Download Biochemistry I course outline - School of Life Sciences, IUB

Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
Lecture
No
Topic
In Brief
Introduction of Biochemis try: What is it?
Why Biochemistry? for fundamental understanding
of life, disease process and application
Biomolecules : definition and type
Micromolecu les : definition and examp le
Macromolecules: definition and three
different type of macromolecules
1
Biomolecules:
Protein
Protein : definition and functions
Amino Acid (AA): building block of proteins
General structure of AA, Isomer, Optical
isomer, Stereoisomer, Enantiomer ,
asymmetry of AA
Classification of AA based on:
1. Structure: AA with aliphatic s ide chain,
hydroxyl group containing AA, sulfur
containing AA, acidic AA and their amides,
basic AA, aromatic AA and Imino Acid
2. Polarity: non polar AA and polar AA
3. Nutritional value: essential AA and non
essential AA
4. Metabolic fate: glycogenic AA, ketogenic AA
and both
Properties of AA :
1. Physical properties: solubility, Meltin g point,
taste, optical properties, AA as ampholytes
(Zwitter ion and P I)
2. Chemical properties : reactions due to -COOH
group, reactions due to –NH2 group
2
Biomolecules:
Protein
Non standard AA: AA derivative in proteins, Nonprotein AA, D-amino acids
Functional characteristics of proteins
Properties of proteins : solubility, molecular weight
shape, P I, acidic and basic protein,
precipitation of proteins, color reactions of
proteins
Date
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
Classification of Proteins:
1. Functional classification: structural protein,
enzyme protein, transport protein, hormonal
protein, contractile protein, storage protein,
genetic protein, defense protein, receptor protein
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4
Class test, problem solving and discussion
Classification of Proteins:
2. Classification based on chemical nature and
solubility: a) simple protein: globular and fibrous
b) conjugated protein c) derived protein: primary
and secondary
3. Classification based nutritional value: complete
protein, partially incomplete protein and
incomplete protein
Denaturation, Coagulation and Flocculation of protein
Biomolecules:
Protein
Structure of protein :
1. Primary structure:
Peptide bond: formation of peptide bond,
characteristics of peptide bond, writing,
shorthand read and naming of peptides
Biologically important peptides
Determination of primary s tructure:
a) determination of AA composition
b) degradation of protein or polypeptide into
smaller fragments
c) determination of AA sequence
5
Biomolecules:
Protein
Secondary Structure: ? -helix and ß-sheet
Tertiary structure of protein : bonds of tertiary
structure, domains
Quaternary structure: bonds of quaternary
structure, importance and examp le of
oligomeric protein
Bond res ponsible for protein structure: covalent
bonds and non-covalent bonds
Example of protein structure
1. Glutathione: Structure and functions
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
2. Insulin: Structure and function
3. Keratin: Structure and function
4. Collagen: Structure and function
6
7
8
Class tes t, problem solving and dis cuss ion
Globular protein: Myoglobin and Haemoglobin
(Hb)
Structure : globin and heme structure
Function of Hb : O2 binding and dissociation of
Hb and Myoglobin
Abnormalities in Hb : Bascic concepts of glob in
synthesis
Sickel cell anemia : Occurrence, mo lecular bas is,
abnormalities associated with it
Thalassemia: Molecu lar basis, a - and ßThalassemia
Biomolecules:
Protein
Tools in biochemistry:
P aper Chromatography
Ion-exchange Chromatography
Gel filtration Chromatography
Affinity Chromatography
Gel Electrophoresis
Enzymes
Definition and functions
Nomeneclature and classifications :
