index
Announcements
Questions
Chapter 10: Introduction to Metabolism
Chapters on Metabolism
Section 10.1: General Concepts in Metabolism
The Metabolic Map
The Metabolic Map, 2
The Metabolic Map (Detail)
Anabolism and Catabolism
Stages of Metabolism
Stages of Catabolism
Section 10.2: Metabolic Pathways
Linear Metabolic Pathways
Cyclic Metabolic Pathways
Spiral Metabolic Pathways
Metabolism Proceeds by Incremental Steps
Section 10.3: Major Pathways in Cells
Overview of Anabolic Pathways
Overview of Catabolic Pathways
Energy and Carbon
Questions
Next Lecture: Sections 10.4 - 10.10

Fundamentals of Biochemistry

Biochem 380 - Fall 2006

Lecture 029

Outline

Quiz
Announcements
Questions from previous lecture
Section 10.1: General Concepts in Metabolism
Section 10.2: Metabolic Pathways
Section 10.3: Major Pathways in Cells

Announcements

Lecture 28 notes are online

Questions

Any questions on the material from the previous lecture?

Chapter 10: Introduction to Metabolism

In the 9 chapters of biochemistry we have covered so far, we have learned some basic concepts:
- Structural building blocks (three of the four classes of biomolecules)
- Functional mechanisms (enzymes, catalytic and regulatory strategies)
The next 9 chapters or so take us into the 'meat and potatoes' of biochemistry:
- Metabolism: the large network of integrated chemical reactions in living cells
- At its core, metabolism consists of a set of reactions for breaking down fuel molecules to produce energy, and corresponding reactions to synthesize new molecules from smaller building blocks

Chapters on Metabolism

The following chapters indicate where we are headed in the coverage of metabolism:
- Chapter 10 - Introduction to Metabolism
- Chapter 11 - Glycolysis
- Chapter 12 - Gluconeogenesis
- Chapter 13 - Citric Acid Cycle
- Chapter 14 - Electron Transport and ATP Synthesis
- Chapter 16 - Lipid Metabolism
- Chapter 17 - Amino Acid Metabolism
- Chapter 22 - Protein Synthesis

Section 10.1: General Concepts in Metabolism

Metabolism refers to the large collection of interconnected sequences of chemical reactions that occur in cells
In any particular sequence of reactions or pathway, a starting molecule is converted step by step into some other molecule or molecules
Even simple metabolic systems consist of thousands of such reactions, but a group of about 100 molecules or so play central roles in the network
In addition, the number of different kinds of reactions is fairly small
Consequently, learning these common elements and motifs will provide a foundation for understanding the overall structure and function of such complex chemical systems

The Metabolic Map

One way to represent the interconnected set of metabolic reactions is with a two-dimensional diagram or map
In a metabolic map, each node or dot represents a particular molecule or metabolite
Each arc or line represents a reaction, generally catalyzed by some particular enzyme
A sequence of connected line segments represents a pathway from some starting molecule to some product
Thicker line segments at the center of the map indicate the most heavily active portions of metabolism, in terms of energy and mass flow

The Metabolic Map

The Metabolic Map (Detail)

Anabolism and Catabolism

Anabolism and Catabolism refer to two complementary pathways of metabolic reactions
Anabolism involves the assembly of smaller biomolecules into larger, more complex ones, requiring an input of energy
Catabolism is like the combustion of larger biomolecules into smaller ones, resulting in the production of energy
Anabolic and Catabolic pathways are not just simple reversals of each other, but generally involve different sets of enzymes and regulatory inputs, and are often spatially separated
An example is seen in the breakdown and synthesis of glucose, which occurs in two distinct pathways: the catabolic pathway of glycolysis and the anabolic pathway of gluconeogenesis

Stages of Metabolism

The many reactions in metabolism can also be thought of in a simpler way by representing them as a set of three overall stages
These three conceptual stages can be applied to both energy production processes (catabolic pathways) and synthesis (anabolic pathways), even though they proceed in opposite directions
The three stages are organized according to size of metabolites
The catabolic stages proceed from larger to smaller molecules
The anabolic stages proceed from smaller molecules to larger ones

