PM Guide to Module 2 - Principles of Biochemistry PDF

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2018 UQ BIOM 1051
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Module 2: Principles of Biochemistry

Luke Guddat

Access to Mastering Biology You will have access through a link in Blackboard to ‘Mastering Biology’, which is linked to the content of your textbook, “Campbell Biology”’. Instructions for access to 'Mastering Biology' are available in the slides for the Introductory Workshop on 19th February 2018 under ‘Lecture Resources’ in ‘Learning Resources’ and you should have established your access to Mastering Biology during that workshop. Please contact one of the course coordinators if you have any issues with accessing Mastering Biology, as you need it for this self-study and also for three On-line Quizzes during the semester.

The Mastering Biology site is best accessed in Google Chrome or Mozilla Firefox. The ‘Concepts & Activities’ listed below can be accessed in the ‘Assignments’, ‘eText’ and ‘Study Area’ on the left panel under ‘Course Materials’.

AFTER you have worked through all activities and concepts below, you can attempt the optional Principles of Biochemistry Test to see how PREPARED you are for this module! The test is located in the Preparatory Material for Module 2-Lecture Resources section of the course Blackboard site.

Concepts & Activities Study the following concepts and activities. The concept can be found in the ‘eText’ section (if purchased) and in the hardcopy of the textbook “Campbell Biology”’. The ‘Activities’ section can be found under the ‘Study Tools’ tab which allows you to select the chapter of interest by use of a drop down menu. Additional multimedia can be found by clicking on the ‘Multimedia’ tab where you will find chapter specific videos.

Refer to the following Concepts & Activities to prepare yourself for this module.

* The content from Chapters 2-4 will be covered in the optional Revision of Chemistry workshops in Week 1 & 2 of the semester, and will be briefly mentioned in the first lecture of Module 2. Chapter 2: The Chemical Context of Life *

Chapter 2: The Chemical Context of Life * 2.1 Concept 2.3 Activity: Hydrogen Bonds 2.2 Concept 2.4 Chapter 3: Water and Life * 3.1 Concept 3.1 Activity: The Polarity of Water 3.2 Concept 3.2 Activity: Cohesion of Water 3.3 Concept 3.3 Activity: Dissociation of Water Molecules Activity: Acids, Bases and pH Chapter 4: Carbon and Molecular Diversity of Life * 4.1 Concept 4.1 4.2 Concept 4.2 Activity: Diversity of Carbon-Based Molecules Activity: Isomers 4.3 Concept 4.3 Activity: Functional Groups Chapter 5: The Structure and Function of Large Biological Molecules 5.1 Concept 5.1 Activity: Making and Breaking Polymers 5.2 Concept 5.2 Activity: Models of Glucose Activity: Carbohydrates 5.3 Concept 5.3 Activity: Lipids 5.4 Concept 5.4 Activity: Protein Functions Activity: Protein Structure 5.5 Concept 5.5 Activity: Nucleic Acid Functions Activity: Nucleic Acid Structure Chapter 8: An Introduction to Metabolism 8.1 Concept 8.1 Activity: Energy Transformations 8.2 Concept 8.2 8.3 Concept 8.3 Activity: The Structure of ATP Activity: Chemical Reactions and ATP 8.4 Concept 8.4

Activity: How Enzymes Work Chapter 9: Cellular Respiration: Harvesting Chemical Energy 9.1 Concept 9.1 Activity: Overview of Cellular Respiration Bioflix: Cellular Respiration 9.2 Concept 9.2 Activity: Glycolysis 9.3 Concept 9.3 Activity: The Citric Acid Cycle 9.4 Concept 9.4 Activity: Electron Transport Glossary Key Molecules of Life Monomers Polymers Carbohydrate Lipid Nucleic acid DNA RNA Nucleotide Protein Amino acid Polypeptide Peptide R group Vitamin Chaperonins Saccharide

