Chemistry of Microbiology
Can Eating Spicy Foods Cause Ulcers?
Ramona is a young mother who takes. For children who drink during the day, put it back a few nights later. Pretty soon she's feeling pain every night.
The clinic takes ex use at and high. Mentions her symptoms to her trainer. Mr. Rowe, who meets the needs of her family and Tells her that he might have an ulcer.
Mr. Know about Rowe her studies mean a busy schedule, Ramona's love of spicy food, and her advice to cut back.
Late nights, very itchy oysters, and eating on the run Rajamona. You can see an improvement in her symptoms with the hot sauce.
Ramona takes Moti loves spicy food and eats a lot. He says His advice is, but the pain and nausea continue. Ever Hot Sauce for Every Meal. That Happens to be Mexican Symptoms occur during the day, but most often they flare up.
Weekends and sneaks in an occasional cigarette when he. During the night the children are not watching. What do you think? Did you eat very spicy food?
One night, Ramona notices a burning pain in her upper back. Ramona an ulcer? The almonds vanish after a few minutes but come again.
Learning some basic concepts of chemistry will enable you to better understand. The diversity of interactions between microorganisms and their environment.
The reactions, growth, and the identification of pathogenic microorganisms in the laboratory. And the microbial chemistry involved in the selection of antimicrobial drugs. Understanding the fundamentals of chemistry will also help you maintain your health.
In this chapter, we study atoms which are the basic constituents of chemistry. And about how atoms react to form chemical bonds and molecules.
We then examine the three major categories of chemical reactions. In this chapter Completion of the molecules. Most important to live—are water, acids, bases, lipids, carbohydrates, proteins, and ATP.
Atoms
Atoms are the smallest chemical units of matter. Atoms are very small and only the largest of them can be seen using a microscope.
Atomic Structure
In 1913, the Danish physicist Niels H. D. Bohr proposed a general model. In which charged subatomic particles orbiting electrons form. The center of a miniature solar system. is called a nucleus.
A nucleus is made up of free neutrons and charged protons. The only exception is the nucleus of a normal hydrogen atom, which is made up of only a proton and a neutron. Protons and neutrons are very small.
If a meterstick were to be stretched between the Sun. And the Earth's neutron or proton would measure only the width of a human hair. The number of electrons in an atom is generally equal to the number of protons. So entire atoms are neutral.
In contrast, the ink in your pen is not an element because it is made up of many types of atoms. Elements differ from each other in their atomic number.
Which is the number of protons in their nucleus. For example, the atomic numbers of hydrogen, and carbon. And oxygen is 1,6, and 8 because all hydrogen nuclei have the same number of protons.
The atomic mass of an atom is the sum of the masses of its protons, neutrons, and electrons. Protons and neutrons each have a mass of about 1 atomic mass unit, also called dalton 3.
An electron is very massive, with a mass of about 0.00054 daltons. Electrons are ignored in discussions of atomic mass. Because their contribution to the total mass is negligible.
So protons and the number of neutrons are approximately equal. To the atomic mass of an atom. There are 93 occurring elements known. But, only 20 are used only by organisms. Each of which has its symbol derived from its English or Latin name.
Isotopes
Each atom of an element has the same number of protons. But atoms of a given element may differ in the number of neutrons in their nuclei.
For example, there are three occurring isotopes of carbon. Each with 6 protons and 6 electrons. More than 95% of carbon atoms also have six neutrons.
Because these atoms have six protons and six neutrons. This isotope has an atomic mass of about 12 neutrons. And is known as carbon-12, which has the symbol C.
An atom of carbon-13 has seven neutrons per nucleus and 1 cm. An unstable atom because of its ratio of protons and neutrons nucleus release energy.
And sub-protons and electrons called radioactive decay. Atoms that have undergone radioactive decay are radioactive isotopes.
Radioactive decay and radioactive isotopes play an important role. In microbiological research, medical diagnosis. Treatment of disease. And the destruction of contaminating microbes of medical equipment and chemicals.
Electron Configuration
Although the nuclei of atoms determine their identity, it is an electron. That determines the chemical behavior of an atom. Nuclei of different atoms rarely come close enough to interact.5.
Generally, but, only the electrons in the atoms interact. So because all isotopes of carbon have the same number of electrons. All isotopes behave the same way in chemical reactions.
