Courses Outline

Module – 1 (Basic Medical Biochemistry and Research Methodology)

1.1. Structure and functions of Biomolecules:

Learning objectives

At the end of the course student should be able to

1. Apply the basic theoretical & practical knowledge of biomolecules in cells and their structure & function relationship in establishment of diagnostic, differential diagnosis, prognostic value of laboratory tests
2. Perform laboratory procedures systematically
3. Select the appropriate tools and techniques of quality control and to identify and assess systematic errors in finding made in the laboratory, control of quality of test performed in the laboratory (Internal & external quality control)
4. Understand the areas of management of laboratory

Contents

1. Biomolecules and cell

Introduction to Biochemistry

Major complex molecule of cells and organelles of eukaryotes

2. Carbohydrate

Chemical structure and function of different classes of carbohydrate found in human body; monosaccharide, disaccharides, polysaccharides, homopolysaccharide, heteropolysaccharide and glycoprotein

3. Amino acid and Protein

Amino acids

Classification according to their structure and charge

Role of amino acid in protein conformation

Protein

Classification of protein

Structural organization of protein

Protein folding and pathologic consequence from perturbation of protein conformation

                        Chaperone

                        Alzheimer's disease, Parkinson’s disease, amyloidosis, Prions disease etc.

Hemoglobin and myoglobin

            Structure and function relationship of hemoglobin

            Structure and function relationship of myoglobin

            Hemoglobinopathies and biomedical implications; HbS, HbM, thalassemia etc.

4. Lipid

Chemical structure and role of different lipids in the body

Fatty acids

Triacylglycerol

Complex lipids; Phospholipids and glycolipids

Lipoproteins

Cholesterol

5. Nucleic acids

Nucleotides

Chemical composition and structure of nucleic acids; DNA and RNA

        6. Extracellular Matrix

                        Molecular composition and structure of extracellular matrix

            Extracelluar matrix in tissue homeostasis and ageing

1.2. Membrane Biochemistry

Objectives

 At the end of the course, students should be able to

1. explain the components, structural organization and functional aspects of biologic membrane
2. understand the fluid mosaic model of membrane structure
3. describe the chemical structure and properties of components in membrane architecture
4. understand the concept of membrane transport process and recognize the importance of transporters and ion channels in membrane functions
5. describe the variety of disorders resulting from abnormalities of membrane structure and functions.
6. understand the  separation and isolation techniques of specific membrane components

Contents

1. Membrane Biology

Structural and molecular basis of biologic membrane

The major lipids in mammalian membranes

Membrane proteins

The fluid mosaic model of membrane structure

Architecture of lipids and proteins in membrane

Turnover of membrane lipids and proteins

Lateral diffusion of lipids and certain proteins

Transverse movements of lipids across the membrane (Flip flop)

Dynamic nature of membrane

Isolation of specific membrane components by appropriate separation techniques

       Isolation of many membranes in a cell plasma membrane, mitochondrial

membrane, nuclear membrane, lysosomal, peroxisomal, endoplasmic 

reticulum, golgi apparatus and others (involving centrifugation)

Determining lipid composition (TLC, GLC and GLC-MS enzymic degradation)

Determination of protein composition (SDS-Gel electrophoresis), complete analysis

of proteins (Sequencing, X-ray crystallography, NMR spectroscopy)

Functions of membrane proteins: measure specific enzymes (eg. Na⁺-K⁺ ATP ase)

Cell biology approach: Use of fluorescent dyes

Diseases or pathologic states resulting from or attributed to  abnormalities of membranes

Mutation in membrane receptors and ion channels 

1. Achondroplasia
2. Familial hypercholesterolemia
3. Cystic fibrosis

Receptor defect due to infection

1. Cholera
2. Recurrent salmonella infection

 Structural abnormalities of membrane

Red cell abnormalities

Lysosomal abnormalities

Hyaline membrane disease

2.1. Enzymology and Bioenergetics

1. Characteristics of enzyme

Definition and Classification,

Basic principle of enzyme catalyzed reaction

Chemical nature of enzyme; elements of enzyme structure that explain their substrate specificity and catalytic activity

