Biochemistry Cell and Molecular Biology and Genetics An Integrated Textbook 1st Edition by Zeynep Gromley, Adam Gromley 162623535X 9781626235359
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ISBN 10: 162623535X
ISBN 13: 9781626235359
Author: Zeynep Gromley, Adam Gromley
Biochemistry, Cell and Molecular Biology, and Genetics: An Integrated Textbook by Zeynep Gromley and Adam Gromley is the first to cover molecular biology, cell biology, biochemistry (metabolism), and genetics in one comprehensive yet concise resource. Throughout the book, these topics are linked to other basic medical sciences, such as pharmacology, physiology, pathology, immunology, microbiology, and histology, for a truly integrated approach.
Key Highlights
- Easy-to-read text enhances understanding of underlying molecular mechanisms of disease
- Nearly 500 illustrations and tables help reinforce chapter learning objectives
- Textboxes throughout make connections with other preclinical disciplines
- End of unit high-order clinical vignette questions with succinct explanations help integrate basic science topics with clinical medicine
This textbook provides a robust review for medical students preparing for courses as well as exams. Dental, pharmacy, physician’s assistant, nursing, and graduate students in pre-professional/bridge programs will also find this a beneficial learning tool.
Table of contents:
Part I
1 Anatomy of the Cell and Organelles
1.1 The Plasma Membrane
1.2 The Nucleus
1.3 The Endoplasmic Reticulum
1.4 The Golgi Apparatus
1.5 Mitochondria
1.6 Lysosomes
1.7 Peroxisomes
2 DNA Replication, Gene Mutations, and Repair
2.1 The Structure of DNA
2.2 DNA Replication
2.3 Replication of Telomeres Requires Telomerase
2.4 DNA Mutations and Repair
2.5 Nucleotide Excision Repair and Base Excision Repair
2.6 Mismatch Repair
2.7 Non-Homologous End Joining and Homologous Recombination
3 Transcription and Regulation of Transcription
3.1 Link to Microbiology
3.2 Structure and Transcription of Prokaryotic Genes
3.3 Structure and Transcription of Eukaryotic Genes
3.4 Assembly of the initiation complex
3.5 Elongation and Termination
3.6 Regulation Mechanisms of Eukaryotic Transcription
4 Translation and Regulation of Translation
4.1 Genetic Code and Mutations
4.2 Basic Components of Translation
4.3 Translation in Prokaryotes
4.4 Translation in Eukaryotes
4.5 Inhibitors of Translation in Eukaryotes
4.6 Regulation of Translation in Eukaryotes
Part II
5 Cytoskeleton
5.1 Actin Cytoskeleton
5.2 Actin Filaments
5.3 Actin Filament Organization and Dynamics
5.4 Actin Bundles and Networks
5.5 Cell Cortex
5.6 Actin Cytoskeleton Motors Myosins
5.7 Cytokinesis
5.8 Muscle Contraction
5.9 Microtubules and Their Organization
5.10 Microtubule Structure and Dynamics
5.11 Kinesins and Dynein Are Microtubule-based Motors
5.12 Spindle Poles in Mitosis
5.13 Cilia and Flagella
5.14 Intermediate Filaments
6 Protein Sorting, Modifications, and Intracellular Traffic
6.1 Vesicular Tubular Clusters
6.2 Retrieval of ER Cargo Receptors and Soluble ER Proteins
6.3 Clathrin Coated Vesicles
6.4 Specificity of Vesicular Targeting and Membrane Fusion
6.5 Endosomes
6.6 Transport of Hydrolases to the Lysosome
6.7 Receptor Mediated Endocytosis
6.8 Secretory Vesicle Formation
6.9 Insulin Secretion in the Pancreas