Scientists know that electrons do not orbit the nucleus. In a two-dimensional circle as predicted by the Bohr model; instead. These nuclei move 100 quadrillion times per second in three-dimensional electron shells.
More put, an electron shell represents the possible locations of electrons. At a given time; besides. Is simpler and more convenient to draw electron shells as circles.
Each electron shell can only hold a certain largest number of electrons. For example, the first shell can accommodate the largest of two electrons.
And the second shell can hold no more than eight electrons. Hydrogen and helium The atoms of Li have one and two electrons. Thus these two elements have only one electron shell.
When the outermost shell is the third shell, it holds eight electrons. But, when the fourth shell holds two electrons, its capacity increases to 18. Heavier atoms have more shells. But these atoms do not play an important role in life.
The electrons in the outermost shell of the atoms are called electrons. Figure 2.4 shows the electron configuration of atoms of some elements.
Important for microbial life. Note that in the given column the atoms of all the elements. Except helium have the same electron configuration. There are some molecules. With the noble gases, helium is placed in the far column.
Because its outer surface is full, although it has two eight polar electrons. The valence electrons are important for interactions between molecules. Next, Let us consider that these reactions are called chemical bonds.
When the outer shell of an atom is not filled with eight electrons. There is either room for more electrons or there are electrons over electrons. For example, an oxygen atom with six electrons.
The Euler shell has two "vacancies" because of the oxygen atom. It takes less energy to gain two electrons than to lose six. In contrast, a calcium atom has two.
The "extra" electrons are in the outer shell because it requires less energy. To lose two of these electrons then to gain six new ones.
When a calcium atom loses two electrons, its third shell is. Which is then its outer shell, is filled with eight electrons, and is stable. As stated earlier, the outermost electrons of an atom are called valence electrons.
And thus the outermost shell of the valence or shell. The valence 6 of an atom, defined as its valence potential, is considered positive.
If its valence shell has extra electrons to give up and be negative. In this fill thus a calcium atom has a valence of +2 in. The valence shell of two electrons while the oxygen atom has to fill it There are two places for this.
Molecules combine in such a way that they fill their valence shells. By sharing or other transfers of balancing electrons. A molecule consisting of atoms of more than one element is a compound.
Two hydrogen molecules bonded together to form a hydrogen molecule. Which is not a compound because Only one element is involved. But, two hydrogen atoms bonded with an oxygen atom form a water molecule, which is a compound.
In this section, we discuss the three major chemical bonds: non-polar covalent bonds. Polar covalent bonds, and ionic bonds, we also consider the hydrogen bond. Polar covalent bonds are weak elements that act with polar covalent bonds.
Nonpolar Covalent Bonds
For example, consider what happens when two hydrogen atoms approach each other. Each hydrogen atom has a single proton orbited by an electron.
Since each atom has two electrons to fill its valence cell Electrons are needed. So one electron from each atom is added to the other to form a hydrogen molecule.
In which both the atoms are complete alcohol oxygen atoms can share electrons. But they have to share a pair of electrons for a complete seal. Because the two pairs of electrons are shared. The oxygen atoms form two covalent bonds or double covalent bonds with each other.
The attraction of electrons to an atom is called its electronegativity. The more electronegative an atom is the more electrons it has in its nucleus. Note Figure 2.6, which displays the electrons in atoms of many elements.
They. -Etronegativities increase from left to right in the chart. The reason is that elements on the right side of the chart have more protons and thus, electrons in the chart.
The electron electronegativities of K decrease because of the distance between the nucleus. And the valence shell increases as the elements become larger.
Two hydrogen atoms or atoms such as hydrogen and carbon have equal or equal electrons. In chemistry and physics "poles" are opposing forces.
Such as the north and south magnetic poles or the positive and negative poles of a battery. negative terminal. On atoms of similar electronegativity. The shared electron pairs spend an equal amount of time around each nucleus and there are no poles.
Hydrogen molecules can symbolize several
H-H H: H H2
The dash in the first symbol represents the chemical bond between the atoms. These two symbols are known as structural formulas. The third symbol is known as the molecular formula.
The superscript "2" refers to the number of hydrogen atoms. That are bonded together, not the number of shared electrons trans. Each of these symbols indicates the same thing—two hydrogen atoms sharing electrons.
Many atoms need more than one electron to fill their valence shell. For example, the carbon molecule has four valences. And needs to gain four more if it wants to keep eight in its chemical shells.
