biob111 - source.endeavourlearninggroup.com.au · biob111 chemistry and biochemistry ......

BIOB111 CHEMISTRY AND BIOCHEMISTRY

STUDENT STUDY GUIDE

2016

This document is the property of Endeavour College of Natural Health and contains confidential information of Endeavour College of Natural Health.

Copyright in the whole and every part of this document belongs to Endeavour College of Natural Health and may not be used, sold, transferred, adapted or modified or reproduced in whole or in part in any manner or form or in any media, to any persons other than in agreement with Endeavour College of Natural Health.

This document remains the confidential information of Endeavour College of Natural Health and should not be used for any other purpose other than that expressly approved by Endeavour College of Natural Health at the time the document was provided by Endeavour College of Natural Health.

July 2015

© Endeavour College of Natural Health 029b9236589d45208d7708434cdf70664 Last updated on 18-Jul-16 of 117

BIOB111 SUBJECT STUDY GUIDE

As students in the ‘knowledge-age’, you are increasingly confronted with a vast array of information that is sometimes conflicting and contested. As students and practitioners, you must be able to seek, evaluate and synthesize information, and be active participants in the development of your own knowledge and understanding. Subsequently, you will become more responsive and dynamic practitioners who are able to ensure your ongoing capacity to effectively work within the changing nature and demands of society and enhance the field of Natural Health Practice.

How to best utilize directed self-learning

This Subject Study Guide (SSG) has been produced to assist you to explore, investigate, critically analyze and evaluate the principles and practice in this subject of study and to encourage you to achieve deeper levels of learning. As an approach to study, it is suggested that you read the questions for each session first. These questions will guide you through your reading, note-taking and research.

The following suggestions will assist you to pre-read effectively:

Highlight the key points during your pre-readings.

In the case of lengthy readings or documents, summarize and write your own synopsis.

Answer questions or complete activities as directed.

Jot down any queries, questions or concerns for discussion in class.

Reference to chapters, sections, paragraph headings, page numbers in this document and the lecture notes refer to the set textbook Stoker (2014). Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn, Brooks/Cole, Cengage Learning, Belmont, CA.

Students may be using other editions of Stoker as their text. The content of this SSG is still relevant; however students will have to source the corresponding material through the text index, using the Topic Headings given.

Students may also be referred to the following textbooks:

1. Tortora, GJ & Derrickson, B 2012, Principles of Anatomy and Physiology, 13th edn, John Wiley.

2. Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008, Molecular Biology

of the Cell, 5th edn, Garland Publishing, New York 3. Timberlake, KC 2013, General, Organic and Biological Chemistry: Structures of Life, 4th

edn, Pearson Higher Ed, Boston, USA.

4. McMurray, JE, Ballantine, DS ,Hoeger, CA, & Peterson, VE 2013, Fundamentals of General, Organic and Biological Chemistry, 7th edn, Princeton Hall, USA.

http://www.amazon.com/s/ref=ntt_athr_dp_sr_4?_encoding=UTF8&sort=relevancerank&search-alias=books&ie=UTF8&field-author=Martin%20Raff

http://www.amazon.com/s/ref=ntt_athr_dp_sr_6?_encoding=UTF8&sort=relevancerank&search-alias=books&ie=UTF8&field-author=Peter%20Walter

© Endeavour College of Natural Health 029b9236589d45208d7708434cdf7066

Last Updated on 2-July-14 of 117

Contents

SESSION 1: Introduction to Chemistry .................................................................................................. 8

Introduction to the Fundamentals of Chemistry .................................................................................. 9

Measurements .................................................................................................................................... 9

Temperature ....................................................................................................................................... 9

Elements Necessary for Health ........................................................................................................ 10

Distribution of Elements in the Human Body .................................................................................... 10

Atoms and Elements ......................................................................................................................... 10

The Atom .......................................................................................................................................... 11

Complete following: ........................................................................................................................... 12

SESSION 2: Chemical Bonding ........................................................................................................... 13

Introduction to Covalent Bonds ......................................................................................................... 15

Introduction to Bond Polarity ............................................................................................................. 15

SESSION 3: Chemical Reactions ........................................................................................................ 17

SESSION 4: Reaction Rates ................................................................................................................ 20

Introduction to types of Reactions .................................................................................................... 21

Factors affecting Rate of Reaction ................................................................................................... 21

Introduction to Oxidation – Reduction ............................................................................................... 21

Introduction to Reversible Reactions and Equilibrium ...................................................................... 21

SESSION 5: Physical States of Matter ................................................................................................. 23

Energy ............................................................................................................................................... 24

Energy and Nutrition ......................................................................................................................... 24

States of Matter ................................................................................................................................. 24

Introduction to Intermolecular Forces ............................................................................................... 24

Introduction to Gases and Pressure ................................................................................................. 24

Water................................................................................................................................................. 25

Types of Solutions ............................................................................................................................ 25

Solubility ............................................................................................................................................ 25

Colloids ............................................................................................................................................. 25

Osmotic Pressure and Dialysis ......................................................................................................... 26

SESSION 6: Acids and Bases .............................................................................................................. 27

Introduction to Acids and Bases ....................................................................................................... 28

Properties of acids and bases .......................................................................................................... 28

pH...................................................................................................................................................... 28

pH Scale ........................................................................................................................................... 29

Electrolytes ....................................................................................................................................... 29

SESSION 7: Introduction to Organic Chemistry ................................................................................... 31

Organic Chemistry ............................................................................................................................ 32

Structure of Organic Compounds ..................................................................................................... 32

Alkanes ............................................................................................................................................. 32

Cycloalkanes ..................................................................................................................................... 33



Physical & Chemical Properties of Alkanes & Cycloalkanes ............................................................ 33

SESSION 8: Properties of the Functional Groups & Examples (I) Unsaturated Hydrocarbons. Alkanes, Alkenes, Alkynes & Aromatics ............................................................................................... 34

Introducing Reactions of Aromatic Compounds ............................................................................... 36

SESSION 9: Properties of the Functional Groups & Examples (II). Phenols, Alcohols, Ethers, Aldehydes, ketones & carboxylic Acids. ............................................................................................... 38

Alcohols ............................................................................................................................................ 39

Carbonyl Group ................................................................................................................................. 40

Aldehydes & Ketones........................................................................................................................ 40

Carboxylic Acids ............................................................................................................................... 40

SESSION 10: Properties of the Functional Groups & Examples (III) Amines, Esters and Amides ..... 43

Esters ................................................................................................................................................ 44

Amines .............................................................................................................................................. 44

Amides .............................................................................................................................................. 45

SESSION 11: An Introduction to the Structure and Function of Carbohydrates .................................. 47

Textbook Location ................................................................................................................................ 48

Introduction to carbohydrates ........................................................................................................... 48

Structure and function of carbohydrates ........................................................................................... 48

Chirality ............................................................................................................................................. 49

Classification of Monosaccharides ................................................................................................... 49

D-Glucose ......................................................................................................................................... 49

D-Galactose ...................................................................................................................................... 49

D-Fructose ........................................................................................................................................ 49

Reactions of Monosaccharides ......................................................................................................... 49

Disaccharides ................................................................................................................................... 50

D-Maltose .......................................................................................................................................... 50

D-Lactose .......................................................................................................................................... 50

D-Sucrose ......................................................................................................................................... 50

Oligosaccharides .............................................................................................................................. 50

Polysaccharides ................................................................................................................................ 51

Starch ................................................................................................................................................ 51

Glycogen ........................................................................................................................................... 51

Cellulose ........................................................................................................................................... 51

Chitin ................................................................................................................................................. 51

Fatty Acids ........................................................................................................................................ 54

Triacylglycerols ................................................................................................................................. 54

Membrane Lipids .............................................................................................................................. 55

Eicosanoids ....................................................................................................................................... 55

Biological Waxes ............................................................................................................................... 55

SESSION 13: An Introduction to the Structure and Function of Amino Acids ..................................... 58

Introduction to Proteins ..................................................................................................................... 59

Amino Acids ...................................................................................................................................... 59



Peptides ............................................................................................................................................ 60

SESSION 14: An Introduction to the Structure and Function of Proteins ............................................ 62

General Structural Characteristics of Proteins ................................................................................. 63

Primary Structure of Proteins ............................................................................................................ 63

Secondary Structure of Proteins ....................................................................................................... 63

Tertiary Structure of Proteins ............................................................................................................ 64

Quaternary Structure of Proteins ...................................................................................................... 64

Protein Hydrolysis ............................................................................................................................. 64

Protein Denaturation ......................................................................................................................... 64

Structural Classification of Proteins .................................................................................................. 65

Functional Classification of Proteins ................................................................................................. 65

SESSION 15: Enzymes and Co-Enzymes ........................................................................................... 67

General Characteristics of Enzymes ................................................................................................ 68

Enzyme Structure ............................................................................................................................. 68

Nomenclature of Enzymes ................................................................................................................ 69

Models of Enzyme Action ................................................................................................................. 69

Enzyme Specificity ............................................................................................................................ 69

Factors Affecting Enzyme Activity .................................................................................................... 69

Enzyme Inhibition .............................................................................................................................. 70

Regulation of Enzyme Activity .......................................................................................................... 70

Medical Uses of Enzymes ................................................................................................................ 70

SESSION 16: Biochemical Nature of the Cell Membrane .................................................................... 72

SESSION 17: Nucleic Acids – Structure, DNA Replication .................................................................. 76

Introduction to Nucleic Acids ............................................................................................................ 77

Nucleotides ....................................................................................................................................... 77

Structure of Nucleic Acids ................................................................................................................. 78

Secondary Structure of DNA ............................................................................................................ 78

DNA Replication ................................................................................................................................ 78

Ribonucleic Acids .............................................................................................................................. 78

SESSION 18: Nucleic Acids – Protein Synthesis ................................................................................. 81

Protein Synthesis Overview .............................................................................................................. 82

Transcription ..................................................................................................................................... 82

Translation ........................................................................................................................................ 82

Mutation ............................................................................................................................................ 83

Genetic Engineering, Recombinant DNA & Polymerase Chain Reaction ........................................ 83

SESSION 19: Bioenergetics- Metabolic Pathways – An Overview ...................................................... 85

Metabolism ........................................................................................................................................ 86

Metabolism & Cell Structure ............................................................................................................. 86

Important Nucleotide-Containing Compounds in Metabolic Pathways ............................................. 87

Overview of Bioenergetics’ Pathways ............................................................................................... 87

Common Metabolic Pathway ............................................................................................................ 87

SESSION 20: Metabolism .................................................................................................................... 88



Digestion & Absorption of Carbohydrates ........................................................................................ 89

Glycolysis .......................................................................................................................................... 89

Fates of Pyruvate .............................................................................................................................. 90

Glycogen Synthesis & Degradation .................................................................................................. 90

Glycogenesis .................................................................................................................................... 90

Glycogenolysis .................................................................................................................................. 90

SESSION 21: Metabolism – Gluconeogenesis, Cori Cycle & Citric Acid Cycle ................................... 92

Gluconeogenesis .............................................................................................................................. 92

The Cori Cycle .................................................................................................................................. 93

Citric Acid Cycle (CAC) ..................................................................................................................... 93

Hormonal Control of Carbohydrate Metabolism ............................................................................... 93

B vitamins & Carbohydrate Metabolism ............................................................................................ 93

SESSION 22: Common Metabolic Pathways Electron Transport Chain, Oxidative Phosphorylation, ATP Production. ................................................................................................................................... 95

Electron Transport Chain (ETC) ....................................................................................................... 95

Oxidative Phosphorylation (OP) ....................................................................................................... 95

ATP Production ................................................................................................................................. 96

ATP Production from Complete Oxidation of Glucose in Skeletal muscles & Nerve cells ............... 96

SESSION 23: Metabolic Pathways – Lipid Metabolism Part 1 ............................................................. 99

Digestion & Absorption of Lipids ..................................................................................................... 100

TAG Storage & Mobilization ........................................................................................................... 100

Glycerol Metabolism ....................................................................................................................... 101

Oxidation of Fatty Acids .................................................................................................................. 101

ATP Production from FA Oxidation ................................................................................................. 102

SESSION 24: Lipid Metabolism Part 2. Ketogenesis and Lipogenesis ............................................. 105

Ketone Bodies ................................................................................................................................. 106

Ketogenesis .................................................................................................................................... 106

Ketosis ............................................................................................................................................ 107

Lipogenesis ..................................................................................................................................... 107

Fate of Fatty Acid Generated Acetyl CoA ....................................................................................... 108

Cholesterol Biosynthesis ................................................................................................................ 108

Relationship Between Lipid & Carbohydrate Metabolism ............................................................... 108

B vitamins & Lipid Metabolism ........................................................................................................ 108

Digestion & Absorption of Proteins ................................................................................................. 111

Amino Acid Utilization ..................................................................................................................... 111

Transamination ............................................................................................................................... 112

Oxidative Deamination .................................................................................................................... 112

The Urea Cycle ............................................................................................................................... 112

Amino Acid Carbon Skeletons ........................................................................................................ 113

Amino Acid Biosynthesis ................................................................................................................ 113

B vitamins & Protein Metabolism .................................................................................................... 113

SESSION 26: Integrating the Metabolic Pathways ............................................................................ 115



Integration of Metabolic Pathways .................................................................................................. 116



SESSION 1: Introduction to Chemistry

Code: BIOB111

Learning outcomes from BIOB111 SO:

#1. Explain elements, atoms, ions, chemical bonding, chemical reactions, the importance of energy transfer and catalysts and state applications in biochemical systems. Illustrate the principles of chemical reactions and predict and balance reactions in inorganic and organic chemistry.

Session Aims: This session will provide opportunities for students to:

Address the learning outcomes listed in the SO BIOB111 and above.

Become familiar with the Student Subject Guide and the Learning Outcomes and Assessment Tasks for this Subject of Study.

Key Concept

Atoms are the smallest units of matter.

Atoms consist of particles including a central nucleus of positively charged protons and non- charged neutrons surrounded by negatively charged electrons. Atoms make up different elements which differ in their characteristics.

Session Overview

This lecture is designed to familiarize students with the nature of matter. The session will introduce students to the atomic structure of matter. They will also learn about the elements from which all matter is constructed and the development and use of the Periodic Table - all of which will underpin the material covered later in the subject.

Session Topics

Atoms and Elements o Atomic structure o Chemical symbols

Elements

The Periodic Table o Using the Periodic Table to predict physical and chemical properties of elements

The Atom o Atomic number, isotopes and mass o Energy shells, electronic configuration and the Octet rule o Formation of ions

Read the BIOB111 Subject Outline (SO) and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully.



Textbook Location

Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn, Brooks/Cole, Cengage Learning, Belmont, CA.

Chapter 1: Basic Concepts About Matter, pp. 1-14 – Sections: 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.9

Chapter 2: Measurements in Chemistry, pp. 24-44 – Sections: 2.1, 2.2, 2.6, 2.9, 2.10

Chapter 3: Atomic Structure and The Periodic Table, p.53-77 – Sections: 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7

Concepts to Remember at the end of each chapter.

Exercises and Problems with odd numbers, at the end of each chapter, are answered at the end of the textbook.

Summary

Introduction to the Fundamentals of Chemistry

All things are composed of chemical matter. The first six sessions of this subject are linked in that they are a general introduction to the concepts and terminology used in chemistry to provide an understanding of organic chemistry in beginning of Session 7. It is important that students understand and integrate the principles learnt in each chapter, into to the relevant topics of health and medicine. Chemistry is the “study of matter”. Matter is anything that has mass and takes up space. Matter makes up everything you can see around you, from the chair you are sitting on to the cells in your body, which is why the study of matter is very important. Chemistry is the science that deals with matter, what it looks like, smells like, acts like (physical properties) and how it changes from one substance to another, or reacts (chemical properties). The different types of matter are classified by their composition.

Measurements

So that chemists around the world can understand each other clearly there is an internationally recognised system of how to measure things, which is called the international system of units (SI). We are lucky because SI units are based on the metric system, which is the standard system of measurement in Australia. The total quantity of matter within an object is measured with Mass (independent of gravity) or Weight (depends on gravity). Volume measures the amount of space occupied by a substance. Density and Specific Gravity Density is a measurement of how heavy something is compared to how much space it takes up (mass per unit volume).

Temperature

Temperature is a measure of how hot or cold a substance is compared to another substance. It is the indication of kinetic energy of the particles in a substance. Read Chapter 2 from Stoker – Sections: 2.1, 2.2, 2.6, 2.9, 2.10



New Terms:

Proton The positive particle found in the nucleus of the atom

Electron The negative particle found orbiting the outside of the atom

Neutron The neutral particle found in the nucleus of the atom

Atomic Number The number of protons an atom has - a very important term, as it is the number of protons that determines the element that the atoms make up

Atomic mass The number of protons & neutrons in the atom

Ions Atoms with unequal numbers of protons and electrons

Isotopes Atoms with unequal numbers of protons and neutrons

Elements Necessary for Health

The Health Notes discussed in chapter 3 in Timberlake outline the elements we need in our bodies to stay alive. The tables below show the distribution of these elements in our bodies as well as a comparison with the distribution of elements in the universe.

Distribution of Elements in the Human Body

Element Distribution (atom %)

Hydrogen 60.5

Oxygen 25.7

Carbon 10.7

Nitrogen 2.4

All others 0.7

Distribution of Elements in the Universe

Element Distribution (%)

Hydrogen 91

Helium 8.5

All others < 0.5

Atoms and Elements

The primary units of all substances are atoms. Different types of atoms are called elements. An element is a pure substance that can’t be broken down into smaller or simpler substances. There are 114 known elements and they are the building blocks of all the substances we have on earth and beyond. Elements are represented by chemical symbols. An example is the element oxygen which we need to live.



Read Chapter 1 from Stoker – Sections: 1.6, 1.9 The periodic table is a way of arranging the elements so that they are put together in columns which have similar qualities. Dimitri Mendeleev (1834 –1907), a Russian chemistry professor, devised the periodic table while preparing to write a chemistry textbook. A periodic table can be found on the inside cover of your textbook. Read Chapter 3 from Stoker – Sections: 3.4, 3.5, 3.6, 3.7

The Atom

All matter is made up of very small indivisible particles called atoms. In fact an atom of gold has a diameter of 0.00000003cm – no wonder we can’t see them. So if we can’t see them how do we know they exist? In ancient Greek times the philosopher Democritus and his followers started the idea that a particular piece of matter can be divided down to its ultimate particles, its atoms, and no further. This theory was built on by the English chemist John Dalton, and makes up what we know as Dalton’s atomic theory.

Pre / Post class readings

In this subject the material is taught from the perspective that the students have no prior knowledge in the field. In this regard there is no compulsory pre-reading associated with this subject. The reading material that the students are directed to can be used either as pre-reading or post-reading dependent on the students individual study requirements

Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn, Brooks/Cole, Cengage

Learning, Belmont, CA.

Chapters 1, 2 and 3

Additional Reading

The reading materials listed below are in addition to the texts recommended for the subject but will add further to the students understanding of the topics covered.

Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H. Freeman and Co, New York.

Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008, Molecular Biology of the Cell, 5th edn, Garland Publishing, New York

Bettelheim, FA, Brown, WH, Campbell, MK, Farrell, SO, Torres, OJ 2013, Introduction to General, Organic and Biochemistry, 10th edn, Brooks/Cole, Cengage Learning, USA.

http://web.visionlearning.com/custom/chemistry/animations/CHE1.3-an-atoms.shtml



http://web.visionlearning.com/custom/chemistry/animations/CHE1.3-an-atoms.shtml



Revision Questions / Activities

Complete following:

1. Define chemistry and matter.

2. Define chemical and physical change.

3. Describe the concept of an atom and describe the electrical charges, and the locations

of the proton, neutron and electron.

4. Define atomic mass, atomic number and isotopes.

5. Write the correct symbols for the major elements in the human body.

6. Describe electron shells.

7. Describe the importance of trace minerals in the body.

Review Questions

Answer the relevant problems at the end of the chapter 1, 2 and 3 in Stocker (See Tutorial Handouts for suggested relevant Questions and Problems)



SESSION 2: Chemical Bonding

Code: BIOB111



Session Aims: This session will provide opportunities for students to:

Address the learning outcomes listed above. Become familiar with the Student Subject Guide and the Learning Outcomes and Assessment Tasks for this Subject of Study

Key Concept:

A compound is formed during a chemical reaction between two or more elements.

The forces that hold atoms together are called chemical bonds. Two principle types of bonds are ionic and covalent bonds.

Session Overview

This lecture will introduce the mole concept and the process by which elements and compounds participate in chemical reactions. Students will be able to write and balance chemical equations and to determine mass relationships for specific chemical reactions. Students will be able to recognize various types of chemical reactions and note their characteristics. This will prepare students to understand chemical reactions that occur in the body.

Session Topics

Chemical Bonding

Valence electrons

Lewis Symbols

The Octet rule

Formation of ions

Ionic bonding

Naming of ionic compounds

Polyatomic ions

Covalent bonding

Naming covalent compounds

Electronegativity

Bond polarity



Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully.

Textbook Location


Chapter 4: Chemical Bonding: The Ionic Bond Model, pp. 85-106 – Sections: 4.1, 4.2, 4.3, 4.4, 4.9, 4.10

Chapter 5: Chemical Bonding: The Covalent Bond Model, pp. 113-138 – Sections: 5.1, 5.4, 5.9, 5.10, 5.11, 5.12





Summary

Matter is made up of atoms and these atoms (elements) bond with each other in various ways to form compounds. Atoms form ions, which have different numbers of protons and electrons. When this happens the atom becomes charged - either positively or negatively. Positive ions are called cations and negative ions are called anions. It is important to remember that there is an enormous difference between an atom and its corresponding ion. It is the atoms’ ability to form ions that determines how these atoms will bond with other atoms to form compounds.

Ionic bonding is the attraction between positive and negative ions to form ionic compounds. Ionic bonds occur between a cation and an anion (a metal and a non-metal). Ionic compounds are usually solids at room temperature and generally have a type of crystal lattice structure. One example of an ionic compound is NaCl (sodium chloride) which you know as table salt. Read Chapter 4 from Stoker – Sections: 4.1, 4.2, 4.3 Read Chapter 4 from Stoker – Sections: 4.4, 4.9, 4.10

Introduction to Covalent Bonds

A covalent bond is one in which two atoms share a pair of electrons to form covalent compounds. Covalent compounds occur in non-metals. Most of the substances that form part of our body are covalent compounds. There are two types of covalent bonds; polar covalent and non-polar covalent bonds. In a non-polar covalent bond the electrons are shared equally, and in a polar covalent bond the electrons are not shared equally. Some elements are ‘greedier’ and take more than their share of the electron pair: this concept is called electronegativity.

