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Biology news sources- 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 Ancient Skeleton May Rewrite Earliest Chapter of Human Evolution By Ann Gibbons ScienceNOW Daily News 1 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." Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Biology news sources- 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. Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Chapter 4 Carbon and the Molecular Diversity of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Overview: Carbon: The Backbone of Life Although cells are 70 95% water, the rest consists mostly of carbonbased compounds Carbon enters the biosphere through the action of plants, which use solar energy to transform atmospheric CO 2 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

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, CH 4 ) to colossal ones (such as proteins) Most organic compounds contain hydrogen atoms in addition to carbon atoms Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 4.1: Organic chemistry is the study of carbon compounds 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

Concept 4.1: Organic chemistry is the study of carbon compounds 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 4.1: Organic chemistry is the study of carbon compounds 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. Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-2 EXPERIMENT Atmosphere Water vapor CH 4 Electrode Condenser Cooled water containing organic molecules Cold water H 2 O sea Sample for chemical analysis

Concept 4.1: Organic chemistry is the study of carbon compounds 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. Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

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

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

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

The Formation of Bonds with Carbon 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-3 Name Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model (a) Methane (b) Ethane (c) Ethene (ethylene)

The Formation of Bonds with Carbon 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-4 Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) H O N C

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

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

Fig. 4-5a (a) Length Ethane Propane

Fig. 4-5b Butane (b) Branching 2-Methylpropane (commonly called isobutane)

Fig. 4-5c 1-Butene (c) Double bonds 2-Butene

Fig. 4-5d Cyclohexane (d) Rings 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-6 Fat droplets (stained red) 100 µm (a) Mammalian adipose cells (b) A fat molecule

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

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

Structural Isomers Fig. 4-7a 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 C 5 H 12-3; C 8 H 18-18; C 10 H 42-366,319 Pentane 2-methyl butane (a) Structural isomers

Fig. 4-7b 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 cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (b) Geometric isomers

Fig. 4-7c 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 asymmetirc carbon in two different ways Like right- and left-handed versions of a molecule L isomer (c) Enantiomers D isomer

Enantiomers 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 http://www.wired.com/images/article/full/2008/09/thalidomide_baby_350px.jpg Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Enantiomers Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules Animation: L-Dopa Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-8 Enantiomers Drug Condition Effective Enantiomer Ineffective Enantiomer Ibuprofen Pain; inflammation S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

SUMMARY Pentane (a) Structural isomers 2-methyl butane L isomer (c) Enantiomers D isomer cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (b) Geometric isomers Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

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

Fig. 4-9 Estradiol Testosterone Both are steroids Differ only in chemical groups attached to the rings Affect function by affecting molecule s shape

Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules 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 Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-10a Hydroxyl NAME OF COMPOUND Alcohols (their specific names usually end in -ol) EXAMPLE (may be written HO ) 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.) Ethanol, the alcohol present in alcoholic beverages FUNCTIONAL PROPERTIES Is polar as a result of the electrons spending more time near the electronegative oxygen atom. Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

Fig. 4-10a CHEMICAL GROUP Carbonyl NAME OF COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton STRUCTURE Ketones if the carbonyl group is within a carbon skeleton EXAMPLE The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. Acetone, the simplest ketone FUNCTIONAL PROPERTIES A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. These two groups are also found in sugars, giving rise to two major groups of sugars: aldoses (containing an aldehyde) and ketoses (containing a ketone). Propanal, an aldehyde

Fig. 4-10c Carboxyl STRUCTURE Carboxylic acids, or organic acids NAME OF COMPOUND EXAMPLE Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, FUNCTIONAL PROPERTIES Acetic acid, which gives vinegar its sour taste Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1 and called a carboxylate ion (here, specifically, the acetate ion).

Fig. 4-10d Amino STRUCTURE Amines NAME OF COMPOUND EXAMPLE Glycine Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms). FUNCTIONAL PROPERTIES Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions.

Fig. 4-10e Sulfhydryl STRUCTURE (may be written HS ) Thiols NAME OF COMPOUND EXAMPLE Two sulfhydryl groups can react, forming a covalent bond. This cross-linking helps stabilize protein structure. FUNCTIONAL PROPERTIES Cysteine Cysteine is an important sulfur-containing amino acid. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be permanently curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds.

Fig. 4-10f Phosphate STRUCTURE Organic phosphates NAME OF COMPOUND EXAMPLE Glycerol phosphate 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). FUNCTIONAL PROPERTIES 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. Has the potential to react with water, releasing energy.

Fig. 4-10g Methyl STRUCTURE Methylated compounds NAME OF COMPOUND EXAMPLE Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. FUNCTIONAL PROPERTIES 5-Methyl cytidine Arrangement of methyl groups in male and female sex hormones affects their shape and function. 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

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

Fig. 4-UN3 Adenosine

Fig. 4-UN4 Reacts with H 2 O P P P Adenosine P i P P Adenosine Energy ATP Inorganic phosphate ADP

SUMMARY Functional groups affect molecular function by being directly involved in chemical reactions The seven most common functional groups ATP Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate methyl Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-10f Phosphate STRUCTURE Organic phosphates NAME OF COMPOUND EXAMPLE Glycerol 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. 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. FUNCTIONAL PROPERTIES

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

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