Figure 25c shows a carbon atom shared with four hydrogen atoms. As before, a line in the structural formula shows a covalent bond formed by the sharing of two electrons.
The oxygen atom in the two covalent bonds formal aldehyde and a carbon atom. This fact is stated in two lines. This shows that the four electrons of the carbon molecule are with the oxygen atom.
Carbon atoms are important for life. Carbon-molecule has four electrons. it has the same tendency to either lose four electrons or gain four electrons due to events. A complete outer shell.
This results in carbon atoms sharing electrons and forming four covalent bonds. With each other and with many other types of atoms. In effect, each carbon atom acts as a four-way.
The junction is where different components of a molecule can join. A consequence of this characteristic. Carbon atoms can form very large chains. That form the "backbone" of many important molecules.
Carbon chains can be branched or unbranched, and some can also close on themselves to form rings. Compounds that contain carbon and hydrogen atoms are called organic compounds.7
Polar Covalent Bond
If the electron goes off two bound atoms. What is different then their electrons will not be shared. Instead, the electron pair will spend more time orbiting the greater electron nucleus.
Thus Bonds in which electrons are shared are polar covalent. bond. An example of a molecule with polar covalent bonds is water. Electrons are more electronegative than hydrogen. So electrons spend more time near hydrogen nuclei than near hydrogen nuclei.
The covalent bond between an oxygen atom and a hydrogen atom. Called polar because the partial electrical charges of the atoms are opposite. Polar covalent bonds can occur between many elements. Usually, molecules with polar covalent bonds are soluble in water.
And non-polar molecules are not. The most important polar covalent bonds for life are bonds involving hydrogen. Because allow binding, which we are discussing shortly.
Both nonpolar and polar covalent bonds form angles between the atoms. Such that the distance of the electron orbits is maximized.
But, it is more convenient to draw molecules as if all the atoms were in a plane; for example H-O-H.
Ionic Bond
Consider that when there are two atoms. For example, sodium has one electron in its valence shell. And chlorine, with seven electrons in its valence shell.
And an electronegativity of 3.0. Then Chlorine has such a high electron affinity. That it attracts sodium's valence electrons very. And as a result, sodium loses electrons to chlorine.
Now that the chlorine atom has one electron instead of a proton. It has an absolute negative charge. And the sodium atom, which has lost an electron.
Now contains an atom or group of atoms with an absolute positive charge 2. Positive charge Ions are called cations, while negative ions are called anions.
Charged ions form ionic bonds 3 and the metal and nonmetal ions form salts. Known as sodium chloride and potassium chloride. Instead, the attraction of opposite electric charges results in bonding.
The polar bonds of the water molecules disrupt the ionic bonds of the salt. Causing dissociation also called ionization. This occurs when the partial negative charge on the oxygen atom of water contracts.
Cation and charged ions on hydrogen atoms. The presence of polar bonds interferes with the attraction between cations and anions.
When the cations and anions are separated from each other and surrounded. Water molecules are called electrolytes because they conduct electricity.
Electrolytes are important to life because they can form a variety of compounds. Stabilize electrolytes, and serve as electron carriers. And use electrical gradients across cells to stay inside cells. We examine these functions of electrolytes in later chapters.
In nature, chemical bonds are nonuniform. The important thing to remember. That electron are shared between atoms. n covalent bonds and transferred from one atom to another in ionic bonds.
Hydrogen Bond
As we have seen, hydrogen atoms are bonded. With oxygen atoms via polar covalent bonds. Resulting in temporary positive charges on the hydrogen atoms. Hydrogen molecules also form polar covalent bonds with atoms of other elements.
The electrical attraction between a charged hydrogen atom. And a full or partial negative charge on a different region of the same molecule.
Hydrogen bonds can be compared to weak ionic bonds. As they result from the attraction of positive and negative charges.
Note also that although they result from polar covalent bonds between hydrogen atoms. and other, more electronegative atoms, hydrogen bonds are not covalent bonds.
As we've seen, covalent bonds are essential to life because they link atoms. Together to form molecules. Hydrogen bonds that are weaker than covalent bonds are also necessary.
The cumulative effect of many hydrogen bonds is to stabilize. The three-dimensional shape of large molecules. For example, D.N. A. The double helix shape of H is.
Due to the stabilizing effects of the hydrogen bonds attached to the molecule. The precise shape is essential for the function of enzymes. Antibodies intracellular chemical messengers and the recognition of target cells by pathogens.
