Organic Chemistry and Biochemistry

Lecture Text Chapter 2

Organic Molecules

• Molecules containing both carbon and hydrogen

• Carbon– 4 valence electrons in

outer orbital– Needs 8 total for full

complement

Carbon

• Can form 4 covalent bonds

• Can form 1-2 bonds with multiple atoms, including other carbon atoms– Form chains of carbons,

rings, etc.

Reactive Groups

• Hydrocarbon chains may be linked to more reactive elements– E.g., oxygen, nitrogen

Chemical Formulas

• Molecular Formulas– Number of atoms of each element in the

molecule• E.g. water = H2O

• E.g. methane = CH4

• E.g. glucose = C6H12O6

– Does not indicate how atoms bond together

Chemical Formulas

• Structural Formulas– Indicate bonds among atoms within molecules– Single line indicates single covalent bond– Double line indicates double covalent bond– E.g. Acetone (C3H6O)

Chemical Formulas

• Condensed Structural Formulas– Not all bonds drawn– Central atoms shown with atoms bonded to

them

– E.g. Acetone (C3H6O)

(CH3)CO(CH3)

(CH3)2CO

CH3CCH3

Oor or

Chemical Formulas

• Line-Angle Formulas– Bonds represented by lines

– Carbon atoms assumed to be present at the end of any line

– Oxygen and Nitrogen shown, Hydrogen is not

– Each carbon is assumed to have enough hydrogens bonded to it by single bonds to give it four bonds total

Chemical Formulas

• Line-Angle Example

Line-Angle Structural Formula

Biomolecules• Complex organic molecules used in biological

systems• Polymers

– Made up of repeated subunits

• Major Groups1. Carbohydrates – energy sources, cell communication2. Lipids – energy storage, cell membrane structure,

cushioning, cell communication3. Proteins – structure, cell function (enzymes) , cell

communication4. Nucleic Acids – information storage

Carbohydrates (Sugars)

• molecules that contain H, O and C

• relative amounts of each are the same in all simple carbohydrates– #C atoms = #O atoms– #H atoms = 2x the number of either C or O

• general formula = (CH2O)n

– e.g. glucose – C6H12O6

Carbohydrates (Sugars)• monosaccharide - individual

unit• basic CH2O formula• name possesses the suffix –ose

– e.g. glucose, galactose, fructose, ribose

• Monosaccharides can have the same formula but different arrangements of atoms– Isomers – molecules of same

formula but different structures

Carbohydrates (Sugars)

• Disaccharide– two monosaccharides linked

together • e.g. sucrose

= glucose + fructose

• e.g. maltose = glucose +

glucose

Carbohydrates (Sugars)

• Polysaccharide– Many monosaccharides

linked together

• E.g. glycogen– Polymer of glucose

Carbohydrate Synthesis

• Monosaccharides are linked together by dehydration synthesis– employs specific enzymes– H is removed from one

monosaccharide, an -OH group from the other

– covalent bond (glycosidic bond) formed between the two

– water formed as an end-product

Carbohydrate Digestion

• polysaccharides are broken apart via hydrolysis– a water molecule is split– H+ added to one of the

free monosaccharides– OH group added to the

other

Lipids (Fats, Oils, Waxes)

• very general category• contain compounds

that are not soluble in water (hydrophobic)

• Major classes– Triglycerides– Phospholipids– Steroids

Triglycerides

• fats and oils• formed by dehydration

synthesis• combine glycerol with

three molecules of fatty acid

Triglycerides

• different types of fatty acids• Saturated

– all carbons in chain linked by single bonds

• Unsaturated– one or more carbons in chain

linked by double bonds

• Unsaturated fatty acids tend to be more fluid

Phospholipids

• contain a phosphate group (PO4)

• commonly a combination of a phosphate group to a glycerol molecule attached to two fatty acids– e.g. lecithin

Phospholipids

• possess both polar an nonpolar ends (amphipathic)

• nonpolar ends aggregate together

• form micelles when mixed in water– interact with water – lowers

surface tension of water

Steroids• Consist of 3 six-carbon rings and a

single five-carbon ring interlocked together

• different functional groups attached to basic structure– e.g. sex steroids – produced by

gonads (testosterone, progesterone)– e.g. corticosterones – produced by

adrenal glands– e.g. cholesterol – precursor for

hormones, regulation of cell membrane fluidity

Proteins

• Diverse in structure and function

• Polymers of amino acids• 20 common amino acids

each with:– an amino group

– a carboxyl group

– a functional side-group (differs among a.a.’s)

Peptide Bonds

• Amino acids are joined together by dehydration synthesis

• NH3 group of one joined to the COOH group of another to form a peptide bond– two joined amino acids =

dipeptide– many joined amino acids =

polypeptide

Protein Structure:Primary Structure

• Sequence of amino acids in a polypeptide chain

• From free amino end (N-terminus) to the free carboxyl end (C-terminus)

• May be 1000’s of a.a.’s long

Protein Structure:Secondary Structure

• Formation of helix or sheet shape in a protein chain

• due to hydrogen bonds forming between the amino group of one peptide bond and the carboxyl group from another peptide bond

Protein Structure:Tertiary Structure

• Twisting and folding of a single protein chain

• due to chemical interactions among the different sidechain groups

Protein Structure:Quaternary Structure

• Bonding and interactions of multiple polypeptide chains– e.g. insulin = two

separate chains– e.g. hemoglobin = four

separate chains

Conjugated Biomolecules

• Combinations of two or more types of biomolecules– Glycoprotein = carbohydrate + protein– Lipoprotein = lipid + protein– Glycolipid = carbohydrate + lipid