Important
words and concepts from Chapter 4, Campbell & Reece, 2002 (1/14/2005):
by Stephen T. Abedon (abedon.1@osu.edu)
for Biology 113 at the Ohio State University
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Course-external links are
in brackets Click [index] to access site index Click here to access
text’s website Vocabulary
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(1) Chapter title: Carbon and the Molecular
Diversity of Life
(a)
Found at this site are additional pages of possibly related interest
including: [organic chemistry primer]
(b)
External links include:
(i)
[carbon and the molecular
diversity of life (Google Search)]
(ii)
[carbon-based compounds, functional
groups, carbohydrates (Biology at Clermont College)
(a)
First we reviewed chemistry, then we considered the chemical and
physical properties of water, now we’ll consider the chemistry of
the complex stuff that floats around in the water found within living things.
(b)
“Biological diversity reflects molecular diversity; and carbon,
of all chemical elements, is unparalleled in its ability to form molecules that
are large, complex, and diverse.”
(c)
The distinction between organic compounds and inorganic compounds was
originally made on the basis of their origin, i.e., the former came from living
things while that latter need not.
(d)
Today we know that the distinction between made by living things and
not necessarily made by living things is somewhat arbitrary, simply reflecting
the complexity of the chemistry of living things versus the simplicity of the
chemistry of non-living things
(e)
Humans have modified this distinction somewhat by creating a gray area
in which living things (humans) direct non-living things (laboratory apparatus)
to produce somewhat complex, carbon-based molecules
(f)
Thus, we now understand that there is nothing inherently magical about
the ability of life to produce complex chemicals
(g)
Instead, we recognize that the chemistry (and physics) of life works
under the same constraints as the chemistry and physics of nonliving things
(that is, we recognize that there exists a mechanistic basis of life)
QUICK INTRODUCTION TO CARBON
CHEMISTRY
(a)
“The foundation of organic chemistry is not some intangible life force,
but the unique chemical versatility of the element carbon.”
(b)
“The carbon atom completes its valence by sharing electrons with other
atoms in four covalent bonds. Each carbon thus acts as an intersection
point from which a molecule can branch off in up to four directions. This tetravalence is one facet of carbon’s
versatility that makes large, complex molecules possible.”
(c)
Upon completing its outer shell, carbon’s four paired electrons attempt
to maximally separate
(d)
See Figure 2.17c, Molecular
shapes due to hybrid orbitals (Methane)
(e)
In three dimensions, this places carbon’s single covalent bonds at angles “toward the corners of an imaginary
tetrahedron.”
(f)
See Figure 4.2, The shapes
of three simple organic molecules
(g)
Note that writing structural formulas as though molecules are flat — See Figure 4.4, Variations in carbon
skeletons — fails to take into account this tetrahedral shape, so
consequently often fails to capture the complexity of organic molecules
(h)
Example structures (no need to know the immediately following names or structures unless
required to elsewhere):
(i)
Methane (CH4)
(ii)
Ethane (3HC-CH3; note that this is hardly a
standard-written molecular formula)
(iii)
Ethene (2HC=CH2; ditto)
(iv)
Carbon dioxide (O=C=O)
(v)
Urea (O=C(NH2)2)
(i)
[organic chemistry (Google Search)] [organic chemistry primer
(MicroDude)] [orientation of bonds about carbon (MicroDude)]
[index]
(a)
A hydrocarbon is a molecule that consists of only hydrogen and carbon atoms
(b)
See Figure 4.4, Variations
in carbon skeletons
(c)
See Figure 4.5, The role of
