Chapter 5 Microbial Metabolism (Pages 114-152)
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Chapter 5 Microbial Metabolism (Pages 114-152) and Chapter 2 Chemical Principles (pages 37-49) Class Notes Power Point 2013. Introduction Metabolism - refers to the sum of all chemical reactions within a living organism. Metabolism can be divided up into two classes of chemical reactions.

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Chapter 5 Microbial Metabolism (Pages 114-152) and Chapter 2 Chemical Principles (pages 37-49)Class Notes Power Point 2013


Metabolism- refers to the sum of all chemical reactions within a living organism. Metabolism can be divided up into two classes of chemical reactions.

Catabolism– the enzyme-regulated chemical reactions that involve the breakdown of complex organic compounds into simpler ones. Energy, generally in the form of ATP is released.

Catabolic reactions are generally hydrolytic, water is used in the break down of chemical bonds.

These reactions are exergonic- produce more energy than they consume energy.


sugar carbon dioxide + water + ATP

Anabolism - the enzyme-regulated energy requiring chemical reactions that involve the building of complex organic compounds from simpler ones. These reactions are anabolic or biosynthetic reactions and involve dehydration synthesis, that is they release water.

These reactions are endergonic- consuming more energy than they produce.


Amino acids protein (Hemoglobin)

Nucleotides nucleic acids (DNA & RNA)

Simple sugars polysaccharides (starch &


Cow Protein



A new protein chain is formed by the instructions in our genes.


Human Protein

II. The Structure and Role of ATP in Coupling

Anabolic and Catabolic Reactions

A. The Structure of Adenosine triphosphate

ATP exists in two forms:

ATP Adenosine Triphosphate - A kind of

chemically charged form of ATP.

ADP Adenosine diphosphate– A kind of

chemically discharged form of ATP.

Adenosine triphosphate ATP


ATP and ADP Conversions

H 2 O + ATP ADP + P

( G = -7.3 kcal / mole) or (–31 kj/ mole)

This reaction represents 7.3 kcal /mole of energy that can be used to do cellular work.

P + ADP ATP + H 2 O

( G = +7.3 kcal / mole) or (+31 kj/ mole)

This reaction represents 7.3 kcal /mole of energy that is needed to replenish or recharge ADP to ATP.

Energy Production: When, where and how is ADP converted to ATP?

  • Nutrients such as carbohydrates, fats, proteins and nucleic acids have energy associated with the electrons that form the bonds between their atoms.

  • When spread throughout a molecule such as glucose this bond energy is difficult for the cell to use.

  • Various reactions in catabolic pathways can

    transfer the bond energy of a molecule

    such as glucose into the bonds of ATP.

  • To extract the bond energy from organic

    compounds such as glucose and store it in the form of ATP, processes in the cells of the organism pass electrons from one compound to another through a series of oxidation-reduction reactions.

Oxidation-Reduction Reactions

  • Oxidation is the removal of electrons(e-) from an atom or molecule. It often produces energy.

  • Reduction is the addition of one or more electrons to an atom or molecule. It can be be viewed as storing energy.

  • Oxidation and reduction are always coupled together.

  • Most biological redox reactions electrons and protons are removed at the same time and involve hydrogen atoms.

III. Catabolism A Closer Look

A. Fermentation – A catabolic process that is a partial degradation of sugars that occurs without the help of oxygen.


Glucose (6 C) 4ADP


2ADP Glycolysis

2 Pyruvic Acid (3C)

Various End Products Depending on the Bacteria

Acids Alcohols CO2 H2

Fermentation can be defined in several ways:

  • A process that releases energy from sugars such as glucose as well as other organic molecules such as amino acids and nucleic acids.

  • A process that does not require oxygen.

  • A process that does not utilize the Krebs cycle or the electron transport chain.

  • A process that does use an organic molecule as the final electron acceptor.

  • A process that produces only small amounts of ATP.

1Mole of glucose yields 6 86kcal

Fermentation produces a net yield of 2 ATP:

2 ATP X 7.3 kcal/mole ATP = 14.6 kcal

14.6kcal/686 kcal ~ 2% Efficiency

B. The most prevalent and efficient catabolic pathway is cellular respiration, in which oxygen is consumed as a reactant along with an organic fuel such as sugars.

