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• http://www.nature.com/news/index.html

• http://sciencenow.sciencemag.org/cgi/content/full/2009/1001/1

• http://news.bbc.co.uk/2/hi/science/nature/default.stm

•Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Ancient Skeleton May Rewrite Earliest Chapter of Human Evolution•By Ann GibbonsScienceNOW Daily News1 October 2009

•Researchers have unveiled the oldest known skeleton of a putative human ancestor--and it is full of surprises. Although the creature, named Ardipithecus ramidus, had a brain and body the size of a chimpanzee, it did not knuckle-walk or swing through the trees like an ape. Instead, "Ardi" walked upright, with a big, stiff foot and short, wide pelvis, researchers report in Science. "We thought Lucy was the find of the century," says paleoanthropologist Andrew Hill of Yale University, referring to the famous 3.2-million-year-old skeleton that revolutionized thinking about human origins. "But in retrospect, it was not."

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• http://www.bbc.co.uk/news/world-middle-east-12084496


•Evidence of early man found in Israel

•27 December 2010 Last updated at 18:50 ET Help

•Archaeologists excavating a cave in central Israel believe they have found teeth belonging to the earliest Homo sapiens that could be around 400,000 years old.

•The team of scientists who have been excavating Qassem cave, a pre-historic site that was uncovered in 2000, say the size and shape of the teeth are very similar to those of modern man.

•Homo sapiens are believed to have originated in Africa and migrated out of the continent.

•Professor Aviv Gopher from Tel Aviv University says that further research is needed to solidify their claim, but if they are proven right, it could change the concept of human evolution.

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Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

PowerPoint® Lecture Presentations for

BiologyEighth Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp

Chapter 4

Carbon and the Molecular Diversity of Life

Overview: Carbon: The Backbone of Life

• Although cells are 70–95% water, the rest consists mostly of carbon-based compounds

• Carbon enters the biosphere through the action of plants, which use solar energy to transform atmospheric CO2 into the molecules of life

• These molecules are passed onto animals that feed on plants

• Carbon is unparalleled in its ability to form large, complex, and diverse molecules

• Has made possible the diversity of organisms that have evolved on Earth

• Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds


Fig. 4-1

Concept in this Chapter

1. Organic chemistry is the study of carbon compounds

2. Carbon atoms can form diverse molecules by bonding to four other atoms

3. A small number of chemical groups are key to the functioning of biological molecules


CONCEPT 4.1:

ORGANIC CHEMISTRY IS THE STUDY OF CARBON COMPOUNDS


Concept 4.1: Organic chemistry is the study of carbon compounds

• Organic chemistry is the study of compounds that contain carbon

• Organic compounds range from simple molecules (such as methane, CH4) to colossal ones (such as proteins)

• Most organic compounds contain hydrogen atoms in addition to carbon atoms



• Overall percentages of the major elements of life- C, H, O, N, S, and P are uniform between organisms.

• A limited assortment of building blocks

• Carbon is versatile• Allows large variety of organic molecules

• Variations in organic molecules distinguish between species and individuals within species


Concept 4.1: Organic chemistry is the study of carbon compounds• The science of organic chemistry began with attempts to purify and

improve the yield of products obtained from organisms.

• Early chemists made simple compounds by combining elements under the right conditions

– Seemed impossible to synthesize complex molecules extracted from living matter

• Jons Jakob Berzelius distinguished between organic compounds (thought to arise only in living organisms) and inorganic compounds (those found only in the nonliving world)

• Vitalism- the idea that organic compounds arise only in organisms

– Believed that physical and chemical laws do not apply to living things



• Organic chemists learned to synthesize complex organic compounds in the laboratory raising doubts about vitalism

• Friedrich Wöhler and his students synthesized urea from totally inorganic materials

– 1828

– Challenged vitalists but was shot down since one of the ingredients had been extracted from animal blood

– Hermann Kolbe (Wohler’s student) made acetic acid from inorganic substances

– Vitalism crumbled

• .



• In 1953, Stanley Miller set up a laboratory simulation of possible chemical conditions on the primitive Earth and demonstrated the abiotic synthesis of organic compounds.


