Essential chemistry for biochemistry

97% by weight of most organism accounted for by 6 elements.
These elements are?

C, H, O, N, P, S.

Water is the major component of most cells.
Last time we discussed the proposition that Life is a water-based phenomenon

C is much more abundant in cells than the environment.

Why is life often called a carbon-based phenomenon?
What are the properties of C that allow its versatility?

• the compounds that make up living organisms are based on C
• C has 4 valence electrons: tetravalent
• C has little tendency to gain or lose electrons to form ions or be involved in ionic or charged interactions
• these chemical properties of C allow it to make large, complex, and diverse chains and rings with the other major constituents of cells, H, O, N, P, S.
• the major biomolecules, nucleic acids, proteins, carbohydrates and lipids, are based on C

Chemistry of C termed organic chemistry.
If biochemistry is the chemistry of life processes,
Then biochemistry is the organic chemistry of life processes.
A knowledge of organic chemistry fundamental to an understanding of biochemistry

What is the atomic structure of C?

• 4 valence electrons , 2s and 2p, which form 4 sp3 bonding orbitals by promotion of an s orbital to the vacant p orbital
• the 4 sp3 orbitals point to the corners of a regular tetrahedron, angle of 109 degrees
• C may form single bonds by sp3 overlap (a sigma bond), double bonds by sp2 and p overlap (a sigma and a pi bond), or triple bonds by sp and two p overlap (a sigma and two pi bonds)
• these bonds form with itself or other elements

• methane, CH4

• ethane, C2H6

• ethanol, CH3CH2OH

• ethanal (acetaldehyde), CH3CHO

• ethanoic acid (acetic acid), CH3COOH

• urea

• ethylamine, CH3CH2NH2

• ethanamide or acetamide, CH3CONH2

Properties of functional groups.

Functional groups are made up of the other common elements in the biosphere, H, O, P, N, S.

Functional groups have particular and individual chemical properties, behave consistently from one molecule to another, and allow us to predict the properties of a molecule.
Note that these properties make use of the non-covalent interactions and acid base properties we discussed previously.

1. Aliphatic:
   • hydrocarbons: methane, ethane, propane, etc
   • uncharged, non-polar, hydrophobic
   • chemically rather inert
   • but >C=C< adds polarity so that it readily undergoes reversible addition/elimination reactions
     -CH=CH- + H2O <--> CH2-CHOH-
   
   
2. Alcohols: R-OH
   • methanol, ethanol, etc
   • uncharged but polar, hydrophilic, dipole and H-bond interactions.
   
   
3. Carbonyl group: >C=O
   • aldehydes, RCHO
   • ketones, R-CO-R
   • uncharged but polar, dipole and H-bond interactions
   
   
4. Carboxyl group: R-COOH
   • weak acids, weak proton donors, partial dissociation, buffers
   • charge interactions
   
   
5. Amines:
   • R-NH2, uncharged but polar, dipole and H-bond interactions
   • a base, like ammonia = proton acceptor, which will then become:
   • R-NH3+, charged, weak acid, proton acceptor.
   
   
6. Phosphate group:
   • derived from phosphoric acid, H3PO4
   • R-CH2-OPO3
   • charge interactions
   • transfer of energy between molecules

Isomerism

What are isomers?
What are the different types of isomers?

If two organic compounds have the same formula, ie. have identical types and numbers of atoms but different chemical structures, they are structural isomers.
eg, butane and isobutane.

If the two isomers have different spatial arrangements about a >C=C< double bond they are geometric isomers. This is due to the fact that the >C=C< is planar and does not allow free rotation of the atoms about the bond axis. This drastically effects the biological activity of the molecules.
When functional groups are on the same side of the >C=C<, they are said to be cis: when they are on opposite sides, they are trans.
eg, fumaric acid (trans, found in the Citric Acid Cycle) and maleic acid (cis, for all intents and purposes not found in nature).

If the two isomers are mirror images of each other they are optical isomers or enantiomers. This occurs when a C has 4 different functional groups attached. Such a C atom is said to be chiral.
eg, the L- and D-isomers of the amino acid Alanine: only the L form is commonly found in proteins.
eg, for the drug Ibuprofen, only one isomer is active in relieving pain. For the drug thalidomide, only one isomer was responsible for birth defects -- the other optical isomer was effective at combating nausea.

