Fall
2020
Biochemistry
Foundations of Medicine I:
Introduction to Human Biology
FM1010
ANTHONY GOODINGS
, 1
Table of Contents
Learning Outcomes ................................................................................................................ 5
1. Introduction to Biochemistry .............................................................................................. 5
Biochemistry..................................................................................................................................5
Chemistry of Living Mater ..............................................................................................................5
Six Kingdoms of Life .......................................................................................................................5
Cells ..............................................................................................................................................5
Molecules than Underpin Cellular Function ....................................................................................6
Biomolecules .................................................................................................................................6
Elements that make up biomolecules: ................................................................................................................. 6
Shared Elements in Cells ................................................................................................................6
Animal Cell Cytoskeleton................................................................................................................6
2. Water in Biological Systems ............................................................................................... 7
Water in Cells ................................................................................................................................7
Ionization of Water and pH ............................................................................................................8
pH in Blood ........................................................................................................................................................... 8
3. Bioenergetics ..................................................................................................................... 9
Energy ...........................................................................................................................................9
ATP ........................................................................................................................................................................ 9
Energy Coupling .................................................................................................................................................... 9
Gibb’s Free Energy and the Laws of Thermodynamics ................................................................... 10
4. Nucleic Acids .................................................................................................................... 11
Information Flow in Cells.............................................................................................................. 11
Composition ................................................................................................................................ 11
DNA Structure ..................................................................................................................................................... 12
DNA Packaging .................................................................................................................................................... 12
5. RNA Structure .................................................................................................................. 13
Types of RNA ............................................................................................................................... 14
Transcription of RNA .................................................................................................................... 14
Transcription Steps ............................................................................................................................................. 14
Anatomy of a Typical Eukaryotic Gene ............................................................................................................... 14
Information Flow ................................................................................................................................................ 15
6. Proteins ........................................................................................................................... 15
Variation of Function ................................................................................................................... 15
Composition of Proteins ............................................................................................................... 15
Amino Acids ........................................................................................................................................................ 15
, 2
Classification of AAs ..................................................................................................................... 16
Non-Polar, Aliphatic R-Groups............................................................................................................................ 16
Aromatic R-Groups ............................................................................................................................................. 17
Polar, Uncharged R-Groups ................................................................................................................................ 17
Positively Charged R-Groups .............................................................................................................................. 17
Negatively Charged R-Groups ............................................................................................................................ 17
Summary of Amino Acids ................................................................................................................................... 18
Uncommon Amino Acids .................................................................................................................................... 18
Formation of Peptide Bonds ............................................................................................................................... 18
7. Protein Synthesis (Translation) ......................................................................................... 19
Genetic Code ............................................................................................................................... 19
Components for Synthesis of Proteins .......................................................................................... 20
tRNA .................................................................................................................................................................... 20
Ribosomes .......................................................................................................................................................... 21
Eukaryotic Protein Synthesis ........................................................................................................ 21
Initiation ............................................................................................................................................................. 21
Elongation ........................................................................................................................................................... 21
Termination ........................................................................................................................................................ 22
Making the Most of an mRNA ...................................................................................................... 22
Antibiotic Inhibitors of Protein Synthesis ...................................................................................... 22
After Translation .......................................................................................................................... 22
8. Protein Structure and Folding ........................................................................................... 23
Primary Structures: ...................................................................................................................... 23
Importance of Primary Structure ....................................................................................................................... 23
Secondary Structure of Proteins ........................................................................................................................ 23
Tertiary Structure of Proteins ............................................................................................................................. 24
Quaternary Structure ......................................................................................................................................... 24
Protein Folding ............................................................................................................................ 24
Disease................................................................................................................................................................ 25
9. Functional Divisions of Proteins ........................................................................................ 26
Ligands / Ligand Binding Proteins .................................................................................................26
Receptors as Ligand Binding Proteins ................................................................................................................ 26
Enzymes ...................................................................................................................................... 26
Enzyme Nomenclature ....................................................................................................................................... 27
How Enzymes Work ............................................................................................................................................ 27
Enzymes and Disease.......................................................................................................................................... 28
Coenzymes, Protein Folding, and Diseases ........................................................................................................ 28
Enzymes that Covalently Modify Proteins.......................................................................................................... 28
ATP ...................................................................................................................................................................... 29
Myristoylation .................................................................................................................................................... 29