Apart from this, due to the weakness of the hydrogen bond, they can be overcome if necessary. For example, D.N. A. The two complementary halves of the molecule.
Are held together by hydrogen bonds and are called D.N. A. Can be taken apart for replication.
Chemical Reactions
You are already familiar with the many consequences of chemical reactions. Put yeast in bread dough and it rises; enzymes.
In your laundry detergent remove grass stains and gasoline burn. What is happening in these reactions? What is the exact definition of a chemical reaction?
All chemical reactions begin with reactants—atoms, ions, or molecules. That is present at the beginning of a reaction. All chemical reactions result.
After the reaction Atoms, ions or molecules are produced when this happens. Biochemistry involves the chemical reactions of life.
The reactants and products can have very different physical cal and chemical characteristics. For example, hydrogen and oxygen are gases.
And have very different properties in water. Which is composed of hydrogen and oxygen atoms. But the type of atoms in a chemical reaction Changes happen. We now turn our attention to three general categories. Biochemical reactions.
Synthesis Reactions
Synthesis reactions involve the formation of larger and more complex molecules. Synthesis reactants can be expressed.
Reactor + Reactant → Product(s)
The arrow indicates the reaction of the new chemical bond and the direction of the form ion. For example, algae make their glucose using the following reaction:
6H2O+6CO2→ C6H12O6 +6O2
The reaction is described as, "Six molecules of water. And six molecules of carbon dioxide produce one molecule of glucose. And six molecules of oxygen are produced."
Note that the total number of atoms on both sides of the reaction and The types are similar.
A common synthesis reaction occurring in biochemistry is dehydrated synthesis. In which two small molecules are linked together by a covalent bond and a water molecule is also formed.
The name of this type of reaction refers to the fact. That dehydration denotes. One of the products is a water molecule formed. By the combination of a hydroxyl ion with a hydrogen ion of a reactant.
Energy is required to break bonds in synthesis reactions. Reactions form new bonds to form reactants and products. The ones that need energy are called endothermic reactions. Because they trap energy within new molecular bonds.
Energy Supplies are a common rule for fueling synthesis reactions. Care of all living things. All synthesis reactions have been collected in one organization is called anabolism.
Decomposition Reactions
Decomposition reactions are the opposite of synthesis reactions. That they break down smaller atoms and ions. And molecules into larger molecules."General, in decomposition.
C6H12O6 +6O2 → 6H2O +6 CO2
Note that this reaction is the exact opposite of the synthesis reaction in algae. That we looked at earlier. A common type of decomposition reaction in biochemistry.
Is hydrolysis,0 followed by dehydration synthesis. In hydrolytic reactions, a covalent bond breaks a large molecule.
And breaks down the ionic components of cations into products. is mixed in. All decomposition reactions in the Jaeger system are called catabolism. Exchange reactions have characteristics.
In stans, they involve breaking and forming covalent bonds. They involve both endothermic and exothermic steps. As the name suggests, atoms are transferred from one molecule to another. In general, these reactions can be represented as the B+ side.
A + BC - AB + C
An important reaction in the exchange of glucose to phosphorus in living organisms. Is adenosine the sum of all chemical reactions? In an organism, Catabolic, anabolic, and exchange reactions are called metabolism.
Water, Acids, Bases, and Salts
As stated earlier, living things depend on organic compounds that contain carbon. And hydrogen molecules. Organisms also need a variety of inorganic chemicals.
Which generally lack carbon, such as water, oxygen, and oxygen. In this section, we examine the characteristics of some of these inorganic materials.
Water
Water is the most abundant substance in living organisms, accounting for 50% to 99% of their mass. The fact that water molecules have two polar covalent bonds.
Allows hydrogen bonding between water molecules. And their neighbors Important characteristics of water are important consequences of this.
Among the characteristic features of water are the following: Water molecules are cohesive. That is, they stick to each other through hydrogen bonding.
This property gives rise to several properties of water. Such as surface tension, which causes water to form a thin layer on the surface of cells. This aqueous layer is needed to carry solutes.
Water is an excellent solvent; it dissolves salts. And charged molecules in themselves. Because it is attracted to both charged molecules.
Water remains a liquid across a wider range of temperatures. Than other molecules of similar size. This is important because living things must water in liquid form.
Water itself can absorb significant amounts of heat energy as the temperature changes. When hot water molecules evaporate. They take most of the absorbed energy with them. These properties are modern.