2. Enzyme kinetics

Michaelis-Menten kinetics

Factors affecting velocity of enzyme reaction

Enzyme Inhibition and kinetic analysis of different types of inhibitors

Drug targeting on enzyme-catalyzed process

Regulation of enzyme activity in body homeostasis

            Regulation of catalytic efficiencies

            Regulation of quantity

       3. Enzyme in clinical medicine

            Laboratory enzymology

            Enzyme and isoenzyme in diagnosis

            Liver enzymes and drug metabolism

2.2. Bioenergetics

1. Application of thermodynamics to biological system

Gibb’s free energy

Free energy change

Coupling of exergonic and endergonic reactions in cellular metabolism

2. Activated carrier molecule and the energy currency of the cell
3. Energy rich compounds  and their role in metabolism
4. Role of mitochondria in ATP synthesis
5. Basal metabolic rate
6. Energy balance and obesity
7. Free radicles and other theories of ageing process

3. Intermediary metabolism

      1. Introduction to metabolism

Major metabolic pathways and their significance

Role of enzyme and compartmentation in regulation of metabolism.

      2. Carbohydrate metabolism

Digestion & absorption of carbohydrate in human GI tract

Major pathways of glucose metabolism; Glycolysis, CAC, the Pentose Phosphate Pathway, Gluconeogenesis and Glycogen metabolism

Blood glucose homeostasis

      3. Lipid metabolism

Digestion & absorption of lipids in human GI tract

Metabolisms and their regulation of major lipids

Fatty acid metabolism

TAG metabolism

Cholesterol metabolism

Ketone body metabolism

       4. Lipid transport and storage

Lipoproteins

Adipose tissue and TAG storage

        5. Disease associated with impaired lipid metabolism

Dyslipidemia and coronary artery disease

Lipid storage diseases

       6. Protein metabolism

Digestion & absorption of protein in in human GI tract

Biosynthesis of non-essential amino acids, synthesis of specialized compounds derived from amino acids

Protein turnover

Amino acid Catabolism

Fate of amino nitrogen

Fate of carbon skeleton

Clinical importance of hyperammonemia

      7. Nucleotide metabolism

Purine metabolism

Biosynthesis of purine nucleotides and its regulation

Catabolism of purine nucleotides and its clinical importance

Pyrimidine metabolism

Biosynthesis of pyrimidine nucleotides its regulation

Catabolism of pyrimidine nucleotides and its clinical importance

     8. Inborn error of amino acid metabolism

4. Research Methodology and Biostatistics

Objective

At the end of this chapter students are expected to gain knowledge on:

1. Understand the basic biostatics concepts and skills.
2. Choose appropriate statistical tests and bio-statistics soft wares in Biomedical fields

    Content

1. Core statistical concepts.
2. Hypothesis testing, errors and estimation
3. Exploratory data analysis
4. Analysis of variance
5. Analysis of contingency tables
6. Logistic Regression
7. Usage of bio-statistics soft wares

Laboratory work

    1. Principles of various laboratory analytical methods

Basic principles of various laboratory analytical methods

Steps in collection of blood samples and anticoagulants

Preparation of reagents

Principles in making a solution

Molarity, percent solution

Storage of  stock solution

Buffer solution    

     2. Basic Laboratory Procedures

2.1  Photometry (Colorimetry, spectrophotometry and enzyme linked immunosorbent                         assay)

• Basic components of colorimeter
• Lambert’s Beer law
• Auto analyzers

Types of autoanalyzers; semi-auto analyzer, Batch analyzer, random access auto-analyzer