Overview: Glucose (6 C)

Input Output




2 Pyruvic Acid (3C)


2 CO2

2 ( 2C ) acetyl Co A


Kreb’s Cycle 6 NADH 4 CO2



Electron Transport &10 NADH

Chemiosmosis2 FADH2

__________________ Total

ATP Yield by Oxidative Phosphorylation 32 – 34 36-38 ATP/

ATP Yield by substrate level Phosphorylation 4 glucose

IIf Energy is released from a fuel all at once, it cannot be harnessed efficiently for constructive work. (ie a gas tank exploding) Glucose and other organic fuels are broken down in a series of steps, each catalyzed by an enzyme. At key steps, electrons are stripped from glucose . These electrons travel with a proton , thus as a hydrogen atom. The H atoms are not transferred to O2 directly but instead are usually passed through first to an electron carrier, o coenzyme called NAD+ (nicotinamide adenine dinucleotide) .

Nicotinamide adenine dinucleotide

IV.The Effect of Oxygen

Prokaryotes display a wide range of responses to molecular

oxygen(O2). (See pgs 165-167)

A. Obligate aerobes require O2 for growth and cannot grow with out it. O2 is used as the final electron acceptor in aerobic respiration. These organisms are at a disadvantage in poor oxygenated waters. Many of the aerobic bacteria have developed or retained the ability to continue to grow in the absence of O2 .Such organisms are called:

B.Facultative anaerobes organisms that can use O2 when it is present but are able to continue growth by using fermentation when O2 is not available. What happens to their efficiency when O2 absent?

E-coli is a familiar example.

C. Obligate anaerobes organisms that are unable to use O2. In fact O2 is a toxic substance, which either kills or inhibits their growth. Obligate anaerobes live by fermentation, bacterial photosynthesis, or methanogenesis. Members of the Clostridium genus that cause tetanus and botulism are examples.

D. Aerotolerant anaerobes are bacteria with an exclusively anaerobic ( fermentative) type of metabolism but they tolerate O2 fairly well. They live by fermentation alone whether or not O2 is present in their environment. They can grow on the surface of a nutrient agar plate with out the special techniques required for obligate anaerobes. Many of these bacteria ferment carbohydrates to lactic acid, which as it accumulates inhibits aerobic competitors.

V. A Bit of Chemistry

  • The carbon atom. A single carbon atom has the ability to form 4 covalent bonds. These 4 bonds can form with a wide variety of other elements to make a number of different compounds.

Organic Compounds

Compounds that contain CARBON are

called organic.

Macromolecules are large organic



  • Carbon can bond with many elements, including hydrogen, oxygen, phosphous, sulfur and nitrogen to form the molecules of life.

  • Carbon has 4 electrons in its outer shell.

  • Carbon can form covalent bonds with as many as 4 other atoms (elements), and even other atoms of carbon.

  • Carbon has the ability to form millions of different large and complex molecules.

B. Examples include:



Molecular Representations

Methyl Alcohol

Ethyl Alcohol

VI. Polymers and Monomers

  • Monomer – a singe building block

    (i.e. sugar)

  • B. Polymer – a macromolecule made up of

  • a characteristic set of monomers .

  • C. Polymers are constructed by way of a

  • dehydration or condensation synthesis

  • reactions.

  • D. Polymers are broken down by

  • hydrolysis reactions.









Monomers linked together to make polymers:


  • How are Macromolecules or Polymers formed?








By Dehydration Synthesis

  • Also called “condensation reaction”

  • Forms polymers by combining monomers and “removing water”.

  • How are Macromolecules separated or digested?








Answer: Hydrolysis

  • Separates monomers by “adding water”.

  • Important Biological Organic Compounds

  • (See Pgs 38 – 49)

  • A. Carbohydrates -A class of biological

  • molecules used for fuel and building

  • blocks. The carbohydrates include:

  • Polysaccharides

  • Disaccharides

  • Monosaccharides

  • (saccharide means sugar)


The arrangement of cellulose in plant cells

Starch-the storage form of carbohydrates in plants. How do plants produce glucose? Why do plants store glucose as starch?