Stages of Catabolism

In the first stage of catabolism, large molecules such as proteins, polysaccharides and fats are broken down into their component monomers such as amino acids and glucose
In the second stage, these smaller molecules are converted into central intermediates such as the acetyl unit in acetyl CoA
In the third stage, ATP is produced by the complete oxidation of acetyl CoA into the final product molecules of CO₂ and water

Section 10.2: Metabolic Pathways

A pathway is a biological sequence of reactions, similar to the multiple steps in a synthesis procedure in organic chemistry
Biological pathways are quite distinct from chemical syntheses however, in their specificity and their ability to be regulated
Pathways can have a number of different forms that describe the start and endpoints of the reaction steps. These forms include linear pathways, cyclic pathways and spiral pathways
In these biological pathways the changes and energies involved occur in small, incremental steps. This is one of the reasons for the high efficiency of energy production in living organisms, compared to some industrial processes.

Linear Metabolic Pathways

A linear metabolic pathway has distinct start and end points. Most of the pathways that we will look at will be linear pathways
An example is the pathway for the synthesis of serine from 3-phosphoglycerate. This consists of three successive enzyme-catalyzed steps with two intermediates

Cyclic Metabolic Pathways

A cyclic metabolic pathway is a sequence of reactions that forms a closed loop, with no distinct start or end points. A completed reaction for each step in the pathway consititutes a single cycle, with possible intermediates entering or leaving the loop
An example is the citric acid cycle, which is used both for the oxidation of carbon compounds and for biosynthesis reactions

Spiral Metabolic Pathways

A third type of pathway is a spiral pathway, where the same set of enzymes can operate repeatedly on a substrate by lengthening or shortening it
In fatty acid biosynthesis, an acyl chain is lengthed by two carbons in a set of repeating reactions

Metabolism Proceeds by Incremental Steps

Section 10.3: Major Pathways in Cells

Anabolism and Catabolism provide two general ways of classifying metabolic pathways. A number of pathways are used by both anabolic and catabolic processes
In such common pathways, the flow of metabolites proceeds in either one direction, or the other, depending upon whether synthesis or breakdown is taking place
The control of flow in either of these two directions occurs through regulation of enzymes at key points in pathways, typically through phosphorylation and dephosphorylation, or through allosteric interactions
Another way of controlling the direction of metabolite flow is through compartmentalization. For example, certain catabolic processes are localized to organelles such as mitochondria, and anabolic processes involving the same metabolites will take place in other parts of the cell

Overview of Anabolic Pathways

Overview of Catabolic Pathways

Energy and Carbon

Two fundamental aspects of metabolism are the sources of energy and carbon. All organisms can be classified by their means for obtaining energy, either from sunlight (phototrophs) or chemical compounds (chemotrophs). Similarly, their source of carbon can be produced either from inorganic sources such as CO₂ (autotrophs) or from organic compounds (heterotrophs):

Carbon Source

CO₂

Organic Compounds

Energy
Source

Photons

Photoautotroph

Pteridium aquilinum
(plant)

Photoheterotroph

Rhodopseudomonas palustris
(purple non-sulfur bacterium)

Chemical
Compounds

Chemoautotroph

Nitrosomonas
(nitrifying bacterium)

Chemoheterotroph

Kittyus catticus
(animal)

Questions

Questions about the material covered today?

Next Lecture: Sections 10.4 - 10.10

Read Sections 10.4 - 10.10

Table of Contents

Fundamentals of Biochemistry

Biochem 380 - Fall 2006

Lecture 029

Outline

Announcements

Questions

Chapter 10: Introduction to Metabolism

Chapters on Metabolism

Section 10.1: General Concepts in Metabolism

The Metabolic Map

The Metabolic Map

The Metabolic Map (Detail)

Anabolism and Catabolism

Stages of Metabolism

Stages of Catabolism

Section 10.2: Metabolic Pathways

Linear Metabolic Pathways

Cyclic Metabolic Pathways

Spiral Metabolic Pathways

Metabolism Proceeds by Incremental Steps

Section 10.3: Major Pathways in Cells

Overview of Anabolic Pathways

Overview of Catabolic Pathways

Energy and Carbon

Questions

Next Lecture: Sections 10.4 - 10.10