MICR130

Living things too small to be seen with the unaided eye

Carolus Linnaeus

Genus and specific epithet, bot are underline or italicized. Genus is always capitalized

Bacteria, Archea, and Eukarya

He observed that cork was composed of “little boxes”; he introduced the term cell. His discovery marked the beginning of cell theory (all living things are composed of cells).

Anton van Leeuwenhoek

Some forms of life could arise spontaneously from nonliving matter

Francesco Redi

John Needham

Lazzaro Spallanzani

Rudolf Virchow

Living cells can arise only from preexisting living cells

He demonstrated that microorganisms are in the air everywhere and offered proof of biogenesis. He used a long-necked flasks, bent the necks into S-shape curved, which trapped any airborne microorganisms. His discoveries led to the development of aseptic techniques.

Pasteur

Pasteurization

Bassi and Pasteur

Joseph Lister

Who proved that microorganisms cause disease?

Robert Koch

A sequence of experimental steps for directly relating a specific microbe to a specific disease

Edward Jenner

Paul Ehrlich. It is used to treat syphilis

He observed that the Penicillium fungus inhibited the growth of bacterial culture.

Antibiotic from fungus

The study of bacteria

The study of fungi, includes medical, agricultural, and ecological branches

The study of protozoa and parasitic worms

The study of immunity

The study of virus

People came to believe that living organisms arise form nonliving matter because they would see flies coming out of manure, maggots coming out of dead animals, and microorganisms appearing in liquids after a day or two.

Electrons (e-), Nucleus → protons (p+), neutron (n0)

The atomic number

The total number of protons and neutrons

An attraction between ions of opposite charge that holds them together to form a stable molecule. Weaker ionic bond are important in biochemical reactions such as antigen-antibody reactions

A bond formed by two atoms that share one or more pairs of electrons. Covalent bonds are the most common type of chemical bond in organisms and are responsible for holding together the atoms of most molecules in organisms

A relatively weak bond in which a hydrogen atom that is covalently bonded to one oxygen or nitrogen atom is attracted to another oxygen or nitrogen atom. Hydrogen bonds do not bind atoms into molecules, but rather serve as bridges between different molecules or different portions of the same molecule, for example, within proteins and nucleic acids.

A chemical reaction that absorbs more energy than it releases

A chemical reaction that releases more energy that it absorbs

• When two or more atoms, ions, or molecules combinr to form new and larger molecules
• A + B → AB
• Pathways of synthesis in living organisms are collectively called anabolic reactions, or anabolism

• The reverse of a synthesis reaction
• AB → A + B
• Decomposition reactions that occur in living organisms are collectively called catabolic reactions or catabolism

• Part synthesis and part decomposition
• AB + CD → AD + BC

Reversible reaction

• When the end product can revert to the original molecule
• A+B ⇔ AB

• Usually small, ionically bonded molecules
• Example: common acids, bases and salts

• Always contains carbon and hydrogen
• Mostly or entirely covalently bonded, and many of them are large molecules

H+

OH-

• referems to the concentration of H+ in a solution
• pH 7 is neutral; pH value below 7 indicates acidity; pH above 7 indicates alkalinity

to stabilized the pH insida a cell and in culture media

A chain of carbon atoms

Carbohydrate, lipids, proteins, and nucleic acids

• Compounds consisting of atoms of carbon, hydrogen, and oxygen. CH20
• Includes sugar and starches
• Can be classified as monosaccharide, disaccharide, and polysaccharides
• Monosaccharide
• Contain from three to seven carbon atoms
• May form disaccharide and polysaccharides by dehydration synthesis

• Two molecules with the same chemical formula but different structure and properties
• Example: glucose (C6H12O6) and fructose (C6H12O6)

• A diverse group of compounds distinguished by their insolubility in water
• Simple lipids
• Consist of a molecule of glycerol and three molecules of fatty acids
• Saturated lipids
• No double bonds between carbon atoms in the fatty acids Higher melting point that unsaturated lipids
• Unsaturated lipids
• One or more double bonds
• Phospholipids
• Complex lipids consisting of glycerol, two fatty acids, and a phosphate group
• Steroids
• Carbon rings structures

• Amino acids are the building blocks of proteins
• Amino acids consist of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur
• Twenty amino acids occur naturally in proteins

• Primary: sequence of amino acids
• Secondary: helices or pleats
• Tertiary: overall three-dimensional structure of a polypeptide
• Quaternary: two or more polypeptide chains

Amino acids combined with inorganic or organic compounds

DNA, RNA- macromolecules consisting of repeating nucleotides

Pentose, a phosphate group, and a nitrogen-containing base.

A pentose and a nitrogen-containing base

Deoxyribose (a pentose) and one of the following nitrogen-containing bases: thymine or cytosine (pyrimidine) or adenine or guanine (purines).