Structure

Water & Bonds

Enzymes

Primary structure Amino acid sequence Protein sequence Genetic sequence Mutation Divergence Secondary structure Alpha Helix Beta Pleated Sheet Tertiary structure Conformation Quaternary structure

Water polarity Acid Base/Alkaline pH Covalent bond Non-covalent bond Ionic bond Hydrogen bond Polar bond Hydrophobic Hydrophilic Peptide bond Glycosidic bond

Enzyme Substrate Active site Competitive inhibitor Metabolism ATP Catabolism Anabolism Cellular respiration Glycolysis Citric Acid Cycle Oxidative Phosphorylation Electron transport chain Chemiosmosis Mitochondria

The following Key Concepts will help you identify the areas in knowledge that may need further preparation

1

Biochemistry is the study of life at a molecular level, and includes the structure, function, synthesis and regulation of biological molecules.

2

Biological structures are formed through the chemical reactions between molecules, and are held together by the bonds they form (covalent and noncovalent bonds).

3

Since water is the major component in all cells, molecular bonds and activity are strongly influenced by water polarity (hydrophobic and hydrophilic) and pH (acids and bases).

4

Carbon atoms are the basis of the structure of diverse organic molecules formed by carbon bonding to four other atoms, and their activity is usually determined by the presence of some biologically important functional groups, with some additional atoms including H, O, N, S and P.

5

Isomers are compounds with the same numbers of atoms of the same elements, but different structures and hence different physical and biological properties.

6

Molecules bond to form increasingly complex structures from monomers (monosaccharides, amino acids and nucleotides) to polymers (carbohydrates, proteins and nucleic acids). Lipids are the one class of large biological molecules that do not form polymers.

7

Carbohydrates include sugar and polymers of sugars (with glycosidic bonds joining the monosaccharide building blocks), and have functions in providing fuel for cells, and as storage molecules and structural materials.

8

Lipids are a diverse group of hydrophobic molecules, including fats (constructed from glycerol and fatty acids), phospholipids (with a hydrophobic lipid tail and a hydrophilic phosphate head) that are the basis of cell membrane structure and steroids (with a carbon skeleton of four fused rings), such as cholesterol.

9

Nucleic acids are polymers of monomers called nucleotides, which consist of a five-carbon sugar, a N-containing base and one or more phosphate groups.

The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), store, transmit and help to express hereditary information. One DNA molecule includes many genes. DNA (double helix with two antiparallel 10 polynucleotide chains) in the nucleus of a eukaryotic cell programs the synthesis of messenger RNA (single polynucleotide strand) which dictates protein synthesis in ribosomes. Proteins have diverse structures, resulting in a wide range of functions, because 11 they are linear polymers of amino acids, which are coded by triplets of DNA bases and are joined in the protein by peptide bonds. Amino acids consist of an asymmetric alpha carbon with an amino group, a carboxyl group, a hydrogen atom and a variable R group (side chain), with 20 12 amino acids that are essential to biological function differentiated by the properties of their R groups (non-polar hydrophobic, polar hydrophilic and electrically charged hydrophilic). There are FOUR levels of protein structure, including primary (the linear amino acid sequence), secondary (twisting of the chain stabilised by hydrogen bonds 13 between atoms of the polypeptide backbone) and tertiary (confirmation stabilised by interactions between amino acid side chains) for all proteins and quaternary for some proteins based on the association of two or more polypeptides. Enzymes are a type of protein that are highly specific catalysts that drive chemical reactions involving the binding of an enzyme to a substrate at the active site of the 14 enzyme, resulting in lowering of the activation energy and production of a final product. 15

Enzyme inhibitors are compounds that compete with enzymes by binding to the active site of substrates, slowing down the rate of a reaction.

Metabolism in the body couples an exergonic process to drive an endergonic 16 process, with the energy coupling in cells usually mediated by the nucleotide, adenosine triphosphate (ATP). 17

Cellular respiration involves glycolysis, the citric acid cycle and oxidative phosphorylation, with energy coupling occurring by chemiosmosis.