Ate fluctuations in temperature which would otherwise harm the living beings. Water molecules take part in many chemical reactions. Inside cells as reactants in hydrolysis. And as products of the process of dehydration.
Acids and Bases
As we have seen, the polar bonds of water molecules dissociate salts. Into their components and ions. In a similar process, some substances are known as acids and bases.
Acid is a substance that dissociates into one or more hydrogen ions and one or more anions. Acids can be inorganic molecules such as hydrochloric acid.
And sulfuric acid or organic molecules such as amino acids and nucleic acids. Well-known organic acids are found in lemon juice, black coffee, and tea.
Organic acids have carbon in their anions, while inorganic acids do not. A base is a molecule that binds with HT when dissolved in water. Some cations are complex and dissociate into hydroxyl ions. Which then combine with hydrogen ions to form water molecules:
H + + OH →H2O
Other bases, such as household ammonia, accept hydrogen ions. And become mixed ions such as NH. Another common household base of baking soda is sodium bicarbonate.
Metabolism requires a stable balance of acids. And bases because of hydrogen ions and hydroxyl ions. Are involved in many chemical reactions.
Complex molecules such as proteins lose their functional shape when acidity changes. Metabolism ceases if the concentration goes far beyond normal.
The concentration of hydrogen ions in a solution is expressed. By the logarithmic pH scale. The term pH comes from the potential of hydrogen. Which is negative in the logarithm of the concentration of hydrogen ions.
On this logarithmic scale, it is worth noting. That Acidity increases with decreasing pH values. And each decrease represents a 10-fold increase in acidity.
For example, a glass of grapefruit juice. With a pH of 3.0 contains 10 times the same amount of hydrogen ions as tomato juice, which has a pH of 4.0.
Tomato juice is 1000 times more acid than water, which has a pH of 7.0. Water is neutral because It dissociates into a hydrogen cation and a hydroxyl anion:
H2O - H+ +OH
Organisms can only tolerate a certain, narrow pH range. Fluctuations outside an organism's preferred range. Inhibit its metabolism and can even be fatal.
Most organisms have buffers that prevent rapid drastic changes. In the laboratory culture, the metabolic activity of microorganisms can change. The pH of microbial growth solutions as nutrients.
Are taken up and waste materials are released. A common buffer is used. In microbiological media is F, PO. Which, depending on the pH of the environment, is present as either a weak acid or a weak base.
Acidic conditions Under K, KH, and PO, are a base that combines. With H, neutralizing the acidic environment. But, under alkaline conditions, K, PO, acts as an acid, releasing hydrogen ions.
Microorganisms differ in their ability to tolerate different ranges of pH. Photosynthetic bacteria known as cyanobacteria grow well in more basic solutions.
But, some bacteria, called acidophiles, must have acidic conditions. Some bacteria are tolerant of acid. One such bacterium is Prinibac.
Skin acne has a pH of 4.0. Another roundworm, Helicobacter pylori. Appears to cause ulcers in the stomach, where the pH can be less than 1.5 when acid is secreted.
Clinical case study: Raw musk and antacids: a deadly mix? Focus on how the use of antacids can increase. The survival rate of bacteria that cause stomach disease.
Microorganisms can change the pH of their environment. By using acids and bases and producing acidic or basic substances waste.
For example, fermentative microorganisms from or decomposition of tannic acid sugar. And Thiobacillus bacteria can lower the pH to 0.0. The acid produced by this bacterium in mine water can be.
Some mines are made profitable by extracting uranium and copper from low-grade ores. Scientists measure pH with a pH meter or impregnated test paper.
Which changes color in response to pH. In a microbiological laboratory, usually. By converting them to the color of pH indicators included in microbial growth media. Used to differentiate bacterial species.
Salt
As we have seen, salt is a compound that dissociates into many ions and cations other than HTiS and OH. During exchange reactions the acid. And the base neutralizes each other yielding hydroxyl, For example, milk.
Magnesia is an antacid used to neutralize stomach acid. The chemical reaction is
Mg(OH)2 + 2HCI → MgCl2 + 2H2O
Magnesium Hydrochloric Magnesium Water Hydroxide acid chloride
The ions of cations and salts are electrolytes. A cell uses electrolytes to create the electrical difference between its inside.
And outside, to move electrons from one place. To another, and as an important component of many enzymes. Some Organisms also use salts. Such as calcium carbonate to give structure and support to their cells.
