Biology Notes Ch. 4 Carbon and Molecular Diversity

Organic Chemistry

The study of compounds containing carbon

• They can range from simple molecules like methane CH4 to colossal ones like proteins

How are different species of organisms and different individuals within a species distinguuished?

• While the overall percentages of the major elements of life — C, H, O, N, S, and P — are quite uniform from one organism to another (and thus reflecting the common evolutionary origin of all life) because of C ability to make four bonds, this limited assortment of atomic building blocks can be used to build an inexhaustible variety of organic molecules

• Different species/individuals are distinguished by variations in the types of organic molecules they make

Electron Configuration

• The key to an atom’s chemical characteristics

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

• only those available in the outermost shell are free for bonding

Electron shells vs. Orbitals

Electron shells are principal energy levels defined by the primary quantum number (n), representing a large group of electrons, while orbitals are specific three-dimensional regions within a shell where an electron is most likely to be found, with each orbital capable of holding a maximum of two electrons with opposite spins.

Which bonds does carbon typically form?

• usually forms single or double covalent bonds

• Each carbon atom acts as an intersection point from which a molecule can branch off in as many as four directions

• This enables carbon to form large, complex molecules

What is the arrangement of carbons four hybrid orbitals?

• Four hybrid orbitals causes the bonds to angle toward the corners of an imaginary tetrahedron

• The bond angles in methane are 109.5 C

• For example, ethane is shaped like two overlapping tetrahedron

How can carbon structures vary in shape?

• carbon chains form the basis of most organic molecules

• Carbon skeletons vary in length and may be straight, branched, or arranged in closed rings

• Some carbon chains have double bonds which vary in number and location

• Variation in carbon chains is one important source of the molecular complexity and diversity that characterize living matter.

Hydrocarbons

Organic molecules consisting of only carbon and hydrocarbon

• Atoms of hydrogen are attached to the carbon skeleton wherever electrons are available for covalent bonding

• Although not prevalent in most living organisms, some of a cell’s organic molecules have regions consisting of only carbon and hydrogen

• Hydrocarbons compounds are non-polar and therefore hydrophobic

Isomers

• compounds that have the same number of atoms of the same elemnts but different structures and hence different properties

Structure isomers

• Differ in the covalent arrangements of their atoms

Cis-trans Isomers (geometric isomers)

• carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds

• single bonds allow the atoms they join to rotate freely about the bond axis without changing the compound

• Double bonds do not permit such rotation, if a double bond joins two carbon atoms, and each C also has two different atoms (or groups of atoms) attached to it, then two distinct cis-trans isomers are possible.

Enantiomers

Isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon, one that is attached to four different atoms or groups of atoms

• usually, only one isomer is biologically active because only that form can bind to specific molecules in an organism

Similarities & Differences of estradiol and testosterone

• Compounds are female and male sex hormones

• both are steroids, organic molecules with a common carbon skeelton in the form of four fused rings

• they differ only in the chemical groups attached to the rings

• These chemical groups are important because they affect molecular shape, contributing to their functions

Functional groups

• chemical groups involved in chemical reactions

• each has certain properties, such as shape and charge, that cause it to participate in chemical reactions in a characteristic way

• Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phospahte, and methyl groups

  • the first six groups can be chemically reactive; of these six, all except the sulfhydryl group are also hydrophilic and thus increase the solubility of organic compounds in water

• The methyl group is not reactive, but instead often serves as a recognizable tag on biological molecules.

Adenosine Triphosphate or ATP

• Where three phosphates are present in series, as in ATP, one phosphate may be split off as a reuslt of a reaction with water

• This inorganic phosphate ion is usually abbrivated

• Having lost one phosphate, ATP becomes adenosine diphosphate, or ADP

• Sometimes stored as energy, it is mor eaccurated to think of it as storing the potential to react with water or other molecules

Components of Living Matter

• consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus.

• These elements all form strong covalent bonds, an essential characteristic in the architecture of complex organic molecules

Hydroxyl Group

• Written as -OH and is used primarily in the structure of alcohols

• Is a polar molecule due to the oxygen hogging the electrons 

• Can be used to form hydrogen bonds within water molecules which helps dissolve organic compounds like sugars. 

Carbonyl Group

• Written as a carbon double bonded to an oxygen and is used primarily in ketones if the carbonyl group is within a carbon skeleton OR they can be used in 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 and these groups are also found in sugars 

Carboxyl Group

• Written as a carbon double bonded with an oxygen and single bonded to an -OH

• Act as acids which donate H+ ions because the covalent bond between the oxygen and hydrogen is so polar. 

Amino Group

• is written as N with two single bonds to hydrogen molecules

• Acts as a base where the H+ ion is absorbed from the surrounding solution which is usually water in living organisms 

Sulfhydryl 

• written as —SH and is found within Thiols 

• When two sulfhydryl groups react, this forms a covalent bond that creates “cross-linking” which helps stabilize protein structure

• 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 and then breaking and reforming the cross linking bonds. 

Phosphate

• Written as P which has 3 single bonds to O and then one double bond to an O. This is commonly found in organic phosphates 

• Because two of the O’s have a negative charge, this contributes a negative charge to the molecule of which it is a part of. 

• Molecules containing this group have the potential to react with water and release energy. 

Meythl

• Written as carbon with 3 single bonds to H and is commonly found in methylated compounds 

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

• Arrangement of methyl groups in male and female sex hormones affect their shape and function