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Chapter 4 Carbon and the Molecular Diversity of Life
Outline
I. Organic compoundsII. Bonding with CarbonIII. IsomersIV. Functional Groups
Organic Compounds
What is organic We think of organic produce “natural”
In chemistry organic refers to molecules that have a carbon backbone, covalently bound to each other
Early chemists thought of organic as coming from plants and animals and inorganic coming from minerals
Overview: Carbon: The Backbone of Life
Living organisms consist mostly of carbon-based compounds
Carbon is unparalleled in its ability to form large, complex, and diverse molecules
Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds
© 2011 Pearson Education, Inc.
Organic Molecules and the Origin of Life on Earth
Stanley Miller’s classic experiment demonstrated the abiotic synthesis of organic compounds
Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life
© 2011 Pearson Education, Inc.
Figure 4.2 EXPERIMENT“Atmosphere”
Electrode
Condenser
CH4Water vapor
Cooled “rain”containingorganicmolecules
Cold water
Sample for chemical analysis
H2O “sea”
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Carbon
Carbon has four electrons in its outer shell. It needs eight electrons to be stable
So, carbon can form up to four covalent bonds.
Carbons can link together to form a backbone – many other elements can bond to this backbone
Carbon – carbon bonds are strong
Carbon compounds
Carbons can form single, double or triple bonds.
Hydrocarbons are made of carbon and hydrogen
Carbons can form chains or rings
Figure 4.3
Name andComment
MolecularFormula
(a) Methane
(b) Ethane
CH4
Ball-and-Stick Model
Space-FillingModel
(c) Ethene(ethylene)
C2H6
C2H4
StructuralFormula
Figure 4.5
(a) Length
Ethane 1-Butene
(c) Double bond position
2-ButenePropane
(b) Branching (d) Presence of rings
Butane 2-Methylpropane(isobutane)
Cyclohexane Benzene
Carbon atoms can partner with atoms other than hydrogen; for example:
Carbon dioxide: CO2
Urea: CO(NH2)2
© 2011 Pearson Education, Inc.
Urea
Isomers
Isomers: compounds with the same molecular formulas, but different structures
Structural isomers Geometric isomers Enantiomers
Isomers do not have identical physical, chemical, or biological properties
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Figure 4.7 (a) Structural isomers
(b) Geometric isomers
(c) Enantiomers
cis isomer: The two Xsare on the same side.
trans isomer: The two Xsare on opposite sides.
CO2HCO2H
CH3
H NH2
L isomer
NH2
CH3
H
D isomer
Structural Isomers
Molecule have different arrangement of their carbon skeleton but still have the same molecular formula:
Geometric Isomers
Have the same arrangement of atoms but the spatial arrangement of the atoms are different.
An example is cis vs trans arrangements across a double bond (cis = large groups are on same side, trans = large groups on opposite side
Enantiomers
Isomers that are mirror images of each other
Must be a chiral molecule –where a carbon is bonded to four different molecules
Referred to as: + or – R or L
Fig. 3.2
Enantiomers
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Web sites
http://scholar.hw.ac.uk/site/chemistry/topic5.asp?outline=no
http://webhost.bridgew.edu/fgorga/Stereochem/default.htm
http://www.mhhe.com/physsci/chemistry/carey/student/olc/ch07enantiomers.html
Why do we care
The function of a protein is determined by its shape.
Usually only one form of an isomer is active in biological systems.
Why do we care
Biological organisms usually synthesize only one form.
However, chemical synthesis usually produces equal amounts of the two enantiomers
Enantiomers are important in the pharmaceutical industry
Two enantiomers of a drug may have different effects
Usually only one isomer is biologically active
Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules
© 2011 Pearson Education, Inc.
© 2011 Pearson Education, Inc.
Animation: L-DopaRight-click slide / select “Play”
Figure 4.8
Drug
Ibuprofen
Albuterol
Condition EffectiveEnantiomer
IneffectiveEnantiomer
Pain;inflammation
Asthma
S-Ibuprofen R-Ibuprofen
R-Albuterol S-Albuterol
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Example: The drug albuterol (e.g., Proventil®) contains equal amounts of two enantiomers.
Another more expensive drug is levalbuterol (Xopenex®) it only contains the active form of the drug, it has fewer side effects
This is an example of what kind of isomer?