Oxidoreductase, Transferases, Hydrolases,
Lyases, Isomerases, Ligases
Chemical nature and properties of enzyme :
holoenzyme and apoenzyme, co-enzyme,
cofactor and prosthetic group
Factor affecting Enzyme activity : concentration
of enzyme, concentration of substrate, effect of
temperature, effect of PH , effect of product
concentration , effect of activators, effect of
time, effect of light and rad iation
Enzyme kinetics and MM equation
Active s ite of Enzyme : features of active site
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
Enzyme inhibition:
1. Reversible: competitive, non-competitive and un competitive
2. Irreversible
3. Allosteric
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10
Class tes t, problem solving and dis cuss ion
Enzyme Specificity:
1. Optical specificity
2. Reaction specificity
3. Substrate specificity: absolute, relative and
broad specificity
Mechanism of enzyme action
Enzyme substrate complex and activation
energy
Enzymes
Lock and key model
Induced fit model
Enzyme activity regulation in living system
1. Allosteric regulation: conformational changes in
allosteric enzyme, feedback inhibition
2. Activation of latent enzymes
3. Compartmentation
4. Control of enzyme synthesis
5. Enzyme degradation
6. Isoenzyme
Non protein enzymes
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
Definition and functions of carbohydrate
Classification: Monosaccharides, Disaccharides,
Polysaccharides
Monosaccharide: Aldose and Ketose and their
structures
Glycosides and their importance
Derivatives of Monosaccharides: sugar acids,
sugar alcohol, aldito ls, amino sugars,
deoxysugars , L-ascorbic acids
Disaccharides
Maltose
Cellobiose
Sucrose
Lactose
Polysaccharides:
Homo polysaccharide
Starch
glycogen,
Cellulose
Dextrin
Inulin
Chitin
11
Biomolecules:
Carbohydrate
12
Class tes t, problem solving and dis cuss ion
Hetaro polysaccharides
Mucopolysaccharide
Hyaluronic acid
Biomolecules:
Chondroitin Sulphate
Carbohydrate
Heparin ,
Determination of starch
13
Biomolecules:
Lipids
Lipids : definition and functions
Classification of lipids
1. Simple lipids
a) Fats and oils
b) Waxs
2. Complex or compound lipids
a) Phospholipid
b) Glycolipids
c) Lipoproteins
d) Other complex lip ids
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
3. Derived lipids
4. Miscellaneous lipids
5. Neutral lipids
Fatty acids (FA): occurrence, even and odd chain
FA, saturated and unsaturated FA,
lengths of FA, shorthand
presentation of FA
Essential FA: b iochemical basis, functions,
deficiency
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15
Biomolecules:
Lipids
Triacylglycerol (TG): fats as stored fuel, structure
of acy lgycero l, s imple TG and mixed TG
Properties of TG:
1. Hydrolysis
2. Saponifications
3. Rancidity
4. Lipid peroxidation
Purity test for fats and oils :
1. Iodine number
2. Saponification number
3. Acid number
Phospholipids:
1. Glycerophospholipid
a) Phosphatidic acid
b) Lecithin
c) Cephalin
d) Phosphatidylinositol
e) Phosphatidylserine
f) Plasmalogen
g) Cardiolipin
2. Sphingomyelin
Functions of phospholipids
Glycolipids
Lipoproteins
Steroids :
Cholestero l: structure and occurrence, properties
and functions
Prostaglandins
Leukotrienes
Class tes t, problem solving and dis cuss ion
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
16
Metabolis m:
Catabolis m,
Carbohydrate
Metabolism:
Catabolism: Three stages
Anabolism
High energy compound: ATP, structure, ATP
cycle, Phosphocreatine, NADH, FAD
Major pathways of carbohydrate metabolism:
1. Glycolysis
2. Citric acid (TCA) cycle
3. Gluconeogenesis
4. Glycogenolys is
5. Pentose phosphate pathway (PPP)
6. Uronic acid pathway
7. Galactose metabolism
8. Fructose metabolism
9. Amino
sugar
and
mucopolysaccharide
metabolism
Entry of glucos e into cell: insulin independent and
