Concepts of Organic Chemistry and Biochemistry...Concepts of Organic Chemistry and Biochemistry...

Santino.diberardino@lneg.pt

MESTRADO INTEGRADO EM ENGENHARIA DA ENERGIA E DO AMBIENTE

Aula N 3

Concepts of Organic Chemistry

and Biochemistry

Santino Di Berardino

Unidade de BIOENERGIA, LNEG, Est. do Paço do Lumiar, 1649-038 Lisboa, Portugal.

(e-mail: santino.diberardino@mail.ineti.pt)

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Bioenergy and organic chemistry

The production of energy from the biomass-organic matter is carried-out by biological, chemical or thermochemical reactions.

The biomass produced by natural systems is available in the form of 3 large groups of compounds: carbohydrates, fats and proteins

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Carbon

Carbon (C) is the fourth most abundant element in the Universe, after Hydrogen (H), Helium (He) and Oxygen (O), and is the pillar of life as we know it.

There are basically two forms of carbon, the organic, present in living and dead organisms, not decomposed, and another inorganic, present in rocks.

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What does the carbon atom so special?

The carbon atom is tetravalent, thus being able to establish 4 covalent bonds.

Carbon has 2 electron pairs available.

The four valencies of carbon are equal.

The carbon atoms are able to establish very strong covalent bonds between each other, forming long chains and rings. Structures called Carbonic Chains.

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PROPERTIES OF THE CARBON ( C )

Properties

Simbol C

Atomic Number 6

Valence Electrons

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Atomic number 12

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Covalent Bonds

Carbon can establish covalents bonds with four different atoms.

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Bond Lengths (d)and Energies.*

Ligação O.L. d (Å = 10-10m) Edis (kJ/mol)

H-H 1 0,74 432

C-H 1 1,09 411

C-C 1 1,54 346

C=C 2 1,34 602

CºC 3 1,20 835

C-N 1 1,47 305

C=N 2 1,29# 615

C-O 1 1,43 358

C=O 2 1,20 799

N-O 1 1,40 1,40

N=O 2 1,21 1,21

N=N 2 1,25 418

NºN 3 1,1 942

Fonte: J.E. Huheey et al., Inorganic Chemistry, 4th. ed., 1993.* Com exceção das ligações H-H e NºN, todos os valores de d e Edisfornecidos são valores médios.#

Fonte: http://chemviz.ncsa.uiuc.edu/content/doc-resources-bond.html

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Organic chemistry

Organic chemistry is the part of chemistry that studies compounds containing carbon (C) atoms.

The organic compounds are composed of a matrix of carbon atoms.

All living things are made up of organic compounds.

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Inorganic Carbon

Some substances, although containing carbon atoms in their molecular structure, have properties similar to those of inorganic compounds (carbon-free). These substances are regarded as inorganic. The most important are:Graphite: C (graf.);Diamond: C (diam.);Carbon Monoxide: CO;Carbon dioxide CO2;Carbonic Acid: H2CO3;Cyanuric Acid: HCN;Carbonates: Na 2 CO 3 etc;Cyanides: NaCN etc.

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Carbon chain

Carbon atoms are present in all organic molecules and form the "skeleton" (carbonic chain);

Hydrogen atoms are present in almost all organic molecules;

Any atom other than C or H present in an organic molecule is called a Heteroatom;

When a heteroatom is found, in the organic molecule, located between two carbons, we say that it is part of the carbonic chain;Examples of heteroatoms are O, S, N and P.A carbon chain is the structure formed by all the carbon atoms of an organic molecule and also by the heteroatoms that are positioned between these carbons.

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Orgânic Compounds Representing FORMULA

ESTRUTURAL

PLANA DOS

COMPOSTOS

ORGÂNICOS:

COMPOSTOS

ORGÂNICOS:

Simplified structured formula

CH3-CH2-O-CH2-CH3

H3C-CH2-O-CH2-CH3

structured formula

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Carbon may form a wide variety of compounds, either single or complex..

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Methane has only 1 Carbon Atom

DNA has 10 billions of carbon atoms

Carbon compounds

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História

Until 1828 it was believed that organic compounds (thecarbon compounds) were produced only by livingorganisms. Such a process of synthesis was explained bythe so-called Vital Force Theory.

The German chemist Friedrich Wohler demonstrated thaturea (substance present in mammalian urine) could besynthesized by the chemical reaction promoted by theheating of ammonium cyanate (an inorganic compoundand experimentally proved that organic compounds couldbe synthesized artificially, just as it did with the urea.

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Urea synthesis

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First organic compound synthesized by man from an

inorganic compound (ammonium cyanate).

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Biochemistry

Biochemistry is a special area of organic chemistry that deals with matter inside living cells, called protoplasm.

Protoplasm is a very complex mixture of organic compounds where a high level of chemical activity occurs.

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Major Organic Compounds - Large Molecules

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

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The organic components of cells are divided into the

following major categories:

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Polymers and monomers

All these molecules are long chain polymers consisting of elemental units called monomers.

