Chemistry of microbes
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LECTURES IN MICROBIOLOGY. Chemistry of Microbes. LESSON 2. Sofronio Agustin Professor. Topics. Fundamental Building Blocks Macromolecules The Cell. Fundamental Building Blocks. Atoms Elements Molecules and compounds. Atoms. Subatomic Particles Proton = positive charge

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Chemistry of Microbes

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Chemistry of microbes



Chemistry of Microbes


Sofronio Agustin




  • Fundamental Building Blocks

  • Macromolecules

  • The Cell

Fundamental building blocks

Fundamental Building Blocks

  • Atoms

  • Elements

  • Molecules and compounds



  • Subatomic Particles

    Proton = positive charge

    Neutron = neutral

    Electron = negative charge

  • Atomic number = no. of protons

  • Atomic mass = no. of protons and neutrons

Chemistry of microbes

Atomic Structure

Models of Atomic Structure



  • Atoms with same number of protons but differ in number of neutrons are called isotopes.

  • Example: 12C, 13C, and 14C are isotopes of carbon.

  • Radioisotopes emit radiation in the form of alpha or beta or gamma rays or photons.

Major elements of life

Major Elements of Life

Molecules and compounds

Molecules and Compounds

  • Molecule = combination of two or more elements (e.g.H2)

  • Compound = combination of two or more different elements (e.g. H2O)

  • Molecules are held together by chemical bonds

Chemical bonds

Chemical Bonds

  • Covalent

  • Ionic

  • Hydrogen

Chemical bonds1

Chemical Bonds

Chemical bonds involve atoms sharing, donating or accepting electrons

Covalent bonding

Covalent Bonding

Examples of covalent bonding

Polar covalent bond

Polar Covalent Bond

  • Polarity occurs when atoms electrons unequally due to differences in electronegativities. This is seen in water (H2O).

  • More electronegative atoms tend to pull electrons toward them creating a polar molecule.

Ionic bonding

Ionic Bonding

Sodium chloride (table salt) is an example of ionic bonding, that is, electron transfer among atoms or redox reaction.



  • Molecules formed by ionic bonding breakup (ionization) when dissolved in water (solvent), producing separate positive (cation) and negative (anion) ions.

  • These ions conduct electricity and thus called electrolytes.

Hydrogen bond

Hydrogen Bond

  • Hydrogen bonding is formed between the partially positive (hydrogen) end of a polar molecule and the negative end of another (e.g. O2 or N2).

  • Example : Water molecules

Chemistry of microbes


  • pH – measurement of the H+ ion concentration in a solution.

  • General rule:

    • Acidic = excess H+ ions in solution

    • Basic = excess OH- ions in solution

    • Neutral = equal amounts of H+ and OH- ions

The ph scale

The pH Scale

The pH of an environment (exterior or interior of a cell) is important for living systems.



Molecules important to life consist of inorganic and organic substances.

  • Inorganic – either C or H maybe present (e,g, CO2, H2)

  • Organic- C and H (hydrocarbons) are present

    (e.g. CH3)

Organic molecules

Organic Molecules

  • Carbon, a tetravalent atom, is an ideal element for life because it serves as the skeleton for macromolecules.

  • Functional groups (R) attached to these carbons confer unique properties to these macromolecules.



  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids



  • Simple Sugars

  • Disaccharides

  • Polysaccharides

Classes of carbohydrates

Classes of Carbohydrates

Major sugars (monosaccharides) in the cell are glucose, galactose and fructose. Several sugars bonded together are called polysaccharides.

Glycosidic bond

Glycosidic Bond

  • Sugars are bonded by special kind of covalent linkage called glycosidic bonds.

  • Water is released (dehydration) after the bond is formed.



Peptidoglycan in bacteria is an example of a polysaccharide.



  • Fats

  • Phospholipids

  • Steroids

Chemistry of microbes


Synthesis and structure of a triglyceride (fat), a storage molecule.



  • Phospholipids serve as a major structural component of cell membranes.

  • It is an amphiphatic molecule. Its phosphate “head” is hydrophilic and its fatty acid “tail” is hydrophobic.

Cholesterol an alcoholic steroid

Cholesterol: An Alcoholic Steroid

Cholesterols are associated with cell membranes of some cells such as those of eukaryotes.



  • Proteins are the predominant organic molecules in cells.

  • Proteins consist of a series of amino acids (e.g. peptides, polypeptides)

  • Peptide bonds link amino acids together.

  • Examples: hormones, enzymes, antibodies, etc.

Amino acids

Amino Acids

  • An amino acid has a central carbon, to which carboxylic, amino and R groups are attached.

  • Amino acid types vary according to the reactive (R) groups present.

The 20 naturally occurring amino acids

The 20 Naturally Occurring Amino Acids

Chemistry of microbes


Peptide Bond

A peptide bond (covalent) forms between the amino group on one amino acid and the carboxyl group on another amino acid with the accompanying loss of water.

Levels of structures of protein

Levels of Structures of Protein

Proteins take on a variety of shapes due to extensive folding of the molecule. This enable them to perform specific functions and interactions with other molecules.

Nucleic acids

Nucleic acids

  • Deoxyribonucleic acid (DNA)

  • Ribonucleic acid (RNA)

  • DNA contains genetic information and transfers it to RNA

  • RNA translates the DNA information into proteins

Nucleic acid polymers

Nucleic Acid Polymers

Nucleic acids are polymers of repeating units called nucleotides.

The sugars and nitrogenous bases

The Sugars and Nitrogenous Bases

The pentose sugars and nitrogen bases determine whether a molecule will be DNA or RNA.

Chemistry of microbes


The DNA Molecule

  • The DNA configuration is a double helix similar to “a spiral staircase”

  • Sugar and phosphate backbones are held together by hydrogen bonds formed between nitrogenous bases.

Dna the molecule of inheritance

DNA : The Molecule of Inheritance

  • DNA serves as a template for the synthesis of new DNA strands as well as mRNA, tRNA and rRNA.

  • DNA replication is an important step in cell reproduction.

The cell

The Cell

Fundamental characteristics shared by all living organisms:

  • Reproduction

  • Metabolism

  • Motility (Response to molecules)

  • Protection and Storage (Cell wall or membrane)

  • Nutrient transport

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