Steps in automated system

Operation procedures and Responsibilities in maintenance of  analyzer

2.2  Separation techniques (Electrophoresis and Chromatography)

            -  Electrophoresis

Introduction to general principles of electrophoresis

Force acting on the component in an electrophoresis system

Factors affecting electrophoresis,

Types of electrophoresis and their applications

- cellulose acetate

- agarose gel, polyacrylamide gel electrophoresis

              2.3. Chromatography

Introduction to general principle of chromatography

Classification of chromatography

Principle of Partition Chromatography & procedure

Other chromatographic techniques- Adsorption chromatography, thin layer chromatograph (TLC), Gas Liquid Chromatography (GLC), High Performance Liquid Chromatography (HPLC), Affinity Chromatography, Ion exchange Chromatography

      3. Laboratory safety

Laboratory common hazards, safety rule and safety procedures

Laboratory safety levels

      4. Quality assurance and quality control of the laboratory

Definition of quality assurance and quality control in the laboratory

Quality control tests in clinical laboratory

Quality Control Manual vs Automation in clinical laboratory

Calibration curve

The Levey-Jennings (L-J) chart

                        Internal and external quality control program- External Quality Control

                        program

Importance of quality control of the laboratory procedures in diagnosis and

management

      5. Blood chemistry

Measures chemical in the sample of blood and its association with functions of organ and

metabolism. It is important for diagnosis and prognosis.  It includes measure of enzyme

activity, lipids, glucose etc.)

      6. Laboratory management; Principles and processes

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Module -2

1. Human genome organization, nucleic acids and gene expression and proteomics

Objective

At the end of this chapter students are expected to

1. Describe human genome, structure and organization of chromosome
2. Describe the mechanism and features of DNA replication and its regulation
3. Comprehend DNA damage, repair mechanisms and mutation and how mutation affects phenotype and diseases
4. Describe gene expression and its regulation with the understanding on epigenetics
5. Understand the fundamental principles of proteomics and its importance in health and disease.
6. Discuss the basic and advanced techniques necessary for analyzing proteomic

Contents

1. Chromosome structure and genome organization
2. DNA replication and its control
3. DNA damage and repair
4. Types & effects of gene mutation and chromosomal translocation
5. Process and regulation of gene expression and protein targeting

6. Genetic code and mutation and phenotypic expression
7. Polygenic and monogenic diseases
8. Proteomic methods and its application to biological problems

    7.   Polygenic and monogenic diseases

2. Molecular oncology (1 credit)

Objective

At the end of this chapter students are expected to

1. Acquire knowledge on ell division, cell cycle regulation and check points and its regulation in mammals
2. Explain the balance of oncogene products, tumor suppressor gene products and DNA repair enzymes in the tissue homeostasis and the development of cancer
3. Basic principles of human molecular genetics and its applications in the improvement of human health.

Contents

       1.  Cell proliferation and its regulation

    Meiosis, Mitosis and the normal cell cycle

Role of cyclin and cyclin dependent protein kinase in cell cycle progression

Retinoblastoma and restriction point

Cell cycle check points and its regulatory proteins

2.  Oncogenes and its importance in the development of cancer

              Protooncogene and oncogene

              Mechanisms of oncogene products in oncogenesis               

3.  Apoptosis

Stimuli for apoptosis

Mechanism of apoptosis

Deviation from normal apoptotic process and diseases

3.  Population Genetics and Bioinformatics

Objectives

At the end of the course, students should be able to

1.  Explain the basic concepts of genetics and population genetics

2.  Discuss the Darwin theory of evolution and Mendel’s law of inheritance

3.  Understand the age of molecular genetics

4.  Discuss the principle behind the nucleotides and protein sequence alignment, PCR

     primer design and protein-protein interactions.

