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The Backbone of Biological Molecules
Although cells are 70–95% water, the rest consists mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex and diverse molecules Proteins, lipids, DNA, carbohydrates and other molecules that distinguish living matter are all composed of carbon compounds
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Organic chemistry is the study of carbon compounds
Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized the compounds in the lab
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Sample for chemical analysis
EXPERIMENT “Atmosphere” CH4 Water vapor Electrode NH3 H2 Condenser Cooled water containing organic molecules Cold water Figure 4.2 Can organic molecules form under conditions believed to simulate those on the early Earth? H2O “sea” Sample for chemical analysis
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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
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The Formation of Bonds with Carbon
With four valence electrons, carbon can form four covalent bonds with a variety of atoms This tetravalence makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, the molecule has a flat shape
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Molecular Formula Structural Formula Ball-and-Stick Model
Space-Filling Model Name (a) Methane (b) Ethane Figure 4.3 The shapes of three simple organic molecules (c) Ethene (ethylene)
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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
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Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4)
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Molecular Diversity Arising from Carbon Skeleton Variation
Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape
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(commonly called isobutane)
Ethane Propane Length Butane 2-methylpropane (commonly called isobutane) Branching 1-Butene 2-Butene Double bonds Cyclohexane Benzene Rings
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Carbon atoms can partner with atoms other than hydrogen; for example:
Carbon dioxide: CO2 Urea: CO(NH2)2 O = C = O
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Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy
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Fat droplets (stained red)
100 µm A fat molecule Mammalian adipose cells
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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
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Pentane 2-methyl butane
Figure 4.7 Three types of isomers (a) Structural isomers
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cis isomer: The two Xs are on the same side.
trans isomer: The two Xs are on opposite sides. (b) Geometric isomers Figure 4.7 Three types of isomers
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L isomer D isomer Figure 4.7 Three types of isomers (c) Enantiomers
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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
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(effective against Parkinson’s disease) (biologically Inactive) L-Dopa
D-Dopa (biologically Inactive)
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Effective Enantiomer Ineffective Enantiomer Drug Condition Pain;
inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Figure 4.8 The pharmacological importance of enantiomers Albuterol Asthma R-Albuterol S-Albuterol
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Functional groups are the parts of molecules involved in chemical reactions
Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it Certain groups of atoms are often attached to skeletons of organic molecules
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The Functional Groups Most Important in the Chemistry of Life
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
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Estradiol Female lion Testosterone Male lion
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The six functional groups that are most important in the chemistry of life:
Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group
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FUNCTIONAL PROPERTIES
STRUCTURE (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Alcohols (their specific names usually end in -ol) 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).
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STRUCTURE EXAMPLE NAME OF COMPOUNDS Acetone, the simplest ketone
Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.
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STRUCTURE EXAMPLE Acetic acid, which gives vinegar its sour taste NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Carboxylic acids, or organic acids Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.
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STRUCTURE 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. NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Amine Acts as a base; can pick up a proton from the surrounding solution: (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions
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STRUCTURE EXAMPLE NAME OF COMPOUNDS
(may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Thiols Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).
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component of DNA that has been modified by addition of a methyl group
Methyl group ( CH3) Methylated compound 5-Methyl cytosine, a component of DNA that has been modified by addition of a methyl group Figure 3.5bc Some biologically important chemical groups (part 9: methyl) 31
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Hydrogen bond Hydrophobic interactions and van der Waals interactions
Figure 3.21d Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Figure 3.21d Exploring levels of protein structure (part 8: tertiary stabilization) Polypeptide backbone 33
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STRUCTURE EXAMPLE NAME OF COMPOUNDS
Glycerol phosphate NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Organic phosphates Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules.
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Adenine Phosphate groups Ribose
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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
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Reacts with H2O Energy ATP Inorganic phosphate ADP Adenosine Adenosine
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Animations and Videos Bozeman - Molecules of Life Bozeman - Biological Molecules Building Biomolecules Properties of Biomolecules Biochemical Pathway A Biochemical Pathway Functional Groups – 1 Functional Groups - 2
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Animations and Videos Chapter Quiz Questions – 1 Chapter Quiz Questions – 2
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What was the first organic molecule to be synthesized in the laboratory?
ammonium cyanate hydrogen cyanide urea acetic acid methane Answer: c
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What was the first organic molecule to be synthesized in the laboratory?