Cellulose – major componebt of plant cell walls.

Glycogen- a polysaccharide and the storage form of glucose in the humans and other vertebrates.

1.Disacccharides- a carbohydrate sugar consisting of two monosaccharide sugars joined by a glycosidic linkage.Important disaccharides include: Sucrose – the transport form of sugar in plants. sucrose = glucose + fructose Lactose – the sugar found in breast milk.Lactose = glucose + galactoseMaltose – malt sugar used in brewing.Maltose = gulcose +glucose

Why is the formula for a disaccharide sugar C 12 H22 O 11 as opposed to C 12 H24 O 12 ? Explain

Dehydration synthesis of sucrose

Hydrolysis of sucrose

2. Important Monosaccharide sugars include:glucose – blood sugarfructose – fruit sugar( the sweetest sugar) galactose – less sweet than glucose

Aldehyde Sugar Ketone Sugar

Monosaccharide sugars – generally have formulas that are some multiple of the unit CH2O. Examples:The 6 carbon sugar: C6H12O6 The 5 carbon sugar: C5H10O5

Carbohydrate sugars – generally have formulas that are some multiple of the unit CH2O. Examples:The 6 carbon sugar: C6H12O6 The 5 carbon sugar: C5H10O5

The structure and classification of some monosaccharide sugars

Lipids – used for structural and long term

energy storage.

Lipids are made up of 1 glycerol molecule linked to 3 fatty acid molecules

1 gram of fat releases 8,893 calories when it is burned. That is ~8.9 Kcals or Food Calories1gram fat ~ 9 kcal/gram

What is the evolutionary significance of fat?

Hummingbird example:

A 5g hummingbird needs ~ 45kcal of stored energy to make it’s annual migration.

Burning fat it needs to add ___________

Burning carbohydrate it needs to add ___________

Glycerol – One of the structural components of a fat and other lipids.

Is glycerol a carbohydrate? Explain.

Hint: Write the molecular formula for glycerol:

Fatty Acids Saturated vs Unsaturated fat

Dehydration reaction in the synthesis of a fat


Bilayer structure formed by self- assembly of phospholipids in an aqueous environment

Plasma Membrane

The structure of cholesterol

Amino Acids are the monomers building blocks of proteins.

Dehydration Synthesis of two different amino acids producing a dipeptide

Proteins can be 100’s of amino acids’s long! And the order of the amino acids, determines the particular protein. There are 1,000’s of different proteins!

Our genes tell our cells how to arrange the amino acids in the correct order to make a particular protein!

Cow Protein


A new protein chain is formed by the instructions in our genes.

Human Protein

Structure of insulin

Glucose/ Insulin animation

Protein Primary structure. The sequence of amino acids, determined by the DNA base sequence.

Protein tertiary structure

Hemoglobin example found in red blood cells is an of 4th level protein structure

Protein Folding Animations

Cytochrome c is primarily known as an electron-carrying mitochondrial protein. Cytochrome c is an efficient biological electron-transporter and it plays a vital role in cellular oxidations in both plants and animals. It is generally regarded as a universal catalyst of respiration, forming an essential electron-bridge between substrates such as NADH and oxygen. Its main function in is to transport electrons from cytochrome C reductase(Complex III) to cytochrome C oxidase(Complex IV).

Collision Theory

Activation energy and enzymes

Mechanism of enzyme action

Protein and non-protein part of an enzyme

Some enzymes do not need any additional components to show full activity. However, others require non-protein molecules called cofactors to be bound for activity. Cofactors can be either inorganic or organic.

Inorganic Organic

Cu, Fe, Mg, Mo, Se Zn Vitamins

Competitive vs Non –competitive Inhibitors

  • Large organic molecules also called POLYMERS.

  • Are made up of smaller “building blocks” called MONOMERS.

  • Examples:

    1. Carbohydrates

    2. Lipids

    3. Proteins

    4. Nucleic acids (DNA and RNA)

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