Fig. 4-2

Water vapor

“Atmosphere”

Electrode

Condenser

Coldwater

Cooled watercontainingorganicmolecules

Sample forchemical analysis

H2O“sea”

EXPERIMENT

CH4


• In 1953, Stanley Miller set up a laboratory simulation of possible chemical conditions on the primitive Earth and demonstrated the abiotic synthesis of organic compounds.

– Evolution- spontaneous synthesis of organic compounds could have been an early stage in the origin of life

– The mixture of gases Miller created probably did not accurately represent the atmosphere of the primitive Earth.

– However, similar experiments using more accurate atmospheric conditions also led to the formation of organic compounds.


Concept 4.1: Organic chemistry is the study of carbon compounds• Shift from vitalism to mechanism.

• Mechanism is the view that physical and chemical laws govern all natural phenomena.

– The laws of chemistry apply to both organic and inorganic compounds

• Organic chemistry was redefined as the study of carbon compounds,

– regardless of their origin.

– Organisms produce the majority of naturally occurring organic compounds.

• The foundation of organic chemistry is not a mysterious life force but rather the unique versatility of carbon-based compounds.


• Organic Chemistry

– The study of carbon compounds

– Percentages of the major elements of life are uniform. How then the diversity?

– Carbon’s versatility.

• Vitalism

– The idea that organic compounds arise only in living organisms

• Mechanism

– is the view that all natural phenomena are governed by physical and chemical laws


Summary

CONCEPT 4.2:

CARBON ATOMS CAN FORM DIVERSE MOLECULES BY BONDING

TO FOUR OTHER ATOMS


Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms

• Electron configuration is the key to an atom’s characteristics

• Electron configuration determines the kinds and number of bonds an atom will form with other atoms


The Formation of Bonds with Carbon

• Carbon has four valence electrons

– Chooses to complete valence shell

• Shares its electrons to form four covalent bonds with a variety of atoms

– Covalent bonds be single or double

• This tetravalence makes large, complex molecules possible



• In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape

– Only happens with single bonds

• When two carbon atoms are joined by a double bond, the molecule has a flat shape


Fig. 4-3

NameMolecular Formula

Structural Formula

Ball-and-StickModel

Space-FillingModel

(a) Methane

(b) Ethane

(c) Ethene(ethylene)

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

• The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules



Fig. 4-4

Hydrogen(valence = 1)

Oxygen(valence = 2)

Nitrogen(valence = 3)

Carbon(valence = 4)

H O N C

• Carbon atoms can partner with atoms other than hydrogen; for example:

– Carbon dioxide: CO2

– Urea: CO(NH2)2

O = C = O


Molecular Diversity Arising from Carbon Skeleton Variation

• Carbon chains form the skeletons of most organic molecules

• Carbon chains vary in length and shape

– May be straight, branched, or arranged in closed rings

– Some carbon skeletons have double bonds

– Atoms of other elements can be bonded to the skeletons at different sites

• Such variation in carbon skeletons in one important source of the molecule complexity and diversity that characterize living matter.


Molecular Diversity Arising from Carbon Skeleton Variation

• Carbon chains form the skeletons of most organic molecules

• Carbon chains vary in length and shape

Animation: Carbon Skeletons


Fig. 4-5a

(a) Length

Ethane Propane

Fig. 4-5b

(b) Branching

Butane 2-Methylpropane(commonly called isobutane)

Fig. 4-5c

(c) Double bonds1-Butene 2-Butene

Fig. 4-5d

(d) RingsCyclohexane Benzene

Hydrocarbons

• Hydrocarbons are organic molecules consisting of only carbon and hydrogen

• Not prevalent in living organisms

– Regions in many of the cell’s organic molecules

• Many organic molecules, such as fats, have hydrocarbon components

– hydrophobic

• Hydrocarbons can undergo reactions that release a large amount of energy

– Gasoline

– Stored fuel for animal bodies


Fig. 4-6

(a) Mammalian adipose cells (b) A fat molecule

Fat droplets (stained red)

100 µm

Isomers

• Variation in the architecture of organic molecules

• Isomers are compounds with the same molecular formula but different structures and properties:

– Structural isomers have different covalent arrangements of their atoms

– Geometric isomers have the same covalent arrangements but differ in spatial arrangements

– Enantiomers are isomers that are mirror images of each other


Isomers

• Isomers are compounds with the same molecular formula but different structures and properties:

– Structural isomers have different covalent arrangements of their atoms

– Geometric isomers have the same covalent arrangements but differ in spatial arrangements

