1. Microbiology- a clinical approach by Anthony Strelkauskas et al. 2010 Chapter 2: : Fundamental chemistry for microbiology

2. © Charles D. Winters / Science Photo Library  An understanding of chemistry is essential to understand cellular structure and function, which are paramount for your understanding of microbiology.  Many of the pathogenic effects of infectious diseases occur at the molecular level.  To understand the infection process, you need to understand basic chemistry.

4.  Tissues are organized in the following way: Atoms Molecules Cells Tissues

5.  Atoms are composed of three types of particles ◦ Protons  Located in the core of the atom  Have a positive charge  The number of protons in an atom is equal to the atomic number of the atom. ◦ Neutrons  Located in the core of the atom  Neutrons have no charge  The number of neutrons is usually equal to the number of protons  The total number of protons and neutrons equals the atomic weight of an atom. ◦ Electrons  Have a negative charge  Located in shells (orbitals) around the outside of the core  In an uncharged atom, the number of electrons is equal to the number of protons.

6.  Shells occupied by electrons have a limited capacity. ◦ First shell can only hold 2 electrons ◦ Second shell can only hold 8 electrons ◦ Third shell can hold 18 electrons but needs 8 to be stable  If the electron shell is not full, it is unstable.  Atoms with unstable electron shells can give or receive electrons to other atoms.  This stabilizes the atom and makes ionic bonding possible.

7.  Ionic bonds (example: salt, NaCl) ◦ Electrons are donated or received by atoms ◦ Cations: donated an electron and are positively charged ◦ Anions received an electron and are negatively charged ◦ Opposite charges are attracted- 2 ions form an ionic bond  Covalent bonds (example: water molecule, methane, CH4) ◦ Electrons are shared in outermost electron shell ◦ Unequal sharing leads to polarity  Hydrogen bonds (example: water) ◦ Form because of polarity of covalent bonds ◦ Found between and within molecular structures, render molecule shape ◦ Affected by temperature and pH

8.  Water may be the most important component for life because it has properties very important for physiological function.  Water has three major properties: ◦ Solubility  Dissociation of molecules  Solvent : water  Solute: what is dissolved ◦ Reactivity  Dehydration  Hydrolysis ◦ Heat capacity  Ability to absorb and retain heat

9.  Microorganisms can live in acidic or alkaline environments.  Acidity can be viewed as excessive numbers of H + ions. ◦ Lower numbers on the pH scale, acidic is low pH.  Alkalinity can be viewed as excessive numbers of OH - ions. ◦ Higher numbers on the pH scale, basic is high pH.  A neutral pH is 7.0.

11.  Biological molecules are also referred to as organic molecules.  There are four major categories of biological molecules: ◦ Carbohydrates ◦ Lipids ◦ Proteins ◦ Nucleic acids  All four categories of biological molecules use carbon as their backbone.

12.  All carbohydrates contain carbon, oxygen, and hydrogen.  Carbohydrates can be viewed as the most easily used and best source of energy.  Organisms and cells can break down or build up carbohydrates.  There are three major categories of carbohydrates: ◦ Monosaccharide – smallest carbohydrate like glucose  Used to build bigger carbohydrate molecules ◦ Disaccharide – two monosaccharides ◦ Polysaccharide – many monosaccharides like glycogen

13. Glucose (monosaccharide) Sucrose (disaccharide) Glycogen (polysaccharide)

14.  Lipids are a chemically diverse group of substances that includes fats, phospholipids, and steroids.  They are relatively insoluble in water which makes them very useful as elements of cellular structure.

15.  Some lipids contain more energy than carbohydrates but are harder to break down.  Fatty acids are a key component of all lipids.

16.  Glycerol + Fatty acids ◦ Monoglycerol ◦ Diglycerol ◦ Triglycerol

17. Phosphate groups are attached to fatty acids Sugars are attached to fatty acids hydrophilic hydrophobic Membranes

18.  4-ring carbon structures  Very hydrophobic  Cholesterol  Hormones

19.  Made out of amino acids  Assume structure ◦ Primary structure: amino acid sequence  Dipeptide, polypeptide, protein ◦ Secondary structure: folding due to amino acids and hydrogen bonds  Alpha helical or beta sheet ◦ Tertiary structure: folding of the chain itself  Renders 3-D structure  Hydrogen bonds and disulfide bridges  Globular or threadlike ◦ Quaternary structure: joining of multiple polypeptide chains

21.  Proteins can be denatured. ◦ Factors such as pH and temperature can break hydrogen bonds. ◦ This damage causes changes in shape. ◦ Changes in shape disrupt function.

22.  Protein functions ◦ Structural ◦ Enzymatic Type III secretion apparatus

23.  Nucleic acids are involved with cellular information and also function as energy molecules.  Nucleic acids are composed of  Nitrogenous base + pentose sugar + phosphate  There are two types of nucleic acid information molecule: ◦ DNA – deoxyribonucleic acid ◦ RNA – ribonucleic acid (DNA)(RNA)

24.  The bases that are used to build nucleic acids:

25.  DNA strands are anti-parallel and form a double helix  The bases point inward  RNA is single stranded and can pair with DNA

26.  The major energy molecule in cells is ATP.  It contains the nitrogenous base adenosine, a ribose sugar, and a chain of three phosphates bonded to the sugar.  The bonds between these phosphates are high- energy bonds that when broken yield energy. ◦ ATP ADP + energy  Energy plus phosphate added can rebuild ATP. ◦ ADP + P i + energy ATP

28.  Atoms are composed of protons, neutrons and electrons.  Atoms join together to make molecules, which can join together to make cells, which can join together to form tissues.  There are three types of chemical bond: ionic, covalent, and hydrogen bond. ◦ Ionic bonds form when electrons are donated or accepted. ◦ Covalent bonds form when electrons are shared and are strong chemical bonds. ◦ Hydrogen bonds form between hydrogen atoms and are the weakest form of chemical bond.

29.  Biological molecules use carbon atoms as their building blocks.  There are four types of biological molecule: carbohydrates, lipids, proteins, and nucleic acids.  ATP is the major energy molecule of the cell.

30.  Which of the following is the type of bond holding Na + and Cl - ions together in NaCl? A. Covalent B. Ionic C. Polar covalent D. None of the above  Which of the following statements is not true? A. Enzymes are used in a chemical reaction. B. Enzymes increase the probability that a reaction will occur. C. Enzymes are proteins. D. Enzymes lower the energy of activation of a reaction. E. None of the above

31.  Which of these molecules make up the plasma membrane of cells? A. Nucleic acids B. Carbohydrates C. Lipids D. Water E. None of the above  Starch and glycogen are made up of A. Amino acids B. Lipids C. Fatty acids D. Carbohydrates E. Glycerol