Chemical Principles (as they pertain to microbiology) Ch. 2

What are all organisms made of?

• All organisms are made up of various structures and molecules that come together to form 'life'' at the cellular level

• Amino acids —> proteins

• Fatty acids—> Phospholipids

• Carbohydrates—>Glycerol—->Phospholipids

• Carbohydrates—→Monosaccharides—→Polysaccharides

• Nucleobases—→Nucleotides—→ DNA/RNA

Chemistry

the study of interactions between atoms and molecules

atom

the smallest unit of matter and cannot be subdivided into smaller substances without losing its properties

molecules

Atoms interact to form molecules

• E.g O2 Oxygen gas=molecule

• NH3 or ammonia =molecule

Atoms are composed of three particles:

• Electrons: negatively charged particles

• Protons: positively charged particles

• Neutrons: uncharged particles

• Protons and neutrons make up the nucleus

• Electrons move around the nucleus in regions called electron shells

chemical element

• Atoms with the same number of protons are classified as the same chemical element

• e.g carbon, Nitrogen, phosphorus, iron, ect are all elements

• Each chemical element has a different number of protons

Atomic number

number of protons in the nucleus

Atomic mass

total number of protons + neutrons in an atom

isotopes

• It is possible for the same element to have atoms with different number of neutrons….if this is the case they are called isotopes.

• O¹⁶₈ 8= atomic number, 16=atomic mass

• O₈¹⁷ 8=atomic number, 17=atomic mass

• Atomic mass differs between isotopes, atomic number stays the same

What are some of the important elements used by living organisms?

• Hydrogen H 1

• Carbon C 6

• Nitrogen N 7

• Oxygen O 8

• Sodium Na 11

• Magnesium Mg 12

• Phosphorus P 15

• Sulfur S 16

• Chlorine Cl 17

• Potassium K 19

• Calcium Ca 20

• Iron Fe 26

• Iodine I 53

What are the most abundant elements in living organims?

• Hydrogen

• Carbon

• Nitrogen

• Oxygen

important isotopes:

C¹² C¹³ C¹⁴

N¹⁴ N¹⁵

Why do microbiologists care about isotopes?

• Some isotopes (e.g., heavy ones are much rarer)

• Also, microbes generally prefer to use lighter isotopes.

• Heavier isotopes can be used in studies to track and enumerate fixation rates!

Electron configuration

• Electrons are arranged in electron shells corresponding to different energy levels

• Electron configuration refers to the arrangement of electrons in these shells

• Each shell can hold a characteristic number of electrons

Innermost shell: up to 2 electrons

Second shell: up to 8 electrons

valence shell

Number of electrons in outermost shell (valence shell) is what determines an atom's reactivity with other atoms

e.g carbon: Valence shell electrons=4, number of empty spaces=4

What element is this? And what is the heaviest isotope? What is the isotopes name?

• This is Carbon: count protons, 6 each=carbon

• Heaviest isotope? count Protons+neutrons, Atomic nucleus 3 has 14 so is heaviest

• Name =C¹⁴

How to form molecules?

• Atoms form molecules by combining with other atoms to fill their outermost shells

• The number of missing or extra electrons in the outermost shell is known as the valence

• This is also considered the combining capacity of an atom

• Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atoms

compound

• A compound is a molecule that contains two or more kinds of atoms

• e.g H₂O, two hydrogens and one Oxygen

Ionic Bonds

• Involve ions.

• Ions specifically are charged atoms that have gained or lost electrons

• Ionic bonds are attractions between ions of opposite charge

Cations

• Atoms that lose electrons and become positively charged ions

• K⁺, Na⁺, Ca²⁺

Anions

• Atoms that gain electrons and become negatively charged ions

• I^- , Cl^- , S^2-

Covalent bonds

• Formed when two atoms share one or more pairs of electrons.

• stronger and more common in organisms than ionic bonds.

• E.g. H2 gas (two hydrogens sharing an electron pair)

• CH4 methane (carbon atom sharing an electron pair with each hydrogen atom)

Hydrogen bonds

• Form when a H atom that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule

• Are weak attractions, that do not bond atoms into molecules

• Serve as bridges between different molecules or between different regions of the same molecule

• Break and reform readily

• Multiple hydrogen bonds stabilize large molecules

Ionic Bond importance

Weaker ionic bonds are important in biochemical reactions such as antigen–antibody reactions.