hydrocarbons in the characteristics of fats
(d)
[hydrocarbon (Google Search)] [hydrocarbon (MicroDude)]
[index]
ISOMERIC VARIATION IN THE
CARBON SKELETON
(a)
Isomers are compounds that share molecular formulas but differ in some
way in terms of their structure
(b)
See Figure 4.6, Three types
of isomers
(c)
[isomer (Google Search)] [isomer (MicroDude)]
[index]
(a)
Structural isomers are the most general case of isomers
(b)
Structural isomers share molecular formulas but differ in structural
formulas
(c)
see Figure 4.6a, Three types
of isomers (a) Structural Isomers
(d)
[structural isomer (Google Search)] [structural isomer (MicroDude)]
[index]
(a)
Geometric isomers share both their molecular and their structural
formulas
(b)
Geometric isomers occur as a consequence of the non-rotatability of
double bonds (this may need to be seen to be appreciated; see figure or link)
(c)
see Figure 4.6b, Three types
of isomers (b) Geometric Isomers
(d)
[geometric isomer (Google Search)] [geometric isomer (MicroDude)]
[index]
(a)
Enantiomers share both molecular and structural formulas
(b)
Unlike geometric isomers, however, they are not
generated by double bonds
(c)
They are, however, like geometric isomers a consequence of the
non-interchangeability of paired electrons around carbon
atoms
(d)
In other words, a carbon atom which is single bonded to four different atoms or groups can have those
groups arranged in up to two different ways (as an aside, these carbons
are then described as being chiral, asymmetric, or to exhibit chirality)
(e)
Furthermore, each of those ways or being orientated constitutes a
different molecule (essential a left-handed
one and a corresponding right-handed
one)
(f)
Each enantiomer is also a mirror image of the other (note that the
definition of enantiomers and stereoisomers differs slightly, but we won’t
worry about this difference here: enantiomers are true mirror images while
stereoisomers are mirror images only in terms of the arrangement of the bonds
immediately around, for example, a chiral carbon atom)
(g)
See Figure 4.6c, Three types
of isomers (c) Enantiomers
(h)
(photograph ball and stick
model for presentation during lecture)
(i)
Molecules of living things are far more likely to display not just
chirality but only one of two (or more) possible enantiomers compared with the
molecules of non-living things
(j)
[enantiomer (Google Search)] [enantiomers (MicroDude)]
[index]
HYDROPHILIC FUNCTIONAL
GROUPS
(a)
Carbon atoms can bond to elements other than carbon and hydrogen
(b)
These other elements or groups of elements are together described as
groups
(c)
They may additionally be described as functional groups because these
other-than-carbon-and-hydrogen groups
tend to be more chemically reactive than hydrocarbons
(d)
Functional groups “behave consistently from one organic molecule to
another, and the number and arrangement of the groups help give each molecule
its unique properties.”
(e)
[functional groups, functional group, functional group chemistry
(Google Search)] [functional group, organic
chemistry primer (MicroDude)] [index]
(10) Hydrophilic functional groups
(a)
Hydroxyl group (-OH)
(b)
Carbonyl group (=O; aldehydes and ketones)
(c)
Carboxyl group (O=C-OH; -COOH)
(d)
Amino group (-NH2)
(e)
Sulfhydryl group (-SH)
(f)
Phosphate group (-O-PO3, i.e., -PO4)
(g)
See Table 4.1, Functional
groups of organic compounds
(h)
[hydrophilic functional group
(Google Search)] [functional group (MicroDude)]
[index]
(a)
The hydroxyl functional group (-OH) is a good hydrogen bonder
(b)
For low molecular weight organic molecules, the hydroxyl group confers water solubility
(c)
When an otherwise simple hydrocarbon contains a hydroxyl functional
group we give the name of the molecule the suffix –ol (i.e., methane becomes
methanol, ethane becomes ethanol, isopropane becomes isopropanol, etc.)