Extra Reading Material for Key Concepts For detailed information on the Key Concepts, refer to the following Chapter sections and figures in the prescribed textbook, Campbell Biology 11th Ed, Reece et al. (2016) or the previous version, Campbell Biology 10th Ed, Reece et al. (2015).

TEXT Key Concept

Pages Content Reference Description Chapter 2

10th Ed

11th Ed

28-43

28-43

2

Covalent bonds, non-polar and polar types

36-38

36-38

2

Ionic and hydrogen bonds

37-39

37-39

44-55

44-55

51-53

51-53

Chapter 4

56-65

56-65

4

Structure of organic molecules

57-60

57-60

4

Biologically important functional groups

62-63

62-63

5

Isotopes

61-62

61-62

66-91

66-91

Chapter 3 3

Acids, bases, pH

Chapter 5 6

Monomers and polymers

66-67

66-67

7

Carbohydrates

68-72

68-72

8

Lipids

72-75

72-75

9-10

Nucleic acid, DNA, RNA, nucleotides

84-87

84-86

11-12

Proteins, amino acids, polypeptides

75-78

75-78

13

4 Levels of protein structure

78-84

78-83

Chapter 8

141-161

145-165

14-15

Enzyme process, specificity and function

151-157

155-161

16

Metabolism and the role of ATP

142-151

146-155

Chapter 9

162-184

166-188

163-176

166-180

17

Cellular respiration

Figures Multiple references to the same Figures reflect 10th / 11th Ed versions of the same textbook

Key Concept

Pages Content Reference Description 10th Ed

11th Ed

1

3

1

Fig 1.2 Some integrative levels in the hierarchy of biological order

2

Fig 2.10 Covalent bonds

37

37

2-3

Fig 2.11 Polar covalent bonds

37

37

2

Fig 2.12 Electron transfer and ionic bonding

38

38

2

Fig 2.14 A hydrogen bond

39

39

2-3

The formation of hydronium and hydroxide ions (concept 3.3)

51

51

3

Fig 3.10/Fig 3.11 The pH of some aqueous solutions

52

52

4

Fig 4.3 The shapes of three simple organic molecules

59

59

4

Fig 4.9 Some biologically important chemical groups

63

63

5

Fig 4.7 Three types of isomers, compounds with the same molecular formula but different structure

61

61

6

Fig 5.2 The synthesis and breakdown of polymers

67

67

7

Fig 5.3-5.5, 5.7 Structure of carbohydrates

68-71

68-71

8

Fig 5.10 & 5.11 Structure of lipids

73-74

73-74

9

Fig 5.24/5.23 Components of nucleic acids

85

85

10

Fig 5.25/5.24 The structure of DNA and tRNA molecules

87

86

10

Fig 5.23/ Fig 5.22 Gene expression: DNA > RNA -> protein

84

84

11

Fig 5.13 An overview of protein functions

76

76

11

Fig 5.14 The 20 amino acids of proteins

77

77

11

Fig 5.15 making a polypeptide chain

78

78

12

Amino Acid Monomers-R group (concept 5.4)

75

75

13

Fig 5.18 Levels of protein structure

80-81

80-81

14

Fig 8.14 The effect of an enzyme on activation energy

153

157

14

Fig 8.16 The active site and catalytic cycle of an enzyme

154

158

15

Fig 8.18 Inhibition of enzyme activity

156

161

16

Fig 8.6 Free energy changes (ΔG) in exergonic and endergonic reactions

147

151

16

Fig 8.9 The structure and hydrolysis of adenosine triphosphate (ATP)

149

153

17

Fig 9.6 An overview of cellular respiration

167

171

17

Fig 9.9 A closer look at glycolysis

168-169

172-173

17

Fig 9.12 A closer look at the citric acid cycle

171

175

17

Fig 9.13 Free-energy change during electron transport

172

176

17

Fig 9.15 Chemiosmosis couples the electron transport chain to ATP synthesis

174

178...