Introduction to Bond Polarity

The difference in electronegativity determines the type of bond that will form. Another important group of ions is the polyatomic ions. Polyatomic ions are compounds that have both ionic and covalent bonds and these are very important in our bodies. Read Chapter 5 from Stoker – Sections: 5.1, 5.3, 5.4, 5.9, 5.10, 5.11, 5.12






Chapters 4 and 5

Additional Reading


Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H. Freeman and Co, New York.


Bettelheim, FA, Brown, WH, Campbell, MK, Farrell, SO, Torres, OJ 2013, Introduction

to General, Organic and Biochemistry, 10th edn, Brooks/Cole, Cengage Learning, USA. http://www.visionlearning.com/library/module_viewer.php?c3=&mid=55&l=


1. Describe the difference between ionic, covalent compounds. 2. Describe polar and non-polar compounds. 3. Write a molecule in structural, Lewis and molecular formulae. 4. Name ionic and molecular compounds. 5. Recognize and name the common polyatomic ions. 6. Describe the polyatomic ions in bone and teeth.

Review questions

Answer the relevant Exercises and Problems at the end of Chapters 4 & 5 in Stoker.



http://www.visionlearning.com/library/module_viewer.php?c3=&mid=55&l



SESSION 3: Chemical Reactions

Code: BIOB111



Session Aims:

This session will provide opportunities for students to:

Address the learning outcomes listed above.


Key Concept:

Law of conservation of mass is used to write a chemical reaction in the form of a balanced of equation. A mole is a collective term for 6.02 x 1023 items The coefficient number in a chemical equation represents the number of moles of reactants and products. The molar mass g/mole of any substance is the mass in grams equal numerically to its atomic mass, or the sum of the atomic masses which have been multiplied by their subscripts in a formula.

Session Overview

This lecture will introduce the mole concept and the process by which elements and compounds participate in chemical reactions. Students will be able to write and balance chemical equations and to determine mass relationships for specific chemical reactions. Students will be able to recognise various types of chemical reactions and note their characteristics. This will prepare students to understand chemical reactions that occur in the body.

Session Topics

Chemical Equations

Balancing a chemical equation

Classification of chemical reactions

Heat of reaction

The Mole

Calculation of Formula Weight and the mole

Mass Relationships in chemical reactions Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully



Textbook Location


Chapter 6: Chemical Calculations: Formula Masses, Moles & Chemical Equations, pp. 1455-167 – Sections: 6.1, 6.2, 6.3, 6.4, 6.6

Chapter 9: Chemical Reactions, pp. 238-264 – Sections: 9.1, 9.2, 9.3



Summary

Chemical reactions are occurring around us all the time. Our bodies are constantly producing chemical reactions. A chemical reaction occurs when one or more original substances are converted or changed into one or more new substances, so even baking cakes involves chemical reactions. Chemical equations actually show us what is happening when two or more substances react with each other to form new substances. In chemical reactions atoms are never created or destroyed (they just join up in a different way) so there must always be the same number of each type of atom, before and after the reaction. Learning how to balance chemical equations requires patience and practice. Just remember the more you have of each, the better you will become. Read Chapter 6 from Stoker – Sections: 6.6 Read Chapter 9 from Stoker – Sections: 9.1, 9.2, 9.3





Chapters 6 and 9

Additional Reading



Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H. Freeman and Co, New York





Bettelheim, FA, Brown, WH, Campbell, MK, Farrell, SO, Torres, OJ 2013, Introduction to General, Organic and Biochemistry, 10th edn, Brooks/Cole, Cengage Learning, USA.

http://video.about.com/chemistry/How-to-Balance-Chemistry-Equations.htm

http://chemistry.about.com/cs/stoichiometry/a/aa042903a.htm http://www.visionlearning.com/library/module_viewer.php?c3=&mid=55&l=


1. Explain how you would calculate a formula (molecular) weight. 2. Define the concept of the mole. 3. Explain chemical equations using five examples. 4. Demonstrate five balancing equations Review Questions

Answer the relevant Exercises and Problems at the end of Chapter 6 & 9 in Stoker.

http://video.about.com/chemistry/How-to-Balance-Chemistry-Equations.htm

http://chemistry.about.com/cs/stoichiometry/a/aa042903a.htm

http://www.visionlearning.com/library/module_viewer.php?c3=&mid=55&l



SESSION 4: Reaction Rates

Code: BIOB111


#2. Discuss states of matter, gases, equilibrium, mixtures and solutions and state applications to physiological processes and in metabolism. Describe Le Châtelier's principle and its role in equilibrium

Session Aims:




Key Concept:

The rate of a chemical reaction can be increased by factors such as increasing the concentrations of reactants, raising the temperature or by adding a catalyst.

In a reversible reaction, a chemical equilibrium can be obtained when the rate of forward reaction equals the rate of reverse reaction. Le Châtelier’s principle is used to describe the changes made in equilibrium when reaction conditions change.

Session Overview

This lecture will introduce students to the factors which determine the rates of chemical reactions. The nature of equilibrium reactions and the application of Le Châtelier’s Principle to systems at equilibrium will also be discussed. This will prepare students to understand chemical reactions that occur in the body.

Session Topics:

Oxidation-Reduction

Energy in Chemical Reactions

Reversible reactions and equilibrium

Collision Theory of Chemical Reactions

Factors Affecting Reaction Rate

Textbook Location


Chapter 9: Chemical Reactions, pp. 235-264 – Sections: 9.4, 9.5, 9.6, 9.7, 9.9

Concepts to Remember at the end of the chapter.




Summary

Introduction to types of Reactions

Now you are looking at types of reactions in detail, specifically oxidation-reduction reactions, the energy in chemical reactions, equilibrium and the factors that affect equilibrium reactions will be explored.

Factors affecting Rate of Reaction

Once a reaction has started, there are several factors that can then affect how long they take to be completed. Some reactions happen very fast (e.g. an explosion) and others are very slow (e.g. the rusting of metal).

Read Chapter 9 from Stoker – Section: 9.6

Introduction to Oxidation – Reduction

The second type of chemical reaction we are going to study in detail is the Oxidation-Reduction reaction. These reactions are some of the most important and common reactions that take place, both in and out of our bodies. When your car rusts, or when our cells respire it is an oxidation – reduction reaction that is occurring. It is important to remember that there can be no oxidation without an accompanying reduction!

Introduction to Energy in Chemical Reactions In almost all reactions there is a gain or loss of heat. This is called the heat of reaction. Some reactions require heat to work. These are called endothermic (e.g. baking a cake); and other reactions give off heat (e.g. lighting a match) - these are called exothermic. Energy is not only heat - it can also take the form of sound, calories, light or electricity.

Introduction to Reversible Reactions and Equilibrium

Many reactions are not reversible - for example, burning paper or wood - but many reactions can be made to go in either direction or are reversible. In equilibrium the forward and reverse reactions are taking place at the same rate, unless we do something to change it. Read Chapter 9 from Stoker – Section: 9.7





Chapter 9

Chemical Connections: Changes in Human Body Temperature & Chemical Reaction Rate – p.253

Additional Reading




http://www.chemguide.co.uk/physical/equilibria/lechatelier.html.

Le Châtelier’s Principle and Chemical equilibria

http://www.wwnorton.com/college/chemistry/chemistry3/chemtours.aspx, then choose Chapter 16 Equilibrium (qualitative)


1. Classify the types of reaction. 2. Define Oxidation and Reduction. 3. Define Exothermic and Endothermic. 4. Define reaction rate and equilibrium. 5. Discuss the factors that affect rate of reaction. 6. Discuss equilibrium and Le Châtelier’s principle.

Review Questions

Briefly explain the Collision Theory of chemical reactions.

Define Activation Energy.

Define Exothermic and Endothermic chemical reactions.

Define Reaction rate and Chemical Equilibrium.

Discuss the factors that affect Reaction rate.

Define a Reversible chemical reaction & Chemical Equilibrium.

Discuss Le Châtelier’s principle

Answer the relevant Exercises and Problems at the end of Chapter 9 in Stoker.

http://www.chemguide.co.uk/physical/equilibria/lechatelier.html

http://www.wwnorton.com/college/chemistry/chemistry3/chemtours.aspx



SESSION 5: Physical States of Matter

Code: BIOB111


#2. Discuss states of matter, gases, equilibrium, mixtures and solutions and state applications to physiological processes and in metabolism. Describe Le Châtelier's principle and its role in equilibrium

Session Aims:




Understand Boyle’s & Dalton’s Laws of gases.

Address the types of intermolecular forces.

Describe Solubility & factors that affect solubility.

Key concept:

Matter exists in three different states. It is the intermolecular forces that determine a state for any substance. Kinetic energy and intermolecular forces determine the temperature of a substance to exist as a solid, liquid or gas.

It is essential to understand the behaviour of gases since they are important to life.

Boyle’s law and Dalton’s law of partial pressures are used to explain the behaviour of gases.

Session Overview:

Students will be introduced to the States of Matter, including the gaseous, liquid and solid states. They will identify the principle determinants of the states that matter adopt. The origin and the practical applications of the Gas Laws will be discussed. The properties of gases, liquids and solids will also be explained. The properties of mixtures including solutions and colloids will be examined. The behaviour and properties of solutions and colloids including a number of the colligative properties will be discussed

Session Topics

States of Matter o Gases o Liquids o Solids

Intermolecular Forces

Gas Laws

Solutions, Colloids and Suspensions

Solubility

Osmotic Pressure and Dialysis



Textbook Location


Chapter 7: Gases, Liquids and Solids, pp. 173-198 – Sections: 7.1, 7.2, 7.4, 7.8, 7.9, 7.13

Chapter 8: Solutions, pp. 205-230 – Sections: 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.9


Exercises and Problems with odd numbers, at the end of each chapter, are answered at the end of the textbook

Summary

Energy

Energy is the ability to do work and can be classified as kinetic energy or potential energy.

Energy and Nutrition

States of Matter

All matter can exist in three forms, or what we call states of matter – solid, liquid and gas. Let us look at water as an example. It can be solid (ice at 0°C), liquid (from the tap at room temperature) or gas (steam when you boil the kettle at 100°C). Whether matter is a solid, liquid or gas is determined by temperature, which is different for each substance. The state of matter is a physical property.

Introduction to Intermolecular Forces

Intermolecular forces are the forces that keep molecules together (don’t confuse them with bonds) and it is the strength of these forces that determine if a substance will be a solid, liquid or gas. It is a combination of kinetic energy and intermolecular forces that determines at what temperature matter will be a solid, a liquid or a gas. Gases are particularly important to living things, as we need them to survive. That is why many laws have been formulated to explain the behaviour of gases. The two which are most important to us at this point are Boyle’s Law and Dalton’s Law.

Read Chapter 7 from Stoker – Section: 7.13

Introduction to Gases and Pressure

Gases are very important to all living things because they form our atmosphere which makes our planet liveable and green. The atmosphere we live in is made up of the following gases:

Nitrogen 78%

Oxygen 20.9%

Argon 0.9%



Carbon dioxide and other gases 0.1%

Read Chapter 7 from Stoker – Sections: 7.4, 7.8

Water

Water is essential. It makes up approximately 60%-75% of the human body and is essential to many reactions occurring in your cells. It is often called the universal solvent because of all the substances it can dissolve. Most of its behaviour is due to its hydrogen bonding ability.

Types of Solutions

Solutions are present in all our lives. When you make a cup of coffee you are making a solution. The sea is a solution of salt in water. Aromatherapy oils are solutions of different oils. Can you think of any others?

Read Chapter 8 from Stoker – Sections: 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.10

Solubility

Solubility is a measure of how much of something will dissolve in water. Every substance has a different solubility (solubility is a physical property). One of the main characteristics of solutions is that you can make them up in different concentrations (dilute to concentrated). There are 3 ways to measure the concentration of a solution, % concentration, molarity and parts per million (ppm). Parts per million is a common measure of the concentration of minerals found in commercially bottled spring water. An example is shown below: Bottled water from France

Mineral Concentration (ppm)

Calcium 78

Magnesium 24

Sodium 5

Potassium 1

Colloids

Colloids are homogeneous mixtures that appear cloudy. Some examples of colloids are toothpaste, milk and smoke.



Osmotic Pressure and Dialysis

Osmosis is the passage of solvent molecules from the dilute to the more concentrated. Animal and Plant cells use the process of osmosis to move fluids around. Our kidneys use the process of dialysis to filter our blood.





Chapters 7 & 8

Chemical Connections: Hydrogen Bonding and Density of Water – p.196.

Additional Reading


http://www.harcourtschool.com/activity/states_of_matter/


http://www.holton.k12.ks.us/staff/mspade/lessons/gaslaws.html

http://legacyweb.chemistry.ohio-state.edu/betha/nealGasLaw/

www.nclark.net/GasLaws Air pressure & a balloon


1. Describe variations of energy output/input. 2. Define potential and kinetic energy 3. Define intermolecular forces and describe the different types of intermolecular forces 4. Define kinetic energy and states of matter relationship. 5. Define Kinetic Molecular Theory of gases in brief. 6. Describe Boyle’s Law and application to breathing. 7. Describe Dalton’s Law of Partial Pressures and gas transport in blood. 8. Explain how the human body takes up oxygen from the air 9. Discuss the properties of water. 10. Define homogenous and heterogeneous solutions. 11. Explain the concept of solubility and the characteristics of solutions. 12. Define colloids. 13. Explain osmosis, osmotic pressure, and dialysis. 14. Demonstrate your ability to calculate concentrations of solutions.

Review Questions

Answer the relevant Exercises and Problems at the end of chapters 7 & 8 in Stoker.

http://www.harcourtschool.com/activity/states_of_matter/


http://www.holton.k12.ks.us/staff/mspade/lessons/gaslaws.html

http://legacyweb.chemistry.ohio-state.edu/betha/nealGasLaw/

http://www.nclark.net/GasLaws



SESSION 6: Acids and Bases

Code: BIOB111


#2. Discuss acids & bases, acid-base reactions, strength of acids & bases, the concept of pH, buffers & electrolytes and their applications to physiological processes and metabolism.

Session Aims:


Address the learning outcomes above.


Describe the 2 definitions of Acids & Bases together with the strength of Acids & Bases.

Discuss the concept of pH in relation to the concentration of H+ in the solution.

Thoroughly explain Buffers & their function in the human body, giving examples.

Key Concept:

Acids are proton donors and bases are proton acceptors. The strength of an acid/ a base is measured on the pH scale. Buffers maintain the pH of the solutions and are important for normal biological functions.

Session Overview

Students will be introduced to the chemical definitions of acids and bases. A comparison of the properties of acids and bases will be made. The significance of pH as a measure of acidity and alkalinity will be discussed. The importance of buffers to maintain a stable pH in body fluids will be emphasized

Session Topics

Acids and Bases o Properties of acids and bases o pH concept o Buffers o Electrolytes o

Textbook Location




Chapter 10: Acids, Bases and Salts, pp. 271-303 – Sections: 10.1, 10.2, 10.3, 10.4, 10.6, 10.7, 10.8, 10.9, 10.12

Concepts to Remember at the end of the chapter. Exercises and Problems with odd numbers, at the end of each chapter, are answered at the end of the textbook

Summary

In this lesson we look at the concept of pH, acids, bases and buffers. Acids by definition produce hydrogen ions (H+) and bases produce hydroxide ions (OH-). The strength of an acid or base is measured on the pH scale, which ranges from 0-14 pH as measured by indicators. Buffers are substances that prevent changes in pH and are very important in our bodies. Acids and bases react to form salts and water.

Introduction to Acids and Bases

Acids and bases (alkalis) are very common in our everyday lives. We drink acidic orange juice and wash our hands with basic soaps. But what makes an acid, an acid?

Acids have the ability to produce H+ ions when added to water, and bases produce OH- ions when added to water. The strength of an acid is measured by how many of these ions it produces.

Properties of acids and bases

A phenomenological definition of acids and bases is a definition that hinges on what you can see, taste, feel or touch. The phenomenological definitions of acids and bases are:

Acids: o Taste sour, turn litmus red, react with metals such as zinc and iron to release

H2 gas.

Bases: o Taste bitter, turn litmus blue and feel slippery.

Tasting any questionable material to learn whether it is sour or bitter or rubbing it between your fingers to see if it slippery is a dangerous activity. This is why we use indicators. Indicators show us how strong an acid or base is. Phenolphthalein is a very common acid-base indicator and is also the active ingredient in laxatives.

Read Chapter 10 from Stoker – Sections: 10.1, 10.2, 10.3, 10.4, 10.6, and 10.7.

pH

pH is a measurement of the strength of an acid or base. The pH scale ranges from 0 – 14, with 0 being the strongest acid (something like HCl which is stomach acid) to 14 being the strongest base (for example NaOH – caustic soda). A list of common substances and their pH is found in table 8.4



pH Scale

Read Chapter 10 from Stoker – Sections: 10.8, 10.9.

Electrolytes

Electrolytes are compounds that are able to conduct electricity when in aqueous solutions. It is important to understand, that acids, bases & salts can form electrolytes.

Electrolytes are classified into strong, weak & non-electrolytes, according to their ability to conduct electric current.

Read Chapter 10 from Stoker – Sections: 10.14.






Chapter 10

Chemical Connections: Composition and Characteristics of Blood Plasma – p.293.

Chemical Connections: Acidosis and Alkalosis – p.297.

Chemical Connections: Electrolytes and Bodily Fluids – p.301.

Additional Reading

http://chemistry.about.com/od/acidsbases/a/strengthacids.htm


1. Discuss the amazing properties of water. 2. Demonstrate your ability to calculate concentrations of solutions. 3. Describe acids, bases, pH and buffers.

4. Describe acids & bases according to Arrhenius & Brønsted-Lowry. 5. Draw a comparison between strong & weak acids, giving examples. 6. Draw a comparison between strong & weak bases, giving examples. 7. Describe conjugate acid-base pairs. 8. Discuss the characteristics of acids & bases. 9. Describe mono-, di- & triprotic acids. 10. Discuss pH concept & the pH scale, giving examples. 11. Describe a buffer. 12. Demonstrate your ability to understand buffer action, giving examples. 13. Describe electrolytes.

Review Questions


http://chemistry.about.com/od/acidsbases/a/strengthacids.htm



SESSION 7: Introduction to Organic Chemistry

Code: BIOB111


#3. Identify and apply the nomenclature and common chemical reactions associated with organic functional groups.

Session Aims:



Become familiar with the Student Subject Guide and the Learning Outcomes and Assessment Tasks for this Subject of Study

Present the bonding ability of different atoms commonly found in Organic compounds.

Explain the main differences between Saturated & Unsaturated Hydrocarbons.

Discuss the nomenclature, isomerism, sources, physical & chemical properties of Alkanes & Cycloalkanes

Key Concept:

Carbon provides a basis of for millions of organic compounds in combination with oxygen, nitrogen, sulphur, and halogens. The presence of a group of atoms that characterise a particular organic compound are called functional groups. Functional groups are responsible for the chemical properties of compounds and help us to classify the organic compounds.

Session Overview

Students will be introduced to Organic Chemistry. The origins of organic compounds and the significance of the functional groups they contain in their classification and as sites of chemical reactions will be discussed.

Session Topics

Saturated & Unsaturated Hydrocarbons

Functional Groups

Structural Isomers

Stereoisomers

Nomenclature

Alkanes & Cycloalkanes

IUPAC Nomenclature

Alkyl Groups

Structural Isomerism of Alkanes

Sources of Alkanes

Physical & Chemical properties of Alkanes



Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully

Textbook Location


Chapter 12: Saturated Hydrocarbons, pp. 339-375 – Sections: 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 12.10, 12.11, 12.12, 12.13, 12.15, 12.16, 12.17, and 12.18.



Summary

Organic Chemistry

Organic chemistry studies compounds that contain carbon. There are more than 8 million organic compounds known, with lots more being discovered every year. Why is organic chemistry so important for you to learn? Well, everything living is made up of organic compounds, including us and all the food we eat. Herbs are also made of carbon compounds and it is these compounds that give the therapeutic value to herbal remedies. Vitamins are also organic compounds and are very important for our health.

Read Chapter 12 from Stoker – Sections: 12.1, 12.2.

Structure of Organic Compounds

Recognition of organic compounds is based on structural formula (not molecular formula). Many organic compounds can have the same molecular formula, but their structures are very different (these are called isomers) and this makes them different compounds with different chemical and physical properties.

Alkanes

Acyclic Saturated Hydrocarbons contain only single covalent bonds between C atoms in their chains & are fully saturated with H atoms. The chemical formulae of alkanes can be written in several ways, including molecular formulas as well as expanded, condensed & line-angle structural formulas, all of which are governed by the rules that are set by the IUPAC system. Alkanes are able to form Constitutional Isomers – molecules that have same molecular formulae but different arrangement of atoms in space – therefore these isomers are different compounds with different physical & chemical properties. Alkanes often form branch-chain molecules that are composed of a straight parent chain, to which branches or Alkyl Groups are attached.




Cycloalkanes

Are cyclic Saturated Hydrocarbons that also contain only single covalent bonds between C atoms & are fully saturated with H atoms just like alkanes, however the C atoms join to form a closed ring structure. The nomenclature & chemical formulae of cycloalkanes are also set by the IUPAC system. Both, alkanes & cycloalkanes, can be found in nature, mainly in crude oil. Read Chapter 12 from Stoker – Sections: 12.12, 12.13, 12.15

Physical & Chemical Properties of Alkanes & Cycloalkanes

Alkanes & Cycloalkanes are non-polar compounds – they are insoluble in water but soluble in non-polar solvents, they are less dense than water – float on water surface (e.g. oil spills), they have low melting & low boiling points that increase the larger the molecule is. Alkanes & Cycloalkanes readily undergo chemical reactions, including Combustion & Halogenation. Halogenated alkanes may potentially be toxic, which is illustrated by the destruction of Ozone layer by Chlorofluorocarbons, halogenated compounds designed as refrigerants. Read Chapter 12 from Stoker – Sections: 12.16, 12.17, 12.18




Chapter 12

Chemical Connections: Occurrence of Methane – p.344.

Chemical Connections: The Physiological Effects of Alkanes – p.372

Chemical Connections: Chlorofluorocarbons and the Ozone Layer – p.378.



Additional Reading


http://www.cartage.org.lb/en/themes/sciences/Chemistry/Organicchemistry/Families/Somefamilies/mainpage.htm

Revision Questions / Activities .

1. Define organic chemistry. 2. Explain the differences between organic & inorganic compounds. 3. Show how carbon atoms can combine to make so many compounds. 4. Draw the expanded, condensed & line-angel formulae for the first 10 alkanes. 5. Explain the nomenclature of alkanes & cycloalkanes, using examples. 6. Explain what an Alkyl Group is, using examples. 7. Discuss Constitutional Isomers, using examples. 8. Describe carbon classification – primary, secondary, tertiary, quaternary. 9. Outline the physical properties of alkanes & cycloalkanes. 10. Describe the chemical properties of alkanes & cycloalkanes. 11. Outline the classification of C atoms – primary, secondary, tertiary, quaternary, using

examples.

