Chapter From Atoms to Cells


Chemical building blocks of matter

Matter. Anything that has mass and occupies space. Ex. atom, air, water, rocks, bacteria

Atom. Smallest chemical unit of matter

Atoms are building blocks for more complex substances. i.e. atoms interact with each other to produce various chemical substances such as the oxygen we breath, water, salt, proteins, etc.

Element. Substance composed of same kind of atoms

Major elements present in living organisms

C = Carbon
H = Hydrogen
N = Nitrogen
O = Oxygen
P = Phosphorus

 

Molecule. Chemical combination of 2 or more atoms

Ex. O2, molecular oxygen (Fig. 2.3)

Compound. Molecule made of 2 or more elements

Ex. carbon dioxide, CO2

 

What are N2 and H2O ?

 

The structure of atoms (See Fig. 2.1)


 Component

 Location

 Charge

 Proton

 Nucleus

 + (Positive)

 Neutron

 Nucleus

None (Neutral)

 Electron

 Orbiting nucleus

 - (Negative)

Electron shell. Region around the nucleus where electrons orbit (See Fig. 2.2)

Inner most shell holds only 2 electrons

The atoms of most elements of living organisms are stable when 8 electrons are in the outer shell

(Hydrogen only has one shell, so it is stable when 2 electrons are present)

An atom has a neutral charge because it has the same number positive (protons) and negative (electrons) charges

Ion. An atom that carries a charge because it has gained or lost electrons in order to acquire a stable outer shell.

The number of protons and electrons are no longer equal (Fig. 2.6)

Ex.

Na+ Sodium ion resulting from the loss of one electron from the outer shell of a neutral Sodium atom

Cl- Chlorine ion resulting from the gain of one electron the outer shell of a neutral Chlorine atom

Ca++ Calcium ion resulting from the loss of 2 electrons from the outer shell of a neutral Calcium atom

 

Cation. A positively charged ion

Anion. A negatively charged ion


Chemical bonds and molecules. Links between atoms, ions or compounds that hold them together (Fig. 2.3, 2.4 and 2.5)

3 Types

1) Ionic bond. Attraction between a cation and an anion (opposite charges attract)

Ex. Na+Cl- (table salt)

 

2) Covalent bond. Sharing of electrons between atoms (represented as a solid line)

Allows both atoms to have completely filled outer electron shells

 

 

3) Hydrogen bond. Attraction between partially postive (d+) hydrogen atom of one molecule and a partially negative (d-) atom of another molecule

(d, "delta" is the symbol used to designate a partial rather than a *full positive or negative charge)

*Note that cations and anions have full positive or negative charges

Partial charges exist when there is unequal sharing of electrons in a covalent bond between two atoms of a molecule.

Ex. H2O (Fig. 2.5)

 

 

See Fig. 2.8

Note: The hydrogen bond is between an oxygen atom of one water molecule and a hydrogen atom of another water molecular (represented as a dashed line). The bond between O and H of the same water molecule is a covalent bond.

 

Comparison of Bond Strengths

Strongest ---------------------------> Weakest

Covalent.......>........Ionic........>...... Hydrogen


Chemical reactions. Formation or breakage of bonds between atoms

Energy is stored in a chemical bond

Bond formation requires input of energy

Chemical reaction

X + Y + energy -----------------------> X-Y

 

Bond breakage releases energy stored in the bond

Chemical reaction

X-Y -----------------------------> X + Y + energy

 

Metabolism. The chemical reactions that occur inside cells of living organisms.

Two types:

Anabolism. Reactions that require energy to form covalent bonds

Involved in biosynthesis of cellular components

Ex. Proteins, cell walls, DNA, lipids

 

Catabolism. Reactions that break bonds, releasing the energy stored in the bonds

Supplies the energy needed for anabolic reactions

Ex. Breakdown of high energy food molecules such as carbohydrates (sugars) and lipids (fats)



D. Water and solutions

Living organisms are mostly water

Has important properties necessary for life

1. A polar solvent

Dissolves ionic and polar compounds to form solutions (Fig. 2.7)

Ex. Salt and sugar solutions

Does not form solutions with nonpolar compounds like oils and fats

Ex. Oil doesn't dissolve in water and floats on the surface when the two are combined

2. Medium for metabolic reactions between dissolved compounds in the cytoplasm of a cell

3. Participates as a reactant or product in many metabolic reactions

Hydrolysis rxn.

