Download 5 The structure and function of large biological molecules

Chapter 5
The structure and function of
large biological molecus
AP minknow
•The role of dehydration synthesis in the formation of organic compounds and
hydrolysis in the digestion of organic compounds.
•How to recognize the four biologically important organic compounds
(carbohydrates, lipids, proteins, and nucleic acids) by their structural formulas.
•The cellular functions of all four organic compounds.
•The four structural levels that protein can go through to reach their final shape
(conformation) and the denaturing impact that heat and pH can have on protein
structure.
Quick on Carbon
Chapter 4: Carbon and the molecular
diversity of life.
• 4.2 – Carbon atoms can form diverse molecules
by bonding to four other atoms
– Carbon has amazing ability to form molecules
because:
•
•
•
•
•
It has 4 valence electrons
It can form up to 4 covalent bonds
These can be single, double, or triple cov. Bonds
It can form large molecules.
These molecules and be chains, ring-shaped, or branched
– Isomers – are molecules that have the same
molecular formula, but different in their arrangement
of these atoms.
• This can result in different molecules with very different
activities.
Isomers
Quick on Carbon
4.3 Characteristic chemical groups help
control how biological molecules function
FUNCTIONAL
GROUP
HYDROXYL
CARBONYL
CARBOXYL
O
OH
(may be written HO
C
C
OH
)
STRUCTURE In a hydroxyl group (—OH),
a hydrogen atom is bonded
to an oxygen atom, which in
turn is bonded to the carbon
skeleton of the organic
molecule. (Do not confuse
this functional group with the
hydroxide ion, OH–.)
Figure 4.10
O
The carbonyl group
( CO) consists of a
carbon atom joined to
an oxygen atom by a
double bond.

When an oxygen atom is doublebonded to a carbon atom that is
also bonded to a hydroxyl group,
the entire assembly of atoms is
called a carboxyl group (—
COOH).
Some important functional groups
of organic compounds
NAME OF
COMPOUNDS
Alcohols (their specific
names usually end in -ol)
EXAMPLE
H
H
H
C
C
H
H
Ketones if the carbonyl group is Carboxylic acids, or organic
within a carbon skeleton
acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
H
OH
H
C
H
C
H
H
Ethanol, the alcohol
present in alcoholic
beverages
H
O
C
H
C
OH
H
H
Acetone, the simplest ketone
H
Figure 4.10
C
O
H
H
C
C
H
H
O
C
Propanal, an aldehyde
H
Acetic acid, which gives vinegar
its sour tatste
Quick on Carbon
4.3 Characteristic chemical groups help
control how biological molecules function
AMINO
SULFHYDRYL
H
N
H
Figure 4.10
O
SH
(may be written HS
The amino group (—NH2)
consists of a nitrogen atom
bonded to two hydrogen
atoms and to the carbon
skeleton.
PHOSPHATE
)
O P OH
OH
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
In a phosphate group, a
phosphorus atom is bonded to four
oxygen atoms; one oxygen is
bonded to the carbon skeleton; two
oxygens carry negative charges;
abbreviated P . The phosphate
group (—OPO32–) is an ionized
form of a phosphoric acid group (—
OPO3H2; note the two hydrogens).
Some important functional groups
of organic compounds
H
O
C
HO
C
H
H
N
H
H
Glycine
Figure 4.10
H
H
C
C
H
H
OH OH H
SH
H
C
C
C
H
H
H
O
O
P
O
O
Ethanethiol
Because it also has a carboxyl
group, glycine is both an amine
and a carboxylic acid;
compounds with both groups
are called amino acids.
Glycerol phosphate
5.1 Macromolecules are polymers
built from monomers.