Review Questions


SESSION 8: Properties of the Functional Groups & Examples (I) Unsaturated Hydrocarbons. Alkanes, Alkenes, Alkynes & Aromatics

Code: BIOB111



Session Aims:






Address the learning outcomes listed above. Become familiar with the 3 types of Unsaturated Hydrocarbons – Alkenes, Alkynes & Arenes, their

nomenclature, chemical properties & Cis-Trans Isomerism.


Key Concept:

Functional groups such as alkenes, alkenes alkynes are discussed with reference to their physical and chemical properties. Alkanes undergo substitution reactions and alkenes undergo addition reactions. Aromatic compounds undergo substitution reactions since their aromatic ring is stable.

Session Overview

.

In this session students with further expand their knowledge in Organic chemistry, discussing Unsaturated Hydrocarbons, which include Alkenes, Alkynes & Aromatic Hydrocarbons (Arenes).

The importance of Functional Groups of Organic compounds is introduced & related to the IUPAC structure & nomenclature of Organic compounds.

All 3 groups of Unsaturated Hydrocarbons are discussed in regards of their functional groups, general molecular formulae, nomenclature, structure, and isomerism as well as physical & chemical properties

Session Topics

Structural chemical properties, Naming and reactions of:

Alkanes

Alkenes and alkynes

Cycloalkanes

Aromatic compounds

Functional Groups

Textbook Location



Chapter 13: Unsaturated Hydrocarbons, pp. 380-417 – Sections: 13.1, 13.2, 13.3, 13.4, 13.6, 13.7, 13.8, 13.9, 13.10, 13.11, 13.12, 13.13, 13.16





Summary

Alkenes and Alkynes Alkenes and alkynes are families of hydrocarbons that contain double and triple bonds respectively. They are called unsaturated compounds because they do not contain the maximum number of hydrogen atoms that could be attached to each carbon atoms as do the alkanes. Alkenes form a special type of isomers – Cis-Trans Isomers, known as Steroeoisomers or Geometric isomers that have the same molecular formula, same order of atom attachment but a different arrangement of atoms in space. This is due to the rigidity & restricted rotation on C=C bond in the molecule of the alkenes. Many alkenes occur naturally, including Terpenes like Limonene, Menthol, Zingiberine as well as Carotenoids like β-Carotene, Lycopene, Zeaxanthin & Lutein that are beneficial to the human body as antioxidant compounds. Alkenes readily undergo several Addition Reactions, esp. Hydrogenation, Halogenation & Hydration as well as Polymerization Alkynes are Acyclic Unsaturated Hydrocarbons containing 1 or more triple covalent bonds between C atoms in their chains & are even more unsaturated with H atoms than Alkenes. The functional group of alkynes is the presence of the triple bond in its molecule, it is here where all the different chemical reactions, that alkynes undergo, take place Read Chapter 13 from Stoker – Sections: 13.1, 13.2, 13.3, 13.4, 13.6, 13.7, 13.8, 13.9, 13.10, 13.11 Aromatic hydrocarbons Aromatic hydrocarbons are based on the structure of the benzene ring. They are important to a great variety of consumer products including plastics, synthetic fibres, pharmaceuticals and food flavourings. Two examples of aromatic compounds that give perfume to plants are cinnamaldehyde (in cinnamon) and methyl salicylate (in oil of wintergreen). Read Chapter 13 from Stoker – Sections: 13.13, 13.14, 13.15, 13.16

Introducing Reactions of Aromatic Compounds

Aromatic compounds perform a set of reactions called substitution reactions. These reactions are different from addition reactions as the double bonds in the benzene ring don’t break. In fact the benzene ring structure is one of the most stable organic compounds.





Chapter 13

Chemical Connections: Ethene: A Plant Hormone and High-Volume Industrial Chemical – p.389.



Chemical Connections: Cis-Trans Isomerism and Vision – p.394.

Chemical Connections: Carotenoids: A Source of Colour – p.397

Additional Reading


http://scienceaid.co.uk/chemistry/organic/alkanes.html


1. Outline the physical properties of alkenes & alkynes in relation to the presence of double

& triple bond in their molecule.

2. Explain the nomenclature of Alkenes & Alkynes, using examples.

3. Explain & draw Cis-Trans Isomers of Alkenes.

4. Outline the chemical properties of alkenes, including the different types of Addition

reactions & Polymerization reaction.

5. Recognise the structure of Benzene & discus its unique properties.

6. Identify & name the Phenyl group.

7. Explain the wide variety of Aromatic Hydrocarbons, using some examples.

Review Questions


http://scienceaid.co.uk/chemistry/organic/alkanes.html



SESSION 9: Properties of the Functional Groups & Examples (II). Phenols, Alcohols, Ethers, Aldehydes, ketones & carboxylic Acids.

Code: BIOB111


#3. Identify and apply the nomenclature and common chemical reactions associated with organic functional groups

Session Aims:


Address Learning Outcome listed above


Become familiar with the Functional Groups of Alcohols, Phenols, Ethers, Aldehydes, Ketones and Carboxylic Acids their nomenclature & chemical properties.

Key Concept:

Functional groups such as alcohols, phenols, ethers, aldehydes, ketones and carboxylic acids are discussed with reference to their physical and chemical properties. The chemical properties of compounds classified as alcohols, phenols, ethers, aldehydes, ketones and carboxylic acids, are due to the presence of the respective functional groups.

Session Overview

Students will be introduced to the functional groups such as alcohols, phenols, ethers, aldehydes, ketones and carboxylic acids, their nomenclature, structure, physical & chemical properties. The functional groups which characterize these molecules and the reactions which occur at these groups will be outlined.

Session Topics

Structural, Chemical Properties, Naming and Reactions of:

Alcohols

Ethers

Phenols,

Aldehydes

Ketones

Carboxylic Acids Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully.

Textbook Location




Chapter 14: Alcohols, Phenols & Ethers, pp. 423-460 – Sections: 14.1, 14.2, 14.3, 14.5, 14.6, 14.8, 14.9, 14.11, 14.12, 14.13, 14.14, 14.15, 14.16, 14.18, 14.19, 14.20

Chapter 15: Aldehydes & Ketones, pp. 469-494 – Sections: 15.1, 15.2, 15.3, 15.4, 15.5, 15.7, 15.8, 15.9, 15.10

Chapter 16: Carboxylic Acids, Esters & Other Acid Derivatives, pp. 503-538 – Sections: 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 16.10, 16.11, 16.12, 16.14, 16.15.



Summary

Alcohols

Alcohols are characterised by the presence of the –OH (=hydroxyl) functional group, which is attached to the hydrocarbon chain. The –OH functional group now takes precedence in naming & numbering of the organic compound, therefore it must be positioned on the C atom with the lowest position number. Alcohols are classified into primary, secondary & tertiary, depending on what type of C atom the –OH group is attached to. Polyols are alcohols that have 2 or more –OH functional groups in their structure. Common alcohols are discussed in this session, including Methanol, Ethanol, 2-Propanol, 1,2-Ethanediol, 1,2-Propanediol & 1,2,3-Propanetriol – it is important to stress the toxicity of some of these alcohols (methanol, ethanol, 2-propanol, 1,2-propanediol) as well as the importance of glycerol, as part of the structure of Triacylglycerol lipids, source of energy for the human body & precursor molecule to gluconeogenesis. Short chain alcohols are polar, however with increasing molecular weight their solubility in water decreases – this needs to be explained in class. Alcohols undergo Combustion, Dehydration & Oxidation chemical reactions, Oxidation being the most important reaction, forming different products from primary, secondary & tertiary alcohols. Primary alcohols oxidise into Aldehydes & Carboxylic Acids, Secondary alcohols oxidise into Ketones, while Tertiary alcohols resist oxidation. Must be discussed! Read Chapter 14 from Stoker – Sections: 14.1, 14.2, 14.3, 14.5, 14.6, 14.8, 14.9 Phenols Also known as Aromatic Alcohols, Phenols are characterised by the presence of the –OH functional group, attached to the benzene ring. The simplest Phenol is named Phenol & other Phenols are derivatives of this Phenol, containing other substituent groups in their structure. Phenols have properties of both, aromatic compounds & alcohols, are weak acids (unlike alcohols), are strong skin & mucous membrane irritants (Poison Ivy toxins) & are hepatotoxic. Phenols exhibit strong antiseptic properties (Lysol, Thymol, Eugenol), antioxidant properties (BHA, BHT, Vitamin E & Resveratrol), some are used as flavouring agents (Vanillin), while others may have physiological activity (Catechol is the basic phenolic compound from which dopamine, adrenalin & noradrenalin messengers are derived). Read Chapter 14 from Stoker – Sections: 14.11, 14.12, 14.13, 14.14



Ethers Ether functional group is an oxygen atom present between 2 C atoms in the hydrocarbon chain. Ethers (particularly Ethoxyethane) were used as the first inhalant anaesthetics in the early 19th century, with severe nausea as a side effect, this was overcome by preparing halogenated ether derivatives that are used as anaesthetics today. Due to low reactivity of Ethers, they are commonly used as solvents in organic chemical reactions that tend to generate unwanted by-products, the use of Ethers reduces the formation of these by-products. Read Chapter 14 from Stoker – Sections: 14.15, 14.16, 14.18, 14.19

Carbonyl Group

Is a unique group, in which C atom forms a double bond to an O atom. The Carbonyl group is part of functional groups of 5 types of Organic compounds – Aldehydes, Ketones, Carboxylic acids, Esters & Amides. Read Chapter 15 from Stoker – Sections: 15.1, 15.2.

Aldehydes & Ketones

Aldehydes & ketones are 2 classes of organic compounds, which have as part of their Functional group the Carbonyl group. The carbonyl group now takes precedence over other functional groups in naming & numbering the parent chain. Aldehydes & Ketones have very strong odours & many are responsible for the fragrance of flowers & fruits, therefore they are commonly used in the production of perfumes & as flavourings in foods. The aldehyde Formaldehyde, although toxic, is commonly used in manufacturing of paper, insulation materials, cosmetics (shampoo) & as a preservative in vaccinations. Other important Aldehydes include Vanillin (from vanilla plant), Benzaldehyde (from Bitter almonds) & Cinnamaldehyde (from cinnamon plant). The ketone Acetone is an important solvent & commonly used in nail polish remover. Other important & physiologically active Ketones include hormones Testosterone, Progesterone & Cortisol, Aldehydes & Ketones have lower boiling & melting points than alcohols, but higher than ethers & alkanes – this is because Aldehydes & Ketones have dipole-dipole intermolecular forces, which are stronger than the London dispersion forces (in alkanes) but weaker than Hydrogen bonding (in alcohols). Aldehydes are prepared by the oxidation of Primary alcohols, whereas Ketones are prepared by the oxidation of Secondary alcohols. The most important chemical reactions that Aldehydes & Ketones undergo are Oxidation & Reduction. Only Aldehydes oxidise to Carboxylic acids, Ketones resist oxidation. Reduction of Aldehydes & Ketones yields Primary & Secondary alcohols respectively. Another important chemical reaction that Aldehydes & Ketones undergo is their reaction with Alcohols, producing Hemiacetals & Acetals – this reaction is important for the structure of Carbohydrates. Read Chapter 15 from Stoker – Sections: 15.3, 15.4, 15.5, 15.7, 15.8, 15.9, and 15.10.

Carboxylic Acids

Carboxylic acids are a diverse group of Organic compounds, whose Functional Group is the Carboxyl Group –COOH. They are weak acids, often commonly used in everyday life: Ethanoic (Acetic) acid is found in vinegar & Citric acid is found in citrus fruits, as well as in the energy producing metabolic pathways in the human body. There are many more important carboxylic acids, often with other Functional groups as part of their molecule & several are produced in the human metabolic pathways, including Lactic acid, which is produced in the muscle tissues during anaerobic metabolism of carbohydrates (e.g. during exercise or during a heart attack). Carboxylic acids, like other acids, taste sour, can be corrosive & turn litmus paper red. They have higher boiling & melting points compared to alcohols, because they can form 2 Hydrogen bonds, which makes them even harder to separate.



One of the common properties of Inorganic & Carboxylic acids is their ability to form salts. Soaps are salts of long-chain carboxylic acids with strong bases. It is believed, that in the ancient Babylonian culture, people knew how to make soap – almost 5,000 years ago. Read Chapter 16 from Stoker – Sections: 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8




Chapter 14

Chemical Connections: Menthol: A Useful Naturally Occurring Terpene Alcohol – p.435.

Chemical Connections: Red Wine & Resveratrol – p.450.

Chemical Connections: Ethers as General Anaesthetics – p.455.

Chemical Connections: Marijuana: The Most Commonly Used Illicit Drug – p.459. Chemical Connections: Garlic & Onions: Odoriferous Medicinal Plants – p.463.

Additional Reading


http://www.execulink.com/~ekimmel/functional.htm

http://www.ausetute.com.au/fungroup.html


8. Define Alcohols & Phenols.

9. Outline the Classification of Alcohols.

10. Discuss Methanol, Ethanol & Glycerol.

11. Outline the physical properties of alcohols in relevance to their molecular weight & hydrogen

bonding.

12. Discuss Oxidation of primary, secondary & tertiary alcohols.

13. Outline the important uses of Phenols.

14. Define Ethers.

15. Outline the uses of Ethers.

16. Draw & define the Carbonyl Group.

17. Define & compare Aldehydes & Ketones, utilizing their functional groups.





18. Explain the nomenclature of Aldehydes & Ketones, using examples.

19. Explain the Tollen’s & Benedicts Tests.

20. Describe uses of important Aldehydes & Ketones, including Methanal & Propanone.

21. Understand the chemical reactions of Aldehydes & Ketones.

22. Define Carboxylic Acids & draw their Functional Group.

23. Explain the nomenclature of Carboxylic Acids, using examples.

24. Outline the physical properties of Carboxylic acids in relevance to their molecular weight &

Hydrogen bonding.

25. Understand the chemical reactions of Carboxylic acids.

26. Outline the uses of important Carboxylic acids.

Review Questions

Answer the relevant Exercises and Problems at the end of Chapter 14, 15, 16 in Stoker.



SESSION 10: Properties of the Functional Groups & Examples (III) Amines, Esters and Amides

Code: BIOB111

Learning outcomes


Session Aims:


Address the learning outcome listed above.


Become familiar with the Functional Groups of Esters, Amines & Amides and their physical & chemical properties.

Key Concept:

Functional groups such as Esters, Amines & Amides are discussed with reference to their physical and chemical properties. The chemical properties of compounds classified as Esters, Amines & Amides, are due to the presence of the respective functional groups.

Session Overview

In this session students will be introduced to the Functional Groups of Esters, Amines & Amides their

nomenclature & chemical properties. The functional groups which characterize these molecules and the reactions which occur at these groups will be outlined.

Session Topics

Structural, Chemical Properties, Naming and Reactions of:

Amines

Amides

Esters


Textbook Location




Chapter 16: Carboxylic Acids, Esters & Other Acid Derivatives, pp. 503-538 – Sections: 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 16.10, 16.11, 16.12, 16.14, 16.15.

Chapter 17: Amines & Amides, pp. 547-581 – Sections: 17.1, 17.2, 17.3, 17.5, 17.6, 17.7, 17.9, 17.10, 17.11, 17.12, 17.13, 17.14, 17.17, and 17.19.



Summary

Esters

Carboxylic esters can be prepared via the Esterification reaction, in which a Carboxylic acid reacts with an Alcohol, in an acidic environment, which serves as the catalyst. Ester nomenclature relates to the parent carboxylic acid & alcohol. Esters usually have strong pleasant odours & are responsible for the flavours & fragrances of many fruits & flowers. The fragrance of fruits like strawberries, raspberries, pineapples & apples are due to esters, however there are some esters, whose odour is not so pleasant (Methyl salicylate in the Oil of wintergreen). Esters undergo 2 important Chemical reactions – Hydrolysis & Saponification. Hydrolysis is the reverse reaction of Esterification. In hydrolysis a molecule of water is added to an ester molecule in an acidic environment, splitting it into the parent carboxylic acid & alcohol. Also known as Acid Hydrolysis. Saponification is also known as Basic Hydrolysis – here an ester reacts with a strong base (NaOH or KOH) producing soap & alcohol. Read Chapter 16 from Stoker – Sections: 16.9, 16.10, 16.11, 16.12, 16.14, 16.15

Amines

Are Organic compounds that contain N atom in their structure in the form of amino group, as they are derivatives of Ammonia. Amines are classified into primary, secondary & tertiary, depending on how many alkyl groups are attached to the N atom. Chemically Amines are weak bases & as such readily undergo neutralization reaction with strong acids, producing Amine salts. This reaction is extremely important, as many high molecular mass amines exhibit biochemical activity & are able to alter the physiology of the human body. However these large molecules are commonly insoluble in water, neutralization of any amines renders them water soluble & therefore soluble in bodily fluids, so they can reach their target cells & produce the desired effect. Heterocyclic amines are cyclic organic compounds in which 1 or more C atoms in their ring structure are replaced with N atoms. Important heterocyclic amines include Caffeine & Nicotine. Many amines are naturally produced by plants & have profound effects on the human body, sometimes highly toxic. Alkaloids are amines, several of which have anaesthetic & hallucinogenic properties, however in high doses may lead to death. The functional group of Amines, the amino group, is one of the 2 functional groups of amino acids, the other being the carboxyl group. Amino acids are the building blocks of proteins & enzymes that are necessary for the structure & function of the human body.



Other biochemically important amines include Neurotransmitters (Acetylcholine, Serotonin, Dopamine, Noradrenalin & Adrenalin), Decongestant & Antihistamine drugs. Read Chapter 17 from Stoker – Sections: 17.1, 17.2, 17.3, 17.5, 17.6, 17.7, 17.9, 17.10, 17.11

Amides

Are Organic compounds that also contain N atom in their structure, however they are derivatives of Carboxylic acids, in which the –OH group of –COOH has been replaced by the Amino group. The classification of Amides groups them into primary, secondary & tertiary amides, depending on how many alkyl groups are attached to the N atom. Amides, unlike amines, are neutral compounds. Preparation of Amides involves the chemical reaction between Carboxylic acids & either Ammonia, primary or secondary amines, removing 1 molecule of water. Such a chemical reaction is known as Dehydration synthesis. This very same reaction is involved in the production of bodily proteins by linking singular amino acids into the peptide chain joining them via a Peptide bond, a type of amide bond. Protein chains are chemically polyamides. Amides, just like Amines can alter the physiology of the human body. Cyclic amides known as β-lactams belong to the penicillin family of antibiotics. Urea, the simplest one-C atom diamide is produced during normal metabolism of amino acids in the human body, eliminating N atoms from the body. The Amide known as Paracetamol / Acetaminophen is the top-selling OTC pain reliever. Many synthetic polyamides have a very broad usage, including Nylon, Kevlar, Nomex & Polyurethane. Read Chapter 13 from Stoker – Sections: 17.12, 17.13, 17.14, 17.17, 17.19




Chapters 16, 17

Chapter 17: Amines & Amides, pp. 547-581 – Sections: 17.1, 17.2, 17.3, 17.5, 17.6, 17.7, 17.9, 17.10, 17.11, 17.12, 17.13, 17.14, 17.17, and 17.19.

Chemical Connections: Diabetes, Aldehyde Oxidation & Glucose Testing – p.484.

Chemical Connections: Aspirin – p.525.

Chemical Connections: Nitroglycerin: A Inorganic Triester – p.535.

Chemical Connections: Caffeine: The Most Widely Used Central Nervous System Stimulant – p.559.

Chemical Connections: Nicotine Addiction: A Widespread Example of Drug Dependence – p.561.

Chemical Connections: Alkaloids Present in Chocolate – p.566.



Chemical Connections: Acetaminophen: A Substituted Amide – p.573.

Additional Reading



http://www.ausetute.com.au/fungroup.html http://wps.prenhall.com/esm_mcmurry_fundamentals_4/38/9916/2538553.cw/index.html (chapters 15, 16, 17)


1. Define Esters & draw their Functional Group.

2. Understand the physical properties of Esters.

3. Explain the chemical reactions of Esters.

4. Outline the uses of important Esters.

5. Outline the number of bonds that C, H & N atoms form in Organic compounds.

6. Define Amines & draw their Functional Group.

7. Explain the nomenclature of Amines.

8. Outline the classification of Amines.

9. Discuss the physical properties of Amines.

10. Outline the Alkaline behaviour of Amines.

11. Discuss the importance of the Neutralization reaction of Amines.

12. Explain Heterocyclic amines, giving examples relating to the human body.

13. Outline the effect of Neurotransmitters in the body, giving examples.

14. Define Alkaloids, using examples.

15. Define Amides & draw their Functional Group.

16. Explain the nomenclature of Amides.

17. Outline the classification of Amides.

18. Give examples of useful Amides.

19. Discuss the preparation of Amides & its relevance to the human body.

20. Outline Polyamides, giving examples.

Review Questions

Answer the relevant Exercises and Problems at the end of Chapters 16, 17 in Stoker.



http://wps.prenhall.com/esm_mcmurry_fundamentals_4/38/9916/2538553.cw/index.html



SESSION 11: An Introduction to the Structure and Function of Carbohydrates

Code: BIOB111

Learning outcomes

#4. Illustrate the chemical nature of the major biochemical groups of carbohydrates, lipids, proteins and nucleic acids.

Session Aims:



Become familiar with the structure, properties, chemical reactions & function of the different types of carbohydrate molecules


Key Concept:

Carbohydrates also called as sugars are compounds of carbon, hydrogen and oxygen. During digestion and metabolism the carbohydrates are converted into glucose which is oxidized further in cells to produce the cells with energy and to provide carbon atoms for building proteins, lipids and nucleic acids. They are classified as mono saccharides, disaccharides and poly saccharides depending upon the number of sugars present in the compound. Mono saccharides contain the hydroxyl functional group and disaccharides and poly saccharides contain hydroxyl functional groups and a glycosidic link.

Session Overview

Students will be introduced to Biochemistry. The importance of the 3-dimensional structure as a determinant of biological function will be discussed. Students will be introduced to the chemistry of the carbohydrates. The basis for the classification of carbohydrates will be discussed. The significance of the cyclisation of monosaccharides in aqueous solution and their polymerization to form disaccharides and polysaccharides will be discussed. The important disaccharides and polysaccharides will be identified and their structure and function examined.

Session Topics

Introduction to carbohydrates

Types

Classification

Monosaccharides

Disaccharides

Polysaccharides



o Specialised Polysaccharides Read the BIOB 111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully.