– Enantiomers are isomers that are mirror images of each other

Animation: Isomers


Fig. 4-7a

(a) Structural isomers

2-methyl butanePentane

Structural Isomers

• Differ in covalent arrangements of their atoms

• May also differ in location of double bonds

• The number of possible isomers increases as the carbon skeletons increase in size

• C5H12- 3; C8H18- 18; C10H42- 366,319

Fig. 4-7b

(b) Geometric isomers

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

Geometric Isomers

• Same covalent arrangements but different spatial arrangements

• Due to inflexibility of double bonds

• Cis and trans isomers

• Subtle differences can affect biological activity

• Rhodopsin- light induced change from cis to trans isomer involved in the biochemistry of vision

Fig. 4-7c

(c) EnantiomersL isomer D isomer

Enantiomers• Mirror images of each other

• Asymmetric carbon

• Attached to four different atoms or groups of atoms

• The four atoms can be arranged in space around the asymmetirccarbon in two different ways

• Like right- and left-handed versions of a molecule

• Enantiomers are important in the pharmaceutical industry

• Two enantiomers of a drug may have different effects

• Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

– Thalidomide- mixture of two enantiomers

• One- reduced morning sickness

• Other- caused severe birth defects


Enantiomers

•http://www.wired.com/images/article/full/2008/09/thalidomide_baby_350px.jpg

• Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

Animation: L-Dopa


Enantiomers

Fig. 4-8

Drug

Ibuprofen

Albuterol

Condition

Pain;inflammation

Asthma

EffectiveEnantiomer

S-Ibuprofen

R-Albuterol

R-Ibuprofen

S-Albuterol

IneffectiveEnantiomer

Enantiomers

• Ibuprofen- sold as a mixture of the enantiomers (S 100X more active)

• Only R albuterol synthesized and sold since S form counteracts the active R form

SUMMARY

• Hydrocarbons– organic molecules consisting of only carbon and hydrogen

• Isomers– compounds with the same molecular formula but different

structures and properties

• Structural – Have different covalent arrangements of their atoms

• Geometric– the same covalent arrangements but differ in spatial arrangements

• Enantiomers– isomers that are mirror images of each other


SUMMARY


(a) Structural isomers2-methyl butanePentane

(b) Geometric isomers

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

(c) EnantiomersL isomer D isomer

CONCEPT 4.3:

A SMALL NUMBER OF CHEMICAL GROUPS ARE KEY TO THE

FUNCTIONING OF BIOLOGICAL MOLECULES


Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules

• Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it

• A number of characteristic groups are often attached to skeletons of organic molecules


The Chemical Groups Most Important in the Processes of Life

• Functional groups

– Affect molecular function by direct involvement in chemical reactions

• The number and arrangement of functional groups give each molecule its unique properties


Fig. 4-9

Estradiol

Testosterone

• Both are steroids

• Differ only in chemical groups attached to the rings

• Affect function by affecting molecule’s shape

• The seven functional groups that are most important in the chemistry of life:

– Hydroxyl group- hydrogen bonded to oxygen bonded to carbon– Carbonyl group- carbon atom joined to an oxygen atom by a double

bond– Carboxyl group- oxygen atom double bonded to a carbon atom that is

also bonded to a hydroxyl group– Amino group- nitrogen bonded to two hydrogen atoms and to carbon– Sulfhydryl group- a sulfur atoms bonded to hydrogen to carbon– Phosphate group- phosphorous atom bonded to four oxygen atoms;

one of the oxygens bonded to the carbon skeleton, two oxygens carry negative charges• Above six are hydrophilic and increase solubility of organic

compounds in water– Methyl group- carbon bonded to three hydrogen atoms; not reactive,

acts as a tag


Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules

Fig. 4-10a

Hydroxyl

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. (Do not confuse this functional group with the hydroxide ion, OH–.)

NAME OF COMPOUND

Alcohols (their specific names usually end in -ol)

EXAMPLE

Ethanol, the alcohol present in alcoholic beverages

• Is polar as a result of theelectrons spending more timenear the electronegative oxygen atom.

• Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars.

FUNCTIONALPROPERTIES

(may be written HO—)

Fig. 4-10aCHEMICALGROUP

STRUCTURE

NAME OF COMPOUND

EXAMPLE


Carbonyl

The carbonyl group ( CO)consists of a carbon atomjoined to an oxygen atom by adouble bond.

