CHAPTER 5: MAJOR METABOLIC PATHWAYS Shuler, M. L. and Kargi. (2002). - - PowerPoint PPT Presentation

CHAPTER 5: MAJOR METABOLIC PATHWAYS

By: Puan Nurul Ain Harmiza 1

PTT203: BIOCHEMICAL ENGINEERING SEMESTER 1 (2014/2015)

Shuler, M. L. and Kargi. (2002). Bioprocess Engineering: Basic Concept. 2nd

• Ed. Upper Saddle River, NJ: Prentice Hall PTR

COURSE OUTCOME 2:

By: Puan Nurul Ain Harmiza 2

Ability to ANALYZE the types of metabolic pathways in microorganisms and their growth kinetics.

CONTENT

5.1 Introduction 5.2 Bioenergetics 5.3 Glucose Metabolism 5.4 Respiration 5.5 Control Sites in Aerobic Glucose Metabolism 5.6 Metabolism of Nitrogenous Compounds 5.7 Nitrogen Fixation 5.8 Metabolism of Hydrocarbons 5.9 Overview of Biosynthesis 5.10 Overview of Anaerobic Metabolism 5.11 Overview of Autotrophic Metabolism 5.12 Summary

This course will only cover the red-colored topics. The blue- colored topics have been taught in PTT103 5.1 Introduction 5.2 Bioenergetics 5.3 Glucose Metabolism 5.4 Respiration 5.5 Control Sites in Aerobic Glucose Metabolism 5.6 Metabolism of Nitrogenous Compounds 5.7 Nitrogen Fixation 5.8 Metabolism of Hydrocarbons 5.9 Overview of Biosynthesis 5.10 Overview of Anaerobic Metabolism 5.11 Overview of Autotrophic Metabolism 5.12 Summary

5.1 INTRODUCTION

• Metabolism is the collection of

enzyme catalyzed reactions that convert substrates that are external to the cell into various internal products.

• Metabolic pathways are series
• f chemical reactions

(metabolism) occurring within a cell.

Why we need to learn the metabolic pathways? Starch  smaller glucose

amylase external internal

• Genetic Engineering allows for the alteration of metabolism by insertion or deletion of

selected genes in a predetermined manner (Metabolic Engineering).

• An understanding of metabolic pathways in the organism of interest is of primary

importance in bioprocess development.

Characteristics of Metabolism

• Varies from organisms to organism.
• Many common characteristics.
• Affected by environmental conditions.

– O2 availability: Saccharomyces cerevisiae

• Aerobic growth on glucose → more cells
• Anaerobic growth on glucose → ethanol

Is S.cerevisiae a obligate anaerobes or facultative anaerobes?

Types of Metabolism

• Catabolism

– Metabolic reactions in the cell that degrade a substrate into smaller / simpler products.

• Glucose → CO2 + H2O

– Produces energy.

• Anabolism

– Metabolic reactions that result in the synthesis of larger / more complex molecules.

• Glucose → glycogen

– Requires energy. Which one is EXERGONIC and which

• ne is ENDERGONIC ?

5.2 BIOENERGETICS

• It is the quantitative study of the energy relationships and energy conversions in

biological systems.

• It concerned with the energy involved in making and breaking of chemical bonds

in the molecules found in biological organisms.

• All organisms need free energy to keep themselves alive and functioning.
• The Sun is the ultimate energy source for the life processes on earth.
• The source of energy is just one; solar energy. Only plants use that energy directly.

What the organisms use is the chemical energy in the form of foods. The very first conversion of solar energy into a chemical energy is the sugar molecule.

• On one side the conversion of solar energy into chemical energy with the help of

photosynthesis happens, and on the other hand this photosynthesis makes it possible with the passage of time on earth to accumulate free oxygen in the earth's atmosphere making possible the evolution of respiration. Respiration is important for bioenergetics as it stores the energy to form a molecule ATP; adenosine triphosphate. This molecule is a link between catabolism and

• anabolisms. The process of photosynthesis is helpful in understanding the

principles of energy conversion i.e. bioenergetics. What is bioenergetics ?