Multifunctional groups within a single molecule.

When a single molecule contains more than one functional group, its properties reflect those of each functional group. This produces a rich, chemical diversity. Sometimes these functional groups have oppsite properties. Lets look at two examples.

1. Amino acids, the building blocks of proteins
Principle of biomolecule structure: large complex molecules are made up of simple monomeric units.
Amino acids contain a carboxyl group, an acid, and an amine, a base. They are dipolar ions containing opposite charges = ampholytes

2. Fatty acids
Fatty acids contain a hydrocarbon chain with a carboxyl group.
They are both hydrophobic and hydrophilic = amphipathic
Palmitic acid is a fatty acid with 16C.
Such lipids form micelles and bilayers in water.
Examples are soaps and detergents.

Chemical reactions of functional groups

What is the product of the oxidation of alcohols?
• oxidation of alcohols to aldehydes
• R-CH2OH --> R-CHO + [2H]

What is the product of the reduction of aldehydes?

• reversible: reduction of aldehydes to alcohols
• R-CHO + [2H] --> R-CH2OH

What is the product of the oxidation of aldehydes?

• oxidation of aldehydes to acids
• R-CHO + [O] --> R-COOH

What is the product of the reduction of acids?

• Reversible: reduction of acids to aldehydes
• R-COOH --> R-CHO + [O]

What is the product of the reduction of a ketone?

• Reversible reduction of a ketone to a secondary alcohol
• R-CO-R + [2H] --> R-CHOH-R

Chemical reactions between functional groups

1. condensation of an acid with an alcohol gives an ester
reversible condensation with dehydration gives the ester and hydrolysis of the ester regenerates the alcohol and acid
R-COOH + HO-R' <--> R-CO-O-R' + H2O

with phosphoric acid the product is a phosphate ester
H3PO4 + HO-R <--> H2PO4-R + H2O
Note: this is the bond in AMP between the ribose and phosphate.

2. condensation of an acid with an acid gives an anhydride
reversible condensation and hydrolysis
R-COOH + HOOC-R <--> R-CO-O-CO-R + H2O
for example condensation of two acetic acids gives acetic anhydride

condensation of two phosphoric acids gives phosphoric anhydride
H3PO4 + H3PO4 <--> H2PO3-O-H2PO3 + H2O
Note: ATP has two and ADP has one phosphoric anhydride. In ATP it is the bond between the alpha and beta phosphates and between the beta and gamma phosphates.

3. condensation of an acid with an amine gives an amide
for 2 amino acids, condensation of the carboxylic acid of one with the amine of the other --> dipeptide

and for multiple amino acids --> protein
R-COOH + H2N-R' <--> R-CO-NH-R' + H20

Can C form cyclic or ring structures as well as straight or branched chains?
How big are the rings?
Are the rings puckered or planar?

C can form stable ring structures as well as straight or branched chains.
stable rings containing 5 or 6 C atoms are common in biochemistry.
eg: cyclohexane
puckered ring because C atom is tetrahedral: chair and boat forms

If ring has alternating >C=C<, it is planar = aromatic
the p electrons are de-localized = more stable and less reactive: eg, benzene

What are examples of heterocyclic rings?
What will be the properties of such compounds?

Glucose and ribose sugars.
Glucose is an energy source.
Ribose and 2-deoxyribose are found in nucleic acids.
• Ribose is in RNA
• Deoxyribose is in DNA

The hydroxyl groups make them polar and good H-bond acceptors and donors.

Substituted pyrimidine and purine bases are found in nucleic acids.

The purines are Adenine and Guanine

The pyrimidines are Cytosine, Uracil and Thymine

Your objectives are to know:

1. the atomic structure of carbon
2. structures of simple organic molecules
3. the properties of functional groups
4. the properties of amino acids and carbohydrates

Your objectives are to recognize:

1. a chiral C
2. alcohols, acids, carbonyls, amines and phosphates
3. an ester
4. an anhydride
5. an amide
6. glucose and ribose
7. purines and pyrimidines

Know the properties of the functional groups.

Recognize the component parts (ribose, purine)

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Bich 107 lecture notes on Essential Chemmistry for Biochemistry last updated 09/19/05

Comments to Martyn Gunn