Ubiquitination ..................................................................................................................................................... 29
10. Carbohydrates and Glycobiology .................................................................................... 30
Carbohydrates ............................................................................................................................. 30
, 3
Monosaccharides................................................................................................................................................ 30
Carbohydrate Nomenclature and Structure ...................................................................................................... 31
Blood-Glucose Measurements in the Diagnosis and Treatment of Diabetes .................................................... 31
Disaccharides ............................................................................................................................... 31
Polysaccharides ........................................................................................................................... 32
Oligo- and Polysaccharides as Information Carriers .......................................................................................... 33
Glycoproteins...................................................................................................................................................... 33
Role of Oligosaccharides in Recognition and Adhesion at the Cell Surface ....................................................... 34
11. Lipids ............................................................................................................................. 35
Fatty Acids ................................................................................................................................... 35
Effects of Saturation ........................................................................................................................................... 35
Nomenclature ..................................................................................................................................................... 35
Free Fatty Acids .................................................................................................................................................. 36
Essential Fatty Acids ........................................................................................................................................... 36
Triglycerides ................................................................................................................................ 36
Function .............................................................................................................................................................. 36
Phospholipids and Glycolipids ...................................................................................................... 36
Sterols ......................................................................................................................................... 37
Lipid Metabolism Disorders ................................................................................................................................ 37
12. Cellular Organisation ..................................................................................................... 38
Prokaryotic Cell............................................................................................................................ 38
Organelles of the Eukaryotic Cell .................................................................................................. 38
Transport of Materials Within Cells .............................................................................................. 40
Relevance of Intracellular Trafficking to Disease ........................................................................... 40
Lecture 13: DNA and RNA Structure...................................................................................... 41
The Genetic Material.................................................................................................................... 41
Lecture 14: Principles of Nucleic Acids Hybridization ............................................................. 45
Denaturation of DNA ................................................................................................................... 45
Lecture 15: RNA Transcription .............................................................................................. 47
RNA Synthesis/Transcription Mechanism ..................................................................................... 50
Lecture 16: Chromatin Structure ........................................................................................... 54
Complexes Formed in Eukaryotic DNA .......................................................................................... 54
Chromatin Organisation ..................................................................................................................................... 54
Lecture 17: The -omes .......................................................................................................... 57
Lecture 18: DNA Replication ................................................................................................. 60
Lecture 19: Polymerase Chain Reaction (PCR) ....................................................................... 70
Lecture 20: Regulation Prokaryotes ...................................................................................... 74
2020
Biochemistry
Foundations of Medicine I:
Introduction to Human Biology
FM1010
ANTHONY GOODINGS
, 1
Table of Contents
Learning Outcomes ................................................................................................................ 5
1. Introduction to Biochemistry .............................................................................................. 5
Biochemistry..................................................................................................................................5
Chemistry of Living Mater ..............................................................................................................5
Six Kingdoms of Life .......................................................................................................................5
Cells ..............................................................................................................................................5
Molecules than Underpin Cellular Function ....................................................................................6
Biomolecules .................................................................................................................................6
Elements that make up biomolecules: ................................................................................................................. 6
Shared Elements in Cells ................................................................................................................6
Animal Cell Cytoskeleton................................................................................................................6
2. Water in Biological Systems ............................................................................................... 7
Water in Cells ................................................................................................................................7
Ionization of Water and pH ............................................................................................................8
pH in Blood ........................................................................................................................................................... 8
3. Bioenergetics ..................................................................................................................... 9
Energy ...........................................................................................................................................9
ATP ........................................................................................................................................................................ 9
Energy Coupling .................................................................................................................................................... 9
Gibb’s Free Energy and the Laws of Thermodynamics ................................................................... 10
4. Nucleic Acids .................................................................................................................... 11
Information Flow in Cells.............................................................................................................. 11
Composition ................................................................................................................................ 11
DNA Structure ..................................................................................................................................................... 12
DNA Packaging .................................................................................................................................................... 12
5. RNA Structure .................................................................................................................. 13
Types of RNA ............................................................................................................................... 14
Transcription of RNA .................................................................................................................... 14
Transcription Steps ............................................................................................................................................. 14
Anatomy of a Typical Eukaryotic Gene ............................................................................................................... 14
Information Flow ................................................................................................................................................ 15
6. Proteins ........................................................................................................................... 15
Variation of Function ................................................................................................................... 15
Composition of Proteins ............................................................................................................... 15
Amino Acids ........................................................................................................................................................ 15
, 2
Classification of AAs ..................................................................................................................... 16
Non-Polar, Aliphatic R-Groups............................................................................................................................ 16
Aromatic R-Groups ............................................................................................................................................. 17
