Ch. 8 - Microbial Metabolism

Metabolism

all chemical and physical workings of a cell

What are two types of chemical reactions?

Catabolism & Anabolism

Catabolism

* degradative
* breaks the bonds of larger molecules forming smaller molecules
* release energy

Anabolism

* biosynthesis
* process that forms larger macromolecules
* requires energy input

What are enzymes?

Biological catalysts that **increase** the rate of a chemical reaction by lowering the energy of activation

Energy of activation

Resistance to a reaction

Simple enzymes

consist of protein alone

Conjugated enzymes or holoenzymes

contains both protein and nonprotein molecules

Apoenzyme

protein portion

Cofactors

nonprotein portion

Inorganic elements

(metal ions): iron, copper, magnesium

Organic molecules

coenzymes

For the enzyme **catalase**, what is the action AND cofactor required?

* Action: breaks down hydrogen peroxide
* Cofactor Required: Iron

For the enzyme **oxidase**, what is the action AND cofactor required?

* Action: Adds electrons to oxygen
* Cofactor Required: Iron, Copper

For the enzyme **nitrate reductase**, what is the action AND cofactor required?

* Action: reduces nitrate to nitrite
* Cofactor Required: Molybdenum

For the enzyme **DNA polymerase**, what is the action AND cofactor required?

* Action: synthesis of DNA
* Cofactor Required: Zinc and Mg

For the enzyme **Botulinim**, what is the action AND cofactor required?

* Action: Hydrolyzes protein needed for vesicle transport
* Cofactor Required: Zinc

What do larger enzymes show?

Quaternary structure

Active site (catalytic site)

Site for specific substrate binding

What is the first level of enzyme structure?

As the polypeptide forms intrachain bonds and folds, it assumes a 3D (tertiary) state that displays an active site

What is the second level of enzyme structure?

Because each unique polypeptide folds **differently**, each apoenzyme will have a **differently shaped active site**

What is the third level of enzyme structure?

* More complex enzymes have a **quaternary structure** consisting of more than one polypeptide


* New active sites may be formed by the junction of polypeptides

Enzyme-Substrate Interactions

\
* depends on the shape of both the enzyme AND substrate


* once it is formed, it then undergoes a chemical reaction to form a product.

Induced Fit

A temporary enzyme-substrate union occurs when substrate \n moves into active site

Why is the process of enzyme-substrate interactions important?

* Helps the functioning of metabolic pathways
* Is affected by factors like temperature, pH and substrate concentration

What are some actions **coenzymes** perform?

* Serve as temporary carrier for some substrates
* Vitamins as the most common

List the 4 steps for the figure of **Coenzyme**

1. An enzyme with a coenzyme is positioned to react w/ two substrates
2. Coenzyme picks up a chemical group from **substrate 1**
3. Coenzyme readies the chemical group for transfer to **substrate 2**
4. Final action is for group to be bound to substrate 2; altered substrates are released from enzyme

Exoenzymes

* transported extracellularly, where they break down large food molecules or harmful chemicals
* cellulase, amylase, penicillinase

Endoenzymes

* retained intracellularly and function there
* most enzymes are endoenzymes

Constitutive enzymes

* always present
* always produced in equal amounts or at equal rates (regardless of the amount of substrate)

Regulated enzymes

* not constantly present
* production is turned on (induced) or turned off( (repressed) in response to changes in the substrate concentration

Condensation Reaction

forming a glycosidic bond between **two glucose molecules,** generate maltose requires the removal of a water molecule

Hydrolysis reactions

* Breakage of a peptide bond between 2 amino acids that requires a **water molecule** that adds OH to one amino acid and H to the other

How is the activity of an enzyme influenced?

By the cell’s environment

How do enzymes operate?

Under temperature, pH, and osmotic pressure of organism’s habitat

How do enzymes become unstable?

When they’re subjected to changes in organism’s habitat they become unstable

Labile

chemically unstable enzymes

Denaturation

weak bonds that maintain the shape of the apoenzyme are broken

Metabolic pathways proceed in a stepwise, highly regulated manner to maximize the use of what two things?

Nutrients and energy

What kind of system regulates the enzymes involved in metabolic reactions?

A checks and balances system

Competitive inhibition

substance that resembles the normal substrate, **competes** with the substrate for the active site

Allosteric Inhibition

form of competitive inhibition in special types of enzymes w/ **two binding sites**:

* active site
* regulatory/allosteric site

How are enzymes regulated in the **regulatory site?**

By negative feedback from the binding of molecules other than the substrate

Noncompetitive inhibition

* Inhibitor binds to the entire enzyme-substrate complex
* Prevents the enzyme from completing its action on the substrate

List the three steps in **competitive inhibition**

1. Both molecules compete for the active site (normal substrate and competitive inhibitor w/ similar shape)
2. Reaction proceeds
3. Reaction is blocked b/c competitive inhibitor is incapable of becoming a product

List the three steps in **allosteric inhibition**

1. Enzyme-substrate reaction proceeds; products are released
2. A product of the enzyme reaction binds to the regulatory site and causes a change in the shape of the active site
3. Substrate cannot fit; enzyme action is blocked

How is the regulation of enzymatic action at the genetic level produced?

By controlling the synthesis of degraded enzymes that need replacement

Enzyme repression

Automatic suppression of **enzyme synthesis** when end product builds to excess

Enzyme induction

enzymes are made only when suitable substrates are present

* enables the organism to adapt to nutrients and prevents waste of energy

What occurs during **enzyme repression?**

1. DNA is transcripted into RNA
2. RNA is translated into a protein
3. Protein folds to form functional enzyme structure
4. Enzyme + Substrate produces products
5. Excess products then bind to DNA which shuts down further enzyme production

Energy

capacity to do work or to cause change

What are some forms of energy?