Textbook Location


Chapter 18: Carbohydrates, pp. 592-643 – Sections: 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 18.10, 18.11, 18.12, 18.13, 18.14, 18.15, 18.16, 18.17, 18.18, and 18.19.



Summary

Introduction to carbohydrates

Carbohydrates are the most abundant biomolecules on Earth, although their abundance in human body is relatively low, they constitute about 75% of dry plant material mass. Plants produce carbohydrates via Photosynthesis. Chemically carbohydrates can be divided into the following groups:

Simple sugars (monosaccharides and disaccharides).

Polysaccharides (starch and glycogen), and

Indigestible carbohydrates which constitute the dietary fibre in our diets (such as cellulose). In this session you will have been introduced to the structure and properties of some monosaccharides, disaccharides and polysaccharides

Structure and function of carbohydrates

Carbohydrates Provide energy for plants & animals; Form supportive structures in plants (cellulose), insects & crustaceans (chitin); Supply a short-term energy storage in plants (starch) & humans (glycogen); Provide C atoms for the synthesis of other biochemical substances in plants (proteins, lipids & nucleic acids); Form important components of DNA & RNA molecules as well as cell membranes (Glycolipids), where they are involved in cell–cell & cell–molecule recognition processes (Glycoproteins).

Each type of carbohydrate affects body metabolism in different ways. The basis of chemistry is that structure determines function. It is important to bear in mind, however, that many foods are a combination of the different types of carbohydrates. In this respect, it is more important to understand the effect of particular foods on metabolism rather than individual components. One example of this is to classify foods by their glycaemic index, that is, their ability to raise blood glucose levels. This will be discussed in greater depth in the nutrition subjects. The first aspect of carbohydrates to note is that they are either aldehydes or ketones and therefore have all the chemical and physical properties of these types of molecules. As you proceed through the chapter, it may be worthwhile revisiting the relevant parts of the textbook.



The principal dietary source of carbohydrates is plant products (grains, fruits and vegetables). Glucose and starch are produced in the plant through the process of photosynthesis.

Chirality

“Handedness” or Chirality (a form of isomerism) is a property of many molecules, including carbohydrates. Molecules exhibiting handedness exist in 2 forms – a “left handed” & a “right handed” form (like hands) that are “mirror images” of each other. All objects, including molecules, have mirror images & can be divided into 2 classes depending on their mirror image: Superimposable mirror images – Images that coincide at all points when the images are laid upon each other (Achiral objects) Non-superimposable mirror images – Images where not all points coincide when the images are laid . 2 types of stereoisomers: Enantiomers – Stereoisomers whose molecules are non-superimposable mirror images of each other. Chiral molecules with a single chiral center. Diastereomers – Stereoisomers whose molecules are not mirror images of each other. Cis-Trans isomers of alkenes. Read Chapter 18 from Stoker – Sections: 18.4, 18.5, 18.6, 18.7

Classification of Monosaccharides

Monosaccharides are carbohydrates that contain 1 single polyhydroxy aldehyde or polyhydroxy ketone unit. Aldose – a monosaccharide with a –CHO functional group Ketose – a monosaccharide with C=O group Monosaccharides usually contain 3-7 C atoms however 5 & 6 C species are more common Pentose – a monosaccharide with 5 C-atoms Hexose – a monosaccharide with 6 C-atoms Aldohexose – a 6C monosachcaride with –CHO functional group Ketopentose – a 5C monosaccharide with C=O functional group

D-Glucose

An aldohexose & the most abundant monosaccharide in nature & most important for human nutrition. Sources: ripe fruits (esp. ripe grapes 20-30% glucose by mass). Blood sugar = blood glucose normal range concentration (3.5 – 5.5 mmol/L of blood) – maintained by Insulin & Glucagon. Blood glucose concentration depends on time since the last meal – in 1 hour after eating 7 mmol/L & returns to normal range over the next 2-3 hours.

D-Galactose

An aldohexose & is seldom found as free monosaccharide, usually forms components of important biomolecules – glycoproteins in the brain & glycoprotein blood group markers of the ABO blood group system. Galactose is also part of disaccharide Lactose – produced in mammary glands during lactation.

D-Fructose

A ketohexose that is also known as Fruit sugar. The sweetest tasting sugar – found in fruit & honey in equal amounts with glucose.

Reactions of Monosaccharides

Oxidation to Acidic Sugars Oxidizing agents (Tollens & Benedict’s solutions) oxidize the aldehyde end to give an aldonic acid (carboxylic acid). A reducing sugar is a carbohydrate that gives a positive test with Tollens and Benedict’s solutions. Reduction to Sugar Alcohols



The carbonyl group in a monosaccharide (aldose or ketose) is reduced to a hydroxyl group using hydrogen as the reducing agent, producing a corresponding polyhydroxy alcohol – sugar alcohol. D-Glucitol = D-Sorbitol – used as moisturizing agent in foods & cosmetics & as a sweetening agent in chewing gum. Glycoside Formation Cyclic monosaccharides are hemiacetals, reacting with alcohols they form monosaccharide acetals known as glycosides. A glycoside is an acetal formed from a cyclic monosaccharide by replacement of the hemiacetal carbon –OH group with an –OR group. Glycosides exist in both α- & β-forms. Amino Sugar Formation Amino sugar is formed if 1 of the –OH groups of a monosaccharide is replaced with an amino group (–NH2). In the 3 common naturally occurring amino sugars (D-glucosamine, D-galactosamine & D-mannosamine) the C2 –OH group is replaced by an –NH2 group. Read Chapter 18 from Stoker – Sections: 18.8, 18.9, 18.10, 18.11, and 18.12.

Disaccharides

Contain 2 monosaccharide units joined via glycosidic linkage – is formed in a reaction between the –OH group of the hemiacetal C atom on 1 monosaccharide & an –OH group on the other monosaccharide. Disaccharides are crystalline & water soluble substances, which upon hydrolysis they produce monosaccharides.

D-Maltose

Is composed of 2 α-D-glucose units joined via α (1→4) glycosidic linkage & produced during starch breakdown in the digestive system. Hydrolysis of Maltose produces 2 D-glucose molecules – requires acidic conditions in the lab or enzyme Maltase in the digestive tract.

D-Lactose

Is composed of D-glucose + β-D-galactose joined via β (1→4) glycosidic bond. Hydrolysis of Lactose by acid or enzyme Lactase forms D-galactose & D-glucose molecules.

D-Sucrose

Is composed of α-D-glucose + β-D-fructose joined via α, β (1→2) glycosidic bond. It is the most abundant of all disaccharides found in plants – commercially produced from the juice of sugar cane or sugar beets. The enzyme Sucrase catalyzed hydrolysis of Sucrose to produce D-glucose & D-fructose. Read Chapter 18 from Stoker – Section: 18.13.

Oligosaccharides

Are carbohydrates that contain 3-10 monosaccharide units bonded via glycosidic linkages. Free oligosaccharides are less common than disaccharides in nature, as they are usually found associated with proteins & lipids in complex molecules. Raffinose & Stachyose are 2 naturally occurring oligosaccharides in onions, cabbage, broccoli, all types of beans & whole wheat. Humans lack the digestive enzymes necessary to metabolize raffinose or stachyose – they pass undigested into large intestine & are acted upon by bacteria producing discomfort & flatulence. Read Chapter 18 from Stoker – Section: 18.14.



Polysaccharides

Are polymers of many monosaccharide units bonded via glycosidic linkages, which do not taste sweet, unlike mono- & disaccharides. Distinctive features of Polysaccharides: 1. The identity of the monosaccharide monomer. Homopolysaccharide contains only 1 type of monomer. Heteropolysaccharide contains usually 2 types of monomers. 2. Length of polymer chain varies from few 100 monomer units to up to 1 million monomers. 3. Type of glycosidic linkage between monomers. 4. Degree of polymer chain branching

Starch

A homopolysaccharide of glucose that stores energy in plants (cereal grains, bread, pasta, potatoes, rice, corn, beans, peas, etc.). 2 types of polysaccharides isolated from starch: Amylose – a straight-chain glucose polymer, composed of 300-500 D-glucose units linked via α (1→4) glycosidic bonds. Amylopectin – a branched chain glucose polymer, composed of up to 100,000 D-glucose units linked via α (1→4) glycosidic bonds. Highly branched – a branch occurs every 25-30 glucose units & involves α (1→6) glycosidic bond. Amylose & Amylopectin have nutritional value for humans & can be hydrolyzed by the enzyme α-amylase in the digestive tract.

Glycogen

A homopolysaccharide of glucose that stores energy in humans & animals within skeletal muscles & liver. Structurally similar to Amylopectin, however glycogen is 3x more branched than Amylopectin.Contains up to 1,000,000 glucose units joined together by α (1→4) glycosidic bonds & α (1→6) glycosidic bond.

Cellulose

Linear structural homopolysaccharide of glucose monomers (up to 5,000 glucose units) joined via β (1→4) glycosidic bonds. The most abundant naturally occurring polysaccharide found in plant cell walls in the “woody” parts of plants (stems, stalks & trunks). Although a glucose polymer, cellulose is not a source of nutrition for humans, who lack the enzyme Cellulase that catalyses hydrolysis of β (1→4) glycosidic bonds in cellulose. Grazing animals (horses, cows, sheep) contain bacteria in their intestines that produce cellulase – can hydrolyse cellulose to glucose & these animals can use cellulose in grasses & other plants as a source of nutrition. Cellulose is the “dietary fibre” for humans – provides bulk to intestinal content, facilitates excretion of solid wastes & aids in formation of softer stools.

Chitin

Structurally identical to cellulose, except the monomer is N-acetyl-D-glucosamine (NAG), a derivative of glucose, linked via β (1→4) glycosidic bonds. The 2nd most abundant naturally occurring polysaccharide found in the exoskeletons of crabs, lobsters, prawns, insects & other arthropods.






Chapter 18

Chemical Connections: Lactose Intolerance & Lactase Persistence – p.625.

Chemical Connections: Changing Sugar Patterns: Decreases Sucrose, Increased Fructose – p.626.

Chemical Connections: Sugar Substitutes – p.628.

Chemical Connections: Blood Types & Oligosaccharides – p.633. Chemical Connections: Glycaemic Response, Glycaemic Index & Glycaemic Load –

p.642.

Additional Reading

The reading materials listed below are in addition to the texts recommended for the subject but will add further to the student’s understanding of the topics covered.

McMurray, JE, Ballantine, DS ,Hoeger, CA, & Peterson, VE 2013, Fundamentals of General, Organic and Biological Chemistry, 7th edn, Princeton Hall, USA.

http://www.visionlearning.com/library/module_viewer.php?mid=61

http://www.wisc-online.com/Objects/ViewObject.aspx?ID=AP13104


1 Define carbohydrates.

2 Outline the functions of carbohydrates.

3 Outline the classification of carbohydrates.

4 Discuss chirality, mirror images, chiral molecules, chiral centres, stereoisomers & optical

activity.

5 Define monosaccharides.

6 Discuss common monosaccharides.

7 Outline the difference between Fisher & Haworth forms of monosaccharides.

8 Discuss the reactions of monosaccharides.

9 Describe the 3 common disaccharides.

10 Outline oligosaccharides.

11 Discuss polysaccharides.

12 Outline the structure & function of starch, glycogen, cellulose & chitin.

Review Questions

Answer the relevant Exercises and Problems at the end of Chapter 18 in Stoker

http://www.visionlearning.com/library/module_viewer.php?mid=61




SESSION 12: An Introduction to the Structure and Function

of Lipids

Code: BIOB111

Learning outcomes


Session Aims:



Become familiar with the structure, properties, chemical reactions & function of the different types of lipid molecules.


Key Concept:

Lipids are fats and oils, waxes, steroids, cholesterol and fat soluble vitamins. Lipids vary considerably in structure and are soluble in non-polar solvents but not in water. They have many functions in the body such as storing energy, protecting and insulating internal organs, acting as chemical messengers, and components of cell membrane.

Session Overview

In this session students will be introduced to the chemistry of the lipids, which include fats & oils, phospholipids, cholesterol, bile acids, steroid hormones, eicosanoids & waxes.

The basis for the classification of lipids will be discussed. The triacylglcerols as the principle storage form of energy in the body and the role of phospholipids as constituents in membranes will be identified. The important sterols and their derivatives will be examined as will the relevance of prostaglandins as mediator of inflammation, pain and fever.

Session Topics

1. Structure & Function of Lipids

Types of Fatty Acids

Triacylglycerols – fats & oils

Chemical Reactions of Triacylglycerols

Phospholipids

Sphingolipids

Cholesterol



Cell Membrane Structure

Bile Acids

Messenger Lipids – Steroid Hormones & Eicosanoids

Biological Waxes

Waxes, Fats and Oils

Chemical Property of Triacylglycerols

Oxidation of Fats

Complex Lipids

Cell Membranes Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully. Textbook Location


Chapter 19: Lipids, pp. 654-698 – Sections: 19.1, 19.2, 19.3, 19.4, 19.6, 19.7, 19.8, 19.9, 19.10, 19.11, 19.12, 19.13, and 19.14.



Summary

Unlike carbohydrates, there are several different types of lipids, each with their distinctive structure, however the one property common to all lipids is their insolubility in water & solubility in non-polar solvents. The classification of lipids outlines the wide variety of different lipid molecules, their structure & function. The 5 categories of lipids include: Energy-storage lipids, Membrane lipids, Emulsification lipids, Chemical messenger lipids & Protective-coating lipids.

Fatty Acids

The physical properties of many lipids are determined by the presence of fatty acids in their structure. The fatty acids found in lipids may be saturated or unsaturated, depending on the presence of single or double bonds in their molecules, respectively. The number of double bonds in the fatty acid structure also plays a role – Monounsaturated fatty acids have 1 C=C bond, whereas Polyunsaturated fatty acids have 2 or more C=C bonds in their molecules. However in animal fats saturated fatty acids predominate & in vegetable oil unsaturated fatty acid are mainly found – the greater degree of unsaturation, the lower the melting point of the fatty acid – Figure 19.2, p.660. Nutritionally, the human body is able to synthesize all the fatty acids it needs with the exception of Essential Fatty Acids, which must be obtained from diet.

Triacylglycerols

These molecules are the principle storage form of energy in plants, animals & humans. The structure of Triacylglycerols is suggested in their name – 3 molecules of long-chain fatty acid residues are attached to 1 molecule of glycerol. The fatty acids in Triacylglycerols can all be



the same or different, producing simple or mixed Triacylglycerols. Animal fats & vegetable oils are a mixture of different Triacylglycerols. The important chemical reactions that Triacylglycerols undergo include – Hydrolysis, Saponification, Hydrogenation & Oxidation. Trans fatty acids are a common by-product of partial hydrogenation of plant oils to produce margarine & are implicated in the development of CVD. The cleansing action of soap & the formation of micelles are also explained in this section. Read Chapter 19 from Stoker – Sections: 19.1, 19.2, 19.3, 19.4, 19.6

Membrane Lipids

Cellular interior is separated from the surrounding environment by a cell membrane – Phospholipids, Sphingolipids & Cholesterol are important lipid components of cell membranes. These lipids, together with proteins, are responsible for the correct structure & function of all body cell membranes. Phospholipids are classed as Glycerophospholipids or Sphingophospholipids, depending on the platform molecule in their structure – glycerol or sphingosine, respectively. The general feature of Phospholipids is their amphipathic characteristic, meaning the same molecule has one part that is hydrophilic & another part with hydrophobic properties. This property of Phospholipids is important for their double layer arrangement in the cell membrane structure, so that the polar heads are in contact with water inside & outside the cell but the non-polar tails are hidden away from water in the core of the cell membrane. Sphingolipids are important components of the myelin sheath & the nervous tissue. Cholesterol is vital for the correct structure & function of cell membranes as well as a precursor to other Steroid molecules – bile acids & steroid hormones. Bile acids are able to emulsify dietary lipids in the aqueous environment of the digestive tract. Steroid hormones include Sex hormones, Mineralocorticoids & Glucocorticoids. Read Chapter 19 from Stoker – Sections: 19.7, 19.8, 19.9, 19.10, 19.11, 19.12

Eicosanoids

Are messenger lipids with hormone-like activity that are derived from Arachidonic acid (20:5) & have a profound physiological effect albeit their short life span. These molecules exert their effects locally, in the tissues where they have been synthesized. Eicosanoids are classed into 3 groups: Prostaglandins, Thromboxanes & Leukotrienes. Prostaglandins are involved with contraction & relaxation of smooth muscles, water & electrolyte balance, enhancing inflammation, pain & body temperature. Thromboxanes are produced by platelets (Thrombocytes) & initiate platelet aggregation & formation of a blood clot (Thrombus). Leukotrienes are generated by the white blood cells (Leukocytes) & promote inflammation & hypersensitivity (allergy) responses. Read Chapter 19 from Stoker – Section: 19.13.

Biological Waxes

Are monoesters of long-chain saturated fatty acid & a long-chain saturated or unsaturated alcohol. Commonly found in plants forming coating of fruits, leaves & stems to prevent water loss & damage from pests. However animals also produce waxes on their skin, fur or coat their feathers with waxy secretions to water-proof these structures.

Read Chapter 19 from Stoker – Section: 19.14.






Chapter 19

Chemical Connections: The Fat Content of Tree Nuts & Peanuts – p.666.

Chemical Connections: Fat Substitutes – p.668.

Chemical Connections: The Cleansing Action of Soap & Detergents – p.672.

Chemical Connections: Trans Fatty Acids Content of Foods – p.675.

Chemical Connections: Anabolic Steroid Use in Competitive Sports – p.691.

Chemical Connections: The Mode of Action for Anti-Inflammatory Drugs – p.694.

Additional Reading



http://wps.pearsoncustom.com/pcp_timberlake_chemistry_9_1491/36/9304/2381889.cw/index.html.

Basic concepts about lipids.

http://www.ausetute.com.au/lipids.html


13 Define Lipids.

14 Outline the differences between saturated & unsaturated fatty acids.

15 Define Monounsaturated & Polyunsaturated fatty acids.

16 Discuss the physical properties of fatty acids.

17 Define the Essential fatty acids & provide their names.

18 Define Triacylglycerols.

19 Outline the chemical reactions of Triacylglycerols.

20 Discuss the cleansing action of soap.

21 Describe the components & structure of Phospholipids & Sphingolipids.

22 Outline the importance of Cholesterol in the human body.

23 Discuss the importance of Lipoproteins & their function.

24 Outline the structure & function of Bile acids.

http://wps.pearsoncustom.com/pcp_timberlake_chemistry_9_1491/36/9304/2381889.cw/index.html


http://www.ausetute.com.au/lipids.html



25 Define Steroid hormones, giving examples.

26 Outline the classification of Eicosanoids, giving examples.

Review Questions




SESSION 13: An Introduction to the Structure and Function of Amino Acids

Code: BIOB111

Learning outcomes


Session Aims:



Become familiar with the structure, properties, chemical reactions & function of the different types of amino acid & protein molecules.


Key Concept:

Proteins are composed of 20 different amino acids. Each protein is composed of amino acids arranged in a specific sequence that determines the characteristics and biological function of protein. Proteins function as enzymes or hormones and are important in structure, transport, protection, and storage and muscle contraction.

Session Overview:

This session is designed to introduce the students to the chemistry of amino acids and proteins. The session will give the students an introduction to the amino acids, their structures and functions. Amino acids, as the building blocks of proteins, are discussed in terms of their unique structure, properties & ability to bond together via peptide bonds into a protein chains Information gained in this session is an absolute requirement in order that students can understand both the anabolic and catabolic processes involved in protein metabolism in future sessions.

Session Topics

General Structure of Amino Acids

Buffering ability of amino acids

Characteristics of Proteins

Structure of Amino Acids

Classification of Amino Acids

Essential Amino Acids

Chirality of Amino Acids

Acid-Base Properties of Amino Acids



Zwitterions

The Unique Feature of the Amino Acid Cysteine

Formation of Peptides

Peptide Bond

Direction of a Peptide Chain

Important Small Peptides

General Structure of Proteins

Protein Classification

Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that you understand what is expected of you to complete this subject successfully. Textbook Location


Chapter 20: Proteins, pp. 707-747 – Sections: 20.1, 20.2, 20.3, 20.4, 20.5, 20.6, 20.7, 20.8, and 20.9.



Summary

Introduction to Proteins

Proteins are the most diverse group of bio-molecules, ranging from small peptides (glutathione) to large proteins (haemoglobin), from water-soluble proteins (insulin) to water-insoluble proteins (collagen). Proteins have a multitude of functions in the human body, including structural protein, contractile proteins, transport proteins, storage protein, protection proteins, enzymes & hormones, just to name a few.

Amino Acids

Amino acids, the building blocks of proteins, are joined together via peptide bonds to produce the protein chain of desired length. There are 20 different standard amino acids found in proteins – in each protein these amino acids are arranged in a specific sequence, unique for that specific protein, which determines the characteristics & biological function of proteins. Table 20.1, p.709 – shows the structures of the 20 standards amino acids & although it is not required to know the structure of each of these amino acids, students should be able to understand the classification of amino acids into polar & non-polar, based on the structure of the side groups (R-groups). Nutritionally, the human body is not able to synthesize all 20 standard amino acids it needs to produce proteins, therefore the amino acids that must be obtained from diet are known as Essential Amino Acids.



Dietary proteins are classified into complete & incomplete proteins based on the content of these essential amino acids. Complete proteins contain all essential AAs in the relative amount required by the body & usually come from animal dietary sources & soy. Incomplete proteins do not contain adequate amount of 1 or more essential AAs, relative to the body’s needs & usually come from plant sources & gelatin. Amino acids are chiral molecules, meaning they form D- & L-isomers. The majority of AAs found in nature & in proteins are L-isomers. Due to the presence of carboxyl & amino functional groups, AAs have the ability to act as both, acids & bases, depending on the pH of the environment they are placed in – this feature is important for the human physiology, as proteins are acting as buffers. Cysteine is a very unique AA, containing the –SH (sulfhydryl group), being able to form dimmers with another Cysteine molecule – this reaction produces disulfides, which are vital to maintain the proper structure of proteins. Read Chapter 20 from Stoker – Sections: 20.1, 20.2, 20.3, 20.4, 20.5, 20.6

Peptides

Peptide is an unbranched chain of amino acids held together by amide linkages, which have in proteins are known as Peptide Bonds. As the AAs are joined together to form peptides, the growing peptide chain has a direction – N-terminal contains a free amino group & C-terminal contains a free carboxyl group – the sequence of AAs in the protein is, by convention, read from the N-terminal to the C-terminal. Some peptides are very small – the endogenous antioxidant molecule glutathione is formed from only 3 AAs & is classified as a tripeptide. Another small peptide is the artificial sweetener Aspartame, which is formed from the AAs Phenylalanine & Aspartic acid. Read Chapter 20 from Stoker – Sections: 20.7, 20.8, 20.9

. Pre / Post class readings




Chapter 20

Additional Reading






27 Define Proteins.

28 Discuss the general structure of Amino Acids.

29 Outline the classification of Amino Acids.

30 Define Essential Amino Acids.

31 Discuss the complete & incomplete proteins.

32 Outline the chirality of Amino Acids & their predominant isomer found in nature.

33 Discuss the Acid-Base properties of Amino Acids.

34 Define Zwitterion.

35 Outline the chemical reactions of Amino Acids in acidic & alkaline solutions.

36 Discuss the unique properties of Cysteine.

37 Define Peptide, Dipeptide, Tripeptide, Oligopeptide & Polypeptide.

38 Outline the formation of Peptide Bond.

39 Describe the direction of a peptide chain.

40 Outline 3 biologically important small peptides.

41 Discuss the general structure of proteins.

42 Outline the classification of proteins

Review Questions




SESSION 14: An Introduction to the Structure and Function of Proteins

Code: BIOB111

Learning outcomes

Illustrate & analyse the chemical nature of major biochemical groups, including carbohydrates, lipids, proteins, enzymes & nucleic acids..