(d)
Alcohol is the general class that is made up of
otherwise simple hydrocarbons that contain a hydroxyl functional group
(e)
Other molecules whose properties are strongly influenced by the
presence of numerous hydroxyl groups are the sugars and, more
generally, the carbohydrates
(f)
[hydroxyl group (Google Search)] [alcohols, hydroxyl group (MicroDude)]
[index]
(a)
The sulfhydryl functional group is very similar to hydroxyl
group except that an S replaces the O
(b)
(Sulfhydryl groups play a role in stabilizing protein tertiary structure as disulfide bridges)
(c)
[sulfhydryl group (Google Search)] [sulfhydryl group, thiols (MicroDude)] [index]
(13) Carbonyl group (aldehydes,
ketones)
(a)
Carbonyl functional groups (=O) are good hydrogen bonders
(b)
Similar to hydroxyl groups, at lower molecular weights the
carbonyl group confers water solubility on
molecules
(c)
Molecules containing carbonyl groups may be differentiated into two
types, aldehydes and ketones:
(i)
With aldehydes the =O is found on an end carbon (formaldehyde, which
contains only one carbon, is the simplest aledehyde)
(ii)
With ketones the =O on a middle carbon (acetone, which contains three
carbons, is consequently the simplest ketone)
(d)
The location of the carbonyl group (i.e., what carbon it is attached
to) affects chemistry of the containing molecule significantly
(e)
See Table 4.1, Functional
groups of organic compounds
(f)
You will see carbonyl groups in carbohydrates,
along with hydroxyl groups, and on some of the sugar-like intermediates of carbohydrate metabolism
(g)
[carbonyl group, aldehyde, ketone (Google Search)] [aldehydes, carbonyl group, ketones (MicroDude)]
[index]
(a)
The carboxyl functional group (-COOH) is a good hydrogen bonder
(b)
Similar to hydroxyl groups and carbonyl groups,
the carboxyl group confers water solubility on
lower molecular weight hydrocarbons
(c)
The salts of carboxyl groups, with their full (as opposed to partial)
negative charge are particularly soluble in water
(d)
When an otherwise simple hydrocarbon contains a carboxyl functional
group we give the name of the molecule the suffix –ic
(i)
(thus, acetic acid is an example of a two carbon organic acid
consisting a single carbon to which a second carbon as a carboxyl group is
attached)
(ii)
(formic acid is the single-carbon example of a carboxyl
group-associated molecule—in this case the carboxyl group is attached only to a
hydrogen atom and the carboxyl group itself supplies the only carbon atom in
this molecule)
(e)
When the hydrogen of a carboxyl group is replaced with a cation the
associated molecule is converted to a salt and subsequently is given the suffix
–ate (e.g., -COOH à -COO- Na+;
note that though I used sodium as the metal ion in this example, the cation
involved in converting the acid to its salt is not limited to sodium)
(i)
(acetic acid becomes acetate)
(ii)
(formic acid becomes formate)
(f)
Note that in water solution the carboxyl group tends to exist
dissociated from both its hydrogen and whatever cation it is otherwise
associated with, i.e., it possesses a negative charge (thus making it very
soluble in water)
(g)
The H+ typically dissociate at physiological pHs;
thus, under typical physiological conditions carboxyl groups often exist as
dissociated salts (try not to get confused on this point, but if you recall
your acid-base chemistry, a dissociated weak acid is a weak base, i.e., a
hydrogen ion acceptor—thus hydrogens tend to come off of and then go back on to
carboxyl groups under physiological conditions)
(h)
You will see carboxyl groups in amino acids (along
with various other functional groups including, particularly, amino
groups)
(i)
[carboxyl group, carboxylic acid (Google Search)] [carboxyl group, carboxylic acids, carboxylic acid salts (MicroDude)]
[weak acids (Caduceus MCAT Review)]
[index]
(a)
The amino functional group (-NH2) is also a good hydrogen bonder
(b)
Contrary to the not-disassociated carboxyl group, the
amino group functions as weak base (i.e., able to accept H+): -NH2
+ H+ à NH3+
(c)
Simple carbon compounds possessing amino groups are called amines
(d)
Amino acids are so-named because they possess
an amino group as one of their core structures (among the other core structures
is a carboxyl group from which the term acid in amino acid is derived)
(e)
[amino group (Google Search)] [amino group (MicroDude)]
[index]
(16) Phosphate group (inorganic phosphate, Pi)
(a)
Replace one H of phosphoric acid with carbon and you have
a phosphate group (attached to that carbon)
|
phosphoric acid (a.k.a.,
inorganic phosphate or Pi):
OH | HO – P = O |
OH |
phosphate group:
OH
| C - O – P = O
|
OH |
(b)
Phosphates and phosphate groups readily lose hydrogen ions (i.e., they
are somewhat acidic)
(c)
At physiological pHs phosphate groups are highly negatively
charged due to their ionization (loss of hydrogen ions)
(d)
On the other hand, phosphoric acid is typically referred to as inorganic phosphate (abbreviated, Pi)
when not bonded to carbon
(e)
Phosphate groups play important roles especially in the structure of nucleic acids, many of the molecules that make up membranes
(phospholipids), and in energy storage
associated particularly with the molecule called ATP
(f)
[phosphate group, inorganic phosphate
(Google Search)] [phosphodiester bond group (MicroDude)]
[index]
OXIDATION OF CARBON
(a)
Carbon atoms display different degrees of oxidation depending on what they are bonded to.