Plants make their own food by photosynthesis. Carbon dioxide and water react together in the presence of light and chlorophyll to make glucose and

• xygen. The glucose is

converted into starch, fats and oils for

• storage. It is used to

make cellulose for cell walls, and proteins for growth and repair. It is also used by the plant to release energy by respiration. Respiration and photosynthesis are the main processes dealing with bioenergetics

Metabolic Reactions

• Can be classified into 3 major categories (refer to figure 5.1 pg 135):

1. Degradatation of nutrients 2. Biosynthesis of small molecules (amino acid, nucleotides) 3. Biosynthesis of large molecules This reaction takes place in the cell simultaneously.

Figure 5.1: Classes of Reactions (Pg. 135)

Energetics of bacterial growth: balance of anabolic and catabolic reactions.

Which Class is CATABOLISM and which is ANABOLISM?

Figure 5.1: Classes of Reactions (Pg. 135)

Energetics of bacterial growth: balance of anabolic and catabolic reactions.

ATP : Metabolic Energy

• Adenosine triphosphate (ATP) stored and

transports ENERGY in cells.

• It is the energy currency of life.
• It is used by the cell as ‘money’.

– Some activities such as breaking down glucose produce ATP (money) others such as making DNA consume ATP

• It contains high-energy phosphate bonds.
• The energy in ATP is obtained from the

breakdown of foods.

ATP

ATP : Metabolic Energy

• ATP: Adenosine triphosphate and ADP: Adenosine diphosphate.
• So when a phosphate is lost, energy is released.
• Technically speaking, the whole enchilada from a biological perspective

is thus: – ADP is the end-product that results when ATP loses one of its phosphate groups located at the end of the molecule. The conversion

• f these two molecules plays a critical role in supplying energy for

many processes of life. – The deletion of one of ATP’s phosphorus bonds generates approximately 7.3 kilocalories per Mole of ATP. – ADP can be converted, or powered back to ATP through the process of releasing the chemical energy available in food; in humans this is constantly performed via aerobic respiration in the mitochondria.”

ATP : Metabolic Energy

ATP : Metabolic Energy

• Analog compounds of ATP (GTP, UTP and CTP) also store and transfer high-

energy phosphate bonds but not to the extent of ATP.

• High-energy phosphate compounds (phosphoenol pyruvate and 1,3-

diphosphoglycerate) produced during metabolism, transfer their ~P group into ATP.

• Energy stored in ATP is later transferred to lower-energy phosphate

compounds (glucose -6-phosphate and glycerol-3-phosphate) – refer Figure 5.2 pg 135.

GLUCOSE METABOLISM

This topic has been thought in PTT103 BIOCHEMISTRY by Pn. Khadijah Hanim. Please refer these three previous slides for your additional references.

5.5 CONTROL SITES IN AEROBIC GLUCOSE METABOLISM

Control in Glycolysis: Feedback Inhibition

• The major control site in glycolysis is the phosphorylation of fructose-6-

phsophate by phosphofructokinase:

fructose-6-phosphate + ATP  fructose-1,6-diphosphate + ADP

• Phosphofructokinase (PFK) catalyzes the rate-limiting step in glycolysis and is

the most important control point.

• The enzyme phosphofructokinase is an allosteric enzyme activated by ADP

and Pi but inactivated by ATP. Explain HOW is the mechanism?

phosphofructokinase (active) phosphofructokinase (inactive)

ATP ADP

When ATP levels are high in the cell, the cell no longer needs metabolic energy production to occur. In this case, PFK's activity is inhibited by allosteric regulation by ATP itself, closing the valve on the flow of carbohydrates through glycolysis. Recall that allosteric regulators bind to a different site on the enzyme than the active (catalytic) site. Thus ATP binds in two places on PFK: in the active site as a substrate and in the regulatory site as a negative modulator. ATP bound in the regulatory site acts as a modulator by lowering the affinity of PFK for its other substrate, fructose-6-phosphate.

Glycolysis

The phosphorylation of fructose 6-phosphate is highly exergonic and irreversible, and phosphofructokinase, the enzyme that catalyzes it, is the key enzyme in glycolysis.