• Monomer – smaller
repeating units of a polymer
• Polymer – large molecule
consisting of many similar or
identical building blocks
• Polymers with
molecular weights
>1000
• Polymerization – process of
joining monomers to form
polymers
The synthesis and breakdown of
polymers
• Dehydration
synthesis
(dehydration
reaction) –
synthesis reaction
forming a
byproduct of water
• Hydrolysis –
degradation of
a molecule
using water to
break down
bonds
– These processes
are often aided by
enzymes
Dehydration Synthesis
The Diversity of Polymers
• Each cell has thousands of
different kinds of
macromolecules.
– The inherent different between
human siblings reflect the
variations in polymers:
• Especially DNA and proteins
• There are four major classes
of biological macromolecules
–
–
–
–
Carbohydrates
Lipids
Proteins
Nucleic Acids
5.2 Carbohydrates serve as fuel
and building material
• Carbohydrates: molecules in
which carbon is flanked by hydrogen
and hydroxyl groups.
H—C—OH
• Main Functions
– Energy source
– Carbon skeletons for many other
molecules
Carbohydrates
• Monosaccharides:
simple sugars
• Disaccharides: two
simple sugars linked
by covalent bonds
• Oligosaccharides:
three to 20
monosaccharides
• Polysaccharides:
hundreds or
thousands of
monosaccharides—
starch, glycogen,
cellulose
Carbohydrates
Cells use
glucose
(monosacchar
ide) as an
energy
source.
Exists as a
straight chain
or ring form.
Ring is more
common—it is
more stable.
Carbohydrates
Carbohydrates
• Monosaccharides
have different
numbers of
carbons.
– Trioses: three
carbons– structural
isomers glyceraldehyde
– Hexoses: six
carbons—structural
isomers
– Pentoses: five
carbons
Carbohydrates
• Monosaccharides bind together in
condensation reactions to form glycosidic
linkages.
• Glycosidic linkages can be
α or β.
Beta – glycosidic linkage
Alpha – glycosidic linkage
Carbohydrates
• Oligosaccharides
may include other
functional groups.
• Often covalently
bonded to proteins
and lipids on cell
surfaces and act
as recognition
signals.
• ABO blood groups
Carbohydrates
• Starch: storage of
glucose in plants
– 1-4 glycosydic linkages
between alpha glucose
• Cellulose: very stable,
good for structural
components (cell walls
of plants
– 1-4 glycosydic linkages
between beta glucose
• Glycogen: storage of
glucose in animals
– 1-4 glycosydic linkages
between alpha glucose
• with branching
Chitin
• Chitin, another important structural
polysaccharide
– Is found in the exoskeleton of arthropods
CH O
– Can
be used as surgical thread
H
2
O OH
H
OH H
OH
H
H
H
NH
C
O
CH3
(a) The structure of the (b) Chitin forms the exoskeleton
of arthropods. This cicada
chitin monomer.
is molting, shedding its old
exoskeleton and emerging
Figure 5.10 A–C
in adult form.
(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.
5.3 Lipids are a diverse group of
hydrophobic molecules
Lipids are nonpolar
hydrocarbons:
•
•
•
•
Fats and oils—energy storage
Phospholipids—cell membranes
Steroids
Carotenoids
Fats serve as insulation in animals,
lipid nerve coatings act as
electrical insulation, oils and
waxes repel water, prevent
drying.
Lipids
Fats and oils are
triglycerides—
simple lipids—
made of three fatty
acids and 1
glycerol.
Glycerol: 3 —OH
groups—an alcohol
Fatty acid: nonpolar
hydrocarbon with a
polar carboxyl
group—carboxyl
bonds with
hydroxyls of
glycerol in an ester
linkage.
Lipids
• Saturated fatty acids:
no double bonds
between carbons—it is
saturated with hydrogen
atoms.
• Unsaturated fatty acids:
some double bonds in
carbon chain.
– monounsaturated: one
double bond
– polyunsaturated: more
than one
Lipids
Animal fats tend to be saturated—packed together tightly—solid at
room temperature.
Plant oils tend to be unsaturated—the “kinks” prevent packing—
liquid at room temperature.
Lipids
Phospholipids:
fatty acids bound
to glycerol, a
phosphate group
replaces one fatty
acid.