Covalent bond importance

Most common type of chemical bond in organisms and are responsible for holding together the atoms of most molecules in organisms

Hydrogen bond importance

bridges between different molecules or different portions of the same molecule, for example, within proteins and nucleic acids

Chemical reactions

• involve the making or breaking of bonds between atoms

• A change in chemical energy occurs during a chemical reaction

Activation energy

Breaking bonds requires Activation energy = energy needed to break a bond

Endergonic reactions

absorb energy

Exergonic reactions

release energy

• 3 Types of Chemical Reactions that are especially important in microbes (and organisms for that matter):

• Synthesis Reactions

• Decomposition Reactions

• Exchange Reactions

Synthesis Reactions

Occur when atoms, ions, or molecules combine to form new, larger molecules

A+B→ AB

Anabolism

the synthesis of molecules in a cell

Decomposition Reactions

Occur when a molecule is split into smaller molecules, ions, or atoms

AB → A+B

Catabolism

includes the decomposition reactions in a cell

Exchange Reactions

• Are part synthesis and part decomposition

• AB+ CD → AD +BC

• NaOH + HCl → NaCl + H₂O
  Sodium hydroxide + Hydrochloric acid → Sodium Chloride + water

The Reversibility of Chemical Reactions

• Some reactions can readily go in either direction

• Each direction may need special conditions e.g heat or water

Organic compounds

always contain carbon and hydrogen; often structurally complex

Inorganic compounds

Typically lack carbon; usually small and structurally simple E.g. water is an important inorganic compound

Why is water an important inorganic compound?

• Excellent Temperature Buffer

• Excellent Solvent (substances dissociate in water)

• Serves as Reactant or Product in Many Cellular Reactions

pH

• pH, like temperature, is very important for cells (including microbes).

• Various compounds will act as either acids, bases, or salts

Acids

• Substances that dissociate into one or more hydrogen ions and one or more negative

• ions A.k.a. Proton (H+) donors

• HCl → H⁺ + Cl^-

Bases

• Substances that dissociate into one or more hydroxide ions and one or more positive ions

• A.k.a. Proton (H+) acceptors

• NaOH →Na⁺ + OH

• OH was the proton acceptor

Salts

• Substances that dissociate into cations and anions, neither of which is H+ or OH

• NaCl → Na⁺ + Cl^-

What is pH is determined by?

• The pH is determined by the acid-base balance

• pH is the concentration of H+ ions or [H+] in solution

• Increasing + [H ] increases acidity, decreasing the value of pH

• Decreasing + [H ] increases the alkalinity, increasing the value of pH

• pH=7 Neutral

• pH<7 Acid

• pH>7 Alkaline (basic)

• certain microbes like to live in each of these pH’s

Why is it important to consider pH?

• Microbes must maintain a fairly constant balance of acids and bases

• Biochemical reactions are extremely sensitive to even small changes in pH

• Acids and bases that are continually formed during cellular reactions must be kept in balance by the microbe.

• Most microbes grow best between pH 6.5 and 8.5.

• But some can grow at pH extremes.

Buffers

• compounds that prevent pH changes

• Often buffers are used to keep cells viable in the lab (also sometimes the microbes make their own cellular buffers)

Mg(OH)₂ + 2HCl → MgCl₂ H₂O

• a chemical reaction where an antacid is neutralizing an acid.

Organic compounds

always contain carbon (and hydrogen if a biological molecule); and they can also contain oxygen and/or nitrogen in addition.

carbon skeleton

The chain of carbon atoms in an organic molecule is called the carbon skeleton

Functional groups

• Functional groups bond to the carbon skeletons and are responsible for most of the chemical properties of a particular organic compound.

• E.g. the hydroxyl (OH) group of alcohols is a functional group

R-O-H

• Hydroxyl

• name of group:alcohol

• Biological importance: lipids, carbohydrates

R-C^-H_=O

Aldehyde

Biological importance: reducing sugars such as glucose, polysaccharides. Donates electrons

R-CH₃

Methyl group

Important in DNA; energy metabolism

R-CH₂-NH₂

Amino group

biological importance in proteins

R=C^=O_-O-R

C doubled bonded to O single bonded to O-R

Eseter

Bacterial and eukaryotic plasma memebranes

R-CH₂-O-CH₂-R

• Ether

• Archaeal plasma membranes

R-C_=O^-OH

Carboxyl

Organic acids, lipids, proteins

R-O-PO₃

• Phosphate

• ATP, DNA

Functional Groups: Amino Acids

• Amino acids are important building blocks of proteins

Have two functional groups: amino group (NH₃) + carboxyl group (−𝐶𝑂𝑂𝐻)