• Deoxyribonucleic acid
• Consist of two strands of nucleotides wound in double helix. The strands are held together by hydrogen bonds between purine and pyrimidine nucleotide: AT and GC

• Ribonucleic acid
• Consist of ribose (a pentose) and one of the following nitrogen-containing bases: cytosine, guanine, adenine, and uracil

• Single-strands in cells and most RNA viruses
• The sugar is ribose
• Adenine, thymine, cytosine, and uracil
• Protein synthesis

• Double-stranded in cells and most DNA viruses to form a single double helix; single-stranded in some viruses (parvoviruses)
• The sugar is Deoxyribose
• Adenine, thymine, cytosine, guanine
• Determines all hereditary traits

Energy is released

To regenerate ATP from ADP and inorganic phosphate

Micrometers and nanometers

temperature, pH, and osmotic pressue

carbon, nitrogen, sulfur, phosphorus, oxygen, trace elements, and organic growth factors

minimum growth temperature

Optimum growth temperature

maximum growth temperature

at pH 6.5 and 7.5

• chemoheterotrophs use an organic molecule
• autotrophs use carbon dioxide

any material prepared for the growth of bacteria in a laboratory

microbes that grow and multiply in or on a culture medium

agar

one in which the exact chemical composition is known

one in which the exact chemical composition varies slightly from batch to batch

• Psychrophiles: cold-loving microbes
• Mesophiles: moderate-temperature-loving microbes
• thermophiles: heat-loving microbes

• Psychrophiles
• Pschrotophs
• Mesophilrs
• Thermophiles
• Hyperthermophiles

25-40° C

• cold-loving microbes
• -8° C (minimum growth temperature)
• 15°C (optimum growth temperature)
• 19° C (maximum growth temperature)

• do not grow well at low temperature, except in comparison with other organisms
• able to degrade food
• 0° C (minimum growth temperature)
• 22°C (optimum growth temperature)
• 31°C (maximum growth temperature)

• moderate-temperature-loving microbe
• 10°C (minumum growth temperature)
• 37°C (optimum growth temperature)
• 58°C (maximum growth temperature)
• most common type of microbe
• include most of the common spoilage and disease organisms

• heat-loving microbes
• 39°C (minimum growth temperature)
• 62°C (optimum growth temperature) about the temperature of hot tap water
• 72°C (maximum growth temperature)

• 66°C (minimum growth temperature)
• 93°C (optimum growth temperature)
• 110°C (maximum growth temperature)
• most live in hot springs associated with volcanic activity

bacteria that are remarkably tolerant of acidity

Lag phase

Log phase

stationary phase

Death phase (logarithmic decline phase)

selective media: inhibits unwanted organisms with salts, dyes, or other chemical which allows growth of only the desired microbes

differential media are used to distinguish different organisms

to encourage the growth of a particular microorganism in a mixed culture

by deepfreezing or lyophilization (freezing-drying)

Plasmolysis

high salt concentrations

loss of water from a cell in a hypertonic environment. 

Cellular water passes through the plasma membrane which goes into the high solute concentration. This happens when the microbial cell is in a solution whose concentration of solutes is higher than in the cell.

an organism that requires high osmotic pressures such as high concentrations of NaCl (in order for growth to occur)

organisms that does not require high salt concentration but are able to grow at salt concentrations up to 2%. 

a few species can tolerate even 15% salt

a complex polysacharride derived from a marine alga and used as a solidifying agent in culture media

Carbon is the structural backbone of living matter.  It is needed for all the organic compounds that make up a living cell. Half the dry weight of a typical bactrial cell is carbon

Nitrogen makes up 14% of the dry weight of bacterial cell, and sulfur and phosphorus together constitue about another 4%

Nitrogen is primarily used to form the amino group of the amino acids of proteins.

Sulfer is used to synthesize sulfur-containing amino acids and vitamins such as thiamine and biotin. Important natural sources of sulfur: sulfate ion (SO₄^2-), hydrogen sulfide, and the sulfur-containing amino acids

Phosphorus is essential for the synthesis of nucleic acids and the phospholipids of cell membranes. phosphate ion (PO₄^3-)

during respiration

the electron transport chain

O₂

sulfate, carbonate, phosphate

• 6 molecules NADH
• 2 molecules FADH₂
• 2 molecules ATP

NADH

38 ATP

36 ATP

Pyruvic acid

Cellular respiration, in which glucose is completely broken down and fermentation, in which it is partially broken down

proteins, produced by licing cells, that catalyze chemical reactions by lowering the activation energy.

Enzyme undergo denaturation and lose their catalytic properties.

