Ch 4 BIO 210

Hydroxyl

-OH Hydrogen atom is bonded to an oxygen atom. Found in Sugars and Alcohols Ex. Ethanol and Glucose Are polar as a result of the electrons spending more time near the electronegative O atom. They can form hydrogen bonds with water molecules/ helping dissolve organic compounds like sugars.

Sulfhydryl

-SH (consists of sulfer atom bonded to an atom of H) Also called Thiols Example cysteine(amino acid) A disulfide bridge with a covalent bond stabilizes a protein (they release Hydrogens when bonding) Found in proteins -links different parts of proteins together.

Ethane

A molecule may have more than one tetrahedral group of single bonded atoms

ATP

Adenosine triphosphate Three phosphate groups attached to adenosine. One phosphate may split off as in reaction with water. Losing one phosphate ATP becomes ADP (diphosphate). ATP stores energy and after the reaction with water ADP is activated and energy is released.

Methyl

Also called Methylated compounds CH3 Three hydrogen bonded to a carbon. The methyl group may be attached to a carbon or to a different atom. Addition of a methyl group to DNA affects expression of genes. They are found in fatty acids Makes molecular region hydrophobic. They are hydrophobic because the difference in electronegativity btw. C and H is small - so there are no charge imbalances in the methyl molecule. Ex. male and female sex hormones and where the methyl group is attached affects its expression.

Enantiomer Isomers

Also called Optical Isomers They cannot be superimposed on each other. Mirror images / they have a CHIRAL carbon which needs four different elements bonded to each bond. Arrangement of unique groups around an asymmetrical carbon atom Middle carbon also called the asymmetric carbon. One isomer is biologically active and the other isnt - sometimes the inactive one produces harmful effects.

Carbonyl

C=O consists of a carbon atom joined to an oxygen atom by a double bond. Name of Compound: Ketones - if the carbonyl group is within a carbon skeleton Ex. Fructose Aldehydes - if the carbonyl group is at the end of the carbon skeleton.Ex Glucose Acetone - the simplest ketone. Ketones and aldehydes may be structural isomers with different properties. Sucrose doesn't react with Benedicts reagent bc it doesn't have a free carbonyl group Ring and linear formation of Glucose affect reactions. Ring form doesn't react because of NO free carbonyl group

Carboxyl

COOH Carbon is double bonded to oxygen which is also bonded to OH group. Name of compound: Carboxylic Acid - Organic Acids. Example - Acetic Acid Has acidic properties (is a source of H ions) because the covalent bond between oxygen and hydrogen is so polar. Found in cells in the ionized form with a charge of 1- (called cacrboxylate ion) The H+ is donated to the environment, increasing the local H ion concentration and making the solution more acidic. They are also a part of fatty acids ..

Carbon bonds

Carbon has 6 electrons with 2 in the first electron shell and 4 in the second shell. - they have to donate or accept 4 electrons to complete its valence shell and become an ion. Instead a carbon atom usually completes its valence shell by sharing 4 electrons with other atoms in covalent bonds - single and double.

Structural Isomers

Different arrangement of carbon skeleton. Differ in the covalent arrangements of their atoms. The number of possible isomers increases more as carbon skeletongs increase in size. Also may differ in the location of double bonds.

Geometric isomers

Different organization across double bond / Cis (same sides) and Trans (opposite sides) Applies to molecules with double bonds. The different arrangements are in relation to the double bonds. Have the same covalent partnerships but they differ in their spatial arrangements. The differences arise from the inflexibility of double bonds. Single bonds allow the atoms they join to rotate around the axid but double bonds can't rotate

Common ingredients of Life

Hydrogen Oxygen Nitrogen Sulfur Phosphorus

Seven Functional Groups

Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate Above six are hydrophilic and INCREASE the solubility of organic compounds in water. Methyl - is not reactive but is also hydrophobic and reduces water absorption? they act as a tag on biological molecules.

Amino Group

NH2 (Amines) - compounds bonded to COOH are called amino acids (acts as the building block of protein) and nucleic acids Acts as a BASE. Makes a molecule alkaline (accepts a proton) Can pick up H+ from the surrounding solution Ionized with a charge of 1+ under cellular conditions Example Glycine The alpha carbon of most amino acids is a chiral carbon. Except for Glycine where the R group is another H (the chiral carbon is attached to two Hydrogens)

Hydrocarbons

Organic molecules consisting of only carbon and hydrogen. Atoms of H are attached to the carbon skeleton wherever electrons are available for covalent bonding. Hydrocarbons are the major componet of petroleum (fossil fuel) All hydrocarbons are hydrophobic because the majority of their bonds are relatively nonpolar C to H links. They also release a large amount of energy when reacted upon.

Phosphate

PO4H2 Participates in 5 covalent bonds. Found in DNA and RNA Used in energy transfer ATP Example glycerol phosphate (provides the backbone for phospholipids) the most prevalent molecule in a cell membrane. Contributes negative charge to the molecule- can donate up to two H ions to the solution. Phosphate increases the acidity of a solution. Has the potential to react with water.

Functional Groups contd.

These are small groups of atoms that function as a UNIT and impart specific characteristics to larger molecules. They are also chemical groups that affect molecular function by being directly involved in chemical reactions. - the different groups react in a different way.

Valence of major elements

Valence is the number of covalent bonds an atom can form, generally is equal to the number of electrons required to complete the valence shell.

Isomers

Variation in the architecture of organic molecules Compounds that have the same numbers of atoms of the same elements but different structures and hence different properties.

Organic Chemistry

compounds containing carbon are said to be organic - organic chemistry is the study of carbon compounds

Tetravalence

each carbon atom acts as an intersection point from which a molecule can branch off in as many as four direction. - make the carbons versatility.

Ability of carbon

of ALL chemical elements carbon is the best in its ability to form molecules that are large, complex and diverse and have made life on earth possible. Include proteins DNA carbohydrates Ability - can form up to 4 covalent bonds with other atoms/ molecules

Tetrahedron

the shape carbon forms when having four single covalent bonds - ch4 = 109.5 degrees when two carbons are joined with a double bond all carbons are in the same plane.

methane

when a carbon atom has four single bonds to other atoms, the molecule is tetrahedral ch4

Ethene

when two carbon atoms are joined by a double bond, all atoms attached to those carbons are in the same plane, the molecule is flat.