Making Larger Molecules

• Small organic molecules can combine into large macromolecules

• Macromolecules are polymers consisting of many small repeating molecules called monomers

• Monomers join by dehydration synthesis or 'condensation reactions' to form macromolecules

R-OH+OH-R’ → R-O-R’ +H₂O

• OH+O is the water that is released when two organic molecules (monomers) join together to form a polymer

Larger organic compounds

• Larger organic compounds are critical for life.

• Includes important compounds like:

• Carbohydrates

• Lipids and steroids

• Proteins

• Nucleic acids

• ATP

Carbohydrates

• Serve as cell structures and cellular energy sources

• Include sugars and starches

• Consist of C, H, and O (often in the ratio of 1:2:1)

Carbohydrate isomers

• Many carbohydrates are isomers (same formula, different structures)

• Examples include: glucose, fructose, sucrose, lactose, maltose, starch, cellulose, and glycogen.

• Categories of carbohydrates include monosaccharides, disaccharides, and polysaccharides.

Monosaccharides

• simple sugars with three to seven carbon atoms

• Examples: Glucose Fructose(isomer of glucose) Deoxyribose(important in DNA)

• Glucose (C6H12O6) is the most important monosaccharide in nature; it may occur as a chain or in alpha or beta ring configurations.

• Glucose is the main source of energy for body cells.

alpha and beta glucose difference

In alpha-glucose, the -OH group on C1 points down (below the ring), whereas in beta-glucose, it points up (above the ring).

Disaccharides

• Disaccharides are formed when two monosaccharides are joined in a dehydration synthesis reaction

• Examples:

• Maltose: disaccharide of two glucoses

• Sucrose: disaccharide of glucose and fructose

• Lactose: disaccharide of glucose and galactose

• Disaccharides can be broken down by hydrolysis reactions

Polysaccharides

• Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis

• Examples (made from glucose molecules) that differ in their bonding and function:

• Starch (important in plant cells)

• Glycogen(Important in animal cells)

• Cellulose(important in many algae and plant cells)

chitin

Polysaccharides can also combine with other chemical groups to form even more complex macromolecules. – For example, chitin, the main component of the hard outer covering of insects, spiders, and crabs, is also found in the cell walls of fungi.

Lipids

• Consist of C, H, and O

• Are nonpolar and insoluble in water

• They include:

• Simple lipids [(fats and oils) triglycerides, and also waxes]

• Complex lipids

Two main lipid functions:

1. They are the primary structural component of cell membranes

2. They can supply energy storage

Simple Lipids

• Fats/oils or triglycerides

• Contain glycerol and fatty acids; formed by dehydration synthesis

• Trigerides(fats/oils): Glycerol + 3 fatty acids

• Glycerol attached through carboxyl group to hydrocarbon chain of fatty acid

Saturated fats vs unsaturated fats

• Saturated fats have no double bonds in the fatty acids

• Unsaturated fats have one or more double bonds in the fatty acids

Examples of Types of Fatty Acids (Saturated vs. Unsaturated)

• Saturated (single bonds between carbons)

• Monounsaturated (Double bond in the carbon chain)

• Polyunsaturated (Two or more double bonds in carbon chain)

• Has to be in the carbon chain, the double bond is carboxyl group doesn’t count

Complex Lipids

• Contain C, H, and O AND P, N, and/or S

• Include phospholipids and steroids

• Cell membranes are made of complex lipids called phospholipids – Glycerol + two fatty acids + a phosphate group

• Phospholipids have polar as well as nonpolar regions

Phospholipids

• Phosphate group, attached to glycerol, that is attached to two fatty acids

• Polar head (loves water)

• non polar tails (hates water)

• cell membrane composed of phospholipids

Structure of Cell Membranes

A cell membrane is a lipid bilayer, consisting of two rows of phospholipids, arranged tail-to-tail.

proteins/ protein channels present

Lipids and other macromolecules

• Lipids can also combine with other macromolecules to give even further molecules.

• Lipopolysaccharides (LPS) come from lipid + piece of polysaccharide

• Lipoproteins come from lipid + protein

• Both LPS and Lipoproteins are important in the outer membrane of some bacterial cell walls.