Each type of macromolecule is made up of different types of monomers.

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Monomers

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Macromolecule Monomer

Carbohydrate Monosaccharide

Lipid Polymer Hydrocarbon Chain

Proteins Amino acids

Nucleic Acids Nucleotides

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How do monomers form the polymers?

By means of condensation reactions (also called dehydration synthesis),

The reaction removes a water molecule from two monomers that are bound.

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Reacção de Desidratação e

Síntese de polímeros

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Hydrolysis

Reaction opposite of condensation. It divides a polymer into two parts by adding a water molecule (supported by an enzyme)

Breaking the connection releases energy

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Carbohydrates

They are the key source of energy used by living things.

They are synthesized through photosynthesis, entering the composition of non-photosynthetic beings in the food chain.

They have several functions: structural and energy storage, especially in the form of polysaccharides.

The most common carbohydrate is glucose, which plays a key role in cellular respiration and photosynthesis.

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Carbohydrates

Molecules with various functional hydroxyl (OH) groups and an aldehyde or ketone, or hydrolyzable polymers consisting of such molecules.

They consist of atoms of carbon, hydrogen and oxygen, always in a ratio of 1: 2: 1.

Sugars such as glucose and fructose are organized blocks of carbohydrates.

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monosaccharides

General formula: (CH 2 O) n. The number of Carbonos goes from 3 to 7.

The monosaccharides meet to form oligosaccharides and polysaccharides.

They are readily harvested by the cells due to the small size.

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Polysaccharides

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LIPIDS

Compounds of various species containing the atoms C, H, O. In some cases the phosphorus is present. The Hydrogen content is much higher than that of Oxygen.

The most common lipids are FATS, OILS and STEROIDS. They have in common the similar physicochemical behavior as, for

example, the low solubility in water. The molecular structure is not similar as in sugars.

The fatty acids make an ester bond with some kind of alcohol. Fats are the molecules with the greatest power of energy storage. 1g of Fat (C57H110O6) releases when oxidized more than double the

calories of 1g of sugar (C6H12O6). The oxidation of fats is more complex than that of sugars, becoming

the energy reserves of living beings.

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Lipids

Lipids are molecules that consist of long chains of hydrocarbons. Usually a glycerol molecule binds three chains together.

Lipids are not polar.

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Saturated and unsaturated fats

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Proteins

Proteins are structures consisting of amino acids. DNA code generates Proteins.

Among amino acids a peptide bond is formed by a synthesys reaction (dehydration).

PROTEINS assume a prominent position, being the mostfrequent and varied cellular components.

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Proteínas structure – Levels

Level

Primary Sequênces of amino-acids

Secondary Hélicx and sheets

Tertiary Dissulfur Bridges

Quaternary Multiple polipeptidicbond

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Amino-acids

Are Quaternary compounds containing carbon (C), hydrogen (H), Oxygen (O) and Nitrogen (N) - and sometimes contain sulfur (S) (cysteine).

The general structure of amino acids involves an amine group and a carboxyl group, both attached to the α-carbon (the first after the carboxyl group).

The α-carbon is also attached to a hydrogen and a side chain, which is represented by the letter R. The R group determines the identity of a specific amino acid.

One of the most important properties of such compounds is the three-dimensional shape.

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Important details about organic matter

In animals LIPIDS are more abundant than GLYCOS. In plants the reverse occurs;

LIPIDS are the most energetic components;

GLYCIDES are the most easily oxidized by cells;

The priorities for the cells to obtain energy are: LIPID GLYCINES -PROTECTS

PROTEINS and NUCLEIC ACIDS are INFORMATIONAL macromolecules;

PROTEINS have the great power to catalyze cellular reactions;

DNA is responsible for coordination information on cellular metabolism;

VITAMINS play a role similar to that of the mineral salts assisting the enzymes in their work;

The organic molecules assume several dimensions from SMALL - molecular weight ranging from 100 to 1,000 to MACROMOLECULES: polysaccharides, polypeptides and polynucleotides.

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Bioenergetics and compounds energy-rich

Knowledge of the chemical composition and structure of biological molecules is not enough to understand how they associate by forming complex systems, or how they function to sustain life.

It is necessary to analyze the reactions that form and degrade the biological molecules.

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Metabolism

The general process by which living systems acquire and use free energy to carry out their functions. It is divided into two parts:

- Catabolism or degradation.

- Anabolism

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Catabolism or degradation

is the process in which nutrients and cellular constituents are degraded to take advantage of its components and / or for energy generation

Perform exergonic oxidation

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Anabolism or biosynthesis

process in which the biomolecules are synthesized from simpler components

endergonic process (uses energy released during catabolism)

Many specific metabolic reactions are common to all organisms, with variations arising from differences in the energy sources that sustain them.

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Fermentation

Fermentation is a process of transforming one substance into another,

performed by microrganisms, such as fungi, bacteria and

yeasts. Biological process that allows to synthesize several compounds

from the glucose.