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review sheet of AP Biology for

Chapter 4* 18.Sep.09

 

Chapter.4 :: Carbon and the Molecular Diversity of Life  [[Page.58]]

Overview ‘Carbon – The Backbone of Biological Molecules [[Page.58]]

-          Although living organisms use water as their universal medium for life, they are made up of chemicals based mostly on the element carbon.

-          Carbon enters the biosphere through the action of plants in the transformation of CO₂

-          Of all chemical elements, carbon is unparalleled (best) in its ability to form molecules that are large, complex and diverse (various), and this molecular diversity had made possible the diversity of organisms that have evolved on Earth.

-          Protein, DNA, carbohydrates, and other molecules that distinguish living matter from inanimate material are all composed of carbon atoms bonded to one another and to atoms of other elements.

·         These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P).

 Concept 4.1 – Organic chemistry is the study of carbon compounds [[Page.58]]

-          The study of carbon compounds, organic chemistry, deals with any compound with carbon (or what we called organic compounds)

·         Organic compounds range from simple molecules, such as CO₂ or CO₄ (methane), to complex molecules such as protein, which may weight more than 1000,000 daltons.

-          The overall percentage of the major elements of life (C, H, O, N, S, P) are quite uniform (alike) from one organism to another. But because of carbon’s versatility (usefulness), this limited assortment of atomic building blocks, taken in roughly the same proportions, can be used to build an inexhaustible (unlimited) variety of organic molecules.

-          Different species of organisms, and different individuals within a species, are distinguished by variations in their organic molecules.

-          The science of organic chemistry began in attempts to purify and improve the yield of products obtained from other organisms.

·         Firstly, chemists learnt to synthesize (combine) only simple compounds in laboratory.

·         However, Jons Jacob Berzelius was the first to make a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds that were found in the nonliving world.

ð This led early organic chemists to propose vitalism, the belief that physical and chemical laws did not apply to living things.

·         But then, vitalism started to chip away when Friedrich Wohler was able to synthesize urea by mixing solutions of ammonium ions (NH₄⁺) and cyanate ions (CNO^-). Although at first he was going to make an inorganic salt.

ð Since cyanate, one of his ingredients, had been extracted from animal blood, his product in this experiment was not completely called inorganic materials. (because animal blood came from animal which is living organisms)  

·         After that, Stanley Miller set up a laboratory simulation (model) of chemical conditions on the primitive (ancient) Earth and demonstrated the spontaneous synthesis of organic compounds, which may have been an early stage in the origin of life.

ð This made the organic chemists to finally shift from vitalism to mechanisms, the view that all natural phenomena, including the processes of life, are governed by physical and chemical laws. 

ð Organic chemistry was redefined as study of carbon compounds, regardless of their origin

ð Organisms do produce the majority of organic compounds.

ð The laws of chemistry apply to inorganic and organic compounds alike.

Concept 4.2 – Carbon atoms can form diverse molecules by boding to four other atoms [[Page.59]]

-          Electron configuration (shape) of an atom determines the kinds and number of bonds an atom will form with other atoms.

-          Carbon has a total of 6 electrons, with 2 in the first electron shell and 4 in second shell

-          Carbon’s second electron shell (outer shell) an hold up to 8 electrons, so by having only 4 valence electrons, it would have to donate or accept 4 more electrons to complete its valence shell and become ion. Instead, a carbon atom usually completes its valence shell by sharing its 4 electrons with other atoms in covalent bonds so that 8 electrons are present.

·         This tetravalence by carbon makes large, complex molecules possible.

a.      When a carbon forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles of 109.5^o

b.      In molecules with multiple carbons, every carbon bonded to four other atoms has a tetrahedral shape (having four triangular surfaces).

c.       However, when two carbon atoms are joined by a double bond, all bonds around those carbons are in the same plane & have a flat, three dimensional structures.

-          The three-dimensional shape of an organic molecule determines its function.

-          The electron configuration of carbon gives it covalent compatibility with many different elements

-          The electron-shell diagrams of the 4 major atomic components of organic molecules are shown at the right. (Valence = number of covalent bonds an atom can form)

-          In carbon dioxide (CO₂), one carbon atom forms two double bonds with two different oxygen atoms (O=C=O), this arrangement completes the valence shells of all atoms in the molecules.

·         While CO₂ can be classified as either organic or inorganic, its importance to the living world is clear. (it’s the source of carbon for all organic molecules found in organisms and usually fixed into organic molecules by photosynthesis)

-          Urea, CO(NH₂)₂ is another simple organic molecule in which each atom forms covalent bonds to complete its valence shell.

-          Carbon chains form the skeletons of most organic molecules.

(a)   Length :: carbon skeletons vary in length

(b)   Branching :: skeletons may be unbranched or branched

(c)   Double bonds :: the skeleton may have double bonds, which can vary in location

(d)   Rings :: some carbon skeletons are arranged in rings.