* Thermal
* Radiant
* Electrical
* Mechanical
* Atomic
* Chemical

Endergonic reactions

* consume energy
* Energy + A + B → C **(→ = enzyme)**
* this reaction is **ANABOLIC**

Exergonic reactions

* release energy
* X + Y → Z + Energy **(→ = enzyme)**
* this reaction is **CATABOLIC**

Where is released energy temporarily stored? Which type of reactions are they used in?

* Stored in high energy phosphate molecules
* Endergonic cell reactions

Redox reactions

* always occur in pairs
* electron donor and acceptor
* saves electrons and their energy

Why do carriers have to repeatedly accept and release electrons and hydrogen?

To facilitate the transfer of redox energy

Most carriers are _____

Coenzymes

* NAD, FAD, coenzyme A

Adenosine Triphosphate

* Metabolic “currency” b/c because it provides the energy necessary for many cellular processes
* 3 part molecule consisting of: adenine, ribose and a 3 phosphate groups

Removal of _______ ________ releases energy

terminal phosphate

What two things are in a constant cycle in active cells?

Utilization and replenishment

Metabolic Roles of ATP

Expenditure of ATP powers nearly all processes that are part of cellular work

What is the equation given as an example of **metabolic roles of ATP**

\

Phosphorylation of Glucose by ATP

* Involves the transfer of a phosphate group from ATP to glucose, which results in the formation of **glucose-6-phosphate** and ADP
* Drives the uptake of glucose into cells to produce energy

What enzyme catalyzes the phosphorylation of glucose?

Hexokinase

What are the 3 different mechanisms of ATP synthesis?

* Substrate-level phosphorylation
* Oxidative Phosphorylation
* Photophosphorylation

Substrate-level phosphorylation

transfer of phosphate group from a phosphorylated compound, (substrate) directly to ADP

Oxidative phosphorylation

series of redox reactions occurring during respiratory pathway

Photophosphorylation

in photosynthetic organisms, utilizing the energy of sunlight

Bioenrgetics

* Study of the mechanisms of cellular energy release
* includes catabolic and anabolic reactions

**Primary catabolism of fuels** proceeds through a series of what three coupled pathways?

1. Glycolysis
2. Kreb’s Cycle
3. Respiratory Chain (electron transport)

Aerobic respiration

* series in which electrons are transferred from **fuel molecules to oxyge**n as a final electron acceptor
* glycolysis, the Kreb’s cycle, respiratory chain

Anaerobic respiration

* glycolysis, the Kreb’s cycle, respiratory chain
* **BUT** molecular oxygen is not the final electron acceptor

Fermentation

* glycolysis, organic compounds are the final electron acceptors
* how we make lactic acids from a **non-oxygen source**

Glycolysis

glucose (6C) is **oxidized** and split into **2 molecules of pyruvic acid** (3C), **NADH** is generated

TCA (Kreb’s Cycle)

processes **pyruvic acid** and generates **3 CO2 molecules**, **NADH and FADH2** are generated

Electron transport chain (ETC)

MAJOR GENERATOR OF ATP!

* accepts electrons from reduced carriers: **NADH and FADH**


* generates energy through sequential redox reactions called **oxidative phosphorylation**

How is energy released in the ETC?

By **ATP synthase** complexes to produce ATP

ATP Synthase

* Unique enzyme located in mitochondrial cristae, bacterial cell membrane and chloroplast grana


* Hyrdrogen ions to the synthesis of ATP

How many ATPS are produced per glucose molecule?

2

How many NADH is produced per glucose molecule

2

Describe the terminal step

* Oxygen accepts **2 electrons** from the ETS
* Picks up **2 hydrogen ions** from the solution to form a molecule of water
* Oxygen is the final electron acceptor

Memorize this equation for Aerobic metabolism

Anaerobic Respiration

* functions like aerobic respiration except it **utilizes oxygen containing ions**, rather than **free oxygen** as the final electron acceptor

What do obligate anaerobes use to reduce some compound other than O2?

H+ generated during glycolysis and the Kreb’s cycle

Nitrification

Ammonium (NH4+) **oxidized >** Nitrite (NO2-) **oxidized >** Nitrate (NO3-)

Dentrification

Nitrate (NO3-) **reduced >** Nitrite (NO2-) **reduced >** N2 (Gas) or Ammonium (NH4+)

Fermentation

* incomplete oxidation of **glucose** or other carbohydrates in the **absence of oxygen**
* uses organic compounds as **terminal electron acceptors**
* yields a small amount of ATP

What does fermentation produce?

* ethyl alcohol by yeasts acting on glucose
* forms acid, gas and other products by the action of various bacteria on pyruvic acid

What two coenzymes are the most important during fermentation, and why are they important?

* NADH and NAD+
* we regenerate NAD to start the electron transport chain

Many pathways of metabolism are _______

bi-directional or **amphibolic** (catabolic + anabolic simultaneously)

What do catabolic pathways contain?

Molecular intermediates that can be diverted into anabolic pathways

How can **pyruvic acid** be converted into **amino acids**?

Through amination

How are amino acids converted into energy **sources**?

deamination

What can glyceraldehyde-3-phosphate be converted into?

Precursors for amino acids, carbohydrates and fats

Proton motive force

Energy that is created by the transfer or protons across a semipermeable membrane

Chemiomosis

Movement of ions across a semipermeable membrane

Where does the ultimate source of all the chemical energy cells come from?

The sun

What is the equation for photosynthesis?

6CO2 + 6H2O + light energy → C6H12O6 + 6O2

On land, what are the **primary photosynthesizers?**

Green plants