Ex. H2O + X-Y -------------------------> X-H + Y-OH

4. Stores or releases heat with little temperature change

Most organisms need a stable temperature to function properly

5. Weakly ionic --some molecules dissociate into H+ and OH- (hydroxyl) ions

 

pH, acids and bases

pH A measure of the concentration of H+ of water (Table 2.2)

Pure water is neutral, i.e. the concentrations of H+ and OH- ions are the same

[H+] = [OH-] = 0.0000001 moles/liter (10-7 moles/liter)

The pH value of a water solution is the negative logarithm of [H+]

-log 10-7 = 7.0; so the pH value of pure water is 7.0

The pH scale

7.0 is the middle of the pH scale (range 0-14, see Fig. 2.13)

Pure water and aqueous solutions have a pH value of 7.0 (called neutral)

A solution with a pH value below 7.0 is acidic (it has a higher concentration of hydrogen ions than pure water)

A solution with a value above 7.0 is basic (it has a lower concentration of hydrogen ions than pure water)

Each whole unit of pH represents a 10-fold increase or decrease in [H+]

Acid. Chemical compound that releases a hydrogen ion (H+)when added to water

Ex. Acetic acid

CH3COOH ----------> H+ + CH3COO-

This increases the concentration of hydrogen ions in the solution, decreasing the pH

Base. Chemical compound that accepts H+ or releases a hydroxyl ion (OH-) in water

Ex. 1. Ammonia

NH3 + H+ ---------> NH4+

 

Ex. 2. Sodium hydroxide

NaOH ---------> Na+ + OH-

OH- + H+ --------> H2O

OH- and H+ combine to form H2O which decreases [H+]

So, both types of bases decrease the concentration of hydrogen ions in the solution, increaseing the pH

Exs.

1. You add acetic acid to pure water which increases the [H+]

If:
pH = 6, the [H+] is 10 X greater than that of pure water

pH = 5, the [H+] is 100 X greater than that of pure water

 

2. You add ammonia to pure water which decreases the [H+]

If:
pH = 8, the [H+] is 10 X smaller than that of pure water

pH = 10, the [H+] is __?__ smaller than that of pure water

 

Remember:

1) Solutions with pH values below 7.0 are acidic and those with pH values above 7.0 are basic

2) A solution with a low pH has a higher [H+] than a solution with a higher pH

Most microorganisms prefer pH near 7.0. The pH of the cytoplasm and of their environment affects their growth and survival.

Acidophiles and alkalophiles are unusual microorganisms that thrive in acidic or basic environments


The Chemical Makeup of Microbial Cells

Organic compounds. Contain C and H (may also contain other elements such as oxygen, nitrogen and phosphorus)

Ex. CH4 (methane)

CH3-COOH (acetic acid)

C6H12O6 (glucose)

 

Why aren't NaOH, NaCl, H2O, CCl4 and NH3 organic compounds?


Reduced organic compounds contain more H and little or no O

Have a high energy content, supports good growth of microorganisms

Ex. CH4

 

Oxidized organic compounds contain less H and more oxygen

Have a lower energy content

E.x.

HCO2H (formic acid)

Can't support as much growth as CH4

CO2 (carbon dioxide)

The most oxidized form of carbon in cells

Not organic by deffinition, but is the waste product produced by catabolism of
organic compounds used to support the growth of microorganisms

Has no usable energy to support growth

 

Functional groups affect the properties of organic compounds (Table 2.3)

 Functional group

 Formula

 Property

 Example
 Hydroxyl  -OH  Polar  CH3-OH
 Carbonyl  -CHO  Polar  CH3-CHO
 Carboxyl  -COOH  Acidic  CH3-COOH
 Amino  -NH2  Basic  CH3-NH2


Complex organic compounds

Contain more atoms and functional groups than simple organic compounds

Many are polymers of simple organic compounds

Ex.

Starch and cellulose are polymers of glucose (Fig. 2.17)

Proteins are polymers of amino acids

DNA (deocyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides

Cellular functions

-Components of cell structures

Ex. Cell walls, membranes, cell capsules, flagella

-Catalysts that speed up metabolic reactions

Ex. Enzymes

-Storage and retrieval of information necessary for life

DNA -----> RNA -----> Proteins

-Storage of energy

Ex. starch, a polymer of glucose


Major classes of organic compounds present in cells (Table 2.4)

1. Carbohydrates (a.k.a sugars or saccharides) (Fig. 2.15)

Monosaccharide. Exists as a single molecule

Ex. Glucose C6H12O6

Disaccharide. 2 Monosaccharides joined by a covalent bond

Ex. Sucrose (table sugar): Glucose + fructose

Polysaccharide A polymer of several monosaccharides (hundreds to thousands) joined together by covalent bonds

Ex. Starch and cellulose are polymers of glucose

Ex.

