Biochemistry Explained

A Practical Guide to Learning Biochemistry

Thomas Millar

• Publisher: CRC Press
• Year: 2018
• eBook ISBN: 9781351991452
• Edition: 1
• Topic: Medicine
• Subtopic: Biochemistry in Medicine

Biochemistry Explained employs an innovative approach which has proven highly successful in the author's own classes. The author establishes a thorough understanding of the foundations of and common linkages between molecular structures and reactions, so that eventual interpretation of complex biochemical pathways and reactions is easy. All of the major molecular structures and biochemical pathways are explained, and, for the most part, these center on mammalian biochemistry. The text is supported by biochemical nomenclature and questions to bear in mind while reading. Higher learning sections are also provided for advanced students. Written in an informal, conversational style, this textbook will serve as an invaluable resource for any student who is struggling with the standard texts and for postgraduate students who need to refresh their knowledge.

1 Fundamental Concepts and an Introduction to the Cell

In this chapter you will:

• be introduced to the idea that lipid and water solubility is a major foundation stone of biochemistry
• learn which chemical structures determine water and lipid solubility
• be introduced to the terms hydrophobic and hydrophilic
• revise subcellular compartments and their functions
• learn the function of the cytoskeleton.

Lipid and water solubility

It will not be a surprise to hear that the major component of our bodies is water. For example, 75% of muscle tissue and 60% of red blood cells is water. What most of you have probably not considered is how do we keep the water inside us and why doesn’t it just run away? Clearly, it is not contained in something that is water soluble, but equally, it is not contained in glass or plastic either. The solution to this problem is found by knowing what happens if you mix oil and water together – they do not mix and oil, which is less dense than water, goes to the top. This means that it would be possible to contain water in a bag of oil and fundamentally, this is what occurs in our bodies. Our cells are lipid bags containing water.

Nomenclature: Another name for oil or fat is lipid.

Major point 1: Lipids and water do not mix.

Major point 1 is the basis for 90% of your biochemistry. We will refer to it time and time again.

Major point 2: Lipids are the basis of cellular membranes.

If we now combine major point 1 with major point 2, we come up with another major point.

Major point 3: For something to readily cross a cell membrane it must be lipid soluble.

The significance of these points lies in the concept that the body uses an aqueous environment, the blood, to transport fuels, nutrients, and chemical signals such as hormones and neurotransmitters. For the most part, these substances are water soluble. Cell membranes, being composed mainly of lipids, provide a barrier to these chemicals, and therefore there must be special (bio)chemical mechanisms for the nutrients or signals to pass across the cell membrane. By contrast, the blood also needs to be able to transport lipids or lipid-soluble substances, and again there is a (bio)chemical process that enables this to happen. It is also clear that a cell will be signaled from time to time to carry out a different function and for this to occur, something must change within a cell. Most often, the something is a small part of a molecule becoming more or less water soluble. This small change in water solubility causes the whole molecule to change its shape and consequently its activity. Therefore, it is essential to understand which chemical structures are likely to be water soluble and which are lipid soluble.

* Logic process: Whenever you look at the structure of biochemical molecules determine if they are lipid or water soluble. If they are lipid soluble, they will readily cross a cell membrane and if they are water soluble, they will not.

Which of the following are lipid or water soluble?

(a) sodium chlonde

(b) cholesterol, oestrogen, testosterone

(c) vitamin Λ, vitamin D, vitamin E, vitamin ढ

(d) vitamin B, vitamin C

(e) ointment

Answer: Sodium chlonde and the vitamins B and C are water soluble, whereas cholesterol, oestrogen, testosterone and the other vitamins are lipid soluble. Ointments are lipid soluble so that the medication they contain passes across cell membranes (i.e. is absorbed through the skin).

From all of these, you may have only known with certainty that sodium chloride (table salt) is water soluble. Other substances which are water soluble are other salts such as potassium chloride, acids such as acetic acid and bases such as sodium hydroxide. Therefore, in terms of their chemical structure, what do these substances have in common that makes them water soluble?

