H
OH OH
Deoxyribose (in DNA) Ribose (in RNA)
Figure 5.26
(c) Nucleoside components
67
Nucleotide Polymers
• Nucleotide polymers
– Are made up of nucleotides linked by
the–OH group on the 3´ carbon of one
nucleotide and the phosphate on the 5´
carbon on the next
68
Gene
• The sequence of bases along a
nucleotide polymer
– Is unique for each gene
69
The DNA Double Helix
• Cellular DNA molecules
– Have two polynucleotides that spiral around
an imaginary axis
– Form a double helix
70
• The DNA double helix
– Consists of two antiparallel nucleotide
strands
5’ end
3’ end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
A
3’
end
Nucleotide
about to be
added to a
new strand
5’ end
3’ end
Figure 5.27
5’ end
New
strands
3’ end
71
A,T,C,G
• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary
fashion (A with T only, and C with G only)
72
DNA and Proteins as Tape
Measures of Evolution
• Molecular comparisons
– Help biologists sort out the
evolutionary connections among
species
73
The Theme of Emergent Properties
in the Chemistry of Life: A Review
• Higher levels of organization
– Result in the emergence of new
properties
• Organization
– Is the key to the chemistry of
life
74