Phosphate group is
hydrophilic—the
“head”
“Tails” are fatty acid
chains—
hydrophobic
Lipid (phospholipid bilayer)
Lipid (Steroids)
• Steroids
– Are lipids
characterized by a
carbon skeleton
consisting of four
fused rings
– Many hormones,
including vertebrate
sex hormones, are
steroids produced
from cholesterol
– Steroids play a role
in regulating cell
activities
Lipids (carotenoids)
Carotenoids: light-absorbing pigments
5.4 Proteins have many structures,
resulting in a wide range of functions
Functions of proteins:
• Structural support
• Protection
• Transport
• Catalysis
• Defense
• Regulation
• Movement
Proteins
• Proteins are made
from 20 different
amino acids
(monomeric units)
• Polypeptide chain:
single, unbranched
chain of amino acids
– The chains are folded
into specific three
dimensional shapes.
– Proteins can consist of
more than one type of
polypeptide chain.
Protein (polypeptide)
The composition of a
protein: relative
amounts of each
amino acid present
The sequence of
amino acids in the
chain determines
the protein structure
and function.
Proteins
• Amino acids have
carboxyl and amino
groups—they
function as both
acid and base.
Functional Group
– The α carbon atom
is asymmetrical.
– Amino acids exist in
two isomeric forms:
• D-amino acids
(dextro, “right”)
• L-amino acids
(levo, “left”)—
this form is
found in
organisms
Proteins (amino acids are grouped
by characteristics)
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
O–
H
Glycine (Gly)
C
H
H3N+
C
O–
CH
CH3
CH3
O
C
H
H3N+
C
CH2
CH2
O
C
O–
Valine (Val)
Alanine (Ala)
CH3
CH3
H
O
H3C
H3N+
C
C
O
C
O–
O–
Leucine (Leu)
CH
H
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
H3N+
C
O–
Methionine (Met)
Figure 5.17
CH2
O
C
H
CH2
O
H3 N+
C
C
O–
Phenylalanine (Phe)
H
O
H2C
CH2
H2N
C
O
C
O–
H
C
O–
Tryptophan (Trp)
Proline (Pro)
Proteins (amino acids are grouped
by characteristics)
OH
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
C
CH2
O
H3N+
C
O–
H
C
CH2
O
C
H
Serine (Ser) Threonine (Thr)
O–
H3N+
C
O
H3N+
C
O–
H
Electrically
charged
C
CH2
H3N+
C
O
H
H3N+
NH3+
O
CH2
C
H3N+
–
O
C
C
H
O
C
O–
H
C
CH2
CH2
CH2
CH2
CH2
C
O
CH2
C
O–
H3N+
C
H
Glutamic acid
(Glu)
NH+
NH2
CH2
H
Aspartic acid
(Asp)
O
C
CH2
C
O–
CH2
Basic
O–
O
CH2
Asparagine Glutamine
(Gln)
(Asn)
Tyrosine
(Tyr)
Cysteine
(Cys)
Acidic
–O
C
NH2 O
C
SH
CH3
OH
NH2 O
C
Lysine (Lys)
H3N+
CH2
O
O–
NH2+
CH2
H3N+
C
H
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg) Histidine (His)
Proteins
• Amino acids
bond together
covalently by
peptide
bonds to form
the
polypeptide
chain.
– Dehydration
synthesis
Proteins
A polypeptide chain is
like a sentence:
• The “capital letter” is
the amino group of
the first amino acid—
the N terminus.
• The “period” is the
carboxyl group of the
last amino acid—the
C terminus.
Proteins
The primary structure of a
protein is the sequence of
amino acids.
The sequence determines
secondary and tertiary
structure—how the
protein is folded.
The number of different
proteins that can be
made from 20 amino
acids is enormous!
