Download Microbiology bio 123

Module C-3
How organisms capture, manufacture, and store energy
Most animals are limited to aerobic metabolism.
Bacteria are not limited to aerobic metabolism.
Enzymes process energy, and are manufactured by the DNA.
Enzymes:
Enzymes are organic catalysts, and therefore determine everything that a cell does. Once a reaction is completed,
the enzyme can be reused because it is not changed by the reaction.
The types of enzymes we produce determine what kinds of catabolic pathways we use.
Enzymatic reactions are reversible.
See this page for more info: http://en.wikipedia.org/wiki/Enzyme
Enzymes are categorized into 2 categories.
1. Endoenzymes – inside the bacterial cell
2. Exoenzymes – outside the bacterial cell
Exoenzymes are used by the bacterial cell to break down the proteins, carbohydrates, and fats into molecular size
that can pass through the cell membrane.
Holoenzyme – a complete functional enzyme. All the parts are there.
Parts of an enzyme:
1. Apoenzyme – Protein part of the enzyme, is organic, typically of high molecular weight
2. Co-enzyme – required by some enzymes, typically a vitamin; is organic. Typically of low molecular
weight (not as large as protein). If absent in a holoenzyme, the enzyme will not work and is then not
called a holoenzyme.
3. Co-factor – required by some enzymes, typically a metallic ion; is inorganic.
Approximate size of an enzyme:
10,000-1,000,000 amu (amu is equal to the weight of a proton, H2O is about 18 amu)
A single molecule of enzyme can change up to 1,000,000 molecules of substrate per minute. (Substrate is a
molecule that the enzyme acts on)
Enzymes are fairly unstable, even minor changes in their environment can inactivate them. Two most dangerous
changes are temperature or pH. They can denature the protein when they are outside the normal operating ranges.
The Specificity of Enzymes:
Every enzyme is specific to a specific substrate.
Oxidation refers to the loss of electrons; reduction refers to a gain in electrons.
Enzymes are categorized according to their reaction: (typically enzymes end in -ase, sometimes they end in -yme)
1. Oxidoreductase - They monitor the change and balance of oxidation/reduction. They happen
simultaneously. Can be abbreviated as redox reactions.
2. Transferases – They transfer functional groups from one molecule to another. (Functional groups are –OH
(hydroxide), -COOH (carboxyl group), and NH2 (amino group), PO4 (phosphate group).
3. Hydrolytic – They break apart molecule by adding water. They place a H2O molecule into another
molecule (carbs, proteins, lipids, nucleic acids) and therefore break them apart..
4. Lyases – Break apart molecules without using water.
5. Isomerases – Molecules that have the same molecular formula but have different arrangements of them.
They change one form of a molecule to another.
6. Ligases – (tying, trying to pull things together) they put together, used in DNA and RNA replication.
Enzyme levels:
Control methods for enzymes:
1. Constitutive enzymes – enzymes that remain constant no matter what. They are typically used with
anything that is necessary for life ( basic metabolic processes such as breathing, HR, etc)
2. Inducible enzymes – they are involved with the breakdown/degredative process. Their synthesis is
triggered by the presence of the compound that needs to be broken down (elevated blood glucose, etc)
3. Repressible enzymes – they are involved in biosynthetic pathways (making larger molecules). There are
typically repressed by the end product of the end of the pathway. There are two ways to inhibit the
synthesis of enzymes. In repression, the end product stops the production of all of the enzymes necessary
for the production of the product. In feedback inhibition, the end product stops the production of the first
enzyme necessary for the production of the end product. The end product of the pathway ends the synthesis
of the enzyme.
How to measure enzyme activity:
1. Look for the product of the reaction being made. (i.e. If substrate A turns into product B, then enzyme E is
present.
2. Enzyme activity: When substrate is infinity and the enzyme is limited. Enzyme activity is always measured
by amount of product.
3. The enzymatic curve has two phases; the first is when the curve steadily rises until the entire enzyme is
being used. The second phase is when the curve tapers off and stabilizes. This occurs when the entire
enzyme is currently being used. Amount plateaus because equal amounts of reactions are going backwards
as well as forwards.
Enzyme activity when the substrate is infinity and the enzyme is infinity:
1. The curve is the same.
2. The second phase is when the enzyme is saturated.
3. E+S→ES→EZ→EP→E+P
When the curve is based on pH, the value rises from 0 to 7, and then falls from 7 to 14 (upside down v).
Activity peaks at neutral (pH of 7).
When the curve is based on temperature, the value is a curve that has the highest point at 35 degrees c. It
begins at 0 degrees and ends at 70 degrees c. The colder the temperature, the slower the molecules move, so
the speed of the enzyme slows when it get too cold but still functions. At about 69 to 70 degrees c., the
enzyme will actually be denatured and is not reversible. Heat kills, cold does not.
Conditions that effect enzyme activity: referred to as inhibitors
1. Some are not reversible, they have a structure similar to the substrate and they will not release the enzyme.
These are typically toxins and poisons.