Session Aims:



Become familiar with the 4 levels of protein structure, protein hydrolysis, and protein denaturation as well as structural & functional classification of proteins.


Key Concept:

Proteins are composed of 20 different amino acids. Each protein is composed of amino acids arranged in a specific sequence that determines the characteristics and biological function of protein. Proteins function as enzymes or hormones and are important in structure, transport, protection, and storage and muscle contraction.

Session Overview:

This session is designed to introduce the students to the chemistry of proteins. The session will give the students an introduction to the chemical structure and functions of proteins. The different types of proteins and their functions in the body are discussed. Different structural levels of proteins are discussed in relation to their biological function. Denaturation and hydrolysis of proteins are also explained. Information gained in this session will help students to understand both the anabolic and catabolic processes involved in protein metabolism in future sessions and gain an overall picture of the diverse role that proteins play in the human body. Students will also gain an understanding of how malfunction of proteins can lead to diseased states.

Session Topics

Types of proteins and their functions

General Structure of Proteins

Primary, Secondary, Tertiary & Quaternary Structure of Proteins

Protein Hydrolysis

Protein Denaturation

Structural Classification of Proteins

Fibrous & Globular Proteins



Functional Classification of Proteins

Glycoproteins & Lipoproteins

Formation of the peptide bond

Types of agents which denature proteins Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and

Assessment Tasks for the Subject of Study. Make certain that you understand what is

expected of you to complete this subject successfully.

Textbook Location


Chapter 20: Proteins, pp. 707-747 – Sections: 20.9, 20.10, 20.11, 20.12, 20.13, 20.14, 20.15, 20.16, 20.17, 20.18, 20.19



Summary

General Structural Characteristics of Proteins

Proteins are classified into monomeric & multimeric, depending on the number of peptide chains in their structure, one or more, respectively. Simple proteins contain only peptides, whereas conjugated proteins also contain a non-amino acid prosthetic group as part of their structure.

Primary Structure of Proteins

Every protein found in nature & in the human body has its own unique sequence of AAs, which denotes the primary structure of the protein chains. The number, type & order of attachment of the AAs in the protein are important for its primary structure & it is dictated by the information stored in the cell’s DNA – this topic is discussed in future sessions.

The primary structure of a specific protein is always the same regardless of where the protein is found within an organism. The structures of certain proteins are even similar among different species – see Chemical Connections 20-A, p. 722 for comparison between human, bovine & porcine insulin. The functional differences between the two peptide hormones oxytocin and vasopressin are an example of a small change causing different functions or biological actions. The genetically inherited disease sickle cell anaemia is another example of altered functional capacity of a protein as a result of an amino acid change. Read Chapter 20 from Stoker – Sections: 20.9, 20.10.

Secondary Structure of Proteins

Refers to the arrangement of the primary protein structure in space due to hydrogen bonds formed between peptide bonds in the protein backbone. The 2 types of secondary protein structure are known as Alpha-Helix & Beta-Pleated Sheet.



-Helix has the shape of a coiled spring with R-groups positioned outside of the helix.

-Pleated Sheet is formed between 2 protein chain segments of the same or different molecules side by side linked by hydrogen bonds.

A single protein molecule may contain -helical segments, -pleated sheet segments & unstructured segments within their structure. Read Chapter 20 from Stoker – Section: 20.11.

Tertiary Structure of Proteins

Is formed by interactions between the side chains of the amino acids in the peptide molecule, resulting in a more complex 3-D arrangement of the protein in space. There are 4 different types of interactions that maintain the tertiary arrangement of proteins, including: Disulfide bonds – formed between 2 Cysteine AAs in the protein, the strongest interaction. Electrostatic interactions (Salt Bridges) – between acidic & alkaline R-groups. Hydrogen bonds – between polar R-groups. Hydrophobic attractions – between non-polar R-groups. Read Chapter 20 from Stoker – Section: 20.12.

Quaternary Structure of Proteins

Is the highest level of protein organization but is only relevant for multimeric proteins with 2 or more peptide chains in their structure. Usually an even number of peptide chains is present in these proteins – 2 chains from a dimmer, 4 chains form a tetramer etc. – these protein subunits are held together mainly by hydrophobic interactions between R-groups, however hydrogen bonds & electrostatic interactions are also involved in the maintenance of the quaternary protein structure. Read Chapter 20 from Stoker – Section: 20.13.

Protein Hydrolysis

Is the reverse chemical reaction to dehydration synthesis (peptide bond formation). Hydrolysis leads to the breakdown of the peptide bond, while the amino & carboxyl groups are regenerated & the protein splits into smaller peptides & AAs. This process is vital for the digestion of dietary proteins & involves digestive enzymes that catalyze protein hydrolysis & the breakdown of the peptide bond to liberate free AAs, so they can be absorbed into the bloodstream & transported to body cells for synthesis of new proteins.


Protein Denaturation

Refers to the disruption of the protein’s characteristic 3-D quaternary, tertiary & secondary structures, while the primary structure is not affected. As function depends on structure, denaturation leads to partial or complete loss of function. Small denaturation changes can be reversed & the protein can “re-fold” = Renaturation. However major denaturation changes are irreversible, leading to precipitation of proteins out of solution & their coagulation.



Heat is the major denaturation agent, closely followed by pH changes – both of these factors are important for correct protein digestion. Read Chapter 20 from Stoker – Section: 20.15.

Structural Classification of Proteins

Based on molecular shape determined by tertiary & quaternary structures, proteins are classified into Fibrous, Globular & Membrane proteins. Fibrous proteins are elongated, water-insoluble & play an important role in structure, support & protection – Keratin & Collagen are examples of fibrous proteins. Globular proteins are spherical, water-soluble & play an important role in metabolism, enzyme function, transport & regulation – Myoglobin & Haemoglobin are examples of globular proteins. Read Chapter 20 from Stoker – Section: 20.16.

Functional Classification of Proteins

Based on the vast diversity of functions that proteins perform in the body proteins are classified into Catalytic proteins (Enzymes), Defence proteins (Immunoglobulins), Transport proteins (Haemoglobin), Messenger proteins (Insulin), Contractile proteins (Actin & Myosin), Structural proteins (Collagen), Trans-membrane proteins (Ion channels), Storage proteins (Ferritin), Regulatory proteins (Receptors) & Nutrient proteins (Casein), just to name a few. Read Chapter 20 from Stoker – Section: 20.17.




Chapter 20

Chemical Connections: “Substitutes” for Human Insulin – p.722.

Chemical Connections: Denaturation & Human Hair – p.734.

Chemical Connections: Protein Structure & the Colour of Meat – p.738. Chemical Connections: Lipoproteins & Heart Disease Risk – p.746.

Additional Reading




McMurray, JE, Ballantine, DS ,Hoeger, CA, & Peterson, VE 2013, Fundamentals of General, Organic and Biological Chemistry, 7th edn, Princeton Hall, USA


1. Describe in detail the Primary Structure of Proteins.

2. Describe the 2 types of Secondary Structure of Proteins & the interactions involved.

3. Describe in detail the Tertiary Structure of Proteins & the interactions involved.

4. Describe in detail the Quaternary Structure of Proteins.

5. Explain the process of Protein Hydrolysis, contrasting the different conditions required

for this process in a laboratory setting & in the living human body.

6. Describe the process of Protein Denaturation, naming 3 denaturing agent & explain how

they are involved in denaturation.

7. Outline the difference between fibrous & globular proteins, giving examples.

8. Describe at least 5 functions proteins perform in the human body.

9. Outline the structure of Glycoproteins, giving examples.

10. Outline the structure of Lipoproteins, giving examples.

Review Questions




SESSION 15: Enzymes and Co-Enzymes

Code: BIOB111

Learning outcomes


#5. Analyze the chemical nature of the major biochemical groups of carbohydrates, lipids, proteins and nucleic acids.

Session Aims:



Understand the structure, nomenclature, properties, function & of enzymes.


Key Concept:

The chemical reactions that happen in the body are catalyzed by enzymes. Every enzyme catalyses the reaction on demand and turns off reactions when the products are not needed. Some enzymes require organic molecules or metal ions for their action.

Session Overview:

This session is a continuation from amino acids and proteins. Enzymes are a large class of

proteins, their structure and function are of particular relevance once students begin to study

metabolism. Here they learn how the structure of the previous lesson impacts on the function

of an enzyme and how various mechanisms of activity, regulation and inhibition allow them to

carry out their functions.

Session Topics

2. Structure & Function of Enzymes

General Characteristics of Enzymes

Enzyme Structure

Enzyme Nomenclature

Enzyme Function

Enzyme Specificity

Factors Affecting Enzyme Activity

Enzyme Inhibition

Regulation of Enzyme Activity



Drugs Inhibiting Enzyme Activity

Medical Uses of Enzymes

Vitamins as Coenzymes


Textbook Location


Chapter 21: Enzymes & Vitamins, pp. 754-791 – Sections: 21.1, 21.2, 21.3, 21.4, 21.5, 21.6, 21.8, 21.9, 21.10, 21.11



Summary

In this session, we looked at some of the functional and regulatory aspects of enzymes. It is important to bear in mind that enzymes are proteins and conform to all the physical properties of proteins. The primary structure determines how the enzyme will fold in terms of secondary and tertiary structures. It also means that enzymes, like all other proteins, can be inactivated and denatured as discussed in the previous chapter.

General Characteristics of Enzymes

Enzymes are usually globular proteins, although some enzymes, participating in biochemical reactions involving nucleic acids, are composed of RNA. Enzymes therefore undergo all the reactions of proteins, including denaturation due to pH or temperature changes. Each cell in the human body contains 1,000s of different enzymes as every reaction in the cell requires its own specific enzyme. Enzymes are most efficient catalysts known (increase the reaction rate by up to 1020 times, compared to non-enzymatic catalysts that increase reaction rate by 102 – 104 times).

Enzyme Structure

Depending on their structure enzymes are classified as simple (composed only of protein) or conjugated (composed of a protein part – apoenzyme & a non-protein part – cofactor). Cofactors are either small organic molecules or inorganic ions (usually metals Zn2+, Mg2+, Mn2+ & Fe2+) & provide additional chemically reactive functional groups besides those present in the AAs of the apoenzyme. Coenzyme is a small organic molecule, acting as a cofactor in a conjugated enzyme – many B vitamins – this will be discussed in later sessions on Bioenergetics.



Nomenclature of Enzymes

Enzymes are named according to the type of reaction they catalyse and/or their substrate – the reactant, upon which the specific enzyme acts. An enzyme is denoted with a suffix –ase (lactase), however some digestive enzymes that have been among the 1st ones to be studied, have the suffix –in (pepsin). Enzymes can also be named according to the type of reaction they catalyse, using the reaction name as prefix (oxidase). The names of the substrate & the chemical reaction are often used together to identify a specific enzyme (pyruvate carboxylase). Read Chapter 21 from Stoker – Sections: 21.1, 21.2, 21.3

Models of Enzyme Action

There is a specific portion of an enzyme, to which the substrate binds while it undergoes the chemical reaction – enzyme active site. The active site is a 3-D ‘crevice-like’ cavity formed by secondary & tertiary structures of the protein part of the enzyme. When a substrate binds to the enzyme active site an Enzyme-Substrate Complex is formed temporarily, enabling the substrate to undergo its chemical reaction much faster. There are 2 recognised models of enzyme action: Lock & Key Model The active site is fixed, with a rigid shape (LOCK) & the substrate (KEY) must fit exactly into it (complementary shape & geometry). Upon completion of the chemical reaction, the products are released from the active site, so the next substrate molecule can bind. Induced Fit Model In reality enzymes are not rigid but more flexible & constantly change their shape. Therefore the shape of the active site changes to accept & accommodate the substrate (like a glove changes shape when a hand is inserted into it).

Enzyme Specificity

Enzymes exhibit different levels of selectivity or specificity for their substrates. Absolute specificity – the enzyme catalyse a particular reaction for only 1 substrate (urease). Group specificity – the enzyme acts on similar substrates with a specific functional group (hexokinase). Linkage specificity – the enzyme acts on a particular chemical bond (phosphatase). Steroeochemical specificity – the enzyme can distinguish between stereoisomers (L-amino acid oxidase). Read Chapter 21 from Stoker – Sections: 21.4, 21.5.

Factors Affecting Enzyme Activity

Enzyme activity is measure of the rate, at which enzyme converts substrate to products in a biochemical reaction. There are 4 factors affecting enzyme activity: Temperature – with increased temperature the reaction rate increases however enzymes exhibit their maximum activity at an optimum temperature, which for the human body is 370C. If temperature increases beyond this point, the enzyme’s tertiary structure changes, inactivating & denaturing it.



pH – enzymes exhibit their maximum activity at an optimum pH, which for most enzymes is a very narrow range. Small changes in pH (low or high) can result in enzyme denaturation & loss of its function. Each enzyme in the human body has its characteristic optimum pH. Substrate concentration – increasing substrate concentration, while enzyme concentration is kept constant, increases reaction rate to a saturation point, at which the enzyme works at its maximum capacity. Enzyme concentration – increasing enzyme concentration, while substrate concentration is kept constant, increases reaction rate in a direct proportion. Read Chapter 21 from Stoker – Section: 21.6.

Enzyme Inhibition

Is the ability of a substance to slow down or stop the normal catalytic function of an enzyme, by binding to it. There are 3 types of inhibition: Reversible Competitive Inhibition – involves a competitive inhibitor, which resembles the substrate & competes with it by binding to enzyme active site. This inhibition can be reversed, by increasing the substrate concentration. Reversible Non-Competitive Inhibition – involves a non-competitive inhibitor, which binds to an enzyme site, other than active site & alters the enzyme tertiary structure, including the active site, thus decreasing the enzyme activity. This inhibition can be reversed, by decreasing the concentration of the non-competitive inhibitor. Irreversible Inhibition – involves an inhibitor permanently binding to the enzyme active site by a strong covalent bond, completely deactivating the enzyme. Read Chapter 21 from Stoker – Section: 21.8.

Regulation of Enzyme Activity

Allosteric enzymes – are composed of 2 or more protein chains & have 2 or more binding sites – one is the enzyme active site & the other one is a regulatory site, to which a regulator molecule attaches. Positive regulator up-regulates, whereas negative regulator down-regulates enzymatic activity. 3 mechanisms are utilized by the cells to regulate enzyme activity: Feedback control – the process, in which activation or inhibition of the 1st reaction in a reaction sequence, is controlled by a product of this reaction sequence. Proteolytic enzymes & Zymogens – proteolytic enzymes are produced in an inactive form (zymogens), which are then activated at the right time & place, to prevent destruction of the tissues that produced them. Covalent modification – is the process of altering enzyme activity by covalently modifying the structure of the enzyme via adding / removing a group to / from the enzyme. Read Chapter 21 from Stoker – Section: 21.9.

Medical Uses of Enzymes

Many prescription drugs function as enzyme inhibitors – ACE inhibitors, Sulfa drugs & Penicillins. Other enzymes are used in diagnosis or treatment of certain diseases – lactate dehydrogenase, plasminogen, and urease. Read Chapter 21 from Stoker – Sections: 21.10, 21.11.




In this subject the material is taught from the perspective that the students have no prior knowledge in the field. In this regard there is no compulsory pre-reading associated with this subject. The reading material that the students are directed to can be used either as pre-reading or post-reading dependent on the students individual study requirements.


Chapter 21

Chemical Connections: Enzymatic Browning: Discoloration of Fruits & Vegetables – p.760.

Chemical Connections: H. pylori & Stomach Ulcers – p.764.

Chemical Connections: Enzymes, Prescription Medications & the “Grapefruit Effect” – p.777.

Additional Reading


http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__enzyme_action_and_the_hydrolysis_of_sucrose.html


11. Describe the nature of enzymes, general characteristics & their function as catalysts.

12. Discuss the enzyme structure – simple & conjugated enzymes.

13. Distinguish between cofactor & coenzyme, giving specific examples.

14. Outline the nomenclature of enzymes.

15. Explain the 2 models of enzyme action.

16. Outline the 4 different levels of enzyme specificity.

17. Describe how the 4 factors (temperature, pH, substrate & enzyme concentrations) affect

enzyme activity, giving specific examples.

18. Explain the 3 types of enzyme inhibition, giving specific examples.

19. Define allosteric enzymes.

20. Outline the principle of feedback control.

21. Discuss the relationship between zymogens & proteolytic enzymes, giving specific

examples.

22. Outline the covalent modification of enzymes, giving specific examples.

23. Describe the medical uses of enzymes, giving specific examples






Review Questions


SESSION 16: Biochemical Nature of the Cell Membrane

Code: BIOB111

Learning outcomes from BIOB111 SO



Session Aims:




Key Concept:

The plasma membrane encloses every cell. It defines the cell's boundary, and provides a barrier which differentiates between an intracellular environment, and the external environment. The existence of the cell membrane allows the cell to maintain concentration and electrochemical gradients and therefore in many ways defines the function of the cell.

Session Overview:

Without the development of the plasma membrane, cellular life is impossible .So far, students have studied the structure and function of three macromolecules of the body - carbohydrates, lipids and proteins. In this session, they will learn how these macromolecules (lipids and proteins) interact with each other to form what we know as the cell or plasma membrane and how they enable the membrane to carry out its functions

Session Topics

Structure of glycerophospholipids, cholesterol, and glycolipids

Membrane fluidity

Selective Permeability

Arrangement of membrane proteins



Glycocalyx


Textbook Location


Timberlake, KC 2010, General, Organic and Biological Chemistry, 3rd edn, Pearson, San Francisco. o Chapter 17

Tortora, GJ & Derrickson, B 2012, Principles of Anatomy and Physiology, 13th edn, John Wiley and Sons, USA. Use Topic headings to find page numbers in 11th /12th ed., Chapter 3. Topic: Membrane structures & the glycocalyx

Summary

Without the development of the plasma membrane, cellular life is impossible. The plasma membrane encloses every cell; it defines the cell's boundary, and provides a barrier which differentiates between an intracellular environment, and the external environment. The existence of the cell membrane allows the cell to maintain concentration and electrochemical gradients and therefore in many ways, defines the function of the cell. So far you have studied the structure and function of 3 macromolecules of the body - carbohydrates, lipids and proteins. In this session, you will learn how these macromolecules combine to form what we know as the cell or plasma membrane and how they enable the membrane to carry out its functions. Cell Membrane Structure In order to understand the function of the cell membrane it is important that you are able to describe the composition of the membrane bi-layer. Cell membranes are semipermeable structures which create a barrier between the internal environment of a cell and its external environment. They are described using a fluid mosaic model. Cell membranes are composed of a glycerophospholipid bi layer which is studded with proteins, glycoproteins, glycolipids, and cholesterol hence the term mosaic. The term fluid relates to the fluidity of the membrane preventing lipids from packing tightly and crystallising.

Read Section 19.10 ‘Cell Membranes’

Read section ‘The Plasma Membrane’ on page 675 and ‘The Lipid Bilayer’ on page 676 of Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn,

Arrangement and Function of Membrane Proteins Because of the arrangement of the lipid bi layer, the cell membrane is permeable to small non polar substances, such as O2, CO2, lipid soluble hormones and vitamins, and some polar substances such as water and urea.



Charged ions and large molecules such as glucose are not permitted through the cell membrane. It is the function of transmembrane proteins to act as channels and transporters of various molecules required by the cell, but not able to cross the cell membrane.

Read Sections ‘Arrangement of Membrane Proteins’, ‘Functions of Membrane Proteins’, ‘Membrane Permeability’ and ‘Gradients across the plasma

Transport across the Plasma Membrane We have just seen that proteins embedded within the cell membrane can function to transport substances across the membrane. These processes include diffusion through ion channels, osmosis, facilitated diffusion, and active transport.

Read Section ‘Transport across the Plasma Membrane’ on pages 678 of Stoker, HS 2014, General, Organic and Biological Chemistry, 7th

Information on ‘Transport in Vesicles’ is not required. Glycocalyx We know that cell membranes have carbohydrate moieties attached to membrane proteins or lipids (glycolipids and glycoproteins). These carbohydrate moieties principally galactose and/or glucose face to the exterior of the cell and form a sugary coating known as a glycocalyx. The glycocalyx can function in areas of cell recognition and forms the basis of our ABO blood typing system.


In this subject the material is taught from the perspective that the students have no prior knowledge in the field. In this regard there is no compulsory pre-reading associated with this subject. The reading materials, that the students are directed to, can be used either as pre-reading or post-reading dependent on the students individual study requirements.

Additional Reading







1. Using the description of a cell membrane as a “fluid mosaic model”, discuss the function of the membrane, and how it is able to carry out those functions.

2. Discuss the term semi-permeable and show why a cell membrane is said to be semi-permeable.

3. What is a concentration gradient and how is it achieved? 4. What are the functions of membrane proteins? 5. How do membrane proteins transport substances?



SESSION 17: Nucleic Acids – Structure, DNA Replication

Code: BIOB111



#6. Describe processes associated with DNA replication and protein synthesis and the types

of nucleic acids associated with these outcomes. #7. Recognize the major biochemical pathways and how they relate to health & disease

states.

Session Aims:



Become familiar with the structure, properties & function of the 2 types of nucleic acids


Key Concept:

Nucleic acids are large molecules found in the nucleus of the cell that store information and direct activities for cellular growth and reproduction. Every time the cell divides the genetic information is passed on to the new cell which is accomplished by DNA replication process. Genes are sections of DNA that contain the information to make a protein.