-          Atoms of other elements can be bonded to the atoms of the carbon skeleton.

-          Hydrocarbons are organic molecules consisting only carbon and hydrogen. 
 ·         Hydrocarbons are the major components of petroleum, a fossil fuel that consists of the partially decomposed remains of organisms that lived millions years ago, as well as fats which are biological molecules that have long hydrocarbon tails attached to a nonhydrocarbon component.
ð Both petroleum and fats are hydrophobic compounds that cannot dissolve in water because of their many nonpolar carbon-to-hydrogen bonds.

-          Hydrocarbons can also undergo reactions that release a relatively large amount of energy.

-          Variation in the architecture of organic molecules can be seen in isomers, compounds that have the same numbers of atoms of the same elements but different structures and hence different properties. There are 3 types of isomers ::

·         Structural isomers differ in the covalent arrangements of their atoms.

ð The number of possible isomers increases tremendously as carbon skeletons increase in size.

·          Geometric isomers have the same covalent partnerships, but they differ in their spatial arrangements. It arises from the inflexibility of double bonds, which will not allow the atoms they join to rotate freely about the bond axis. 

·          Enantiomers are molecules that are mirror images of each other. In the picture, the middle carbon (black one) is called an asymmetric carbon because it is attached to four different atoms or groups of atoms

ð The four groups can be arranged in two different ways that are mirror images; they’re like left-handed and right handed versions of molecules and usually one isomer is biologically active while the other is inactive.

ð For example, L-dopa isomer is an effective treatment of Parkinson’s disease, but D-dopa isomer is inactive.

Concept 4.2 –Functional groups are the parts of molecules involved in chemical reactions [[Page.63]]

-          The distinctive properties of an organic molecule depend not only on the arrangement of its carbon skeleton, but also on the molecular components attached to the skeleton.

-          The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups.

·         Each functional group behaves consistently from one organic molecule to another, and the number & arrangement of the groups help give each molecule its unique properties

ð For example, the basic structure of testosterone (a male sex hormone) and estradiol (a female sex hormone) is the same. Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings. These functional groups interact with different target in male and female bodies.

-          The six functional groups most important to the chemistry of life are hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups. (all of them are hydrophilic and increase the solubility of organic compounds in water)

1.       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.  

·         Name of compounds :: Alcohols (their specific names usually end in –ol)

·         Example :: Ethanol, the alcohol present in alcoholic beverages

·         Functional properties ::

ð Is polar as a result of electronegative oxygen atom drawing electrons toward itself

ð Attracts water molecules, helping dissolve organic compounds such as sugar

2.       The carbonyl group(>CO) consists of a carbon atom joined to an oxygen atom by double bond

·         Name of compounds ::

ð Ketones = the carbonyl group is within a carbon skeleton

ð Aldehyde = the carbonyl group is on the end of a carbon skeleton

·         Example :: Acetone (simplest ketone) & Propanal (an aldehyde) 

·         Functional properties :: a ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

3.       When an oxygen atom is double bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (---COOH).

·         Name of compounds :: Carboxylic acids, or organic acids.

·         Example :: Acetic acid, which gives vinegar its sour taste.

·         Functional properties ::

ð Has acidic properties because it is a source of hydrogen ions

ð The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H⁺) tend to dissociate reversibly

ð In cells, found in the ionic form, which is called a carboxylate group.

4.       The amino group (---NH₂) consists of a nitrogen atom bonded to two hydrogen & to the carbon skeleton.

·         Name of compounds :: Amines

·         Example :: Glycine (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 ::

ð Acts as a base; can pick up a proton from the surrounding solution

ð Ionized with a charge of 1+, under cellular conditions.

5.       The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group is shape.

·         Name of compounds :: Thiols

·         Example :: Ethanethiol

·         Functional properties :: 2 sulfhydryl groups can interact to help stabilize protein structure

6.       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. The phosphate group (---OPO₃^2-) is an ionized form of a phosphoric acid group (---OPO₃H₂)

·         Name of compounds :: Organic phosphates

·         Example :: Glycerol phosphate

·         Functional properties :: 

ð Makes the molecule of which it is a part an anion (negatively charged ion)

ð Can transfer energy between organic molecules.

-          A more complicated organic phosphate, adenosine triphosphate, or ATP is the primary energy-transforming molecule in the cell. It consists of an organic molecule called adenosine attached to a string of three phosphate group. 

·         When ATP loses one phosphate, it becomes adenosine diphosphate, or ADP. This reaction releases energy that can be used by the cell.

-          Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphate.

·         These elements are linked by strong covalent bonds.

-          Carbon, with its four covalent bonds, is the basic building block in molecular architecture.

-          The great diversity of organic molecules with their special properties emerges from the unique arrangement of the carbon skeleton & the functional groups attached to the skeleton.

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