Chemistry and Biochemistry for Microbiology

Part 1

By BugLady

Structure and Function

Atoms and molecules

Chemical bonds strength

Water: the molecule of life

Carbohydrates: (energy source, storage, and cell structure)

Lipids (energy storage and membrane main component)

Proteins (enzymes, transporters, movement)

Nucleic acids (genetic material, small effector molecules)

Apr 11, 2023 3

Check point

Electron

Nucleus

Neutron

Proton

Apr 11, 2023 4

Biologically Important Elements

Present in large amounts

C= every organic molecule, CO2

H= water, H+ , all organic molecules

O=water, e- acceptor, all organic molecules

N= proteins, nucleic acids, some vitamins

P= phospholipids, inorganic P, nucleic acids

S= proteins, some vitamins

Apr 11, 2023 5

Why isn’t calcium mentioned as a most abundant element in this class?

Biologically Important Elements

Elements required in smaller amounts

Electrolyte balance, protein stabilization, shells of some microorganisms o Cations: K+ (potassium), Na+ (sodium), Fe2+/3+

(iron), Ca2+ (calcium), Mg2+ (magnesium)

o Anions: Cl- (chlorine), PO4-3 (inorganic

phosphate)

Apr 11, 2023 6

Biologically Important Elements

Essential elements required in trace amountsoMetals: Zinc, Vanadium, Chromium, Molybdenumo Lithium, Iodine, Selenium etc…

Found in vitamins and enzymesEssential functions in a cell will be compromised if trace elements are missing in a diet.

Apr 11, 2023 7

Chemical Bonds

Chemical bond: Atoms form interactions involving their outer most electrons

There are 4 main types of chemical bonds.

Covalent bonds

Ionic Bonds

Hydrogen Bonds

Hydrophobic (non polar) Interactions

Apr 11, 2023 8

Comparison of Chemical BondsStrength of Bonds:

Covalent>ionic>hydrogen bonds>non polar interactions

Non covalent interactions are individually weak but collectively strong.

Ionic bonds and hydrogen bonds are polar or hydrophilic

Non polar interactions are hydrophobic

Apr 11, 2023 9

Covalent BondsCovalent bonds may have an equal or unequal attraction for the shared electrons

Nonpolar covalento Bonds formed between identical atoms or

between atoms that have similar attraction of electrons H-H or C-H

Apr 11, 2023 10

National Institute of General Medical Sciences

Apr 11, 2023 11

Covalent Bonds

Polar covalento One atom has a greater attraction to the

electrons than the othero Produces a slight charge within the molecule

Ionic Bonds

Loss and gain of electrons leads to charged atoms (ions)

Ionic bonds are attractions between ions of opposite charge.

Apr 11, 2023 12

Ionic Bonds

Ionic bonds in solution are weaker than covalent bonds

o Bonds dissociate in water Easily broken at room temperature Approximately 100 time weaker than covalent

bonds

Important among weak forces holding biological molecules together

Apr 11, 2023 13

Hydrogen BondsWeak bonds formed from the attraction of positively charged hydrogen atoms

o Hydrogen atoms in polar molecules are attracted to negatively charged atoms or molecules Most commonly oxygen or nitrogen

Apr 11, 2023 14

Hydrogen Bonds

Hydrogen bonds occur between molecules and within molecules (water, proteins, DNA)

Covalent bonds occur within moleculeso Hydrogen bonds hold molecules togethero Covalent bonds hold atoms together

Apr 11, 2023 15

Nonpolar (Hydrophobic) Interactions

Nonpolar residues (lipids or hydrophobic regions of proteins) are exposed at the surface of two different molecules.It is energetically more favorable for polar water molecules to approach each other closely displacing the "oily" non-polar molecules from between them.

o Example: plasma membranes.

Apr 11, 2023 16

Properties of Water

Stabilized by hydrogen bonds in liquid state: H----O

High heat capacity

High surface tension

Excellent solvent

H+ and OH participate in chemical reactions

Apr 11, 2023 17

National Institute of General Medical Sciences

The Universal Solvent

Ionic compounds dissociate, forming soluteso Salts, acids, bases

Polar compounds form hydrogen bonds with water moleculeso Small alcohols, aldehydes, quaternary

ammonium compounds, vitamins

Apr 11, 2023 18Figure 2.5

Interaction with Water

Hydrophilic- “water-loving”o Readily dissolve in watero Ions and molecules that contain polar covalent

bonds Sugars, salts, protein hormones, some vitamins, small

organic molecules

Apr 11, 2023 19

Courtesy USDA

Interaction with Water

Hydrophobic- “water-fearing”o Do not readily dissolve in watero Hydrocarbons, lipids, non polar solvents, lipid

soluble vitamins, steroidsAmphipathic moleculeo Have both polar or ionized regions at

one or more sites and nonpolar regions at other sites Detergents are amphipatic

Apr 11, 2023 20

Renee Comet NCi

Micelle by SuperManu CC BY-SA 3.0

Acid-Base Balance

pH is a measure of the concentration of H+ in a solution.

pH =7.0 is neutral (pH of freshly distilled water)

pH>7.0 is basic

pH<7.0 is acidic pH = log 1/[H+]=log[H+]

Apr 11, 2023 21

Apr 11, 2023 22

Acid-Base Balance

Increasing [H+] increases acidity. pH decreases.

Increasing [OH] or pH increases alkalinity.

Most organisms grow best between pH 6.5 and 8.5

Optimal pH for most bacterial growth is slightly basic.

Optimal pH for fungal growth is slightly acidic.

Why Measure pH?Acidic pH of skin and stomach are part of our innate immune system

Proper function of proteins requires a specific pH.

DNA stability is dependent on pH.

Most biochemical assays used for bacteria identification measure changes in pH.

Apr 11, 2023 24

Lactose positive and lactose negative colonies of Escherichia coli on Mac Conkey agar

Buffers

Buffered solutions resist change in the pH of a solution when hydrogen ions (protons) or hydroxide ions are added or removed.

Buffers are critical to the maintenance of life.

Buffered systems mean that organisms can maintain a suitable pH environment in their cells and tissues.

One of the most common buffers is the bicarbonate buffer.

Apr 11, 2023 25