      5. Understand the principles of phylogenetic tree and on interpretation of the results

      6. Edit and analyze the sequences using relevant square such as BioEdit and MEGA.

    Contents

1. History of genetics

Cell theory

Mendel’s law of heredity

Darwin’s theory of evolution

Chromosome theory of inheritance

   Elucidation of DNA structure to exploration of the human genome project

2. Genetic epidemiology

1. DNA variation across the human genome and Genome-wide association study (GWAS)
2. Allele frequency, Hardy-Weinberg equilibrium and Linkage equilibrium
3. High throughput genotyping and sequencing
4. Applications of GWAS
5. Database-NCBT, SNP, UCSC Genome Browser protein database.
6. Base local Alignment Search Tool (BLAST) Nucleotide database (BLAST)
7. Protein BLAST (BLASTP)
8. Sequence Alignment (BioEdit, MEGA)
9. Principle of phylogentis Tree Drawing
10. Protein structure prediction, Database for protein structure 
11. Protein – Protein interaction Analysis

4. Biochemical immunology

Objectives

At the end of the student course, students should have a good understanding of ;

1. The molecular and cellular mechanisms in the development and regulation of the immune response
2. The molecular and biochemical basis of manipulation of immune system in the treatment of disease, autoimmunity  and cancer
3. The major immunological  laboratory techniques and their application to both clinical analysis and biomedical research
4. Immunodiagnostic and laboratory skills and techniques

Contents

1. Cells of immune system and messenger proteins

2. Three levels of defense

Physical barrier

Innate immunity

Adaptive immunity

3. Complement proteins

4. Cellular basis of antibody production

5. The structure and function of the immunoglobulins

6. Membrane receptors for antigen

7. Molecular basis and signaling of immune effector molecules

 Cytokines, chemokines and their signaling mechanisms

8. Regulatory mechanisms of immune system

9. Clinical applications of immunology

 Stem cell therapy and transplantation, immunotherapy

 Tumor immunology, immunodeficiency

 Autoimmune diseases

 Vaccine development

10. Immunological methods and applications

Immunodiagnostic and laboratory skills and techniques

Laboratory Works

 Recombinant DNA Technology

Objective

1. Acquire the principle underlying the key recombinant DNA technologies used in the biotechnology industry today.

      2.   Demonstrate the practical laboratory skills in DNA extraction and amplification by

            polymerase chain reaction.

      3.   Know the basic concepts on analysis human genes and chromosomes

Content

Nucleic acid extraction by various methods

PCR and quantification

Gel electrophoresis for DNA separation and identification

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Module -3

1. Nutrition and Health

Learning objectives

At the end of the course student should be able to

1. Discuss principles on human nutrition and balance diet
2. Identify the major nutrient classes and  the role of nutrients in normal metabolism, growth and health of human
3. Discuss diseases associated with malnutrition and the nutritional problems in community
4. Analyze and evaluate the data of nutritional studies
5. Attain the knowledge of the methods used to carry out nutritional assessment, to screen nutritional deficiency, excess and to support health care.

Contents

1. Food and balance diet

Essential nutrients and dietary reference intake

Requirement of major nutrients at different physiological states of life cycle and ill

patients

2. Metabolism of micronutrients; vitamins and minerals

            Dietary sources, absorption, transport and storage

            Elimination from body

3. Micronutrients and their role in growth, metabolism, wellbeing and disease prevention

            Role of vitamins and minerals in metabolism, oxidative stress, bone growth

            Role of vitamins and minerals in blood functions (oxygen transport, coagulation, blood

                                                                                         cell maturation)

4. Malnutrition

            Nutritional deficiency and related diseases

            Nutrition and development of chronic diseases, such as obesity, cardiovascular

            disease, cancer, diabetes, etc.

5. The biological determinants of nutritional requirements and the assessment of nutritional

    status in individuals

            Anthropometry

            Laboratory tests

            Dietary history and other relevant history

6. Nutrigenomics

The relationship between nutrition and genetics

Role of genetic variation and individual dietary response

Role of nutrients in gene expression

2. Acid base, body fluid and electrolytes (Renal, blood  and respiration)

Objective

At the end of the course student should be able to

1. Describe normal acid base regulatory mechanisms in human body
2. Apply acid base principles in diseases associate with acid-base disturbances
3. Discuss arterial blood gas analysis, its uses and interpretation in acid-base disorders
4. Acquire knowledge of clinical manifestation of renal diseases, select appropriate renal function test and discuss on the patient’s data