7 Membrane Transport
7.1 Passive Transporters
7.2 Active Transporters
7.3 Channels
8 Extracellular Matrix
8.1 Basal lamina
8.2 Collagen
8.3 Fibronectin
8.4 Glycosaminoglycans and Proteoglycans
8.5 Elastic Fibers
8.6 Extracellular Matrix Degrading Enzymes
9 Cell Adhesion and Membrane Junctions
9.1 I-CAMs
9.2 Cadherins
9.3 Integrins
9.4 Fibronectin
9.5 Selectins
9.6 Membrane Junctions in Epithelia
9.7 Tight Junctions
9.8 Adherens Junctions
9.9 Gap Junctions
9.10 Desmosomes
9.11 Hemidesmosomes
10 Signal Transduction
10.1 General Principles of Signal Transduction
10.2 Extracellular Signaling
10.3 Hormones
10.4 Growth Factors
10.5 Cytokines
10.6 Membrane Diffusible Molecules
10.7 Receptors
10.8 Ligand-gated Ion Channel Receptors
10.9 Nicotinic Acetylcholine Receptors
10.10 Enzyme-coupled Receptors
10.11 Receptor Tyrosine Kinases
10.12 Insulin Signaling
10.13 Ras-MAP Kinase Signaling
10.14 Receptor Serine/Threonine Kinases
10.15 Cytokine Receptors
10.16 G-protein–coupled Receptors (GPCRs)
10.17 Second Messengers
10.18 cAMP
10.19 IP3 and DAG
10.20 Ca2 +.
10.21 Other GPCRs
10.22 Receptor Desensitization
10.23 Other Types of Cell-Cell Communication
10.24 Delta-notch Signaling
10.25 Death Signals and Apoptosis
10.26 Synaptic Signaling
10.27 Integrin Signaling
10.28 Nitric Oxide
11 Cell Cycle and Control of the Cell Cycle
11.1 G1 Phase
11.2 S phase
11.3 G2 Phase
11.4 Mitosis
11.5 Prophase
11.6 Prometaphase
11.7 Metaphase
11.8 Anaphase
11.9 Telophase
11.10 Partitioning of Other Organelles
11.11 Cell Cycle Regulation
11.12 Cyclin-Cdk Activation
11.13 Termination of Cyclin Signals
11.14 Cyclin D-Cdk4/6 and Transition to S-phase
11.15 Cyclin E-Cdk2 and S-phase Initiation
11.16 Activation of Mitotic Cyclin-cdk
11.17 Checkpoints in the Cell Cycle
12 Stem Cells and Hematopoiesis
12.1 What is a Stem Cell?
12.2 Stem Cell Potency
12.3 Asymmetric Divisions
12.4 Cellular Differentiation
12.5 Extracellular Matrix
12.6 Stem Cell Genes
12.7 Stem Cell Niches
12.8 Stem Cell Niches of the Skin
12.9 Gut Epithelium Stem Cells
12.10 Notch Signaling in Gut Epithelium
12.11 Neural Stem Cells
12.12 Skeletal Muscle Stem Cells
12.13 Hematopoietic Stem Cells
12.14 Hematopoietic Cell Surface Markers
12.15 Hematopoietic Stem Cell Maintenance
12.16 Exogenous Sources of Stem Cells
12.17 Somatic Cell Nuclear Transfer
12.18 iPS Cells
13 Cell Injury, Apoptosis, and Necrosis
13.1 Cellular Responses to Stress
13.2 Hypertrophy
13.3 Hyperplasia
13.4 Atrophy
13.5 Metaplasia
13.6 Necrosis
13.7 Apoptosis
13.8 Caspases
13.9 Intrinsic Pathway
13.10 Extrinsic Pathway
14 Hallmarks of Cancer and Cancer Biology
14.1 Replicative Capacity
14.2 Persistent Proliferative Signal
14.3 Inactivation of Anti-proliferative Signals
14.4 Resistance to Cell Death
14.5 Angiogenesis
14.6 Metastasis
14.7 Causes of Cancer
14.8 Tests for Mutagenic Potential of Compounds
14.9 Infectious Agents
14.10 Tumor Growth Rate
14.11 Multistep Carcinogenesis
14.12 Histologic Changes Leading to Cancer
15 Molecular Principles of Cancer Treatments and Therapies
15.1 Surgical Therapy
15.2 Chemotherapy
15.3 Mitotic Inhibitors
15.4 Antimetabolites
15.5 DNA Damaging Agents
15.6 Targeted Therapy
15.7 Small Molecule Inhibitors
15.8 Therapeutic Monoclonal Antibodies
15.9 Radiation Therapy
15.10 Cancer Immunotherapy
