BCH 201- GENERAL BIOCHEMISTRY I 2019/2020
BCH 201 - General Biochemistry I 2019/2020
PART 1
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BCH 201 - GENERAL BIOCHEMISTRY I 2019/2020
PROF. O. ADEMUYIWA
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OVERVIEW
- The Nature of Biochemistry
- Cellular Basis of Life
- Cell Composition
- Organelles in the Cell
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NATURE OF BIOCHEMISTRY
- Definition: Biochemistry is the study of the chemistry of life.
- Biochemistry can also be defined as the study of the molecular events that correspond to the phenomenon of life.
- The term "study" indicates that Biochemistry is both a theoretical and a laboratory-based science.
- Chemistry refers to the chemical processes taking place within cells.
- Objective: The major objective of Biochemistry is to achieve a complete understanding of all the chemical processes associated with living cells at the molecular level.
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CELLULAR BASIS OF LIFE
- Organisms are composed of membrane-enclosed objects called cells.
- Cells are the fundamental units of life (living organisms) and vary in size and shape.
- Two types of cells:
- Plant cells
- Animal cells
- The cell is enclosed by a delicate, semi-permeable structure called the plasma membrane.
- Many plant and bacterial cells have a cell wall surrounding the plasma membrane.
- Contents enclosed by the plasma membrane: cytoplasm.
- Liquid portion of the cytoplasm is called cytosol.
- The plasma membrane contains transporters and receptors.
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PLANT AND ANIMAL CELLS
Cross-Section of an Animal Cell:
- Cell Membrane
- Centrosome
- Lysosome
- Nucleus
- Nucleolus
- Nuclear Membrane
- Vacuole
- Mitochondrion
- Rough ER
- Smooth ER
- Ribosomes
- Golgi Body
- Other organelles as shown in the diagram.
Cross-Section of a Plant Cell:
- Similar structure to animal cells; notable differences include:
- Cell Wall
- Chloroplasts
- Vacuoles
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CELL COMPOSITION
- A cell consists of:
- Small molecules
- Macromolecules
- Organelles
- Water is the most abundant molecule in cells, accounting for 70% of cell weight, with other components existing in an aqueous environment.
- Except for water, most molecules in the cell are macromolecules classified into four groups:
- Lipids
- Carbohydrates
- Proteins
- Nucleic acids
- Each macromolecule has distinct chemical properties that suit its specific function in the cell.
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CELL COMPOSITION CONTD - STRUCTURES OF SOME LIPIDS
Lauric Acid:
- A fatty acid commonly found in coconut oil.
Cholesterol:
Triglyceride:
Phospholipid:
Structures:
Lauric Acid:
HO-C-C-C-C-C-C-C-C-C-C-C-C-H
HHHHHHHHHHHHHHHHHHOther structures include hydrocarbon chains and functional groups as depicted in diagrams.
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CELL COMPOSITION CONTD
- Carbohydrates:
- Composed primarily of hydrocarbon structures with many polar hydroxyl (OH) groups, making them highly soluble in water.
- Large carbohydrate molecules (Polysaccharides) are formed by many small sugar molecules linked by glycosidic bonds.
- Function: Storage (e.g., starch, glycogen) and providing carbon skeletons for synthesis of other compounds.
- Structural Functions:
- Linear polysaccharides are major components of plant cell walls; bacterial cell walls are composed of cross-linked polysaccharides.
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CELL COMPOSITION CONTD
- Proteins:
- Most complex macromolecules; made up of linear polymers called polypeptides.
- Polypeptides consist of amino acid monomers joined by peptide bonds.
- Each amino acid has:
- Central carbon atom
- Carboxyl group
- Amino group
- Hydrogen atom
- Unique R group
- Properties of proteins determined by the sequence of amino acids in the polypeptide chain.
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CELL COMPOSITION CONTD - AMINO ACID, PEPTIDE BOND AND POLYPEPTIDE
- Peptide Bond:
- Formed by the removal of a molecule of water from two amino acids.