• Protein structure
–Primary
–Secondary
–Tertiary
–Quartinary
Proteins (primary structure)
Proteins (secondary structure)
Secondary structure:
• α helix—right-handed coil resulting from hydrogen
bonding; common in fibrous structural proteins
• β pleated sheet—two or more polypeptide chains are
aligned
Proteins (tertiary structure)
Tertiary structure: Bending and folding results in a
macromolecule with specific three-dimensional shape.
The outer surfaces present functional groups that can
interact with other molecules.
Proteins (tertiary structure)
Tertiary structure
is determined
by interactions
of R-groups:
• Disulfide bonds
• Aggregation of
hydrophobic
side chains
• van der Waals
forces
• Ionic bonds
• Hydrogen
bonds
•
Proteins (Quartinary
structure)
Quaternary
structure
results from
the
interaction of
subunits by:
–
hydrophobic
interactions
– van der
Waals
forces
– ionic bonds
– hydrogen
bonds.
Proteins (Sickle-cell Disease)
– Results from a single
amino acid
substitution in the
protein hemoglobin
Hemoglobin structure and
sickle-cell disease
Primary
structure
Normal hemoglobin
Val
His Leu Thr
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Figure 5.21
Val
His
Leu Thr
structure 1 2 3 4
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Sickle-cell hemoglobin
Pro
GlulGlu . . . Primary


Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Quaternary
structure
...
Val
5 6 7
Pro
 subunit




Function
10 m
10 m
Red blood
cell shape
Exposed
hydrophobic
region
Glu
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.
EnzymeSubstrate
Complex
Proteins (Denaturing)
• Conditions that affect
secondary and tertiary
structure:
• High temperature
• pH changes
• High concentrations of
polar molecules
• Denaturation: loss of 3dimensional structure
and thus function of the
protein
Proteins (folding)
• Proteins can sometimes fold incorrectly and bind to the wrong ligands.
• Chaperonins are proteins that help prevent this.
Polypeptide
Cap
Correctly
folded
protein
Hollow
cylinder
Chaperonin
(fully assembled)
Figure 5.23
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from one end.
2 The cap attaches, causing
3 The cap comes
the cylinder to change shape in off, and the properly
such a way that it creates a
folded protein is
hydrophilic environment for the released.
folding of the polypeptide.
5.5 Nucleic acids store and
transmit hereditary information
Nucleic acids: DNA—
(deoxyribonucleic
acid) and RNA—
(ribonucleic acid)
Polymers
(polynucleotides) —
made of the
monomeric units are
nucleotides.
Nucleotides consist of a
pentose sugar, a
phosphate group, and
a nitrogen-containing
base.
5.5 Nucleic acids store and transmit
hereditary information
DNA—deoxyribose
RNA—ribose
5.5 Nucleic acids store and transmit
hereditary information
The “backbone” of DNA
and RNA consists of the
sugars and phosphate
groups, bonded by
phosphodiester
linkages.
The phosphate groups link
carbon 3′ in one sugar to
carbon 5′ in another
sugar.
Antiparallel The two
strands of DNA run in
opposite directions.
5.5 Nucleic acids store and transmit
hereditary information
DNA bases: adenine
(A), cytosine (C),
guanine (G), and
thymine (T)
Complementary
base pairing:
A—T
C—G
Purines pair with
pyrimidines by
hydrogen bonding.
•
A particular small polypeptide is nine amino acids long.
Using three different enzymes to hydrolyze the
polypeptide at various sites, we obtain the following five
fragments (N denotes the amino end of the chain):
Ala-Leu-Asp-Tyr-Val-Leu
Tyr-Val-Leu
N-Gly-Pro-Leu
Asp-Tyr-Val-Leu
N-Gly-Pro-Leu-Ala-Leu
Determine the primary structure of this polypeptide.