Part III
16 Enzymes and Enzyme Kinetics
16.1 Enzymes: Definition and Fundamental Properties
16.2 Substrate Binding Site is Highly Specific to Substrate
16.3 The Active Site is the Catalytic Site
16.4 Role of Coenzymes and Cofactors in Enzyme Catalysis
16.5 Principles of Enzyme Catalysis
16.6 Factors Affecting Enzyme’s Activity
16.7 Enzyme Kinetics
16.8 Michaelis-Menten Graph
16.9 Significance of Km and Vmax values
16.10 Determining Vmax and Km by a Lineweaver-Burk or “Double Reciprocal” Plot
16.11 Enzyme Inhibition
17 Regulation of Enzyme Activity
17.1 Reasons for the Regulation of Enzymes
17.2 Zymogen Activation
17.3 Conversion of Proinsulin to Insulin
17.4 Allosteric Regulation
17.5 Covalent Modifications
17.6 Regulation by Protein-Protein Interactions
17.7 Feedback Regulation
17.8 Compartmentalization
18 Structure and Function of Proteins
18.1 Proteogenic Amino Acids
18.2 Hydrophobic Amino Acids
18.3 Hydrophilic Amino Acids
18.4 Structure of Proteins
18.5 The Structure of Hemoglobin
18.6 Structure of Hemoglobin Facilitates Cooperative Binding to Oxygen
18.7 Oxygen Saturation Curve
18.8 Agents That Affect O2 Binding to Hemoglobin
18.9 Fetal Hemoglobin
18.10 Protein Folding Errors
19 Molecular and Biological Techniques
19.1 Gel Electrophoresis
19.2 Polymerase Chain Reaction
19.3 Restriction Enzymes
19.4 Recombinant DNA and DNA Cloning
19.5 Fluorescent Proteins
19.6 Nucleic Acid Probes
19.7 Southern Blot
19.8 DNA Sequencing
19.9 Protein Techniques
19.10 Western Blot
19.11 ELISA
19.12 Southwestern
19.13 Microarray
19.14 Proteomics
19.15 Gene Therapy
19.16 Transgenics and Knockout Technologies
19.17 RNA Interference
20 Plasma Proteins and the Diagnostic Use of Enzymes
20.1 Composition of Blood
20.2 Plasma Proteins and Their Functions
20.3 Clotting Cascade
20.4 Fibrinolysis
20.5 Anticoagulation
20.6 Plasma Proteins in the Diagnosis of Diseases
20.7 Clinical Importance of Plasma Enzymes
20.8 Tumor Biomarkers
Part IV
21 Digestion and Absorption of Carbohydrates
21.1 Link to Pharmacology: Gliflozins Are SGLT2 Inhibitors
21.2 Link to Pharmacology
21.3 Link to Pathology: D-xylose Absorption Test:
21.4 Link to Pathology: Crohn’s Disease
21.5 Link to Pathology: Lactose Intolerance
22 Glycolysis
22.1 Link to Pathology
22.2 Pathways of Glycolysis: Aerobic vs Anaerobic Glycolysis
22.3 Link to Pathology: Lactic acidosis
22.4 Reactions and Regulation of Glycolysis
23 Metabolism of Fructose, Galactose and the Pentose Phosphate Pathway (HMP Shunt)
23.1 Metabolism of Other Sugars
23.2 Fructose Metabolism
23.3 Disorders of Fructose Metabolism
23.4 Sorbitol (polyol) Pathway: Fructose Production
23.5 Galactose Metabolism
23.6 Disorders of Galactose Metabolism
23.7 Pentose Phosphate Pathway (PPP) or Hexose Mono Phosphate (HMP) Shunt
23.8 Roles of NADPH in Cellular Processes
23.9 Classification of G6PD Deficiency
24 Glycogen Metabolism and Regulation
24.1 The Pathways of Glycogenesis and Glycogenolysis
24.2 Glycogenolysis
24.3 Coordinated Regulation of Glycogenesis and Glycogenolysis
24.4 Regulation of Glycogenolysis
24.5 Regulation of Glycogenolysis in the Liver
24.6 Regulation of Glycogenolysis in the Muscle
24.7 Regulation of Glycogenesis
24.8 Glycogen Storage Diseases
25 Gluconeogenesis
25.1 Reactions of Gluconeogenesis
25.2 Substrates for Gluconeogenesis