ammonium cyanate hydrogen cyanide urea acetic acid methane
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Carbon is an unusual atom in that it can form multiple bonds
Carbon is an unusual atom in that it can form multiple bonds. Which statement is NOT true? A carbon-to-carbon cis double bond is the type found in nature and is associated with cardiovascular health. A carbon-to-carbon trans double bond is made artificially in food processing and is associated with poor cardiovascular health. Multiple carbon-to-carbon double bonds located near each other can absorb light, so they are found in molecules in the eye or in chloroplasts. Multiple carbon-to-carbon bonds are stronger than single bonds. Saturated fats are those that have a carbon-to-carbon double bond and are associated with good health. Answer: E This question emphasizes the application of material in Concept 3.1. 42
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Carbon is an unusual atom in that it can form multiple bonds
Carbon is an unusual atom in that it can form multiple bonds. Which statement is NOT true? A carbon-to-carbon cis double bond is the type found in nature and is associated with cardiovascular health. A carbon-to-carbon trans double bond is made artificially in food processing and is associated with poor cardiovascular health. Multiple carbon-to-carbon double bonds located near each other can absorb light, so they are found in molecules in the eye or in chloroplasts. Multiple carbon-to-carbon bonds are stronger than single bonds. Saturated fats are those that have a carbon-to-carbon double bond and are associated with good health. 43
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What type of chemical bond joins a functional group to the carbon skeleton of a large molecule?
covalent bond hydrogen bond ionic bond double bond disulfide bond Answer: a
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What type of chemical bond joins a functional group to the carbon skeleton of a large molecule?
covalent bond hydrogen bond ionic bond double bond disulfide bond
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Which of the following is NOT one of the seven functional groups found in biological molecules?
amino hydroxyl carboxyl cyanate phosphate Answer: d
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Which of the following is NOT one of the seven functional groups found in biological molecules?
amino hydroxyl carboxyl cyanate phosphate
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Which functional group behaves as a weak acid in organic molecules?
amino carboxyl carbonyl sulfhydryl hydroxyl Answer: b
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Which functional group behaves as a weak acid in organic molecules?
amino carboxyl carbonyl sulfhydryl hydroxyl
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Which functional group behaves as a weak base in organic molecules?
amino carboxyl carbonyl sulfhydryl hydroxyl Answer: a
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Which functional group behaves as a weak base in organic molecules?
amino carboxyl carbonyl sulfhydryl hydroxyl
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Which type of molecule always contains phosphate groups?
carbohydrates lipids proteins nucleic acids none of the above Answer: d
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Which type of molecule always contains phosphate groups?
carbohydrates lipids proteins nucleic acids none of the above
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What type of isomer is propanal compared to acetone?
cis-trans isomer structural isomer enantiomer none of the above; these are not isomers Answer: b
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What type of isomer is propanal compared to acetone?
cis-trans isomer structural isomer enantiomer none of the above; these are not isomers
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Which type of molecule may contain sulfhydryl groups?
carbohydrate lipid protein nucleic acid all of the above Answer: c
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Which type of molecule may contain sulfhydryl groups?
carbohydrate lipid protein nucleic acid all of the above
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Which functional group is best known for its ability to change the shape of a molecule without affecting its reactivity? amino carboxyl sulfhydryl phosphate methyl Answer: e
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Which functional group is best known for its ability to change the shape of a molecule without affecting its reactivity? amino carboxyl sulfhydryl phosphate methyl
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Scientific Skills Questions
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The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. What is the molar ratio of serine? 1 mole of serine per mole of glycine 3.0 x 102 moles of serine per mole of glycine 3.0 x 102 moles of glycine per mole of serine 1 mole of serine per 3.0 x 102 moles of glycine Answer: b
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The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. What is the molar ratio of serine? 1 mole of serine per mole of glycine 3.0 x 102 moles of serine per mole of glycine 3.0 x 102 moles of glycine per mole of serine 1 mole of serine per 3.0 x 102 moles of glycine
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The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. Which amino acid is present in higher amounts than glycine? serine methionine alanine serine and methionine Answer: c
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The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. Which amino acid is present in higher amounts than glycine? serine methionine alanine serine and methionine
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Based on these results, how many molecules of methionine are present per mole of glycine?
1.08 x 1070 molecules 1.8 x 103 molecules 1.08 x 1021 molecules 6.02 x 1023 molecules Answer: c
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Based on these results, how many molecules of methionine are present per mole of glycine?
1.08 x 1070 molecules 1.8 x 103 molecules 1.08 x 1021 molecules 6.02 x 1023 molecules
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The synthetic atmosphere in this experiment contained H2S instead of water vapor. Which of these amino acids could not have been produced in Miller’s original abiotic synthesis experiment? serine methionine alanine glycine Answer: b
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The synthetic atmosphere in this experiment contained H2S instead of water vapor. Which of these amino acids could not have been produced in Miller’s original abiotic synthesis experiment? serine methionine alanine glycine
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