- Structure of a peptide chain:
Example: Glycine Amino Acids
N-C-C
O R
H—N—C-C
HAA
H-C
- Important Terms:
- N-terminus: Beginning of a polypeptide chain
- C-terminus: End of a polypeptide chain
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CELL COMPOSITION CONTD
- Nucleic Acids:
- Largest macromolecules composed of long linear polymers called polynucleotides.
- Made of nucleotide monomers, comprising a five-carbon sugar, phosphate groups, and nitrogenous bases.
- Two types:
- Deoxyribonucleic acid (DNA): Contains genetic information inherited during cell division.
- Ribonucleic acid (RNA): Involved in protein synthesis.
- Chromosomes contain specific genetic information required for synthesis of cell compounds and replication processes.
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CELL COMPOSITION CONTD - NUCLEOTIDE AND POLYNUCLEOTIDE
- Structure of a Nucleotide:
- Composed of:
- Nitrogenous base (purines and pyrimidines)
- Pentose sugar (ribose or deoxyribose)
- Phosphate group
- Purines: Adenine (A), Guanine (G)
- Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)
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CELL COMPOSITION CONTD
- Each chromosome carries a single DNA molecule with approx. 10^6 or more nucleotides in a specific arrangement.
- The sequence of bases in chromosomal DNA determines amino acid sequences in proteins.
- RNA Types:
- Messenger RNA (mRNA): Transmits genetic information from DNA to the cytoplasm for protein synthesis.
- Ribosomal RNA (rRNA): Found in ribosomes, facilitates protein synthesis.
- Transfer RNA (tRNA): Transports amino acids to ribosomes.
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CELL COMPOSITION CONTD
- Additional Cell Components:
- Inorganic components:
- Metal ions (Na+, K+, Mg2+, Ca2+, Zn2+, Fe2+/Fe3+)
- Other trace elements (molybdenum, selenium, copper, etc.)
- Organic/inorganic molecules involved in normal cellular functions.
- Bioinorganic molecules and coenzymes work with enzymes to maintain homeostasis.
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CELL COMPOSITION CONTD - ORGANELLES IN CELLS
- Organelles: Subcellular membranous structures.
- Nucleus: Repository of genetic information.
- Endoplasmic Reticulum (ER): Site of protein and lipid synthesis (Rough ER and Smooth ER).
- Golgi Complex: Processing and sorting of proteins.
- Lysosomes: Sites of degradative reactions (animal cells only).
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CELL COMPOSITION CONTD - ORGANELLES IN CELLS
- Plant Cells: Do not contain lysosomes; vacuoles serve similar functions.
- Peroxisomes: Break down hydrogen peroxide.
- Mitochondria: Power plants of eukaryotic cells, responsible for ATP production and have their own DNA.
- Chloroplasts: Convert solar energy to chemical energy in plants.
- Cytoskeleton: Interlocking filaments that stabilize cell shape and organize the cytoplasm.
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BCH 201 - pH and BUFFERS
- pH: Defined as –log aH+.
- The activity of ions in a solution can be expressed as:
- $a = c imes ext{γ} $
- where $a$ is activity, $c$ is concentration, $ ext{γ}$ is activity coefficient.
- In dilute solutions, $ ext{γ}
ightarrow 1$, and at infinite dilution, $a = c$.
- For hydrogen ions:
- $aH+ = [H+]$
- pH = –log10$[H+]$
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DISSOCIATION OF H2O AND ITS ION PRODUCT
- Water is a weak electrolyte:
- $H2O
ightleftharpoons H^+ + OH^-$ - Equilibrium constant $K_{eq} = [H^+] imes [OH^-] = 1.8 imes 10^{-16}$ mole/Litre at 25° C.
- $H2O
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DISSOCIATION OF H2O AND ITS ION PRODUCT
- Given that water is slightly dissociated, we consider
- Substituting moles/Litre results in:
- Relationship between [H+] and [OH-] holds true with:
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DISSOCIATION OF H2O AND ITS ION PRODUCT
- Taking logarithm gives:
- The equations result in the definitions of pH and pOH, leading to the relationship of their sum equaling 14.