25.3 Regulation of Gluconeogenesis
26 Pyruvate Dehydrogenase and Tricarboxylic Acid (TCA) Cycle
26.1 TCA cycle intermediates as precursors
26.2 Link to Pathology: Deficiency of Thiamine causes Beriberi and Wernicke-Korsakoff Syndrome
26.3 Link to Pharmacology and Toxicology: Mercury and Arsenic Poisoning
26.4 Link to Pathology: Genetic Mutations of the PDH Complex
26.5 Regulation of the PDH Activity
26.6 Reactions of the TCA Cycle
27 Electron Transport Chain (ETC) and Oxidative Phosphorylation
27.1 Purpose of the Electron Transport Chain (ETC), Localization and its Components
27.2 Regulation of the Rates of ETC and Oxidative Phosphorylation
27.3 Genetic mutations in the mitochondrial DNA
27.4 Sources of NADH and the Entry of NADH Electrons into the ETC
27.5 Inhibitors and Uncouplers of the ETC and Oxidative Phosphorylation
27.6 Inhibitors and Genetic Mutations that Disrupt the Respiratory Chain
28 Oxygen Toxicity and Antioxidants
28.1 Generation of Superoxide Radical (O2-)
28.2 Link to Pharmacology and Toxicology
28.3 Link to Pathology: Myocardial Reperfusion Injury
28.4 Generation of Hydroxyl Radical (OH•)
28.5 Generation of Superoxide Radical by Enzymatic Reactions
28.6 How Do Free Radicals Cause Cell Injury?
28.7 Cellular Defenses against Radical Damage
29 Oxidation of Fatty Acids and Ketogenesis
29.1 Fatty Acid Uptake
29.2 β-oxidation of Fatty Acids
29.3 Regulation of β-oxidation
29.4 Oxidation of Odd-Carbon Fatty Acids
29.5 Oxidation of Mono-Unsaturated Fatty Acids
29.6 Oxidation of Poly-Unsaturated Fatty Acids
29.7 Peroxisomal β-oxidation of Very Long-Chain Fatty Acids (VLCFA)
29.8 Peroxisomal α-oxidation of Branched Chain Fatty Acids
29.9 ω-oxidation of Fatty Acids
29.10 Ketone Bodies
29.11 Ketogenesis
29.12 Oxidation of Ketone Bodies
29.13 Regulation of Ketogenesis
30 Acid Base Chemistry and Acid Base Disorders
30.1 Acids, Bases, and Buffers
30.2 Understanding the pH Scale
30.3 Definition of Acids and Bases
30.4 Plasma Buffer Systems
30.5 Metabolic and Respiratory Components of the Acid-Base Balance
30.6 Primary Acid-Base Disorders
30.7 Compensatory Mechanisms of the Acid-Base Disorders
30.8 Respiratory Acidosis
30.9 Respiratory Alkalosis
30.10 Metabolic Acidosis
30.11 Anion Gap
30.12 Metabolic Alkalosis
31 Glucose Homeostasis and Maintenance of Blood Glucose Concentrations
31.1 Metabolic Fuels
31.2 Glucose Homeostasis
31.3 Action of Insulin and the Regulation of Blood Glucose Levels During the Fed State
31.4 Action of Glucagon and Epinephrine in the Maintenance of Blood Glucose Levels During Fasting and Exercise
Part V
32 Digestion and Absorption of Proteins
32.1 Protein Digestion in the Stomach
32.2 Protein Digestion in the Small Intestine
32.3 Absorption of Amino Acids and Small Peptides by Enterocytes
32.4 Essential Amino Acids
32.5 Intracellular Protein Degradation
33 Nitrogen Metabolism
33.1 Nitrogen Balance
33.2 Nitrogen Entering the Urea Cycle
33.3 Urea Cycle
33.4 Regulation of the Urea Cycle
33.5 Nitrogen in Circulation
34 Amino Acid Metabolism
34.1 Synthesis of Nonessential Amino Acids
34.2 Serine, Glycine, Alanine and Cysteine are Derived from the Intermediates of Glycolysis
34.3 Glutamate, Glutamine, Proline, Arginine, Aspartate and Asparagine are Derived from the Intermediates of the TCA Cycle