Glucose is a good source of energy and carbon for anabolic reactions that produce cellular components during growth

Ribose is a 5-carbon monosaccharide that is a component of RNA

2. Lipids

Nonpolar. Not soluble in water ("oil and water don't mix")

3 major classes

1) Triglycerides (Fig. 2.18)

Composed of glycerol (a carbohydrate) linked to 3 long-chain fatty acids

Used by cell to store energy

 

2) Phospholipids (Fig. 2.19)

Fat with phosphate group substituted in place of 1 fatty acid

Negative charge of phosphate interacts with polar water molecules

Major component of cell membrane

Interactions of the hydrophobic (nonpolar) fatty acid chains with each other and the hydrophilic (polar) phosphate with water are responsible for formation of the bilayer structure of membranes.

 

 

3) Steroids (See Fig. 2.20)

Four fused carbon rings linked to a side chain

Component of cell membrane of plants, animals and some microorganisms

 

3. Proteins. Polymers of amino acids

General structure of an amino acid

The R groups of the amino acids present in a protein determine its properties and its interactions with other cellular components

20 different R groups = 20 different amino acids (Table 2.5)

R groups may be nonpolar, polar, acidic or basic

 

 

Peptide bond: covalent bond that links amino acids together to form a protein. (See Fig. 2.21)

 

Proteins consists of many (often several hundred) amino acids linked together by peptide bonds.

Another name for a protein is a polypeptide.

 

Protein Structure

1. Primary structure. Order of occurrence of amino acids in a polypeptide

Ex. Methionine-Valine-Serine-Aspartic acid-Lysine-......etc.

2. Secondary structure. Conformation of the polypeptide backbone

Helix or sheet

3. Tertiary structure. Overall shape of completely folded polypeptide

4. Quaternary structure. Combination of 2 or more polypeptides

Only proteins consisting of more than one polypeptide have this structure

 

Ex.

High temperature

High or low pH

Chemicals (Ex. alcohol, acids, bases)

 

Classification of proteins

1) Structural proteins

Components of cell structures

Ex. flagella for motility (movement)

2) Enzymes

Catalysts that speed up metabolic reactions in cells


Ex. X + Y ----------------> X-Y

Too slow to support life

Enzymes increase reaction rates by thousands to millions of times, making life possible

3) Other

Regulatory proteins. Control expression of genetic information and metabolism

Receptors. Sense environmental stimuli

Transport proteins. Move substances across the cell membrane as they enter or exit the cell

Antibodies

Produced by immune system of higher organisms (not produced by microorganisms, but inhibit or prevent infections by pathogenic microorganisms)

 

4. Nucleotides and nucleic acids

Nucleotides

Three components (Fig. 2.23)

1) Organic base that contains nitrogen (Adenine, Guanine, Cytosine, Thymine or Uracil)

2) Five carbon sugar (Ribose or Deoxyribose)

3) Phosphate group(s)

 

Two main functions in cells:

1) Source of energy

Ex. Adenosine triphosphate (ATP) (Fig. 2.27)

 

2) Building blocks of nucleic acids

Nucleic acids

Polymers of nucleotides (Fig. 2.23)

Used for storage and expression of genetic information


Sugar-phosphate backbone links nucleotides together

Nitrogen bases extend out from the sugars

1 Deoxyribonucleic acid (DNA) -Blueprint for synthesis of all proteins needed by the cell

Consists of two strands (Fig. 2.23 and 2.25)

Held together by hydrogen bonds between nitrogen bases of opposite strands

Nitrogen bases: Adenine, Thymine, Guanine, Cytosine (no Uracil) (Fig. 2.24)

A of one strand hydrogen bonds only to T of the adjacent strand

G hydrongen bonds only to C

5-C sugar is deoxyribose (Fig 2.24)

2. Ribonucleic acid (RNA) -Involved in expression of the information in DNA during protein synthesis

Consists of a single strand

Nitrogen bases: A, Uracil, G, C (no T)

5-C sugar is ribose (Fig. 2.24)

 

DNA -----> RNA ----->Protein

 

The information is encoded as a sequence of the 4 nitrogenous bases (A, T, G, C)

Ex. T-A-T-C-G-T-A-A-C-A------etc. determines the sequence of amino acids of a protein

 

 

 

Summary of DNA and RNA properties

 Nucleic acid

# of strands

 5-C sugar

 Nitrogen base
 1. Ribonucleic acid

 1

 Ribose

 Adenine (A)

 (RNA)
   

 Uracil (U)
     

 Guanine (G)
     

 Cytosine (C)
       
 2. Deoxyribonucleic acid

 2

 Deoxyribose

 A

 (DNA)
   

 Thymine (T)
     

 G
     

 C

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