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ACIDS AND BASES IN CHEMISTRY
- Bronsted theory: - Acid: Donates a proton. - Base: Accepts a proton. - Example:
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HENDERSON-HASSELBALCH EQUATION
- pH = pKa + ext{Log} rac{[A^-]}{[HA]}
- This equation is used to describe the relationship between pH, pKa, and the concentrations of acid and its conjugate base. Buffers contain weak acids and their conjugate bases.
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BUFFER
- A buffer is defined as a compound that in solution resists a change in pH upon the addition of an acid ($H^+$) or base ($OH^-$). Example: Acetic acid and its salt sodium acetate.
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PREPARATION OF BUFFERS
- Example: Preparing a buffer with a pH of 5 using acetic acid and sodium acetate by applying the Henderson-Hasselbalch equation.
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AN EXAMPLE OF BUFFER SYSTEM IN TISSUES
- Lymph, cerebrospinal fluid, and tissue fluids utilize similar buffering systems (HCO3- and H2CO3).
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ACIDOSIS AND ALKALOSIS
- Definitions and implications of changes in pH due to metabolic processes.
- Metabolic and respiratory acidosis and alkalosis described with examples.
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ACIDOSIS AND ALKALOSIS
- Conditions leading to acid or base accumulation and their physiological effects noted.
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CHEMISTRY OF CARBOHYDRATES
- Overview of carbohydrates as organic molecules and their roles in energy production, structure, and cellular components.
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FUNCTIONS OF CARBOHYDRATES
- Breakdown of carbohydrates provide energy and are key in cell structure (e.g., ribose in RNA).
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STRUCTURE AND CLASSIFICATION OF CARBOHYDRATES
- Definition and classification into monosaccharides, disaccharides, and polysaccharides.
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MONOSACCHARIDES
- Simplest carbohydrates and their roles as building blocks of more complex carbohydrates.
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MONOSACCHARIDE CLASSIFICATION
- Types based on carbon count and functional groups (aldoses and ketoses).
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STEREOCHEMISTRY IN CARBOHYDRATES
- Identification of isomers, chirality, and reference carbons, discussions of stereoisomers and their significance.
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ENANTIOMERS
- Definition and examples including chiral centers, optical activity and its implications.
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PROJECTION FORMULAS
- Fischer and Haworth projection formulas for depicting carbohydrate structures clearly.
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CYCLIZATION OF SUGARS
- Formation of cyclic structures and their biological relevance in aqueous solutions.
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REDUCING SUGARS
- Characteristics of reducing sugars, distinctions in reactivity among aldoses and ketoses.
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EPIMERS AND DIASTEREOMERS
- Definitions with examples highlighting structural differences.
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L AND D ISOMERS
- Designation of isomer forms based on hydroxyl group position relative to chiral center.
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OPTICAL ISOMERISM AND ACTIVITY
- Interactions of chiral compounds with polarized light, importance of racemic mixtures.
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FISCHER AND HAWORTH FORMULAS
- Distinctions in representation of carbohydrate structures, their relevance in biochemical contexts.
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SUGARS IN ACYCLIC AND CYCLIC FORM
- The formation of ring structures from open-chain forms and their implications.
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COMMON BIOLOGICAL FATTY ACIDS
- Overview of biological roles and structures of essential fatty acids.
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FAT AND ENERGY STORAGE
- Roles of triglycerides, chemical structures, and saturated vs. unsaturated differences.
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FATTY ACIDS CLASSIFICATION
- Classification based on saturation levels and implications for metabolism.
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FATTY ACIDS AND OXIDATION
- Biological and physiological aspects of fatty acids in energy metabolism.
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SUGAR DERIVATIVES AND BIOSYNTHESIS
- Overview of sugar derivatives, implications in biological processes and metabolism.