34.4 Amino Acids Degradation
34.5 Amino Acids Degraded to Intermediates of the TCA Cycle
34.6 Methionine, Threonine, Valine and Isoleucine are Degraded to Propionyl CoA.
34.7 Phenylalanine and Tyrosine Metabolism
35 Amino Acid Derivatives
35.1 Introduction
35.2 Cofactors Important for the Synthesis of Amino Acid Derivatives
35.3 Action and Fate of Neurotransmitters
35.4 Derivatives of Tyrosine
35.5 Derivatives of Tryptophan
36 Porphyrin Heme Metabolism and Iron Homeostasis
36.1 Heme Synthesis
36.2 Heme Degradation
36.3 Iron Homeostasis
37 Nucleotide Metabolism
37.1 Do Novo Synthesis versus Salvage Pathways of Purines and Pyrimidines
37.2 Synthesis of 5-Phosphoribosyl-Pyrophosphate (PRPP)
37.3 Synthesis of Deoxyribonucleotides (dNDP) by Ribonucleotide Reductase (RR)
37.4 De Novo Purine Synthesis
37.5 Regulation of De Novo Purine Synthesis
37.6 Purine Salvage Pathway
37.7 Purine Degradation
37.8 Purine Nucleotide Cycle in Muscle
37.9 De Novo Pyrimidine Synthesis
37.10 Pyrimidine Salvage Pathways
37.11 Degradation of Pyrimidines
38 Vitamins in One-Carbon Metabolism
38.1 Absorption of Folate
38.2 Tetrahydrofolate Derivatives Function as One-Carbon Donors in Nucleotide Synthesis
38.3 Functions of Vitamin B12
38.4 Folate Trap Hypothesis
38.5 Absorption of Vitamin B12
Part VI
39 Digestion and Absorption of Lipids
39.1 Fatty Acids Nomenclature and Classification
39.2 Cis vs Trans Unsaturated Fatty Acids
39.3 Digestion and Absorption of Dietary Lipids
39.4 Function of Bile Acids and Bile Salts in the Digestion of Lipids
39.5 Synthesis and Fate of Chylomicrons
40 Synthesis of Fatty Acids and Triacylglycerols
40.1 Regulation of Fatty Acid Synthesis
40.2 Further Elongation
40.3 Desaturation of Fatty Acids
40.4 Synthesis of Triacylglycerols
41 Metabolism of Membrane Lipids and Lipid Derivatives
41.1 Glycerophospholipids
41.2 Synthesis of Glycerophospholipids
41.3 Functions of Glycerophospholipids
41.4 Degradation of Glycerophospholipids
41.5 Eicosanoid Synthesis
41.6 Cyclooxygenase Pathway
41.7 Functions of Prostaglandins
41.8 Lipoxygenase Pathway
41.9 Metabolism of Sphingolipids
42 Cholesterol Metabolism
42.1 Biosynthesis of Cholesterol
42.2 Regulation of Cholesterol Synthesis
42.3 Absorption of Cholesterol
42.4 Fate of Cholesterol
42.5 Bile Acid Synthesis
43 Blood Lipoproteins
43.1 Composition of Lipoproteins
43.2 Chylomicrons
43.3 VLDL to LDL Pathway
43.4 IDL and LDL
43.5 HDL
43.6 Receptor Mediated Lipoprotein Endocytosis
43.7 Atherosclerosis
43.8 Role of Lipoprotein (a) in Heart Disease
44 Steroid Hormones and Vitamin D
44.1 Classes of Intracellular Receptors
44.2 The Common Pathway of Steroid Hormone Synthesis
44.3 Synthesis of Cortisol and Physiological Effects of Cortisol
44.4 Synthesis of Aldosterone and Physiological Effects of Aldosterone
44.5 Synthesis of Sex Hormones
44.6 Synthesis of Vitamin D
44.7 Calcium Hemostasis and Bone Remodeling
45 Nutrition and Metabolism
45.1 Recommendations for Macronutrient Composition of the Diet