The reaction rate decreases.

from the oxidation of carbohydrates

glucose

• 2 ATP
• 2 NADH

refers to the chemical reactions that result in the breakdown of more complex organix molecules into simpler substance. 

refers to chemical reactions in which simpler substance ar combined to form more complex molecules

ATP

• Photosynthesis
• the chemical energy is used for carbon fixation

the sum of all chemical reactions within a living organism

catabolism and anabolism

cofactor (or coenzyme; if cofactor is organic) & apoenzyme.

the apoenzyme will not function

• NAD⁺ (nicotinamide adenine dinucleotide)
• NADP⁺ (nicotinamide adenine dinucleotide phosphate)

both compound contain derivatives of the B vitamins niacin ( nicotinic acid). both function as electron carriers: NAD⁺ catabolic (energy-yielding) and NADP⁺ is primarily involved in anabolic reactions (energy-requiring)

• FMN (flavin mononucleotide)
• FAD (flavin adenine dinucleotide)
• contain derivatives of the B vitamins riboflavin, function as electron carriers

a coenzyme that contains a derivative of pantothenic acid, another B vitamin.  CoA plays and important role in the synthesis and breakdown of fats and in a series of oxidizing reactions called the Krebs cycle.

• 1. any compound with which an enzyme reacts
• 2. a region on an enzyme that interacts with the substrate
• 3. a temporary union of an enzyme and its substrate

• 1. At high temperatures, enzymes undergo denaturation and lose their catalytic properties; at low temperatures, the reaction rate decreases.
• 2. The pH at which enzymatic activity is maximal is known as the optimum pH.
• 3. Within limits, enzymatic activity increases as substrate concentration increases.
• 4. Competitive inhibitors compete with the normal substrate for the active site of the enzyme. Noncompetitive inhibitors act on other parts of the apoenzyme or on the cofactor and decrease the enzyme's ability to combine with the normal substrate by altering the shape of the active site.

Energy released during certain metabolic reactions can be trapped to form ATP from ADP and P (a single phosphate ion). Addition of P to a molecule 

• substrate-level phosphorylation, a high-energy P from an intermediate in catabolism is added to ADP. 
• oxidative phosphorylation, energy is released as electrons are passed to a series of electron acceptors (an electron transport chain) and finally O₂ or another inorganic compound.
• photophosphorylation, energy from light is trapped by chlorophyll, and electrons are passed through a series of electron acceptors. The electron transfer releases energy used for the synthesis of ATP.

a coupled reaction in which one substance is oxidized and one is reduced

• 1. Oxidation is the removal of one or more electrons from a substrate. Protons (H+) are often removed with the electrons.
• 2. Reduction of a substrate refers to its gain of one or more electrons.
• 3. Each time a substrate is oxidized, another is simultaneously reduced.
• 4. NAD⁺ is the oxidized form; NADH is the reduced form.
• 5. Glucose is a reduced molecule; energy is released during a cell's oxidation of glucose.

When an enzyme and substrate combine, the substrate is transformed, and the enzyme is recovered. Enzymes are characterized by specificity, which is a function of their active sites.

fill the active site of an enzyme and compete with the normal substrate for the active site. this is possible because its shape and chemical structure are similar to those of the normal substrate

do not compete with the substrate for the enzyme's active site; instead, they interact with another part of the enzyme

inhibition of an enzyme in a particular pathway by the accumulation of the end-product of the pathway; also called end-product inhibition

stops the cell form making more of a substance than it needs and thereby wasting chemical resources

acts on the first enzyme in a metabolic pathway

the sum of all chemical reactins within a living organism

• release energy- catabolism
• require energy- anabolism

Catabolism is the breakdown of complex organic compounds into simpler ones

releases energy

are called catabolic or degradative reactions

hydrolytic reactions (use water in which chemical bonds are broken)

exergonic (produce more energy than the consume)

example: cells break down sugars into CO₂ and H₂O

Anabolism is the building of complex organic molecule from simpler ones

are called anabolic or biosynthetic reaction

involves dehydration synthesis reactions (release H₂0)

endergonic (consumes more energy than they produce)

example: formation of proteins from amino acids, nucleic acids from nucleotides, polysaccharides from simple sugars

Catabolic reactions provide the building blocks for anabolic reactions and furnish the energy needed to drive anabolic reactions.

through the molecule ATP (adenosine triphosphate)

• 1. stores
• 2. catabolic
• 3. releases
• 4. anabolic

• adenine
• ribose
• 3 phosphate group

ADP (adenosine diphosphate)

enzymes

when chemical bonds are formed or broken

atoms, ions, or molecules must collide

explains how chemical reactions occur and how certain factors addect the rates of those reactions

all atoms, ions, and molecules are continuously moving and are thus continuously colliding with one another

the velocities of the colliding particles, their energy, and their specific chemical configurations

activation energy

reaction rate

raise its temperature

substances that can speed up a chemical reaction without being permanently altered themselves

enzymes

catabolism is energy forming (ADP+P --> ATP) so in catabolism ATP is the product. anabolism: is energy storing (ATP --> ADP +P) in anabolism ATP starts the reaction. SO: ADP + P --> <-- ATP