Lipopolysaccharides

• Lipopolysaccharides (LPS) come from lipid + piece of polysaccharide

• E.g. if you recall lipids are generally insoluble…the LPS helps protect some bacterial cells from harsh environments (also gives more structural support)

Steroids

• Another complex lipid (also hydrophobic like other lipids).

• Contain four carbon rings

• A subset contain an –OH group attached to one ring = Sterol

Sterols are part of membranes that keep them fluid- separate fatty acid chains

Cholesterol

• sterol

• found in animal cell membranes and mycoplasma membranes (type of bacteria)

Ergosterol

• Sterol

• found in fungal cell membranes

Proteins

• Are made of C, H, O, N, and sometimes S

• Essential in cell structure and function

• Proteins include:

– Enzymes that speed up chemical reactions

– Transporter proteins that move chemicals across membranes

– Flagella that aid in movement

– Some bacterial toxins

– Structural components

• Proteins are polymers of amino acid building blocks...are typically 50 to several thousand amino acids in length

Amino Acids

• Proteins consist of subunits called amino acids

• Amino acids contain a carbon that has an attached: Carboxyl group (-COOH) Amino group 2 ( NH ) - Side group (-R group)

side groups change between amino acids

Amino Acids (microbes vs. humans)

• Humans can synthesize certain amino acids, but not others. e.g his and met cannot be synthesized

• Microbes typically synthesize most amino acids

Proteins…how do they form?

Are formed through the joining of amino acids via peptide bonds that are formed via dehydration synthesis reactions.

Protein Structure

• There are different levels of protein structure.

• The primary structure is a single polypeptide chain

• Is stabilized by peptide bonds

secondary structure of Protein

• The secondary structure occurs when the amino acid chain folds and coils in a helix or pleated sheet

• Is stabilized by hydrogen bonds

2= forming of helices and sheets

Tertiary structure of proteins

• The tertiary structure occurs when the helix or sheet folds irregularly into a specific 3D structure

• Tertiary structure is stabilized by: – Various types of bonds (more than only hydrogen bonds)

overall 3D shape

quaternary structure

The quaternary structure consists of two or more polypeptides

4= multiple polypeptide chains together

denaturation

• Proteins can also undergo denaturation

• Occurs when proteins encounter hostile environments (e.g. high temperature and unfavorable pH) and lose their shapes and functions

Conjugated proteins

Conjugated proteins are important and consist of amino acids and other organic molecules

– Glycoproteins (contain sugars)

– Nucleoproteins (contain nucleic acids)

– Metalloproteins (contain metal atoms)

– Lipoproteins (contain lipids)

– Phosphoproteins (contain phosphate)

Enzymes

• Enzymes are specialized protein molecules produced by living cells.

• They are known as biologic catalysts; that is, they speed up metabolic reactions.

• Most chemical reactions in cells requires a specific enzyme

• Enzymes are usually named by adding the ending “-ase” to the word. Hemolysins and lysozyme are examples of enzymes not ending in “ase.”

catalyst

A catalyst is an agent that speeds up a chemical reaction without being consumed in the reaction.

substrate

The specific molecule on which an enzyme acts is referred to as that enzyme’s substrate.

Nucleic acids

Nucleic acids are another type of large organic molecule.

• Carry genetic information

• Include DNA and RNA

• Consist of nucleotides

nucleotides contain:

– A five-carbon (pentose) sugar

– Phosphate group (nucleosides lack this)

– A nitrogen-containing (purine or pyrimidine) base

There are DNA nucleotides and RNA nucleotides One for each nitrogenous base, A, T, C, G, [U (in RNA)]

DNA

• Deoxyribonucleic acid

– Contains deoxyribose

– Exists as a double stranded helix

Nitrogenous bases from separate strands are bonded:

– Adenine hydrogen bonds with Thymine

– Cytosine hydrogen bonds with Guanine

DNA is the the “hereditary molecule”—the molecule that contains the genes and genetic code.

Missing oxygen on sugar compared to RNA

RNA

Ribonucleic acid

– Contains ribose – Is single-stranded

– Contains Uracil instead of Thymine for its nitrogenous bases

• RNA molecules participate in the conversion of the genetic code into proteins and other gene products.

There are several kinds of RNA…these play specific roles in protein synthesis