Session Overview:

This session is designed to introduce the students to the structure and function of nucleic acids - DNA and RNA. Nucleic acids make up the fourth type of macromolecule of the body (carbohydrates, lipids and proteins have been already covered). They serve as a code from which cellular growth and function are controlled. Nucleotides are found primarily as the monomeric units comprising the major nucleic acids of the cell.

Our genetic code is stored on chromosomes which need to be replicated during cell division. This session will focus on the structure of nucleic acids and their replication. This topic is taught and assessed to the detail given in the set text

Session Topics

Types of Nucleic Acids

Chromosomes

Nucleotides

Nucleosides

Structure of Nucleic Acids



Primary Structure of Nucleic Acids

Secondary Structure of DNA

DNA Double Helix

Complementary Base Pairing

DNA Replication

RNA

Secondary Structure of RNA

Types of RNA


Textbook Location


Chapter 22: Nucleic Acids, pp. 798-839 – Sections: 22.1, 22.2, 22.3, 22.4, 22.5, 22.6, 22.8.



Summary:

Introduction to Nucleic Acids

Nucleic acids (NAs) are found in the nucleus of a cell & have acidic properties. There are 2 types of NAs – DNA (deoxyribonucleic acid) & RNA (ribonucleic acid) – where DNA stores the hereditary information required for protein synthesis & RNA is directly involved in protein synthesis within the cell.

Nucleotides

Both NAs are polymers of nucleotides, which in turn consist of 3 parts. Nitrogen-containing base – heterocyclic amines, derived from 2 structures (pyrimidine & purine). There are 3 derivatives of pyrimidine (thymine, cytosine, and uracil) & 2 derivatives of purine (adenine & guanine). Pentose monosaccharide – ribose & deoxyribose – found in RNA & DNA respectively. Phosphate group – is the hydrogen-phosphate ion, derived from phosphoric acid. Nucleoside is the combination of a base & a sugar, whereas a Nucleotide contains all 3 components (base, sugar & phosphate). Read Chapter 22 from Stoker – Sections: 22.1, 22.2, 22.3



Structure of Nucleic Acids

Just like proteins, NAs have both, a primary & secondary structure. The primary structure of both NAs is the sequence of nucleotides & is usually divided into 2 parts – phosphate-sugar backbone & nitrogen bases attached to the sugar parts of the backbone. The sequence of bases attached to the backbone is variable & determines the primary structure of NAs. It is important to understand, that the strand of primary structure has a direction – 5’ end carries a free phosphate group & 3’ end carries a free –OH group on the sugar unit. By convention the sequence of bases on a NA strand (DNA or RNA) is read from the 5’ end to the 3’ end.

Secondary Structure of DNA

The secondary structure of DNA takes the shape of a double helix, in which 2 strands of DNA in their primary structure are wound up around each other like a spiral staircase (imagine the phosphate-sugar backbones forming the banisters of this staircase), running in an anti-parallel direction. The bases of both strands extend inwards towards the bases of the other strand & are bonded together via hydrogen bonds. As the interior of the DNA double helix is small, there is always 1 large purine base linked together to 1 small pyrimidine base via hydrogen bonds – there is always adenine opposite thymine & guanine opposite cytosine – these bases are referred to as complementary base pairs. Read Chapter 22 from Stoker – Sections: 22.4, 22.5.

DNA Replication

Is the process, taking place in the nucleus, in which DNA produces an exact duplicate of itself using the principle of complementary base pairing – the parent DNA molecule divides & produces 2 daughter DNA molecules, each containing 1 strand from the parent & 1 newly synthesized strand. Both of the daughter DNA molecules are identical to the parent DNA. Replication starts with the enzyme DNA-helicase unwinding the double helix & breaking the hydrogen bonds between the bases – this generates a “replication fork”, as the 2 parent strands are separating & becoming a template for the new strand to be synthesized. Following the separation of the strands, free nucleotides found in the nucleus can now pair up with the complementary bases on the separated strand & form new hydrogen bonds. The enzyme DNA-polymerase checks if the base pairing is correct & joints the new bases to a new backbone. The Leading strand is synthesized continuously, whereas the Lagging strand is synthesized in short segment (Okazaki fragments) with gaps between them, which are joined together by the enzyme DNA-ligase. Read Chapter 22 from Stoker – Section: 22.6.

Ribonucleic Acids

There are 4 major differences between DNA & RNA. In a living cell there are 5 different types of RNA, however in this module, only 3 types will be considered. Messenger RNA (mRNA) – carries the genetic information from the DNA in the nucleus to the site of protein synthesis in the cytoplasm. Ribosomal RNA (rRNA) – combines with specific proteins & forms ribosomes = the site of protein synthesis. Transfer RNA (tRNA) – transport amino acids to the site of protein synthesis (ribosomes).







Chapter 22

Chemical Connections: Antimetabolites: Anticancer Drugs than Inhibit DNA Synthesis – p.813.

Chemical Connections: Antibiotic Protein Synthesis Inhibitors – p.831.

Additional Reading


http://www.wiley.com/college/boyer/0470003790/animations/animations.htm

http://www.hhmi.org/biointeractive/dna/animations.html


24. Define the 2 types of nucleic acids.

25. Outline the structure of chromosomes.

26. Define the monomers of nucleic acids.

27. Discuss the 3 components of nucleotides.

28. Describe the structure of nucleosides.

29. Define the structure of nucleotides.

30. Outline the primary structure of nucleic acids, including the backbone & direction.

31. Discuss the secondary structure of DNA.

32. Outline the principle of complementary base pairing.

33. Describe the process of DNA replication in detail.

34. Outline the differences between DNA & RNA.

35. Discuss the 3 types of RNA.

http://www.wiley.com/college/boyer/0470003790/animations/animations.htm

http://www.hhmi.org/biointeractive/dna/animations.html



Review Questions




SESSION 18: Nucleic Acids – Protein Synthesis

Code: BIOB111



#6. Describe processes associated with DNA replication and protein synthesis and the types

of nucleic acids associated with these outcomes. #7. Recognize the major biochemical pathways and how they relate to health & disease

states.

Session Aims:



Become familiar with the function of nucleic acids in protein synthesis.


Key Concept:

Genes are sections of DNA that contain the information to make a protein. This information is copied from the gene in DNA to make messenger RNA (mRNA), a process called transcription. The mRNA moves out of the nucleus into the cytoplasm where they combine with ribosomes and translate the information into a protein with the help of tRNA.

Session Overview:

This session is designed to give the students an introduction to protein synthesis - transcription and translation. They will also learn how the different types of antibiotics work in inhibiting stages of protein synthesis and be introduced to applications of genetic engineering.

Session Topics

Viruses

Transcription – RNA Synthesis

Gene

Splicing

Nucleosides

Translation – Protein Synthesis

Genetic Code

Anticodons & tRNA

Mutations



Mutagens

Recombinant DNA & Genetic Engineering

Polymerase Chain Reaction

Viruses


Textbook Location


Chapter 22: Nucleic Acids, pp. 798-839 – Sections: 22.7, 22.9, 22.10, 22.11, 22.12, 22.13, 22.15, 22.16.



Summary

Protein Synthesis Overview

Protein synthesis within body cells is under the direction of DNA & occurs in 2 phases – transcription (RNA synthesis) & translation (protein synthesis).

Transcription

Is the process by which DNA directs the synthesis of mRNA (rRNA & tRNA are produced in the same way). Only 1 strand of DNA molecule is transcribed. The enzyme RNA-polymerase unwinds a portion of DNA double helix exposing one particular gene, which contains an Initiation signal & Termination signal – these are recognised by the enzyme as Start & Stop, respectively. A gene is a DNA segment, containing the base sequence for the production of a specific RNA molecule & is composed of exons (coding sequences) & introns (non-coding sequences). After transcription is complete, the mRNA transcript is spliced, utilizing enzymes that excise introns & keep only exons, producing a mature mRNA molecule. Read Chapter 22 from Stoker – Sections: 22.7, 22.9.

Translation

Is the process by which the information encoded in a mRNA molecule is deciphered & used to synthesise a specific protein molecule – now the mRNA becomes a template itself, onto which the information written in the form of nucleotides is translated into the amino acid sequence, forming a specific protein. Each amino acid in the protein molecule has a corresponding 3-nucleotide sequence in the mRNA, known as the Codon – this correspondence is the genetic code.



The Genetic Code is universal – (the same codon specifies the same AA in a cell of all living organisms) & highly degenerate (meaning that some amino acids are coded for by more than 1 codon). The initiation & termination codons exist: Start codon = AUG (codes for Met) & 3 Stop codons = UAA, UAG & UGA (do not code for any amino acid). The translation process involves also tRNA molecules, as amino acid carriers – all tRNA molecules have a general structure, which contains a 3’ end (amino acid binds here) & a loop, which contains Anticodon (a sequence of 3 nucleotides, complementary to the Codon). Proteins synthesis takes place within the ribosomes & involves several steps: Activation of tRNA – a specific AA binds onto the 3’end of its specific tRNA via ester bond forming an activated tRNA molecule. Initiation – the mRNA attaches to small ribosomal unit with its 1st codon (Initiation codon AUG), the activated tRNA molecule, with its complementary anticodon (UAC), attaches to the AUG codon & the large subunit of ribosome completes the initiation. Elongation – the codon next to AUG is read & specific tRNA with a complementary anticodon binds to it. Now there are 2 AA next to each other & the enzyme peptidyl transferase links them with a peptide bond, forming a dipeptide. The ribosome moves along the mRNA molecule via translocation & reads the next codon. Termination – when the ribosome reads one of the 3 “STOP” codons, no more AAs can be added, the protein is cleaved from the last tRNA molecule & the ribosomal subunits separate. Many ribosomes move simultaneously along a single mRNA & many identical proteins are synthetised at the same time from 1 single mRNA – energy efficient process. The complex of mRNA & several ribosomes is called Polysome. Read Chapter 22 from Stoker – Sections: 22.10, 22.11, 22.12

Mutation

Is an error in base sequence of a gene, that alters the DNA structure, which is reproduced during replication of DNA & passed on during transcription onto mRNA, altering the function of the resulting protein with potentially lethal consequences. Mutations in reproductive cells are involved in genetic diseases, whereas mutations that accumulate during the lifetime in somatic cells may lead to cancer. Substitution mutation – involves the substitution of a correct base in DNA sequence by an incorrect one – leading to a change in the mRNA codon & the incorrect AA is incorporated into the protein Frame Shift mutation – occurs when a base is added or deleted from the correct DNA sequence, shifting the sequence frame of the DNA – leading to a shift in the mRNA codon sequence & subsequently in the AA sequence in the protein. Mutagens are chemicals (nitrous acid) or agents (ionizing radiation) that cause mutation – Read Chapter 22 from Stoker – Section: 22.13.

Genetic Engineering, Recombinant DNA & Polymerase Chain Reaction

Genetic engineering (Biotechnology) – a process in which an organism is intentionally changed at the molecular (DNA) level, so that it exhibits different traits. Recombinant DNA – DNA molecules that contain genetic material from 2 different organisms, produced by splicing a desired gene from one organism to the DNA of another organism. Polymerase Chain Reaction (PCR) – is a method for rapidly producing multiple copies of a DNA nucleotide sequence (gene), utilizing DNA-polymerase enzyme. It is used for disease diagnosis (genetic disorders like cystic fibrosis), detecting pathogens (HIV) in the body & in forensics (DNA fingerprinting). Read Chapter 22 from Stoker – Sections: 22.15, 22.16.






Chapter 22 Chemical Connections: Antibiotic Protein Synthesis Inhibitors – p.831.

Additional Reading


http://www.wiley.com/college/boyer/0470003790/animations/translation/translation.htm

http://learn.genetics.utah.edu/content/begin/dna/transcribe/

http://www.scq.ubc.ca/a-brief-tour-of-dna-fingerprinting


1. Outline the general overview of protein synthesis.

2. Describe Transcription in detail.

3. Define a gene.

4. Discuss the principle of the genetic code.

5. Distinguish between a codon & an anticodon.

6. Describe Translation in detail.

7. Define mutation, giving examples.

8. Outline mutagens, giving examples.

9. Define genetic engineering & recombinant DNA, giving examples of its application.

10. Outline the principle of PCR, giving examples of its application.

Review Questions


http://www.wiley.com/college/boyer/0470003790/animations/translation/translation.htm

http://learn.genetics.utah.edu/content/begin/dna/transcribe/

http://www.scq.ubc.ca/a-brief-tour-of-dna-fingerprinting/



SESSION 19: Bioenergetics- Metabolic Pathways – An Overview

Code: BIOB111


#7. Recognize the major biochemical pathways and how they relate to health, nutrition and disease states.

#8. Apply the knowledge gained of the major biochemical pathways and relate to health, nutrition and disease states.

#9. Compare and contrast different metabolic states, their biochemical basis and efficacy.

Session Aims:


Address the learning outcomes listed above. Become familiar with the major biochemical pathways involved with energy production from

carbohydrates, fats & proteins.


Key Concept:

The metabolic processes are the basis of life, allowing cells to grow and reproduce, maintain their structures, and respond to their environments. Metabolism refers to all chemical reactions that provide energy and substances for cell growth. The knowledge of cell structure and the coenzymes are essential to understand the oxidation reduction reactions happening in the cell to extract energy from food.

Session Overview:

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed into another by each step requiring a specific enzyme. This session is designed to introduce the students to the concept of metabolism and energy requirements. Students will discover the key components and the biochemical pathways involved in generating ATP.

Session Topics

Metabolism

Metabolic Pathways

Metabolism & Cell Structure

Mitochondria



Compounds in Metabolic Pathways

Adenosine Phosphates

Other Nucleotide Triphosphates

Flavin Adenine Dinucleotide

Nicotinamide Adenine Dinucleotide

Coenzyme A

Overview of Bioenergetics Pathways

Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that the students understand what is expected of them to complete this subject successfully.

Textbook Location


Chapter 23: Biochemical Energy Production, pp. 847-880 – Sections: 23.1, 23.2, 23.3, 23.6



Summary

Metabolism

Is the total sum of all biochemical reactions that take place in a living cell / organism – there are 2 types of metabolic reactions. Catabolism – metabolic reactions in which large bio-molecules are broken down into smaller ones, while energy is released. Anabolism – metabolic reactions in which small bio-molecules are joined together to form larger ones, while energy is required. Metabolic pathway – is a series of consecutive biochemical reactions, used to convert a starting material into an end product. The major metabolic pathways are similar for all life forms – scientists study metabolic reactions in simple life forms to understand the same reactions in humans. Linear pathways – a series of biochemical reactions that generates a final product. Cyclic pathways – a series of biochemical reactions that generates the first reactant.

Metabolism & Cell Structure

In the cytoplasm of a eukaryotic cell there are several organelles – minute structures that carry out a specific cellular function. The 3 most important organelles for human metabolism: Ribosomes – protein synthesis (discussed in Session 17) Lysosomes – contain hydrolytic enzymes needed for cell repair, rebuilding & degradation.



Mitochondria – the cellular organelles responsible for generation of most of the cellular energy. The structure of mitochondria is unique, in that they have a double membrane – outer & inner membrane. The inner membrane is highly folded into cristae to increase surface area – here enzymes involved in energy production are attached. Between the 2 membranes there is the intermembrane space & the very core of the mitochondrion is called the matrix. Read Chapter 23 from Stoker – Sections: 23.1, 23.2.

Important Nucleotide-Containing Compounds in Metabolic Pathways

These molecules are important intermediates that play a vital role in the metabolic pathways – their structure & function are of great importance to understanding the topics discussed in the future sessions, as well as in Nutritional Biochemistry. Adenosine Phosphates – AMP, ADP, ATP Other Nucleotide Triphosphates – GTP, UTP, CTP Flavin Adenine Dinucleotide – FAD Nicotinamide Adenine Dinucleotide – NAD Coenzyme A – CoA Read Chapter 23 from Stoker – Section: 23.3.

Overview of Bioenergetics’ Pathways

The energy, required to run the human body, is obtained from ingested foods that are broken down in several different catabolic pathways. There are 4 general stages in the biochemical energy production: Digestion – results in the production of small molecules that are able to move across the intestinal wall into the bloodstream, including monosaccharides, amino acids & fatty acids. Acetyl Group Formation – several chemical reactions are involved in this stage, some of which occur in the cytosol & others in the mitochondria, resulting in the production of Acetyl groups, which attach to Coenzyme A, forming Acetyl CoA. Citric Acid Cycle – takes place in the mitochondria – acetyl groups from Acetyl CoA are oxidized & produce CO2 & some energy, most of the energy however is captured in the reduced coenzymes NADH & FADH2 & carried to the 4th stage. Electron Transport Chain & Oxidative Phosphorylation – takes place in the mitochondria – the NADH & FADH2 provide H+ & electrons needed for ATP production, which is catalysed by the enzyme ATP-synthase.

Common Metabolic Pathway

The reactions in stages 3 & 4 (above) are the same for all types of foods (carbohydrates, fats & proteins) – these reactions therefore constitute the Common Metabolic Pathway, involved in energy production in the form of ATP. Read Chapter 23 from Stoker – Section: 23.6.


In this subject the material is taught from the perspective that the students have no prior knowledge in the field. In this regard there is no compulsory pre-reading associated with this subject. The reading material that the students are directed to can be used either as pre-reading or post-reading dependent on the students individual study requirements.




Chapter 23

Additional Reading


http://www.wiley.com/college/fob/quiz/quiz16/16-1.html

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_nad__works.html


1. Define metabolism, catabolism & anabolism, giving examples.

2. Define metabolic pathway, distinguishing between linear & cyclic pathways.

3. Describe in detail the structure of mitochondria.

4. Discuss the structure & function of adenosine phosphates.

5. Describe in detail the structure & function of FAD.

6. Describe in detail the structure & function of NAD.

7. Describe in detail the structure & function of Coenzyme A.

Outline the 4 stages of biochemical energy production.

Review Questions Answer the relevant Exercises and Problems at the end of Chapter 23 in Stoker

BIOB111

CHEMISTRY AND BIOCHEMISTRY

SESSION 20: Metabolism

Learning outcomes

5. Discuss the major biochemical pathways & relate the knowledge to nutrition & health.

Session Aims



Become familiar with the major catabolic pathway of carbohydrates – Glycolysis & calculate the amount of ATP produced from complete oxidation of glucose.







Session Overview

This session will discuss digestion & absorption of carbohydrates as well as Glycolysis – the main catabolic pathway for carbohydrates.

Textbook Location


Chapter 24: Carbohydrate Metabolism, pp. 886-915 – Sections: 24.1, 24.2, 24.3, 24.4



Digestion & Absorption of Carbohydrates

Digestion – hydrolysis of food molecules into simpler chemical units that can be used by cells for their metabolic needs. Begins in the mouth – salivary α-amylase catalyzes hydrolysis of α-glycosidic bonds of starch – producing smaller polysaccharides & disaccharide (maltose). No digestion in stomach. Small intestine – majority of carbohydrate digestion – pancreatic α-amylase catalyzes hydrolysis of α-glycosidic bonds in polysaccharides to finally produce maltose. Disaccharidase enzymes (maltase, sucrase & lactase) break down disaccharides maltose, sucrose & lactose into monosaccharides glucose, fructose & galactose – absorbed via active transport into bloodstream – transported into liver – fructose & galactose are converted into compounds that enter the same pathway as glucose – Glycolysis. Read Chapter 24 from Stoker – Section: 24.1.

Glycolysis

The catabolic pathway in which Glucose (C6) is broken down into 2 molecules of pyruvate (C3), 2ATP & 2NADH are produced. It is a series of 10 steps – each is catalyzed by a different enzyme that takes place in the cytosol. It involves an oxidation process where no O2 is used – anaerobic process – the agent that accepts e- here is the coenzyme NAD+. There are 2 stages: C6 & C3 stage of glycolysis. C6 Stage – Steps 1-3 The energy-consuming stage, as 2 ATPs are consumed – the intermediates of the C6 stage are glucose or fructose derivatives. C3 Stage – Steps 4-10 The energy-generating stage, as 2 ATPs are consumed – the intermediates are C3-compounds. Steps 7 & 10 produce 4 ATPs. Note that each molecule of glucose (C6) forms 2 C3-compounds & each of these produces 2 ATPs (2x2 = 4ATP). In the energy-consuming phase 2 ATPs were used up, so the overall energy production for glycolysis = 2 ATPs. Note that the other monosaccharides, Fructose & Galactose, can also enter glycolysis but must be first converted to intermediates that can enter the pathway.



Glycolysis is regulated at steps 1, 3 & 10 – all these steps are catalysed by kinase enzymes. Read Chapter 24 from Stoker – Section: 24.2.

Fates of Pyruvate

Pyruvate is produced via glycolysis in most cells – the fate of pyruvate varies with cellular conditions & the type of organisms. There are 3 important ways in which pyruvate is converted into other substances & NADH is oxidized into NAD+ & recycled for glycolysis so it can continue. Oxidation to Acetyl CoA In the presence of O2 – aerobic conditions – pyruvate is transported from cytosol through both mitochondrial membranes into the matrix, where it is oxidized & decarboxylated to Acetyl CoA. Catalyzed by Pyruvate dehydrogenase complex. Most pyruvate formed during glycolysis is converted to Acetyl CoA & enters the CAC & ETC, in which NADH is recycled into NAD+. Lactate Fermentation When O2 is deficient in tissues (hypoxia) – anaerobic conditions – an enzymatic anaerobic reduction of Pyruvate to Lactate occurs mainly in muscles – leads to tiredness & pain. Purpose – conversion of NADH to NAD+ for increased rate of glycolysis. Lactate is converted back to Pyruvate when aerobic conditions are re-established in the cell. Muscle fatigue associated with strenuous physical activity is attributed to increased build-up of Lactate. Ethanol Fermentation Enzymatic anaerobic conversion of Pyruvate to Ethanol & CO2 – in simple organisms (yeast & bacteria) – NADH is regenerated to NAD+ for glycolysis. Involves 2 reactions: Pyruvate decarboxylation – Pyruvate decarboxylase Acetaldehyde reduction – Alcohol dehydrogenase Read Chapter 24 from Stoker – Section: 24.3.