Rate-limiting enzyme for glycolysis is phosphofructokinase

Control in Glycolysis: Pasteur Effect

– The Pasteur effect is an inhibiting effect

• f
• xygen
• n

the fermentation process (Louis Pasteur, 1857). – The rate of glycolysis under anaerobic conditions is higher than that under aerobic conditions. – In the presence of O2, ATP yield is high since the TCA cycle and ETC are

• perating.

– So, ADP and Pi become limiting and phosphofructokinase becomes inhibited. – A high NADH/NAD+ ratio also reduces the glycolysis rate.

Control in TCA Cycle: Feedback Inhibition

• Certain enzymes of the Krebs cycle are also regulated by feedback inhibition.
• Pyruvate dehydrogenase is inhibited by ATP, NADH, and Acetyl CoA and

activated by ADP, AMP, and NAD+.

• Citrate synthase is inhibited by NAD+.
• In general, high ATP/ADP and NADH/NAD+ ratios reduce the processing rate
• f the TCA cycle. Explain HOW?

Citric acid cycle

5.6 METABOLISM OF NITROGENOUS COMPOUNDS

• Most organic nitrogen compounds have an oxidation level between

carbohydrates and lipids.

• Nitrogeneous compounds can be used as nitrogen, carbon, and energy

source.

• Proteins are hydrolyzed to peptides and further to amino acids by

proteases.

• Amino acids are first converted to organic acids by deamination (removal
• f amino group).

Deamination Reaction

• Deamination reaction may be oxidative, reductive, or dehydrative,

depend on the enzyme system involved.

• A typical oxidative deamination reaction is as in Eq. 5.10 (pg 143).
• Ammonia released from deamination is utilized in protein and nucleic acid

synthesis as a nitrogen source.

• And organic acids can be further oxidized for energy production (ATP).

Transamination Reaction

• Is another mechanism for conversion of amino

acids to organic acids and other amino acids.

• The amino group is exchanged for the keto

group of α-keto acid.

• A typical transamination reaction is in Eq.5.11

(pg.143).

Nitrogen Fixation

• Certain microorganisms fix atmospheric

nitrogen to form ammonia under reductive or microaerophilic conditions.

• Eg.: Azotobacter, Azotomonas, Azotococcus.
• Nitrogen fixation is catalyzed by the enzyme

“nitrogenase”.

Metabolism of Hydrocarbons

• This metabolism require oxygen but only few
• rganisms can metabolize hydrocarbons.
• The first step in metabolism of hydrocarbons

is oxygenation by oxygenases.

• Hydrocarbon molecules alcohol 

aldehyde  organic acid  acetyl-CoA  TCA cycle.

Overview of Biosynthesis

• Pentose-phosphate pathway:

– Produce significant reducing power  energy supply to cell – Important for biosynthesis process and this energy is used for the anabolism processes.

• The main component of biosynthesis is the production
• f amino acids.
• The cell must be able to synthesize lipids and

polysaccharides (fatty acids). The key precursor is acetyl-CoA.

• If the carbon source energy source < 6 carbons, EMP

pathway needs to be operated in reverse reactions.

Gluconeogenesis pathway with key molecules and enzymes. Many steps are the opposite of those found in theglycolysis.

Difference between glycolysis, gluconeogenesis, glycogenesis, and glycogenolysis.

Overview of Anaerobic Metabolism

• The production of energy in the absence of
• xygen can be accomplished by anaerobic

respiration.

• Use the same pathways as in aerobic metabolism

but differ in the use of an alternative electron acceptor.

• Eg.: Nitrate, NO3-
• Many organism grow without using the ETC. the energy generated

without ETC is called FERMENTATION.

• Since no electron transport is used, the organic substrate must

undergo a balanced series of oxidative and reductive reactions.

Overview of Autorophic Metabolism

• Autotrophs obtain their carbon from CO2.
• Calvin cycle provides the building block for

autotrophs growth.

• Photosysthesis.

What is the difference between heterotroph and autotroph?

END OF CHAPTER 5

By: Puan Nurul Ain Harmiza 36