45.2 Carbohydrates and Their Health Effects
45.3 Proteins and Their Health Effects
45.4 Fats and Their Health Effects
45.5 The Ratio of ω-3/ω-6 PUFA in Diet
45.6 Cholesterol and Its Health Effects
45.7 Thyroid Hormones Regulate the Metabolic Rate
45.8 Hormones that Regulate Eating, Appetite, and Weight Homeostasis
45.9 Unbalanced Diet: Excess Energy Intake
45.10 Obesity Causes Insulin Resistance and Metabolic Syndrome
45.11 Mechanisms of Insulin Resistance
45.12 Type-2 Diabetes Mellitus
46 Vitamins and Minerals
46.1 Lipid-Soluble Vitamins
46.2 Vitamin A
46.3 Vitamin D
46.4 Vitamin E
46.5 Vitamin K
46.6 Water-Soluble Vitamins
46.7 Thiamine (B1)
46.8 Riboflavin (B2)
46.9 Niacin (B3)
46.10 Pantothenic Acid (B5)
46.11 Pyridoxine (B6)
46.12 Biotin (B7)
46.13 Folate (B9)
46.14 Cobalamin (B12)
46.15 Vitamin C
46.16 Minerals
Part VII
47 DNA Packaging and Meiosis
47.1 DNA Packaging
47.2 Meiosis
48 Cytogenetics: Chromosomal Basis of Human Diseases
48.1 Parts of a Chromosome
48.2 Chromosome Identification
48.3 Chromosome Abnormalities
48.4 Aneuploidies
48.5 Structural Variations
48.6 Translocations
48.7 Mosaicism
48.8 Cytogenetic Clinical Laboratory Tests
49 Single Gene Disorders: Autosomal Dominant and Recessive Inheritance
49.1 Punnett Square
49.2 Pedigree Analysis
49.3 Pedigree Analysis of Autosomal Dominant and Recessive Diseases
49.4 Genome Analysis Can Reveal Mendelian Inheritance Patterns
50 Sex-linked and Non-traditional Modes of Inheritance
50.1 Sex Linked Inheritance
50.2 X-linked Dominant Inheritance
50.3 X-Linked Recessive Inheritance
50.4 Mitochondrial Inheritance
50.5 Non-Mendelian Inheritance
51 Population Genetics
51.1 Example 1: Determining Carrier Frequency in a Population
51.2 Example 2: Determining Genotype Frequencies
51.3 Factors in Nature that Disrupt the Hardy-Weinberg Equilibrium
52 Genomic Imprinting and Epigenetics
52.1 Link to Pathology
53 Gene Interactions and Multifactorial Inheritance
53.1 Polygenic Inheritance
53.2 Multifactorial Inheritance
53.3 Determination of Recurrence Risk for Multifactorial Diseases
53.4 Traditional Ways to Study Multifactorial Traits
53.5 Genome-Wide Association Studies
54 Personalized Medicine
54.1 Cytochrome p450
54.2 Pharmacodynamics
54.3 Pharmacogenomics
55 Developmental Genetics
55.1 Overview of Embryonic Development
55.2 Tissues and Organs that Derive from Ectoderm
55.3 Tissues and Organs that Derive from Mesoderm
55.4 Tissues and Organs that Derive from Endoderm
55.5 Molecular Mediators of Development and Their Functions
55.6 Axis Specification
55.7 Limb Development
56 Cancer Genetics
56.1 Li-Fraumeni Syndrome
56.2 Hereditary Breast and Ovarian Cancer syndrome
56.3 von Hippel-Lindau Syndrome
56.4 APC-Associated Polyposis Conditions
56.5 Lynch syndrome
56.6 Retinoblastoma
56.7 Neurofibromatosis
56.8 Multiple Endocrine Neoplasia type 2
56.9 Multiple Endocrine Neoplasia type 1
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Tags: Zeynep Gromley, Adam Gromley, Biochemistry, Biology