2. Some are competitive inhibitors, they compete for the enzyme. (i.e. a→b→c→PABA+E→folic acid,
Sulfonamide (synthetic antibiotics) competes with PABA for enzyme E.)
Metabolism includes two major types of reactions:
1. Endergonic reactions require energy to be placed into the reaction to complete the metabolism; typically
biosynthetic reactions. Referred to as anabolism.
2. Exergonic reactions produce energy when the reaction takes place in the form of ATP. Typically occurs
when molecules are broken down. Referred to as catabolism.
When metabolism occurs, they are nothing more than a series of redox reaction (oxidation/reduction). The most
important thing to remember about these pathways is to think of Hydrogen equaling electrons. Aerobic respiration
always begins with glucose, C6H12O6. Hydrogen (H) atoms can be split into an electron and a proton, thence e⁻
and H+. Any molecule with large amounts of hydrogen has a lot of energy.
Aerobic respiration can be broken down into three parts:
1. Glycolysis, which produces pyruvic acid, has a net production of 2 ATP, and has a total production of 4
ATP. Also releases 1 H, gets bound to NAD which becomes NADH.
2. Intermediate Reaction: Pyruvic acid gets changed to acetyl CoA
3. Krebs Cycle/TCA/Citric acid cycle: Produces CO2, two ATP, H which is picked up by NAD making
NADH, releases a second H which is bound to FAD to make FADH2.
4. Electron Transport - Produces 34 ATP molecules. It is when oxidative phosphorylation uses chemiosmosis
to produce large amounts of ATP.
5. Aerobic or Anaerobic acceptor – O₂ or C (from glucose), or SO₄ →H₂ S or NO₃ →NO₂ or N₂ O or N₂
or CO₃ →CH₄
Chemiosmosis –When hydrogen ions (H+) rush back in to cell through channels, ATP synthase stores this energy.
This is called “chemiosmosis.”
Oxidative Phosphorylation – The process of H⁺ ions moving across the membrane and concentration gradient,
Chemiosmosis, and bind with the e⁻ .
The entire process of aerobic respiration ends with a total of 38 ATP.
Nitrate reductase – bacteria that produce this enzyme reduce NO3.
Chemotrophic (aerobic)
1. NO2 – NO3 +e⁻ →ETS→O2
2. NH4 – NO2 +H2 O+e⁻ →ETS→O2
3. Produces variable amounts of ATP (minimal amounts)
Fermentation
1. Glucose →Pyruvic Acid (also final e⁻ acceptor) →Acids or Alcohols (CO2, H2, aldehyde, acetones)
(depends on the enzymes that are present in the cell) (S. Lactis turns milk into lactic acid very quickly,
produces cottage cheese) (L. Bulgaricus turns lactose into lactic acid very slowly, produces yogurt)
(Propionibacterium turns the lactose into lactic acid quickly and also produce O2, producing Swiss
cheese.)
2. Only produces 2 ATP per glucose molecule.
Bacterial Photosynthesis vs. Plant photosynthesis –
Green pigment (chlorophyll) is necessary for the production of glucose, takes CO2 and H2O and uses chlorophyll
and energy from the sun to produce C6H12O6 and O2. Bacterial photosynthesis uses bacterial chlorophyll to
produce glucose, CO2 and H2S and uses chlorophyll and energy from the sun to produce CH2O and S.
Saccromyces = yeast
Propionibacterium = bacteria
Bacillus lactobacillus streptococcus = bacteria
Clostridium = bacteria
Escherichia coli = bacteria
Aerobic respiration begins with glucose:
Glucose
Production of 2 ATP (net);
Total production is 4
Glycolysis
Pyruvic acid
Removal of 1 Hydrogen (oxidized)
H+NAD=NADH (reduced)
Acetyl CoA
2 more ATP produced
H removed; FAD reduced w/ 2 H= FADH2
One H removed (oxidation)
H+NAD=NADH
CO2 removed
Electron Transport Chain: Creates 34 ATP
All hydrogen atoms removed during respiration goes to the cell membrane.
Hydrogen is split; + hydrogen ions go out of cell and electrons are kept in cell membrane to be passed along by
cytochromes. This creates a concentration gradient with more hydrogen ions outside of the cell than inside.
Within the membrane, there is an enzyme called ATP synthase. When hydrogen ions rush back in to cell through
channels, ATP synthase stores this energy. This is called “chemiosmosis.”
When back inside cell, hydrogen is put back together; this creates water because we already have oxygen
available.
This process is called oxidative phosphorylation and creates 38 ATP from beginning to end.
Things that use aerobic respiration tend to be more successful because it is highly efficient and creates 38 ATP.
Anaerobic respiration does not have oxygen as the final electron receptor inside the cell; common ones include
sulfate (creates hydrogen sulfide – NO3+H), nitrate or nitrogen gas using nitrate reductase enzyme. Also uses (?),
creating methane.