Chapter 4

How does carbon account for the large diversity of biological molecules? Organic chemistry – study of compounds containing carbon Accounts for small molecules (methane) to large molecules (proteins)

What are the hypotheses about the natural origin of life on Earth? Vitalism – Belief in a life force outside the jurisdiction of physical and chemical laws – Provided for foundation of organic that eventually began to undermine its very foundation – Who first provide great doubt about vitalism? Wohler who made urea Followed by Kolbe who made acetic acid

Stanley Miller

Who was Stanley Miller and what was his contribution? – Experimented to see if complex organic molecules could arise spontaneously under conditions thought to have existed on the early Earth – His experiment supported the idea that abiotic synthesis of organic compounds could have been an early stage in the origin of life

LE 26-2 Water vapor CH 4 NH 3 H2H2 Electrode Condenser Cold water Cooled water containing organic molecules Sample for chemical analysis H2OH2O

Energy Source

Who was Stanley Miller and what was his contribution? – Helped shift from vitalism to mechanism

What is mechanism? View that physical and chemical laws govern all natural phenomena, including the processes of life

How does carbon form a wide selection of diverse molecules? Carbon has 6 electron – 2 first electron shell – 4 in second shell (4 valence electrons) This shell can hold 8 Would have to donate or accept 4 to complete valence shell and become ion – Generally complete valence shell by covalently bonding sot that 8 electrons (4 from itself, 4 from another) are shared Called tetravalence – Leads to carbon’s versatility to make complex molecules – Generally forms a tetrahedral shape

Most Frequent Partners Oxygen Hydrogen Nitrogen

Can also form covalent bonds to other carbon atoms, linking the atoms into chains of a huge variety

What is the benefit of having a carbon skeleton? Vary in length Can be straight, branched, or in rings, double bonds, single bonds, etc

What is a hydrocarbon? Organic molecules consisting of only carbon and hydrogen Wherever electrons are available for covalent bonding, atoms of hydrogen are attached to the carbon skeleton Many of cell’s organic molecules have regions consisting of only carbon and hydrogen Many of the compounds are hydrophobic because of the non-polar carbon-to-hydrogen linkages Reactions generally release a relatively large amount of energy

What is an isomer? Compounds that have the same number of atoms and the same element composition, but are arranged differently

Kinds of Different isomers Structural Geometric enantiomers

Kinds of Different isomers Structural – Differ in the covalent arrangement of atoms – two substances having the same molecular formula but different physical and chemical properties because the arrangement of their component atoms is different.molecular formula but different physical and chemical properties because the arrangement of their component atoms is different. – Also known as Constitutional ISomers

Kinds of Different isomers Geometric – Have same covalent partnerships but differ in spatial arrangement – Due to inflexibility of double bonds – two or more coordination compounds which contain the same number and types of atoms, and bonds (i.e., the connectivity between atoms is the same), but which have different spatial arrangements of the atoms. – Not all coordination compounds have geometric isomers.

Kinds of Different isomers Geometric – Due to inflexibility of double bonds Two types: – cis isomer- » the two groups are on the same side of the double bond – trans isomer- » the two groups are on opposite sides

Note that these two structures contain the same number and kinds of atoms and bonds but are non-superimposable. The isomer in which like ligands are adjacent to one another is called the cis isomer. The isomer in which like ligands are opposite one another is called the trans isomer. Kinds of Different isomers

enantiomers – isomers that are mirror images of each other – Occurs when there are asymmetric carbons Carbon is attached to 4 different atoms or groups of atoms – Two forms: Right-handed Left-handed – Generally one is biologically active, while the other is not Kinds of Different isomers

What chemical groups are key to the functioning of biological molecules? chemical groups are key to the functioning of biological molecules? – Hydrocarbons- Simplest organic molecules Underlying framework for more complex organic molecules

Hydrocarbon tails

Hydrocarbon Tails of a Phospholipid Structural formula Space-filling model Phospholipid symbol Hydrophilic head Hydrophobic tails Fatty acids Choline Phosphate Glycerol Hydrophobic tails Hydrophilic head

Cell Membranes

What chemical groups are key to the functioning of biological molecules? – The groups attached to the hydrocarbons can participate in chemical reactions or can contribute to function indirectly by their effects on molecular shape – These chemical groups can affect molecular function by becoming directly involved in chemical reaction

Functional Groups Participates in chemical reactions in a characteristic ways 7 chemical groups are important to biological processes

Functional groups serve important purposes in molecules Estradiol Testosterone Male lion Female lion

7 Chemical Groups Important to Biological Processes Hydrophilic and can act as functional groups – Hydroxyl – Carbonyl – Carboxyl – Amino – Sulfhydryl – Phosphate

LE 4-10aa STRUCTURE (may be written HO—) NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ethanol, the alcohol present in alcoholic beverages FUNCTIONAL PROPERTIES 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).

LE 4-10ab STRUCTURE NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton EXAMPLE Acetone, the simplest ketone A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Aldehydes if the carbonyl group is at the end of the carbon skeleton Acetone, the simplest ketone Propanal, an aldehyde FUNCTIONAL PROPERTIES

LE 4-10ac STRUCTURE NAME OF COMPOUNDS Carboxylic acids, or organic acids EXAMPLE Has acidic properties because it is a source of hydrogen ions. Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H + ) tend to dissociate reversibly; for example, Acetic acidAcetate ion In cells, found in the ionic form, which is called a carboxylate group.

LE 4-10ba STRUCTURE NAME OF COMPOUNDS Amine EXAMPLE 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 Acts as a base; can pick up a proton from the surrounding solution: (nonionized) Ionized, with a charge of 1+, under cellular conditions Glycine (ionized)

LE 4-10bb STRUCTURE (may be written HS—) NAME OF COMPOUNDS Thiols EXAMPLE Ethanethiol FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).

LE 4-10bc STRUCTURE NAME OF COMPOUNDS Organic phosphates EXAMPLE Glycerol phosphate FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules.

Not reactive and acts as a recognizable tag on biological molecules – methyl 7 Chemical Groups Important to Biological Processes