Glycogen Synthesis & Degradation

Glycogen is a branched polymer storage form of glucose in humans & animals. Glycogen is stored: In muscles – the source of glucose for Glycolysis In the liver – the source of glucose to maintain normal blood glucose levels

Glycogenesis

Is the metabolic pathway by which glycogen is synthesized from glucose – this occurs in fed state & operates when high levels of glucose-6-phosphate are formed in the 1st step of glycolysis. The hormone Insulin activates Glycogenesis – when glycogen stores are full any additional glucose is converted to body fat & stored. Liver can store about 100-120g, muscle about 200-300g glycogen Involves 3 steps: Formation of Glucose 1-phosphate Formation of UDP Glucose Glucose transfer to a Glycogen Chain

Glycogenolysis

Is the breakdown of glycogen to Glucose-6-phosphate but is not just the reverse of Glycogenesis because it does not require UTP or UDP. This process is activated by Glucagon when blood glucose levels are low (hypoglycaemia) in the liver & by Adrenalin in muscles. Insulin inhibits Glycogenolysis. Involves 2 steps: Phosphorylation of a glucose residue



Glucose 1-phosphate isomerization Glycogenolysis in muscles – Glucose 6-phosphate directly enters glycolysis pathway. Glycogenolysis in liver cells – stimulated by low blood glucose levels – Glucose 6-phosphate is converted to free Glucose – catalyzed by Glucose 6-phosphatase – an enzyme found in liver, kidneys & intestines but not in muscles. The free glucose is released into the bloodstream & transported to muscles & brain tissue. Read Chapter 24 from Stoker – Section: 24.5.

Pre / Post-class Readings



Chapter 24

Chemical Connections: Lactate Accumulation – p.900.

Additional Reading


McMurray, JE, Ballantine, DS ,Hoeger, CA, & Peterson, VE 2013, Fundamentals of General, Organic and Biological Chemistry, 7th edn, Princeton Hall, USA. http://www.science.smith.edu/departments/Biology/Bio231/glycolysis.html http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_glycolysis_works.html http://www.execulink.com/~ekimmel/biofax12.htm (Link verified 19 Nov 2013)


27. Outline the digestion & absorption of carbohydrates.

28. Describe glycolysis – include an overview, the purpose of glycolysis, end products, energy

requirements, where in the cell does glycolysis take place.

29. Outline the control points of glycolysis.

30. Discus the 3 fates of pyruvate.

31. Briefly describe Glycogen & the tissues where it is synthesized.

32. Discuss Glycogenesis & Glycogenolysis – draw a comparison & contrast between these 2

pathways, where in the body do these pathways occur & what their purpose is.

Review Questions

http://www.science.smith.edu/departments/Biology/Bio231/glycolysis.html

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_glycolysis_works.html

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_glycolysis_works.html

http://www.execulink.com/~ekimmel/biofax12.htm




SESSION 21: Metabolism – Gluconeogenesis, Cori Cycle & Citric Acid Cycle

Code: BIOB111

Learning outcomes


Session Aims



Become familiar with the other pathways involved in carbohydrate metabolism – Gluconeogenesis, Cori Cycle and Citric Acid Cycle.

Session Overview

This session will discuss the remaining pathways involved in carbohydrate metabolism – Gluconeogenesis, Glycogenesis & Glycogenolysis, as well as the hormonal control of carbohydrate metabolism.

Textbook Location


Chapter 24: Carbohydrate Metabolism, pp. 886-915 – Sections: 24.5, 24.6, 24.9, and 24.10.



Gluconeogenesis

The metabolic pathway by which glucose is synthesized from non-carbohydrate sources, including pyruvate, lactate (from muscles & RBCs), glycerol (from TAG hydrolysis) & certain AAs (from dietary protein hydrolysis or from muscle protein during starvation). Glycogen stores in muscle & liver tissue are depleted within 12-18 hours of fasting or in even less time from heavy work or strenuous physical activity Without gluconeogenesis, the brain, which is dependent on glucose as a fuel, would have problems functioning if food intake were restricted for even one day. Gluconeogenesis helps to maintain normal blood glucose levels in times of inadequate dietary carbohydrate intake.



About 90% of Gluconeogenesis takes place in the liver. Gluconeogenesis is not the exact opposite process to Glycolysis – Glycolysis (10 steps) vs. Gluconeogenesis (11 steps). 7 reactions are the reverse of Glycolysis & use the same enzymes. 3 reactions are not reversible – catalyzed by kinase enzymes. Reaction 1 of Glycolysis – Hexokinase Reaction 3 of Glycolysis – Phosphofructokinase Reaction 10 of Glycolysis – Pyruvate kinase Gluconeogenesis requires different enzymes to bypass these steps. Bypass of Reaction 10 – Pyruvate carboxylase & Phosphoenolpyruvate carboxykinase Bypass of Reaction 3 – Fructose 1, 6-bisphosphatase Bypass of Reaction 1 – Glucose 6-phosphatase Glycolysis produces 2 ATP. Gluconeogenesis requires equivalent of 6 ATP (4ATP & 2GTP). Whenever Gluconeogenesis occurs it is at the expense of other ATP-producing metabolic processes.

The Cori Cycle

Gluconeogenesis using Lactate as a source is particularly important because of Lactate formation during strenuous exercise. Lactate produced in working muscles diffuses from muscle cells into the bloodstream & is transported to liver, where the enzyme Lactate dehydrogenase converts lactate back to Pyruvate, which is then via Gluconeogenesis converted to Glucose – enters the bloodstream & is transported back to the muscles. Read Chapter 24 from Stoker – Section: 24.6.

Citric Acid Cycle (CAC)

Is a series of biochemical reactions taking place in the mitochondrial matrix in the presence of oxygen, in which the Acetyl portion of Acetyl CoA is oxidized to 2CO2 & reduced forms of coenzymes 3NADH & 2FADH2 (they carry electrons & protons into the ETC) as well as 1GTP are produced? The Acetyl group that enters the CAC is the final product of the breakdown of foods – carbohydrates, fats & proteins. 4 B vitamins are required for the correct function of the CAC – Thiamin, Riboflavin, Niacin & Pantothenic acid. CAC is regulated by ATP & NADH – high levels of ATP inhibit & low levels of ATP speed up Step 1 of the CAC, whereas high levels of ADP & NADH speed up & low levels of ADP & NADH inhibit Step 3 of the CAC. Read Chapter 23 from Stoker – Section: 23.7.

Hormonal Control of Carbohydrate Metabolism

The 3 hormones involved in control of carbohydrate metabolism are Insulin, Glucagon & Adrenalin. Insulin is secreted in the fed state & stimulates Glycolysis & Glycogenesis, at the same time Insulin inhibits Gluconeogenesis & Glycogenolysis. Glucagon is secreted in the fasting state & produces the opposite effect to Insulin, therefore Glucagon stimulates Gluconeogenesis & Glycogenolysis, and at the same time Glucagon inhibits Glycolysis & Glycogenesis. Adrenalin functions similarly to Glucagon & primarily targets muscle cells, where it promotes energy generation for quick action during a short-term stress response. Read Chapter 24 from Stoker – Section: 24.9.

B vitamins & Carbohydrate Metabolism

Many B vitamins function as coenzymes in carbohydrate metabolism – without these the body would be unable to utilize carbohydrates as an energy source.



The 6 B vitamins in carbohydrate metabolism: Thiamin – as TPP Riboflavin – as FAD, FADH2 & FMN Niacin – as NAD+ & NADH Pantothenic acid – as CoA Pyridoxine – as PLP (pyridoxal 5-phosphate) Biotin Read Chapter 24 from Stoker – Section: 24.10.




Chapter 24

Chemical Connections: Diabetes Mellitus – p.913.

Additional Reading


http://www.wiley.com/college/boyer/0470003790/animations/gluconeogenesis/gluconeogenesis.htm

http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/animations/gluconeogenesis/gluconeog

enesis.htm (accessed on 19 Nov 2013)


33. Describe Gluconeogenesis – draw a comparison & contrast to Glycolysis.

34. Outline the Cori Cycle & explain its function.

35. Explain what metabolic states will initiate Glycolysis, Gluconeogenesis & Glycogenolysis – name

the hormones involved in these processes.

Review Questions



http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/animations/gluconeogenesis/gluconeogenesis.htm

http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/animations/gluconeogenesis/gluconeogenesis.htm



SESSION 22: Common Metabolic Pathways Electron Transport Chain, Oxidative Phosphorylation, ATP Production.

Code: BIOB111

Learning outcomes


Session Aims



Become familiar with the Common Metabolic Pathway involved with energy production from carbohydrates, fats & proteins.

Session Overview

This session will discuss in detail the processes occurring in the Common Metabolic Pathway, including the Citric Acid Cycle, the Electron Transport Chain & the Oxidative Phosphorylation.

Textbook Location


Chapter 23: Biochemical Energy Production, pp. 847-880 – Sections: 23.7, 23.8, 23.9, 23.10, 23.11, and 23.13.



Electron Transport Chain (ETC)

Is a series of biochemical reactions, in which e- & H+ from NADH & FADH2 (produced in the CAC) are passed to intermediate carriers within the inner mitochondrial membrane (IMM) & are finally accepted by molecular O2 to produce H2O. The enzymes & electron carriers of the ETC are located within the IMM as 4 distinct protein complexes, tightly bound to the IMM. Complex I: NADH-Coenzyme Q Reductase Complex II: Succinate-Coenzyme Q Reductase Complex III: Coenzyme Q-Cytochrome c Reductase Complex IV: Cytochrome c Oxidase There are 2 mobile electron carriers – Coenzyme Q & Cytochrome c – that shuttle electrons between the complexes & are not tightly bound to the IMM. Read Chapter 23 from Stoker – Section: 23.8.

Oxidative Phosphorylation (OP)

Is the process, by which ATP is synthesized from ADP & Pi, using the energy released in the ETC. The interdependence (coupling) of ATP synthesis & the ETC is related to the movement of H+ across the IMM, hence the OP & the oxidation reactions of ETC are coupled systems.



Besides of e- transport, Complexes I, III & IV of the ETC have a 2nd function as “proton pumps” transferring H+ from the mitochondrial matrix into the intermembrane space. Coupled reactions – are pairs of concurrently occurring biochemical reactions, in which energy released by one reaction is used in another reaction. For every 2e- passed through the ETC, 10H+ cross the IMM through Complexes I, III & IV – this causes the build-up of H+ in the intermembrane space. The protons have the tendency to flow from high [H+] to low [H+], however the IMM is not permeable for H+. Therefore they pass through an enzyme complex – ATP-synthase within the IMM & provide energy for ATP synthesis. The ETC / OP are: Down-regulated by low levels of ADP, Pi, O2 & NADH. Up-regulated by high levels of ADP. Uncoupling agents – allow the ETC to take place but the energy that would usually be used for ATP synthesis is released as heat – include Thyroid hormones & Thermogenin (a protein found in brown adipose tissue of newborn mammals & hibernating mammals).

ATP Production

1 mole of NADH form the CAC produces 2.5 ATP in the ETC/OP 1 mole of FADH2 from the CAC produces 1.5 ATP in the ETC/OP 1 mole of GTP is an equivalent to 1 mole of ATP Therefore the total energy yield in the CMP for each Acetyl CoA, is 10 moles of ATP. Read Chapter 23 from Stoker – Sections: 23.9, 23.10, 23.11, and 23.13.

ATP Production from Complete Oxidation of Glucose in Skeletal muscles & Nerve cells

CYTOSOL (Glycolysis) ATP Yield

– 2 ATP in energy-consuming stage

+ 4 ATP produced in energy-generating stage 2 ATP

+ 2 NADH (shuttled to ETC) 3 ATP

MITOCHONDRIA (CAC, ETC & OP)

Oxidation of Pyruvate to Acetyl CoA 5 ATP

CAC (2 GTP) 2 ATP

ETC & OP (6 NADH from CAC) 15 ATP

(2 FADH2 from CAC) 3 ATP

NET energy yield

30 ATP per glucose molecule







Chapter 23

Chemical Connections: Cyanide Poisoning – p.875.

Chemical Connections: Brown Fat, Newborn Babies & Hibernating Animals – p.876.

Additional Reading


http://www.wiley.com/college/pratt/0471393878/student/animations/citric_acid_cycle/index.html

http://wps.prenhall.com/esm_mcmurry_fundamentals_4/38/9917/2538976.cw/index.html (Chapter 23, 25, 26, 28)


http://www.youtube.com/watch?v=A1DjTM1qnPM

http://www.wiley.com/college/boyer/0470003790/animations/electron_transport/electron_transport.htm


http://bcs.whfreeman.com/thelifewire/content/chp07/0702001.html

http://highered.mcgraw-

hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1

_.html (Accessed on 18 Nov 2013)

http://www.wiley.com/college/boyer/0470003790/animations/electron_transport/electron_transport.htm Make sure you hit the link to <location> to see the inner mitochondrial membrane)



(There is also a short quiz with feedback)

(Links verified 19 Nov 2013)


36. Define the CAC & summarize the products of this pathway.

37. Write an overview of 1 turn of the CAC.

38. Briefly describe the 2 functions of ETC, including the products.

39. Discuss the OP, including the product.

40. Outline the interdependence of OP & the ETC.

41. Define the amount of ATP produced in the ETC/OP per mole of NADH, FADH2 & GTP.

42. Calculate the amount of ATP produced in the CMP per Acetyl CoA.

http://www.wiley.com/college/pratt/0471393878/student/animations/citric_acid_cycle/index.html

http://wps.prenhall.com/esm_mcmurry_fundamentals_4/38/9917/2538976.cw/index.html


http://www.youtube.com/watch?v=A1DjTM1qnPM




http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html








43. Calculate the amount of energy yielded by complete oxidation of glucose.

Review Questions




SESSION 23: Metabolic Pathways – Lipid Metabolism Part 1

Code: BIOB111


#7. Recognize the major biochemical pathways and how they relate to health and disease states.

#8. Apply the knowledge gained of the major biochemical pathways and relate to health and disease states.


Session Aims:



Become familiar with the major catabolic pathway of Lipids – Lipolysis & calculate the amount of ATP produced from complete oxidation of any fatty acid.


Key Concept:

Lipids also play an important role in metabolism and energy production. A large amount of energy is obtained when fatty acids undergo oxidation in the mitochondria to yield acetyl CoA. When carbohydrates are not available to meet energy needs the body breaks down the fat. The acetyl CoA molecules accumulate and a process called ketogenesis is initiated.

Session Overview:

This session will discuss digestion & absorption of Lipids as well as β-Oxidation – the main catabolic pathway for fatty acids Students will learn that in response to energy demands, the fatty acids of stored triacylglycerol’s can be mobilized for use by tissues. The process of fatty acid oxidation called beta oxidation will be studied, and the resultant energy yield from fatty acids calculated. In addition, the biosynthesis of lipids will also be covered, as lipids are an absolute requirement of the body for energy storage, as well as synthesis of various other essential compounds.

Session Topics

Lipid Metabolism – Part 1

Digestion & Absorption of Dietary Lipids

TAG Storage & Mobilization

Glycerol Metabolism



Oxidation of Fatty Acids

ATP Production from Fatty Acid Oxidation

Read the BIOB111 SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that the students understand what is expected of them to complete this subject successfully

Textbook Location


Chapter 25: Lipid Metabolism, pp. 920-946 – Sections: 25.1, 25.2, 25.3, 25.4, 25.5

Concepts to Remember at the end of the chapter. Exercises and Problems with odd numbers, at the end of each chapter, are answered at the end of the textbook

Summary

Digestion & Absorption of Lipids

Most dietary lipids (98%) are Triacylglycerol’s (TAGs) in the form of fats & oils – this session focuses on TAG metabolism. Mouth – salivary enzymes (water soluble) have no effect on lipids, which are non-polar. Stomach – most TAGs change physically to small droplets within the chyme – this is a physical process, not chemical. Lipid digestion starts in the stomach – gastric lipase hydrolyzes ester bonds, forming 2 FAs & 1 Monoacylglycerol (MAG) – about 10% of TAGs are hydrolyzed in the stomach. Small intestines – entry of chyme triggers CCK (Cholecystokinin) & bile is released from gallbladder – bile acts as emulsifier to keep the TAG droplets in aqueous solution & pancreatic lipases continue digestion of TAGs. With the help of bile the free FAs & MAGs combine into Micelles – small spherical droplets much smaller than the original TAG droplets that are readily absorbed into intestinal cells. Within intestinal cells the free FAs & MAGs are reassembled into TAGs, which combine with phospholipids, cholesterol & proteins into Chylomicrons. Chylomicrons are lipoproteins that transport TAGs from intestinal cells, via the lymphatic system, into the bloodstream. TAGs constitute 95% of core lipids in chylomicrons. Once in the bloodstream TAGs are hydrolyzed again into FAs & Glycerol by lipoprotein lipases located on the blood vessel lining in muscles & other tissues. The FAs & Glycerol are absorbed by body cells & either broken down into Acetyl CoA for energy or stored as lipids in adipocytes (they are repackaged again into TAGs). Read Chapter 25 from Stoker – Section: 25.1.

TAG Storage & Mobilization

Most body cells have limited ability to store TAGs, which are stored in specialized cells – adipocytes found in adipose tissue. Adipocytes are the largest cells in the body (most of the cytoplasm contains a large TAG droplet) that are located primarily beneath the skin, esp. on abdomen & around vital organs.



Adipose tissue also insulates against excess heat loss in cold environments & protects organs from physical shock. Several hormones, incl. adrenalin & glucagon trigger the hydrolysis of TAGs via activation of hormone sensitive lipase (HSL). TAG mobilization – the hydrolysis of TAGs into FAs & glycerol by HSL in adipocytes, followed by the release of FAs & glycerol into the bloodstream. This is an ongoing process – about 10% of TAGs are replaced daily by new TAGs. TAGs energy reserves (fat reserves) are the major source of stored energy for humans – energy reserves associated with protein, glycogen & glucose are small to very small compared to fat reserves. Read Chapter 25 from Stoker – Section: 25.2.

Glycerol Metabolism

Glycerol produced in TAG mobilization enters bloodstream & is taken up by liver or kidneys – converted to dihydroxyacetone phosphate in 2 steps: – Phosphorylation of hydroxyl group – Oxidation of secondary alcohol to ketone Dihydroxyacetone phosphate is an intermediate in glycolysis & gluconeogenesis. Read Chapter 25 from Stoker – Section: 25.3.

Oxidation of Fatty Acids

Is the process in which FAs are broken down to produce energy – it is divided into 3 steps. Activation of FA Takes place on the outer mitochondrial membrane where the FA reacts with Co-A in the presence of 1 ATP, forming AMP, 2 PPi & Acyl CoA – the energy for this reaction comes from hydrolysis of 1 ATP → 1AMP, where both high-energy phosphate bonds are broken, producing AMP + 2 PPi – this is energetically equivalent to breaking down 2 ATPs. The FA is converted into a high-energy derivative of CoA (Acyl CoA) & so becomes activated. Transport of FA into the mitochondrial membrane The Acyl CoA is too large to pass through the inner mitochondrial membrane (IMM) into the matrix where the enzymes for β-oxidation are located, therefore a shuttle mechanism involving Carnitine transports the activated Acyl CoA into the matrix as Acyl carnitine. When inside the mitochondrion the Acyl group is transferred from the carnitine back to CoA & Acyl CoA reforms. β-Oxidation of FA Takes place in the mitochondrial matrix, where the Acyl CoA is oxidized in a repetitive sequence of 4 reactions until the whole FA is degraded by removing 2C atoms at a time in the form of Acetyl CoA, while coenzymes FADH2 & NADH are also produced. Step 1 – 1st Oxidation / Dehydrogenation

2H atoms are removed (1 each) from & C atoms of the FA, forming a trans double bond, while FAD (the oxidizing agent) forms FADH2, which in turn enters the ETC. Step 2 – Hydration

A molecule of H2O is added across C=C in an alkene, producing a secondary alcohol on the -C atom. Step 3 – 2nd Oxidation / Dehydrogenation

The –OH group on -C atom is oxidized to a ketone, while NAD+ (the oxidizing agent) forms NADH, which in turn enters the ETC.



Step 4 – Thiolysis

The chain cleavage reaction, in which the FA C-chain is broken between & C atoms, while reacting with CoA – the products = Acetyl CoA & a NEW Acyl CoA, that is 2C atoms shorter, which now enters the same set of 4 reactions. The FAs found in dietary TAGs contain an even No. of C atoms – thus the No. of Acetyl CoA molecules produced in β-Oxidation is half the No. C-atoms in the FA, however the No. of turns of the β-Oxidation spiral is 1 less because the last turn produces 2 Acetyl CoA molecules. C18 FA → 9 Acetyl CoA & 8 turns of β-Oxidation C16 FA → 8 Acetyl CoA & 7 turns of β-Oxidation Read Chapter 25 from Stoker – Section: 25.4.

ATP Production from FA Oxidation

The Complete Oxidation of 1 molecule of Stearic acid (C18) forms: 9 Acetyl CoA – enter the CAC & each generates 10 ATP 8 turns of β-Oxidation – each turn producing 1FADH2 & 1NADH – these coenzymes enter ETC & OP to produce more ATP.

Note that for FA activation 1 ATP → 1AMP, which is energetically equivalent to breaking down 2 ATPs – hence the net ATP production = 120 ATP. Comparison of Fatty Acids & Glucose Oxidation Complete oxidation of Stearic acid (C18) & Glucose (C6):

Based on equal numbers of C atoms in both molecules – lipids are 33% more efficient in storing energy than carbohydrates.



In this subject the material is taught from the perspective that the students have no prior knowledge in the field. In this regard there is no compulsory pre-reading



associated with this subject. The reading material that the students are directed to can be used either as pre-reading or post-reading dependent on the students individual study requirements


Chapter 25

Chemical Connections: High-Intensity versus Low-Intensity Workouts – p.932.

Additional Reading



http://www.ann.com.au/MedSci/fasting.htm (Read the section on “ATP production without glucose” Australian Naturopathic Network. Stevenson, P. Revised May 18 2002. Fasting. ANN. http://www.wiley.com/college/fob/quiz/quiz19/19-9.html (Pathway animation β-oxidation)

http://www.wiley.com/college/boyer/0470003790/animations/fatty_acid_metabolism/fatty_acid_metabolism.htm (also has good information on metabolic states and fatty acid metabolism)

http://www.chem.purdue.edu/courses/chm333/fatty_acid.swf (From the drop down menu, choose sections that are formatively assessed in Review Questions 1 & 2. Also choose synthesis vs oxidation and steps to fatty acid synthesis)


8. Outline the digestion & absorption of lipids.

9. Discuss TAG storage & mobilization, including the hormones involved.

10. Briefly outline Glycerol metabolism & fate.

11. Describe briefly the 3 parts of Oxidation of Fatty acids – include the activation &

transport of FA into the mitochondrial matrix.

12. Discuss an overview of β-Oxidation, its purpose, the end products, energy requirements

& where in the cell does β-Oxidation take place.