–
–
–
–
N-Gly-Pro-Leu-Ala-Leu-Asp-Tyr-Val-Leu
Asp-Tyr-Val-Leu-Gly-Pro-Leu-Ala-Leu
N-Gly-Pro-Leu-Ala-Leu-Ala-Leu-Asp-Tyr-Val-Leu
N-Gly-Pro-Leu-Asp-Tyr-Val-Leu-Tyr-Val-Leu
• (a) You are studying a cellular enzyme involved in
breaking down fatty acids for energy. Looking at
the
R groups of the amino acids in the following
figures, what amino acids would you predict to
occur in the parts of the enzyme that interact with
the fatty acids? *
–
–
–
–
–
non-polar
polar
electrically charged
polar and electrically charged
all of these
The 20 Amino Acids of Proteins
The 20 Amino Acids of Proteins
(cont.)
• (b) You are studying a cellular enzyme
involved in breaking down fatty acids for
energy. Where would you predict to find the
amino acids in the parts of the enzyme that
interact with the fatty acids?
– On the exterior surface of the enzyme
– Sequestered in a pocket in the interior of the
enzyme
– Randomly dispersed throughout the enzyme
• The R group or side chain of the amino acid
serine is –CH2 –OH. The R group or side chain of
the amino acid alanine is –CH3. Where would you
expect to find these amino acids in globular
protein in aqueous solution?
– Serine would be in the interior, and alanine would be
on the exterior of the globular protein.
– Alanine would be in the interior, and serine would be
on the exterior of the globular protein.
– Both serine and alanine would be in the interior of the
globular protein.
– Both serine and alanine would be on the exterior of
the globular protein.
– Both serine and alanine would be in the interior and
on the exterior of the globular protein.
• (a) The sequence of amino acids of the
enzyme lysozyme is known. Following is a
list of amino acids and the number of each
in the lysozyme molecule. Based on this
list and the structures of the amino acids
how many S-S bonds are possible in
lysozyme?
–
–
–
–
–
0
2
4
6
8
Amino Acids in the Lysozyme
Type
Number
in
Type
Number in
Molecule
Lysozyme
Lysozyme
Alanine
Arginine
Asparagine
Aspartic acid
12
11
13
8
8
2
Leucine
Lysine
Methionine
Phenylalanin
e
Proline
Serine
Cysteine
Glutamic
acid
Glutamine
Glycine
Histidine
8
6
2
3
2
10
3
12
1
Threonine
Tryptophan
Tyrosine
7
6
3
The 20 Amino Acids of Proteins
The 20 Amino Acids of Proteins
(cont.)
• (b) The sequence of amino acids of the
enzyme lysozyme is known. Following is a
list of amino acids and the number of each
in the lysozyme molecule. Based on this
list and the structures of the amino acids is
the net charge on lysozyme positive or
negative?
– positive
– negative
Amino Acids in the Lysozyme
Type
Number
in
Type
Number in
Molecule
Lysozyme
Lysozyme
Alanine
Arginine
Asparagine
Aspartic acid
12
11
13
8
8
2
Leucine
Lysine
Methionine
Phenylalanin
e
Proline
Serine
Cysteine
Glutamic
acid
Glutamine
Glycine
Histidine
8
6
2
3
2
10
3
12
1
Threonine
Tryptophan
Tyrosine
7
6
3
The 20 Amino Acids of Proteins
The 20 Amino Acids of Proteins
(cont.)
• Polymers of glucose units are used as
temporary food storage in both plant and
animal cells. Glucose units are connected to
one another by 1, 4-linkages to make a
linear polymer and by 1, 6-linkages to make
branch points.
• (cont.) Polysaccharides of glucose units
vary in size. The three most commonly
Type of
Cell Type
Polymer
Average
encountered
are:
Starch
Size
Amylopectin Plant
Number of
1,4-Bonds
Between
Branches
100,000,000 24 to 30
Amylos
Glycogen
500,000
3,000,000
Plant
Animal
Linear
8 to 12
• (cont.) When each polymer bond is made, a
water molecule is released and becomes part
of the cell water. How many water molecules
were released during formation of each of the
Glycogen?
–
–
–
–
–
1,000,000
2,000,000
2,666,666
3,000,000
3,300,000