dependent pathway
Glycolysis: Salient features
Reactions of Glycolys is :
1. Energy investment phase
2. Splitting phase
3. Energy generation phase
Regulations of glycolysis
Metabolis m:
Catabolis m,
Carbohydrate
17
Metabolis m:
Catabolis m,
Lipid
Conversion of pyruvate into Acetyl CoA:
reaction and regulation
TCA cycle:
the central metabolic pathway
location and overview
reactions
inhibitors
Regulations of TCA cycle
Amphibolic nature of TCA cycle
TG: the body fuel reserve
Reasons for TG as body fuel reserves
Mobilization of fat: chylomicrons and lipoproteins
Lipoprotein lipase activity and its regulations
Fate of glycerol
Fate of free FA
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
18
19
Class tes t, problem solving and dis cuss ion
Fatty acid oxidation: stages and tissues
1. FA activation
2. Transport of acyl CoA to mitochondria: four
stages
3. ß-oxidation: reactions
Oxidation of Palmityl CoA and its energetic
SIDS-disorder due to ß-oxidation blockade
Oxidation of odd chain FA
Metabolism:
Methylmalonic acidemia
Catabolism,
Oxidation of unsaturated FA
Lipid
Ketone bodies:
Ketogenesis
Utilization of Ketone bodies
Overproduction of Ketone bodies
Starvation
Diabetes mellitus
Regulation of ketogenesis
Ketoacidosis
AA pool:
Sources of AA pool
Protein turnover
Dietary protein
Synthesis of non essential AA
Utilization of AA acid from body pool
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Metabolism:
Catabolism,
Protein
Metabolism of AA: general aspects
Transamination: salient features
mechanisms of transamination
Deamination
Oxidative deamination
Non-oxidative deamination
Metabolism of Ammonia
1. Formation
2. Transport and storage
3. Function
4. Disposal
5. Toxicity
Urea Cycle:
1. Formation of carbamy l phosphate
2. Formation of citruline
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
3. Synthesis of arginosuccinate
4. Cleavage of arginosuccinate
5. Formation of urea
Regulations of urea cycle
Disposal of urea
Integration between urea and TCA cycle
Metabolic disorders of urea cycle
Blood urea: clinical importance
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22
Class tes t, problem solving and dis cuss ion
Gluconeogenesis: Location and importance
Reactions of gluconeogenesis
Gluconeogenesis from:
1. Amino acids
2. Glycerol
3. Propionate
4. Lactate
5. Glucose-alan ine cycle
Regulations
of gluconeogenesis
Metabolism:
Why man cannot synthesize glucose from fat?
Anab olism,
Carbohydrate Glycogenesis: four steps
Glycogenolys is: overall steps
Regulations of glycogenes is and glycogenolysis
Glycogen storage diseases
Pentose phos phate pathway (PPP): location
Significance of PPP
23
Metabolism:
Anab olism,
Lipid
Biosynthesis of FA:
1. Production of acetyl CoA and NADPH
2. Conversion of acetyl CoA to malonyl CoA
3. Reactions of fatty acid synthase (FAS) complex
Regulations of FA synthesis
Synthesis of TG:
1. Synthesis of glycerol3-phosphate
2. Adition of acyl group
Cholesterol: Importance and synthesis
Regulations of cholesterol synthesis
Plasma lipoproteins : classifications
Metabolism of HDL
Disorders of plasma lipoproteins
1. Hyperlipoproteinemia
Independent University, Bangladesh
School of Life Sciences
Bio 103: Biochemistry I course outline
2. Hypolipoproteinemia
24
25
Integrated
metabolism
Fatty liver
Obesity: Nutritional bas is and types
Integration of major metabolic pathways :
1. Glycolysis
2. FA oxidation
3. AA degradation
4. TCA cycle
5. Oxidative phosphorylation
6. PPP pathway
7. Gluconeogenesis
8. Glycogen metabolism
Organ specialization and metabolic integration:
1. Liver
2. Adipose tissue
3. Skeletal muscle
4. Brain
Metabolism in s tarvation:
1. Liver in starvation
2. Brain in starvation
3. Skeletal muscle in starvation
4. Adipose tissue in starvation
Reserve day for class
Final Exam