Acetone, the simplest ketone

Propanal, an aldehyde

Aldehydes if the carbonyl groupis at the end of the carbonskeleton

Ketones if the carbonyl group iswithin a carbon skeleton

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.

These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).

Fig. 4-10c

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Carboxyl

Acetic acid, which gives vinegar its sour taste

Carboxylic acids, or organic acids

Has acidic propertiesbecause the covalent bond between oxygen and hydrogen is so polar; for example,

Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

Acetic acid Acetate ion

Fig. 4-10d

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Amino

Because it also has a carboxyl group, glycine is both an amine anda carboxylic acid; compounds with both groups are called amino acids.

Amines

Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms).

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

(ionized)(nonionized)

Glycine

Fig. 4-10e

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Sulfhydryl

(may be written HS—)

Cysteine

Cysteine is an important sulfur-containing amino acid.

Thiols

Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.

Cross-linking ofcysteines in hairproteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breakingand re-forming thecross-linking bonds.

Fig. 4-10f

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Phosphate

In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.

Glycerol phosphate

Organic phosphates

Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates).

Has the potential to react with water, releasing energy.

Fig. 4-10g

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Methyl

5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

5-Methyl cytidine

Methylated compounds

Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes.

Arrangement of methyl groups in male and female sex hormones affectstheir shape and function.

ATP: An Important Source of Energy for Cellular Processes

• One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell

• ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

– One phosphate can react with water and split off, living ADP and releasing a lot of energy

– Energy used by the cell


Fig. 4-UN3

Adenosine

Fig. 4-UN4

P P P P i P PAdenosine Adenosine Energy

ADPATP Inorganic phosphate

Reacts with H2O

SUMMARY• Functional groups

– affect molecular function by being directly involved in chemical reactions

• The seven most common functional groups

– Hydroxyl

– Carbonyl

– Carboxyl

– Amino

– Sulfhydryl

– Phosphate

– methyl

• ATPCopyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-10d

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Amino

Because it also has a carboxyl group, glycineis both an amine anda carboxylic acid; compounds with both groups are called amino acids.

Amines

Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms).

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

(ionized)(nonionized)

Glycine

Fig. 4-10e

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Sulfhydryl

(may be written HS—)

Cysteine

Cysteine is an important sulfur-containing amino acid.

Thiols

Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.

Cross-linking ofcysteines in hairproteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breakingand re-forming thecross-linking bonds.

Fig. 4-10g

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Methyl

Methylated compounds

Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes.

Arrangement of methyl groups in male and female sex hormones affectstheir shape and function.

5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

5-Methyl cytidine

Fig. 4-10c

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Carboxyl

Acetic acid, which gives vinegar its sour taste

Carboxylic acids, or organic acids

Has acidic propertiesbecause the covalent bond between oxygen and hydrogen is so polar; for example,

Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

Acetic acid Acetate ion

Fig. 4-10aCHEMICALGROUP

STRUCTURE

NAME OF COMPOUND

EXAMPLE


Carbonyl

The carbonyl group ( CO)consists of a carbon atomjoined to an oxygen atom by adouble bond.

Acetone, the simplest ketone

Propanal, an aldehyde

Aldehydes if the carbonyl groupis at the end of the carbonskeleton

Ketones if the carbonyl group iswithin a carbon skeleton

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.

These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).

Fig. 4-10a

Hydroxyl

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. (Do not confuse this functional group with the hydroxide ion, OH–.)

NAME OF COMPOUND

Alcohols (their specific names usually end in -ol)

EXAMPLE

Ethanol, the alcohol present in alcoholic beverages

• Is polar as a result of theelectrons spending more timenear the electronegative oxygen atom.

• Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars.


(may be written HO—)

Fig. 4-10f

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Phosphate

Organic phosphates

Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates).

Has the potential to react with water, releasing energy.In addition to taking part in

many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.

Glycerol phosphate

You should now be able to:

1. Explain how carbon’s electron configuration explains its ability to form large, complex, diverse organic molecules

2. Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules

3. Distinguish among the three types of isomers: structural, geometric, and enantiomer


4. Name the major functional groups found in organic molecules; describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur

5. Explain how ATP functions as the primary energy transfer molecule in living cells


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