Polar, Uncharged R-Groups ................................................................................................................................ 17
Positively Charged R-Groups .............................................................................................................................. 17
Negatively Charged R-Groups ............................................................................................................................ 17
Summary of Amino Acids ................................................................................................................................... 18
Uncommon Amino Acids .................................................................................................................................... 18
Formation of Peptide Bonds ............................................................................................................................... 18
7. Protein Synthesis (Translation) ......................................................................................... 19
Genetic Code ............................................................................................................................... 19
Components for Synthesis of Proteins .......................................................................................... 20
tRNA .................................................................................................................................................................... 20
Ribosomes .......................................................................................................................................................... 21
Eukaryotic Protein Synthesis ........................................................................................................ 21
Initiation ............................................................................................................................................................. 21
Elongation ........................................................................................................................................................... 21
Termination ........................................................................................................................................................ 22
Making the Most of an mRNA ...................................................................................................... 22
Antibiotic Inhibitors of Protein Synthesis ...................................................................................... 22
After Translation .......................................................................................................................... 22
8. Protein Structure and Folding ........................................................................................... 23
Primary Structures: ...................................................................................................................... 23
Importance of Primary Structure ....................................................................................................................... 23
Secondary Structure of Proteins ........................................................................................................................ 23
Tertiary Structure of Proteins ............................................................................................................................. 24
Quaternary Structure ......................................................................................................................................... 24
Protein Folding ............................................................................................................................ 24
Disease................................................................................................................................................................ 25
9. Functional Divisions of Proteins ........................................................................................ 26
Ligands / Ligand Binding Proteins .................................................................................................26
Receptors as Ligand Binding Proteins ................................................................................................................ 26
Enzymes ...................................................................................................................................... 26
Enzyme Nomenclature ....................................................................................................................................... 27
How Enzymes Work ............................................................................................................................................ 27
Enzymes and Disease.......................................................................................................................................... 28
Coenzymes, Protein Folding, and Diseases ........................................................................................................ 28
Enzymes that Covalently Modify Proteins.......................................................................................................... 28
ATP ...................................................................................................................................................................... 29
Myristoylation .................................................................................................................................................... 29
Ubiquitination ..................................................................................................................................................... 29
10. Carbohydrates and Glycobiology .................................................................................... 30
Carbohydrates ............................................................................................................................. 30
, 3
Monosaccharides................................................................................................................................................ 30
Carbohydrate Nomenclature and Structure ...................................................................................................... 31
Blood-Glucose Measurements in the Diagnosis and Treatment of Diabetes .................................................... 31
Disaccharides ............................................................................................................................... 31
Polysaccharides ........................................................................................................................... 32
Oligo- and Polysaccharides as Information Carriers .......................................................................................... 33
Glycoproteins...................................................................................................................................................... 33
Role of Oligosaccharides in Recognition and Adhesion at the Cell Surface ....................................................... 34
11. Lipids ............................................................................................................................. 35
Fatty Acids ................................................................................................................................... 35
Effects of Saturation ........................................................................................................................................... 35
Nomenclature ..................................................................................................................................................... 35
Free Fatty Acids .................................................................................................................................................. 36
Essential Fatty Acids ........................................................................................................................................... 36
Triglycerides ................................................................................................................................ 36
Function .............................................................................................................................................................. 36
Phospholipids and Glycolipids ...................................................................................................... 36
Sterols ......................................................................................................................................... 37
Lipid Metabolism Disorders ................................................................................................................................ 37
12. Cellular Organisation ..................................................................................................... 38
Prokaryotic Cell............................................................................................................................ 38
Organelles of the Eukaryotic Cell .................................................................................................. 38
Transport of Materials Within Cells .............................................................................................. 40
Relevance of Intracellular Trafficking to Disease ........................................................................... 40
Lecture 13: DNA and RNA Structure...................................................................................... 41
The Genetic Material.................................................................................................................... 41
Lecture 14: Principles of Nucleic Acids Hybridization ............................................................. 45
Denaturation of DNA ................................................................................................................... 45
Lecture 15: RNA Transcription .............................................................................................. 47
RNA Synthesis/Transcription Mechanism ..................................................................................... 50
Lecture 16: Chromatin Structure ........................................................................................... 54
Complexes Formed in Eukaryotic DNA .......................................................................................... 54
Chromatin Organisation ..................................................................................................................................... 54
Lecture 17: The -omes .......................................................................................................... 57
Lecture 18: DNA Replication ................................................................................................. 60
Lecture 19: Polymerase Chain Reaction (PCR) ....................................................................... 70
Lecture 20: Regulation Prokaryotes ...................................................................................... 74