(b)
In order of increasingly oxidized carbon
atoms we have:
(i)
-C-H (carbon bonded to hydrogen)
(ii)
-C-OH (carbon bonded to a hydroxyl group, an alcohol, for example, 3H-C-OH,
for example)
(iii)
-C=O (carbon double-bonded to oxygen, 2H-C=O, for example)
(iv)
–COOH (carbon as part of a carboxyl group, HO-C=O)
(v)
CO2 (carbon double-bonded, O=C=O, to two oxygen atoms)
(c)
In terms of molecules that contain only a single carbon atom plus
various permutations of hydrogen and oxygen, in order of increasing oxidation
of carbon:
(i)
CH4 (methane)
(ii)
CH3OH (methanol)
(iii)
CH2O (formaldehyde)
(iv)
H-COOH (formic acid)
(v)
CO2 (carbon dioxide)
(d)
Note that in the above compounds you see a monotonic decline in the
number of hydrogen atoms attached to the carbon in the above molecules such
that the hydrogen to carbon ratio (or just plain number of hydrogen atoms) is
reduced by one for each increase in oxidation:
(i)
CH4 (methane), 4 hydrogens (0 oxygens)
(ii)
CH3OH (methanol), 3 hydrogens (1 oxygen)
(iii)
CH2O (formaldehyde), 2 hydrogens (1 oxygen)
(iv)
H-COOH (formic acid), 1 hydrogen (2 oxygens)
(v)
CO2 (carbon
dioxide), 0 hydrogens (2 oxygens)
(e)
So what?
(i)
As carbon becomes more
oxidized the total energy associated with the
bonds about that carbon decreases
(ii)
Roughly, a carbon-containing molecule becomes more soluble in water the
more oxygens associated with the molecule
(iii)
As organisms extract energy from carbon-containing molecules, they tend
to remove hydrogen atoms and add oxygen atoms
(iv)
Ultimately oxidizing a molecule that contains abundant obtainable
energy down to the most oxidized carbon, carbon dioxide
(v)
Carbon dioxide, which contains no obtainable energy, is released as a
waste product (e.g., you exhale)
(f)
(To help bring some of these points home I will go through
the structure of glucose, a partially oxidized
carbon-containing molecule)
(g)
(I will then drive home the
point that extraction of energy often involves the oxidation by once-again
walking through glycolysis)
(h)
[oxidation of carbon
(Google Search)] [cellular respiration:
harvesting chemical energy (MicroDude)]
[index]
VOCABULARY
(a)
Aledehydes
(b)
Amino group
(c)
Carbon
(d)
Carbonyl group
(e)
Carboxyl group
(f)
Enantiomers
(h)
Geometric isomer
(i)
Hydrocarbon
(j)
Hydrophilic functional groups
(k)
Hydroxyl group
(m)
Isomers
(n)
Ketones
(p)
Oxidized carbon
(q)
Phosphate group
(r)
Pi
(t)
Sulfhydryl group