"Chemical Bonds and Biological Molecules Reference Sheet"

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106
PANEL 2–1: Chemical Bonds and Groups Commonly Encountered in Biological Molecules
CARBON SKELETONS
Carbon has a unique role in the cell because of its
ability to form strong covalent bonds with other
carbon atoms. Thus carbon atoms can join to form
or branched trees
or rings
chains.
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
also written as
also written as
also written as
HYDROCARBONS
COVALENT BONDS
A covalent bond forms when two atoms come very close
together and share one or more of their electrons. In a single
Carbon and hydrogen combine
bond one electron from each of the two atoms is shared; in
together to make stable
a double bond a total of four electrons are shared.
compounds (or chemical groups)
Each atom forms a fixed number of covalent bonds in a
called hydrocarbons. These are
defined spatial arrangement. For example, carbon forms four
nonpolar, do not form
single bonds arranged tetrahedrally, whereas nitrogen forms
hydrogen bonds, and are
three single bonds and oxygen forms two single bonds arranged
generally insoluble in water.
as shown below.
Atoms joined by two
or more covalent bonds
C
N
O
cannot rotate freely
H
H
around the bond axis.
H
C
H
H
C
This restriction is a
Double bonds exist and have a different spatial arrangement.
major influence on the
H
H
three-dimensional shape
of many macromolecules.
methane
methyl
group
C
N
O
H
C
2
CH
2
ALTERNATING DOUBLE BONDS
H
C
2
The carbon chain can include double
Alternating double bonds in a ring
CH
2
bonds. If these are on alternate carbon
can generate a very stable structure.
H
C
atoms, the bonding electrons move
2
within the molecule, stabilizing the
CH
2
structure by a phenomenon called
H
C
resonance.
H
H
2
CH
2
H
H
H
H
H
C
C
C
C
C
C
2
´
CH
C
C
C
C
C
2
H
H
H
H
H
C
2
the truth is somewhere between
CH
2
H
H
these two structures
benzene
H
C
3
C
C
C
C
C
often written as
part of the hydrocarbon “tail”
C
C
C
C
C
of a fatty acid molecule
106
PANEL 2–1: Chemical Bonds and Groups Commonly Encountered in Biological Molecules
CARBON SKELETONS
Carbon has a unique role in the cell because of its
ability to form strong covalent bonds with other
carbon atoms. Thus carbon atoms can join to form
or branched trees
or rings
chains.
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
also written as
also written as
also written as
HYDROCARBONS
COVALENT BONDS
A covalent bond forms when two atoms come very close
together and share one or more of their electrons. In a single
Carbon and hydrogen combine
bond one electron from each of the two atoms is shared; in
together to make stable
a double bond a total of four electrons are shared.
compounds (or chemical groups)
Each atom forms a fixed number of covalent bonds in a
called hydrocarbons. These are
defined spatial arrangement. For example, carbon forms four
nonpolar, do not form
single bonds arranged tetrahedrally, whereas nitrogen forms
hydrogen bonds, and are
three single bonds and oxygen forms two single bonds arranged
generally insoluble in water.
as shown below.
Atoms joined by two
or more covalent bonds
C
N
O
cannot rotate freely
H
H
around the bond axis.
H
C
H
H
C
This restriction is a
Double bonds exist and have a different spatial arrangement.
major influence on the
H
H
three-dimensional shape
of many macromolecules.
methane
methyl
group
C
N
O
H
C
2
CH
2
ALTERNATING DOUBLE BONDS
H
C
2
The carbon chain can include double
Alternating double bonds in a ring
CH
2
bonds. If these are on alternate carbon
can generate a very stable structure.
H
C
atoms, the bonding electrons move
2
within the molecule, stabilizing the
CH
2
structure by a phenomenon called
H
C
resonance.
H
H
2
CH
2
H
H
H
H
H
C
C
C
C
C
C
2
´
CH
C
C
C
C
C
2
H
H
H
H
H
C
2
the truth is somewhere between
CH
2
H
H
these two structures
benzene
H
C
3
C
C
C
C
C
often written as
part of the hydrocarbon “tail”
C
C
C
C
C
of a fatty acid molecule
CHAPTER 2 PANELS
107
C – O CHEMICAL GROUPS
C – N CHEMICAL GROUPS
Many biological compounds contain a carbon
Amines and amides are two important examples of
bonded to an oxygen. For example,
compounds containing a carbon linked to a nitrogen.
H
+
alcohol
Amines
in water combine with an H
ion to become
The –OH is called a
positively charged.
C
OH
hydroxyl
group.
H
H
H
+
+
C
C
N
H
N
H
aldehyde
O
H
H
C
Amides
are formed by combining an acid and an
H
The C—O is called a
amine. Unlike amines, amides are uncharged in water.
carbonyl
group.
ketone
An example is the peptide bond that joins amino acids
C
in a protein.
C
O
O
O
C
C
H
N
C
C
H
O
2
2
C
OH
N
O
carboxylic acid
The –COOH is called a
acid
amine
amide
carboxyl
group. In water
H
C
+
this loses an H
ion to
_
OH
Nitrogen also occurs in several ring compounds, including
become –COO
.
important constituents of nucleic acids: purines and pyrimidines.
esters
Esters are formed by a condensation reaction
NH
2
between acid and an alcohol.
H
O
O
N
C
cytosine (a pyrimidine)
C
C
C
HO
C
C
H
O
2
C
C
OH
O
C
H
N
O
acid
alcohol
ester
H
SULFHYDRYL GROUP
The
C
SH
is called a sulfhydryl group. In the amino acid cysteine the sulfhydryl group
may exist in the reduced form,
C
SH
or more rarely in an oxidized, cross-bridging form,
C
S
S
C
PHOSPHATES
Inorganic phosphate is a stable ion formed from
Phosphate esters can form between a phosphate and a free hydroxyl group.
phosphoric acid, H
PO
. It is often written as P
.
Phosphate groups are often attached to proteins in this way.
3
4
i
O
O
O
also
written as
_
_
_
HO
P
O
C
OH
HO
P
O
C
O
P
O
H
O
2
C
O
P
_
_
_
O
O
O
The combination of a phosphate and a carboxyl group, or two or more phosphate groups, gives an acid anhydride.
H
O
2
O
O
O
also written as
_
high-energy acyl phosphate
C
HO
P
O
C
O
O
bond (carboxylic–phosphoric
_
_
OH
C
O
P
O
O
acid anhydride) found in
H
O
2
O
some metabolites
P
_
O
H
O
2
O
O
O
O
phosphoanhydride—a high-
also written as
_
_
energy bond found in
O
P
OH
HO
P
O
O
P
O
P
O
O
P
P
molecules such as ATP
_
_
_
_
O
O
O
O
H
O
2
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