13. Outline the products & ATP yield from the complete oxidation of Stearic acid.

14. Compare the energy yield from complete oxidation of stearic acid to the energy yield

from the complete oxidation of glucose, include calculations in your answer.


http://www.ann.com.au/MedSci/fasting.htm


http://www.wiley.com/college/boyer/0470003790/animations/fatty_acid_metabolism/fatty_acid_metabolism.htm

http://www.wiley.com/college/boyer/0470003790/animations/fatty_acid_metabolism/fatty_acid_metabolism.htm

http://www.chem.purdue.edu/courses/chm333/fatty_acid.swf



Review Questions




SESSION 24: Lipid Metabolism Part 2. Ketogenesis and Lipogenesis

Code: BIOB111





Session Aims:


Address the learning outcomes listed above. Become familiar with the other pathways involved in lipid metabolism – Ketogenesis &

Lipogenesis (Fatty acid synthesis).


Key Concept:

A comparison of fatty acid synthesis and degradation helps to distinguish the purpose and significance of these two pathways

Session Overview:

This session carries on from the last session, in that it continues to discover the process of fatty

acid synthesis, and compares and contrasts the synthetic pathway with the oxidative pathway

of fatty acid metabolism. This session will discuss the remaining pathways involved in lipid

metabolism – Ketogenesis & Lipogenesis, as well as the relationship between lipid &

carbohydrate metabolism

Session Topics

Lipid Metabolism – Part 2

Ketone Bodies

Ketogenesis

Ketosis

Lipogenesis

Fate of Acetyl CoA



Relationship between Lipid & Carbohydrate Metabolism

B vitamins & Lipid Metabolism


Textbook Location


Chapter 25: Lipid Metabolism, pp. 886-915 – Sections: 25.6, 25.7, 25.9, 25.10, and 25.11.



Summary

Ketone Bodies

Ketogenesis is the process in which ketone bodies (KBs) are generated when there is too much of Acetyl CoA produced in β-Oxidation. The Acetyl CoA produced from β-Oxidation enters the CAC & interacts with Oxaloacetate (OA) – therefore adequate balance between lipid & carbohydrate metabolism is required. Sufficient OA must be present for Acetyl CoA to be able to enter CAC, however OA production depends on pyruvate generated in glycolysis, as pyruvate can be converted to OA via (pyruvate carboxylase). Certain conditions upset this lipid-carbohydrate balance: Diet high in fat & low in carbohydrates Diabetes mellitus – glucose is present but can’t be processed Fasting & starvation – insufficient glucose as glycogen is depleted When OA supply is too low, the excess of Acetyl CoA from β-Oxidation is converted to ketone bodies (KBs) – Acetoacetate, β-Hydroxybutyrate & Acetone.

Ketogenesis

The 4-step metabolic pathway by which KBs are formed from Acetyl CoA, primarily in the liver mitochondria. The 1st KB produced is Acetoacetate – some is converted to β-Hydroxybutyrate & both diffuse from the liver into the bloodstream, where Acetone is produced. This is due to the fact that Acetoacetate is unstable & can be spontaneously or enzymatically converted to Acetone – hence Acetone is not a product of ketogenesis. Acetone is volatile & is mainly excreted by exhalation (sweet odour of a diabetic’s breath) – the amount of Acetone present is usually small compared to the concentration of the other 2 KBs.



Ketosis

Under normal metabolic conditions (appropriate glucose-fatty acid balance), the concentration of KBs in the blood is very low – about 1mg/100ml. Abnormal metabolic conditions (mentioned earlier) lead to elevated blood KBs (50-100x more than normal). Ketonemia = excess accumulation of KBs in blood (20mg/100ml). Ketonuria – at 70mg/100ml the renal threshold is exceeded & KBs are excreted in the urine. Ketosis = an overall accumulation of KBs in the blood & urine – it is often detected by the smell of Acetone on a person’s breath. Read Chapter 25 from Stoker – Section: 25.6.

Lipogenesis

Is the biosynthesis of fatty acids from Acetyl CoA, which occurs in the cytosol, however it is not simply the reversal of β-Oxidation. It is catalyzed by a multi-enzyme complex Fatty acids synthase, which ties the Lipogenesis steps closely together & uses a Acyl carrier protein (ACP) to which the intermediates of this pathway are bonded. The reducing agent in Lipogenesis is the coenzyme NADPH (NADH + Pi). Fatty acids are build up 2C at a time from Acetyl CoA, which is used to form Malonyl ACP – this molecule becomes the carrier of the 2C. Lipogenesis occurs any time dietary intake provides more nutrients than needed for energy requirements. As Lipogenesis takes place in the cytosol but the Acetyl CoA is produced in the mitochondrion, it has to be first transported to the cytosol, however although the outer mitochondrial membrane is freely permeable for Acetyl CoA but the IMM is not – therefore a Citrate – Malate shuttle system is used. There are 2 ACP complexes that are needed to start Lipogenesis – Acetyl ACP (C2 – ACP) & Malonyl ACP (C3 – ACP) – additional Malonyl ACP molecules are needed for the process to continue. Cytosolic Acetyl CoA = the starting material for the production of both complexes. Acetyl ACP is formed by direct reaction of Acetyl CoA & ACP, whereas the formation of Malonyl ACP requires carboxylation of Acetyl CoA to Malonyl CoA & subsequent attachment of the Malonyl group to the ACP. Fatty Acid chain elongation involves 4 reactions that occur in a cyclic pattern within the multienzyme Fatty acid synthase complex to produce a fatty acid. 1) Condensation 2) 1st Reduction 3) Dehydration 4) 2nd Reduction Steps 2 through to 4 involve a sequence of functional group changes that occur in reverse order

to -oxidation. The 1st turn of the cycle produces a C4 species that enter the 2nd turn forming a C6 species & further cycles add C2 groups to form C6, C8, C10 .… Acyl groups – the elongation usually stops when the C16 Acyl group (Palmitic acid) is formed. To produce longer saturated FAs & unsaturated FAs different enzymes & different cellular locations are required. Relatively large input of energy is needed to biosynthesize a FA molecule.




Fate of Fatty Acid Generated Acetyl CoA

The Acetyl CoA produced in -oxidation can be: 1) Processed further in the CMP to produce ATP. 2) Converted to KBs, which can be re-converted to Acetyl CoA when needed for ATP production. 3) Converted to FAs, which are stored in the body as TAGs. 4) used as starting material to produce cholesterol. 5) NOT used for the synthesis of glucose in humans & animals

Cholesterol Biosynthesis

Occurs primarily in the liver, when the body is in an Acetyl CoA-rich state – 18 Acetyl CoA molecules are required & 27 separate enzymatic steps are involved. The rate-determining step in cholesterol biosynthesis is the multistep formation of Mevalonate (C6) from 3 Acetyl CoA molecules. The body synthesizes 1.5 - 2.0 g of cholesterol every day from Acetyl CoA units, whilst the average daily dietary cholesterol intake is about 0.3 g. Read Chapter 25 from Stoker – Section: 25.9.

Relationship Between Lipid & Carbohydrate Metabolism

Acetyl CoA is the primary link between lipid & carbohydrate metabolism. Acetyl CoA is the degradation product from glucose, glycerol & FAs. Acetyl CoA is the starting material for biosynthesis of FAs, cholesterol & ketone bodies Lipogenesis occurs in the fed state, when high blood glucose levels & insulin stimulate glycolysis & pyruvate oxidation to Acetyl CoA, which is then available for Fatty acid synthesis. Lipolysis occurs in the fasting state, when blood glucose levels are low & glucagon stimulates this process. Adrenalin also stimulates Lipolysis & Fatty acid mobilization during a stress response. Read Chapter 25 from Stoker – Section: 25.10.

B vitamins & Lipid Metabolism

Many B vitamins function as coenzymes in lipid metabolism – without these the body would be unable to utilize lipids as an energy source. 4 B vitamins in lipid metabolism: Riboflavin – as FAD, FADH2 & FMN Niacin – as NAD+ & NADH as well as NADP+ & NADPH Pantothenic acid – as CoA Biotin Read Chapter 25 from Stoker – Section: 25.11.






Chapter 25

Chemical Connections: High-Intensity versus Low-Intensify Workouts – p.932.

Chemical Connections: Statins: Drugs That Lower Plasma Levels of Cholesterol – p.932.

Additional Reading




15. Describe Ketone bodies & the conditions under which they are produced.

16. Describe Ketogenesis.

17. Briefly describe Ketosis & the potential dangers associated with it.

18. Describe Lipogenesis.

19. Discuss Lipogenesis & Lipolysis – draw a comparison & contrast between these 2

pathways, where in the body do these pathways occur & what their purpose is.

20. Explain what metabolic states will initiate Lipolysis & Lipogensis – name the hormones

involved in these processes.

21. Outline the fates of Acetyl CoA generated from fatty acids.

22. Briefly outline cholesterol synthesis.

Discuss the relationship between Lipid & Carbohydrate Metabolism – name the hormones involved.

Review Questions

Answer the relevant questions at the end of the chapter 24 in Timberlake


(See Tutorial Handouts for suggested relevant Questions and Problems)




SESSION 25: Metabolic Pathways – Protein Metabolism

Code: BIOB111





Session Aims:


Address the learning outcomes listed above. Become familiar with the metabolic pathways of Proteins & Amino acids.

– Transamination, Deamination & the Urea cycle, Catabolism of the Carbon skeletons & Amino Acid Biosynthesis.


Key Concept:

Amino acids enter the amino acid pool in the liver not only from digestion but also from the breakdown of old protein. Elimination of excess nitrogen in amino acids occurs through urea cycle in which urea is synthesized in the liver to be excreted by the kidney. The carbon atoms of amino acids are converted to compounds that can enter the citric acid cycle.

Session Overview:

This session will discuss digestion & absorption of Protein as well as the metabolic pathways, catabolic & anabolic, concerning proteins. The catabolic pathways, including the urea cycle are covered, and then the fates of carbon skeletons in the amino acids are discussed. Here students will see that protein metabolism is linked both with carbohydrate and lipid metabolism.

Session Topics:

Protein Metabolism

Digestion & Absorption of Dietary Proteins

Amino Acid Utilization

Amino Acid Degradation

Transamination

Oxidative Deamination

The Urea Cycle

Amino Acid Carbon Skeletons



Amino Acid Biosynthesis

B vitamins & Protein Metabolism

Read the BIOB111_ SO and pay particular attention to the Learning Outcomes, Set Texts and Assessment Tasks for the Subject of Study. Make certain that the students understand what is expected of them to complete this subject successfully. Textbook Location


Chapter 26: Protein Metabolism, pp. 953-978 – Sections: 26.1, 26.2, 26.3, 26.4, 26.5, 26.6, 26.8, 26.9



Summary

Digestion & Absorption of Proteins

Protein digestion starts in the stomach – involves denaturation & hydrolysis of peptide bonds. Dietary protein entering the stomach promotes the release of hormone Gastrin, which stimulates secretion of Pepsinogen & HCl. HCl denatures proteins, kills most bacteria (pH = 1.5-2.0) & activates Pepsinogen (inactive) to Pepsin (active). Pepsin (enzyme) hydrolyzes about 10% peptide bonds Small batches of acidic chyme containing large polypeptides enter the small intestine (SI) & stimulate secretion of hormone Secretin, which promotes pancreatic production of bicarbonate ions (HCO3

-) that in turn help neutralize the acidic chyme (SI pH = 7-8) & allows activation of pancreatic protolytic enzymes Trypsin, Chymotrypsin & Carboxypeptidase to break peptide bonds in proteins, liberating amino acids. The “free” amino acids are absorbed via intestinal wall into the bloodstream. Read Chapter 26 from Stoker – Section: 26.1.

Amino Acid Utilization

AAs produced from protein digestion enter the amino acid pool in the body – the total supply of free AAs available for use in the human body, which is derived from 3 sources – dietary protein, protein turnover & biosynthesis of non-essential AAs in the liver. Nitrogen Balance The state that results when the amount of nitrogen taken into the human body as protein equals the amount of nitrogen excreted from the body in waste materials – in a healthy adult the nitrogen intake equals the nitrogen excretion. However nitrogen imbalance may occur in 2 forms: Negative nitrogen balance – protein degradation exceeds protein synthesis – the amount of nitrogen in urine exceeds the amount of nitrogen ingested (dietary protein), leading to tissue wasting (starvation, protein-poor diet, wasting illness). Positive nitrogen imbalance – protein synthesis (anabolism) exceeds protein degradation (catabolism) – results in large amounts of tissue synthesis (during growth & pregnancy). Amino Acids There is no specialized storage form of AAs in the body, hence a constant source of AAs is needed to maintain normal metabolism. The AAs from the “AA pool” are used for synthesis of proteins, non-protein N-containing compounds & non-essential AAs, as well as energy production.



Amino Acid Degradation takes place in the liver in 2 stages: Removal of the –NH2 group – involves transamination, oxidative deamination & urea cycle. Degradation of the remaining carbon skeleton Read Chapter 26 from Stoker – Section: 26.2.

Transamination

Involves the transfer of the –NH2 group of an α-AA to an α-keto acid. Usually 2 AA (1 as a reactant & 1 as a product) & 2 keto acids (1 as a reactant & 1 as a product) participate in this process – 2 keto/amino acid pairs are involved, each pair has a common C-chain base. Transamination involves several steps & requires pyridoxal phosphate (coenzyme derived from Pyridoxine) & it is catalyzed by enzyme Transaminase / Aminotransferase.

Oxidative Deamination

Involves the removal of the –NH2 group from Glutamate in the form of ammonium ion (NH4+) & α-

Ketoglutarate is regenerated for transamination. This process occurs in liver & kidney mitochondria, is catalyzed by the enzyme Glutamate dehydrogenase & requires NAD+ as coenzyme, which produces NADH that in turn enters the ETC & forms ATP. Read Chapter 26 from Stoker – Section: 26.3.

The Urea Cycle

Is a series of biochemical reactions, in which urea is produced from NH4+ & Aspartate as nitrogen sources.

The NH4+ produced in oxidative deamination is relatively toxic – it enters the Urea cycle (in mammals) &

is converted to Urea. Urea cycle occurs in the liver – urea is transported in the blood to the kidneys & eliminated from the body via urine. Urea is highly water-soluble but doesn’t contribute to the odour or colour of urine). An adult with normal metabolism excretes about 30g of urea daily in urine, although the exact amount varies with dietary protein intake. The fuel molecule for the Urea cycle is carbamoyl phosphate – produced from NH4

+, CO2, H2O & 2 ATP in the mitochondrial matrix. Part of the UC occurs in the mitochondrion & part in the cytosol. Step 1: Carbamoyl Group Transfer Carbamoyl phosphate transfers its carbamoyl group to Ornithine to from Citruline & Pi. Occurs in the mitochondrial matrix & is catalyzed by Ornithine transcarbamoylase. Step 2: Citruline-Aspartate Condensation Citrulline is transported into cytosol & reacts with Aspartate (from transamination of Glutamate) to produce Argininosuccinate utilizing ATP. Catalyzed by Arginosuccinate synthase. Step 3: Arginosuccinate Cleavage Argininosuccinate is cleaved to Arginine (standard AA) & Fumarate (CAC intermediate). Catalyzed by Argininosuccinate lyase. Step 4: Hydrolysis of Arginine Produces Urea & regenerates Ornithine – transported back into the mitochondria to participate in the Urea cycle again. Catalyzed by Arginase. Urea Cycle Net Reaction



The equivalent of a total 4 ATP molecules are expended in the Urea cycle. 2 ATP molecules are used to produce Carbamoyl phosphate. The equivalent of 2ATP molecules is consumed in Step 2 of the Urea cycle, when ATP is hydrolyzed to AMP. Read Chapter 26 from Stoker – Section: 26.4.

Amino Acid Carbon Skeletons

The removal of –NH2 group from an AA in transamination & oxidative deamination produce an α-keto acid that contain the carbon skeleton from the original AA. Each of 20 AAs have a different carbon skeleton, hence each carbon skeleton undergoes a different degradation pathway, eventually forming 7 degradation products – Pyruvate, Acetyl CoA, Acetoacetyl CoA, α-Ketoglutarate, Succinyl CoA, Fumarate & Oxaloacetate. Glucogenic Amino Acids converted to CAC intermediates can be used to produce glucose via Gluconeogenesis. Ketogenic Amino Acids converted to Acetyl CoA or Acetoacetyl CoA can be used to produce ketone bodies. The AAs that are degraded to Pyruvate are either Glucogenic or Ketogenic, as pyruvate can be metabolized into Oxaloacetate (glucogenic) or Acetyl CoA (ketogenic). There are only 2 purely Ketogenic AAs = Leu & Lys. Read Chapter 26 from Stoker – Section: 26.5.

Amino Acid Biosynthesis

In humans non-essential AAs can be made in the body from other compounds, whereas essential AAs cannot be synthesized in the human body, therefore they have to be supplied in the diet! Non-essential AA in humans are synthesized from: Glycolysis Intermediates – 3-Phosphoglycerate & Pyruvate CAC Intermediates – Oxaloacetate & α-Ketoglutarate The essential AA Phenylalanine – produces Tyrosine via oxidation with molecular O2, NADPH & phenylalanine hydroxylase – lack of this enzyme causes the metabolic disease Phenylkenonuria (PKU). 3 non-essential AA (Alanine, Aspartate & Glutamate) are biosynthesized by transamination of the appropriate α-keto acid. Read Chapter 26 from Stoker – Section: 26.6.

B vitamins & Protein Metabolism

Many B vitamins function as coenzymes in protein metabolism – without these the body would be unable to undertake the various degradation & biosynthesis pathways of AAs. B vitamins involved in protein metabolism: Niacin – as NAD+ & NADH – in oxidative deamination Pyridoxine – as PLP – in transamination reactions All 8 B vitamins – involved in degradation & biosynthesis of AAs Read Chapter 26 from Stoker – Section: 26.9.



Pre / Post class readings & Additional Reading


Chapter 26

Chemical Connections: The Chemical Composition of Urine – p.968.



http://nutrition.jbpub.com/resources/animations.cfm?id=18&debug=0

http://emedicine.medscape.com/article/944996-overview - Ammonia & body systems


23. Outline the digestion & absorption of proteins.

24. Discuss the 3 sources of the amino acid pool.

25. Briefly outline Nitrogen balance & 2 possible imbalances.

26. Describe briefly how amino acids are utilized in the body, include the possible fates of

the amino acid degradation products.

27. Outline Amino acid degradation – where does it take place & what are the 2 stages.

28. Discuss an overview of Transamination, its purpose, the end products & where does it

take place.

29. Outline Oxidative deamination, its purpose, the end products & where does it take place.

30. Discuss the Urea cycle, its purpose, the end products, ATP expenditure & where does it

take place.

31. Discuss the fates of Amino acid carbon skeletons & name the 7 degradation products

formed in this process.

32. Distinguish between Glucogenic & Ketogenic amino acids, giving an example of each.

33. Outline Amino acid biosynthesis in the human body.

34. Briefly discuss Phenylketonuria.

Review Questions



http://nutrition.jbpub.com/resources/animations.cfm?id=18&debug=0

http://emedicine.medscape.com/article/944996-overview



SESSION 26: Integrating the Metabolic Pathways

Code: BIOB111





Session Aims:


Address the learning outcomes listed above. Integrate the knowledge obtained about all the metabolic pathways of Carbohydrates, Lipids &

Amino acids.

Understand the interrelationship among all these pathways & their hormonal control


Key Concept:

Carbohydrate, protein and lipid metabolism are linked by acetyl CoA which goes through the Krebs cycle and electron transport chain to produce energy. This compound is a critical intermediate that centralizes the metabolic reactions and at the same time aids in improving the efficiency. The integration of all metabolic reactions can be explained by flow diagrams.

Session Overview:

This session is a revision session, whereby we are able to pull together the metabolic pathways of Carbohydrates, Lipids and Proteins and show how each of these individual pathways can affect the others. This session will summarize all the learned metabolic pathways in this whole module, including catabolic & anabolic pathways for Carbohydrates, Lipids & Amino Acids.

Session Topics:

Revision of all Metabolic Pathways Studied in BIOB111

Metabolism of Carbohydrates

Metabolism of Lipids

Metabolism of Amino Acid

Interrelationship Among Metabolic Pathways

Feasting

Fasting



Starvation

Absorptive State

Post-Absorptive State


Textbook Location


Chapter 26: Protein Metabolism, pp. 953-978 – Sections: 26.8.



Additional resource:

Tortora, GJ & Grabowski, SR 2003, Principles of Anatomy and Physiology, 10th edn, John Wiley & Sons, New York, NY.

Chapter 25: Metabolism, pp. 907-931

Summary

Integration of Metabolic Pathways

Having studied all the individual metabolic pathways of Carbohydrates, Lipids & Proteins, it is important to understand that these pathways are interrelated & influence one another. This knowledge is paramount to the further studies of Nutrition & Nutritional Biochemistry. Metabolism is essentially about the maintenance & supply of energy sources for ATP production to all tissues. These energy sources can be stored in the absorptive state & mobilized in the post-absorptive state. It is important to look at each pathway & understand the following: 1. What is the overall function of this pathway? 2. What are the molecules entering & exiting this pathway? 3. Under which metabolic states does this pathway operate? 4. When is this pathway turned on / off? 5. In what tissues does this pathway occur? 6. How is this pathway integrated into the function of other tissues & organs? Metabolism interconnects the reserves stored in glycogen, adipose tissue & muscle tissue with the body’s ability to retrieve the glucose, fatty acids, glycerol & amino acids from these stores. Drawing a flow chart of the different metabolic pathways may help to summarize & remember them for future reference. Please understand that the knowledge of these pathways is the basis of the Nutrition studies the students are undertaking at Endeavour College of Natural Health! Read Chapter 26 from Stoker – Section: 26.8.





Chapters 23, 24, 25, 26

Additional Reading

Metabolism video: http://www.youtube.com/watch?v=eFCa5hqBAdE

http://www.youtube.com/watch?v=z3X2UowIzBM Review (no narration)


As such you need to: 1. Look at the overall function of each pathway. This involves knowing the molecules

entering the pathway and those being produced. 2. What are the metabolic states that require the pathway to function ie. When is the pathway

turned on / off? 3. Which tissues use the pathway and why? 4. Is the behaviour of the pathway integrated into the function of organs and tissues?

Metabolic pathways interconnect glycogen, fat, and protein reserves to store and retrieve ATP and glucose. Metabolism should therefore make sense.

Drawing flow diagrams of the different metabolic pathways is a good way to summarize the pathways, and remind you of its functions or reasons for existence.

As you continue to progress with your studies at Endeavour College of Natural Health, these pathways will form a basis on which you will continue to add and grow your understanding of the physiology of the human body. It is therefore, important that you are able to get a good grasp on their functions.

http://www.youtube.com/watch?v=eFCa5hqBAdE

http://www.youtube.com/watch?v=z3X2UowIzBM

biob111 - source.endeavourlearninggroup.com.au · biob111 chemistry and biochemistry ......

Documents