Post on 05-Jan-2016
Chapter 4Carbon & the Molecular Diversity of Life
The Backbone of Biological Molecules• What compound makes up the majority of
matter in cells?
• Carbon is unparalleled in its ability to form large, complex, and diverse molecules• Proteins, DNA, carbohydrates
• Why is carbon so versatile?
Where do we ultimately get carbon to make the molecules necessary for life?
What about life elsewhere?
Do you think it is carbon-based life?
• Organic compounds range from simple molecules to colossal ones
• Most organic compounds contain hydrogen atoms in addition to carbon atoms• Hydrocarbons
Quick Review: What are the elements that are most common in biological compounds?◦O, H, S, P, and of course C
Organic chemistry is the study of carbon compounds
Vitalism - the idea that organic compounds arise only in organisms
Swedish scientist, Berzelius - The idea that there was a “life force” outside of physical & chemical laws
Organic chemistry - study of carbon based compounds
Organic Chemistry - OriginsFriedrich Wöhler accidentally created urea
in his labHermann Kolbe created acetic acid from
inorganic substanceStanley Miller demonstrated possible
origin of life through synthesis of organic compounds
Vitalism Mechanism◦the view that all natural phenomena, are subject to physical & chemical laws
Paradigm shift…
The Structure of Carbon Atoms
What is the electron configuration of carbon?
Why is the electron configuration important?
What kind of bond is carbon going to form?
The Formation of Bonds with Carbon
Four valence electrons = four covalent bonds (tetravalence)
Structure of Organic MoleculesWhat shape is a carbon molecule with four
single bonds?
Why is the bond angle the same for each bond?
LE 4-3
MolecularFormula
StructuralFormula
Ball-and-StickModel
Space-FillingModel
Methane
Ethane
Ethene (ethylene)
Structure of Organic Molecules
Carbon most commonly forms bonds with:OxygenNitrogenHydrogen
Brainstorm: Why do you think that these elements are the most likely to form organic compounds?
LE 4-4
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
Hydrocarbons
Carbon is able to form long chains that vary in length and shape
LE 4-5
LengthEthane Propane
Butane 2-methylpropane(commonly called isobutane)
Branching
Double bonds
Rings
1-Butene 2-Butene
Cyclohexane Benzene
Hydrocarbons
Only contain carbon and hydrogenMany organic molecules, such as fats,
have hydrocarbon components
Brainstorm: Why do you think that hydrocarbons might be important for biological processes?
LE 4-6
A fat molecule Mammalian adipose cells
100 µm
Fat droplets (stained red)
Isomers
Compounds with multiple possible structures and functions◦Structural isomers- arrangement of bonds and
atoms◦Geometric isomers- same covalent placement,
different spatial arrangements (e.g. cis/trans)◦Enantiomers- mirror images
LE 4-7
Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane.
Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon.
cis isomer: The two Xsare on the same side.
trans isomer: The two Xsare on opposite sides.
L isomer D isomer
Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.
Enantiomers
Thalidomide ◦Treatment for morning sickness◦Causes limb deformities in newborns
Ethambutol◦Treatment for tuberculosis◦Causes blindness
Naproxen◦Treatment for arthritis◦Causes liver poisoning
Why is thalidomide especially dangerous?
LE 4-8
L-Dopa(effective againstParkinson’s disease)
D-Dopa(biologicallyInactive)
Functional GroupsMolecular structures that are responsible for
the chemical characteristics of a compoundMost reactions (in organic chemistry)
depend on the functional groups
Methylamine
LE 4-9
Estradiol
Testosterone
Male lion
Female lion
Know these functional groups!
◦Hydroxyl group OH◦Carbonyl group CO◦Carboxyl group COOH◦Amino group NH2
◦Sulfhydryl group SH◦Phosphate group PO4
LE 4-10aa
STRUCTURE
(may be written HO—)
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
Ethanol, the alcohol present in
alcoholic beverages
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
LE 4-10ab
STRUCTURE
NAME OF COMPOUNDS
Ketones if the carbonyl group is
within a carbon skeleton
EXAMPLE
Acetone, the simplest ketone
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
Acetone, the simplest ketone
Propanal, an aldehyde
FUNCTIONAL PROPERTIES
LE 4-10ac
STRUCTURE
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
EXAMPLE
Has acidic properties because it isa source of hydrogen ions.
Acetic acid, which gives vinegarits sour taste
FUNCTIONAL PROPERTIES
The covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,
Acetic acid Acetate ion
In cells, found in the ionic form,which is called a carboxylate group.
LE 4-10ba
STRUCTURE
NAME OF COMPOUNDS
Amine
EXAMPLE
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
Ionized, with a charge of 1+,under cellular conditions
Glycine
(ionized)
LE 4-10bb
STRUCTURE
(may be written HS—)
NAME OF COMPOUNDS
Thiols
EXAMPLE
Ethanethiol
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
structure (see Figure 5.20).
LE 4-10bc
STRUCTURE
NAME OF COMPOUNDS
Organic phosphates
EXAMPLE
Glycerol phosphate
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
ATP: An Important Source of Energy for Cellular Processes
Adenosine triphosphate (ATP)- primary energy-transferring molecule in the cell
The Chemical Elements of Life: A Review
Why is the versatility of carbon so important for biological processes?
Exam practiceWhat is the reason why hydrocarbons are not
soluble in water? A) The majority of their bonds are polar
covalent carbon to hydrogen linkages. B) The majority of their bonds are nonpolar
covalent carbon-to-hydrogen linkages. C) They are hydrophilic. D) They exhibit considerable molecular
complexity and diversity. E) They are lighter than water.
Exam practice
Hydrocarbons mainly consist of H-C nonpolar covalent bonds and thus not soluble in water
The answer is B
Exam
Exam practice The two molecules shown in Figure 4.1 are
best described as A) optical isomers (enantiomers). B) radioactive isotopes. C) structural isomers. D) nonradioactive isotopes. E) geometric isomers.
Exam practice
The answer is C structural isomersThis is because structural isomers differ in
covalent patternsGeometric isomers differ in arrangement
about a double bondEnantiomers differ in spatial arrangement
around an asymmetric carbon (mirror images)
Functional Group Activity