Q&A 1: Draw the chemical structures of sodium chloride, acatic acid, and sodium hydroxide.

You will be aware from your previous chemistry that all of these substances prefer to exist in their ionic or charged form. Now let us examine the structures of some lipid-soluble substances. These often have a long chain of carbon atoms as their backbone, others are ring structures. Therefore, the molecule carries no charge or the vast proportion of the molecule carries no charge.

By comparing the structures of the water-soluble salts and acids with the fat-soluble substances, there is a major difference that determines water or lipid solubility.

Major point 4: A substance that readily dissolves in water is charged and a substance that readily dissolves in lipids is uncharged.

Some molecules are particularly interesting because part of their structure is charged and part is uncharged, examine the following molecules and determine which part would be water soluble and which part would be lipid soluble.

Answer: The parts that are circled are water soluble because they are charged and the rest of the molecule is non-charged and would dissolve easily in lipid (hydrophobic or lipophilic), sis indicated, one is a soap and the other a detergent This property of both water and lipid solubility enables soaps and detergents to be used in water to remove grease from surfaces.

Nomenclature: hydro = water; phobia = fear; lipo = fat; philus = beloved.

Q&A 2: Use the Latin terms above to form a word that means: fear of water; water loving; fear of fats; fat loving.

* Logic process: You would already know that glucose is our main energy source and is needed by cells in high concentrations. To get glucose inside the cell, it must be helped from its aqueous environment where it is in low concentration, across the lipid membrane to the inside of the cell where it is in high concentration. The structure of glucose will be dealt with in a later chapter, but it is enough here to realise that it is strongly water soluble and weakly lipid soluble. Being partially lipid soluble, and with a high concentration of glucose inside a cell, there is a strong tendency for glucose to leak back out of the cell towards extracellular fluid where it is in low concentration. Having spent a large amount of effort getting the glucose to the inside of the cell, the cell does not want the glucose to leak out again. How can it be prevented? The cell makes the glucose less lipid soluble by adding negative charges to it. The negative charges come from a phosphate group that is transferred from adenosine triphosphate (ATP) which is found inside cells.

This example of a biochemical process illustrates how water and lipid solubility can be exploited by a cell to its advantage, i.e. to retain glucose inside the cell. In the next section, as the structure of a cell is reviewed, we will see how this property of lipid and water solubility is exploited even further.

The structure of a cell

A cell is more than a lipid bag containing water as was described earlier. It is really an outer lipid bag or cell membrane containing several smaller lipid bags or compartments. One such bag, or subcellular compartment is the nucleus.

Q&A 3. What is contained within the nucleus?

Q&A 4. List 4 other subcellular compartments

Note that each of the subcellular compartments is surrounded by a lipid membrane and sometimes two. These membranes, like the cell membrane, are neither freely permeable to positive nor negative ions because these are water soluble.

* Logic process: This simple fact means that you can packa...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright Page
• Table of Contents
• Dedication Page
• Preface
• For the Lecturer
• Chapter 1 Fundamental Concepts and an Introduction to the Cell
• Chapter 2 Basic Biochemicdl Structures
• Chapter 3 Sugars
• Chapter 4 Amino Acids and their Functions
• Chapter 5 Peptides, Proteins and Enzymes
• Chapter 6 Complex Sugars and their Functions
• Chapter 7 Metabolism of Sugars
• Chapter 8 Metabolism of Amino Acids
• Chapter 9 The Tricarboxylic Acid Cycle
• Chapter 10 The Electron Transport Chain, Oxidative Phosphorylation and Photosynthesis
• Chapter 11 Lipid Structure and Metabolism
• Chapter 12 Nucleotides and their Derivatives
• Chapter 13 The Structures and Functions of DNA and RNA
• Chapter 14 Metabolism and its Control
• Chapter 15 Cellular Communication
• Index