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DISACCHARIDES
- Formation of disaccharides, linkage types and examples including lactose and sucrose.
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IMPORTANT DISACCHARIDES IN NUTRITION
- Lactose, maltose, and sucrose characteristics and nutritional importance outlined.
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STRUCTURE AND FUNCTION OF POLYSACCHARIDES
- Overview of polysaccharides as structural and energy storage molecules.
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IMPORTANCE OF STARCH
- Starch and its role in plants as a polysaccharide; structure and types.
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FUNCTIONS OF CELLULOSE AND CHITIN
- Overview of structural polysaccharides in plants and their significance.
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ANIMALS AND POLYSACCHARIDES
- Glycogen functions in mammals, storage properties, and metabolic implications.
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BIOSYNTHESIS, STRUCTURE AND FUNCTION
- Overview of polysaccharide biosynthesis, structural roles, and metabolic importance.
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OVERVIEW OF PROTEINS AND AMINO ACIDS
- Proteins as polymers, their functions, and the role of amino acids in structure and function.
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AMINO ACIDS AND THEIR CHARACTERISTICS
- Overview of amino acids, their structure, classification, and biological importance.
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DESCRIPTIVE EXAMPLES OF AMINO ACIDS
- Discussion of polar, charged, and nonpolar amino acids, their properties, and use in proteins.
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AMINO ACID SYNTHESES AND REACTIONS
- Overview of the synthetic pathways of amino acids and their metabolic implications.
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PEPTIDES AND PROTEINS
- Detailed discussion of peptide bond formation, sequences in proteins, and terminology.
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PRIMARY, SECONDARY, TERTIARY, AND QUATERNARY STRUCTURES IN PROTEINS
- Differences between structures in proteins and their biological implications.
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CHEMISTRY OF LIPIDS
- Overview of lipids, their biochemical functions, and structural differences.
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FUNCTIONS OF LIPIDS
- Membrane components, energy storage, and signaling roles of lipids outlined.
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FATTY ACIDS DEFINED
- Structure, classification, and roles of fatty acids in larger biological contexts.
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STEROIDS
- Structure and biological roles of steroid lipids discussed.
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TRIACYLGLYCEROLS, WAXES, AND PHOSPHOLIPIDS
- Overview of their structure, roles, structural elements in membranes, and biological significance.
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SPHINGOLIPIDS AND GLYCOSPHINGOLIPIDS
- Description of sphingolipids structures and functions.
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BIOSYNTHESIS OF LIPIDS
- Pathways involved in lipid biosynthesis and their physiological implications.
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NUCLEOTIDES AND NUCLEIC ACIDS
- Journey through the structure, function, and examples of nucleotides and nucleic acids.
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FUNCTIONS OF NUCLEOTIDES
- Overview of diversity and roles of nucleotides within biological systems.
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STRUCTURES OF NUCLEOTIDES AND NUCLEOSIDES
- Detailed diagrams and types of nucleotides related to DNA and RNA.
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DNA AND RNA STRUCTURAL COMPONENTS
- Key differences and similarities between DNA and RNA related to nucleotides.
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DNA SEQUENCE AND STRUCTURE
- Explanation of how nucleotides link to form structures and chains in DNA.
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BIOCHEMISTRY OF VITAMINS
- Overview of vitamins, their classifications, structures, and significance in metabolic processes.
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FUNCTIONS OF VITAMINS IN METABOLISM
- How vitamins support and catalyze metabolic reactions, energy production, and health.
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VITAMINS AND DISEASES
- Discussing conditions resulting from vitamin deficiencies and their physiological effects.
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VITAMINS AS CO-ENZYMES
- Roles vitamins play as coenzymes in conjunction with enzymes in metabolic processes.
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MECHANISMS OF VITAMINS IN BIOLOGICAL CONTEXTS
- Overview of specific examples of vitamins in metabolic pathways and molecular responses.
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COFACTORS
- Relationship between enzymes and metal ions or organic molecules in catalysis.