1. Geometric2. Enantiomers3. Structural4. None of the above
Geo
metric
Enantio
mers
Structu
ral
Non
e of th
e abo
ve
25% 25%25%25%
Functional Groups
Functional groups are the components of organic molecules that are most commonly involved in chemical reactions
The number and arrangement of functional groups give each molecule its unique properties
© 2011 Pearson Education, Inc.
Figure 4.UN02
Estradiol
Testosterone
Functional Groups
Groups of atoms; determines the types of chemical reactions and associations
1. Hydroxyl2. Carbonyl3. Carboxyl 4. Amino5. Sulfhydryl6. Phosphate7. Methyl
Polarity
Remember that C-H and C-C bonds are non polar
S, N, and O are electronegative atoms and can make a molecule more polar.
Polar and ionic functional groups are hydrophilic, and strongly associate with water
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Fig. 3.1 Fig. 3.1
Properties of functional Groups
1. Hydroxyl – polar, can form hydrogen bonds
2. Carbonyl – polar, can form hydrogen bonds
3. Carboxyl – very polar, weakly acidic and can ionize to become -COO- + H+
Important in amino acids
4. Amino - Polar and weakly basic, can accept a H+ to become –NH3
+
Important in amino acids and nucleic acids
Properties of functional Groups
5. Sulfhydryl – also called thiol, polar, important in proteins, can form strong S-S bonds that stabilize structure
6. Phosphate – polar and weakly acidic. Can dissociate to –PO4
-2
Important in nucleic acids and some lipids
7. Methyl – nonpolar hydrocarbon
Figure 4.9a
STRUCTURE
EXAMPLE
Alcohols(Their specificnames usuallyend in -ol.)
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
(may be written HO—)
Ethanol
• Is polar as a resultof the electronsspending moretime near theelectronegativeoxygen atom.
• Can form hydrogenbonds with watermolecules, helpingdissolve organiccompounds suchas sugars.
Hydroxyl
Figure 4.9bCarbonyl
STRUCTURE
EXAMPLE
Ketones if the carbonylgroup is within acarbon skeleton
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Aldehydes if the carbonylgroup is at the end of thecarbon skeleton
• A ketone and analdehyde may bestructural isomerswith different properties,as is the case foracetone and propanal.
Acetone
Propanal
• Ketone and aldehydegroups are also foundin sugars, giving riseto two major groupsof sugars: ketoses(containing ketonegroups) and aldoses(containing aldehydegroups).
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Carboxyl
STRUCTURE
EXAMPLE
Carboxylic acids, or organicacids
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Acetic acid
• Acts as an acid; candonate an H+ because thecovalent bond betweenoxygen and hydrogen is sopolar:
• Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion.
Nonionized Ionized
Figure 4.9c
Amino
Amines
Glycine
STRUCTURE
EXAMPLE • Acts as a base; canpick up an H+ from thesurrounding solution(water, in livingorganisms):
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
• Found in cells in theionized form with acharge of 1.
Nonionized Ionized
Figure 4.9d
Sulfhydryl
Thiols
(may bewritten HS—)
STRUCTURE
EXAMPLE • Two sulfhydryl groups canreact, forming a covalentbond. This “cross-linking”helps stabilize proteinstructure.
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
• Cross-linking of cysteinesin hair proteins maintainsthe curliness or straightnessof hair. Straight hair can be“permanently” curled byshaping it around curlersand then breaking andre-forming the cross-linkingbonds.
Cysteine
Figure 4.9e Figure 4.9f
Phosphate
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Organic phosphates
Glycerol phosphate
• Contributes negativecharge to the moleculeof which it is a part(2– when at the end ofa molecule, as at left;1– when locatedinternally in a chain ofphosphates).
• Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.
Figure 4.9g
Methyl
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Methylated compounds
5-Methyl cytidine
• Addition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.
• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.
Carboxyl functional groups are:
1. Polar2. Acidic3. Nonpolar4. Polar and acidic
Polar
Acid
ic
Non
polar
Polar an
d acid
ic
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Important Concepts Read Chapters 5 for next lecture
Know the vocabulary of the lecture
Understand the importance of carbon in organic molecules
Understand Stanley Miller’s experiments
What are the different types of isomers, be able to identify examples of each type of isomer?
What is the structure and the properties of the common functional groups?
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