Contents

1. Importance of acid base homeostasis for normal cellular processes

2. Acid base principles and Regulation of pH

       Application of Henderson Hasselbalch equation

       Role of buffers, lungs and kidney in acid base regulation

3. Acid base disorders: definition, causes, compensation, correction and approach to

    differential diagnosis

                   Metabolic acidosis

Metabolic alkalosis

                   Respiratory acidosis

Respiratory alkalosis

4. Assessment of electrolytes and anion gap in acidosis

5. Arterial blood gas analysis

Components of arterial blood gas analysis

Step wise interpretation of data of patient’s ABG

3. Endocrinology

Objective

At the end of the course student should be able to

1. Discuss various signaling pathways and their effects and integration in regulation of cellular processes
2. Describe hormones in terms of structure, synthesis and its regulation, mechanism of action, functions and degradation
3. Describe biochemical basis of endocrine disorders
4. Apprehend the biochemical investigations and interpret the laboratory results of common endocrine disease

Content

1. Endocrine glands, chemical structure of hormones and their properties

2. Components of signaling pathways and their biomedical importance

Receptors of signaling molecules

            Role of intracellular mediators, different kinases in signaling and pharmacological

            agents targeting them in treatment of a variety of diseases

3. Biosynthesis, secretion, regulation of secretion, functions of hormones and their 

    association with disease;

      Hormones of Hypothalamo pituitary thyroid glands

      Hormones of Hypothalamo pituitary adrenal glands

      Hormones of Hypothalamo gonadal axis

      Hormones of pancreas

      Hormones of adrenal medulla

      Hormones of posterior pituitary

      Sex hormones

Adipokines

4. Biochemical basis of the development of endocrine disorders

      Insulin resistance, diabetes mellitus

Metabolic syndrome

      Thyroid disorders

      Osteoporosis

      Cushing’s syndrome and Addison’s disease

5. Signal transduction and oncogenesis

      Deregulation of signaling pathways and oncogenesis

      Association of growth factors signaling and cell cycle activation and cancer

6. Laboratory diagnosis of endocrine disorders and interpretation of data of clinical cases

7. Fluid and electrolyte disturbances in endocrine disorder and other diseases

4. Hepatobiliary and Gastrointestinal function

Objective

At the end of the course student should be able to

1. Describe the role of liver in intermediate metabolism and metabolism of drugs and xenobiotics
2. Apply biochemical knowledge in the pathogenesis and clinical manifestation of various liver diseases
3. Describe the liver function tests with the basic principles and applications
4. Analyze and interpret the laboratory data of liver function test of the patients

Contents

1. Role of liver in carbohydrate, fat, nitrogen and bile acid metabolism
2. Biotransformation functions of liver and its clinical importance

• bilirubin
• Steroid
• nucleotides
• ammonia
• drugs and xenobiotics

3. Alcohol metabolism in liver and genetic influence of alcoholism
4. Biochemical basis of fatty liver
5. Bile formation and importance of its composition
6. Liver diseases and liver function tests

Markers of liver dysfunction

Markers of hepatocellular injury

Markers of cholestasis

Markers of hepatocellular carcinoma

Laboratory work

Renal function tests

• Urinalysis
• Proteinuria
• Determination of blood urea,
• Serum and urine creatinine and GFR and eGFR

Liver function tests

• Total and differential plasma proteins
• Liver enzymes

Hormone assays

       -Determination of thyroid hormones and insulin by ELISA

Determination of commonly measured analytes of the given sample or subject

• Determination of blood glucose and oral glucose tolerance test and interpretation of the result
• Determination of serum lipid profile and interpretation of the result
• Determination of uric acid and interpretation of result
• Rapid diagnostic tests commonly used

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Clinical based-training (Clinical Biochemistry Part II)

Biochemical aspects of medical problems solving in

1. Cardiovascular and respiratory disorders (1 credit)
2. Nutrition
3. Renal disorder
4. Liver and biliary disorder
5. Major metabolic diseases and ageing