Biochemistry PDF

NATURE AND SCOPE Cellular Foundations Atoms to Biomolecules OF BIOCHEMISTRY - Biomolecules are organized in a hierarchy, starting from simple Bio...

NATURE AND SCOPE Cellular Foundations Atoms to Biomolecules OF BIOCHEMISTRY - Biomolecules are organized in a hierarchy, starting from simple Biochemistry atoms (C, H, O, N) to more - Basic unit of life complex structures. - Biomolecules still follow the same Inorganic Precursors chemical laws as non-living matter. - Biomolecules originate from - Purpose of Biochemistry: Studies simple precursors like water, how molecules in living things carbon dioxide, and nitrogen work together compounds (NH4+, NO3-, N2). - Mixes ideas from different Metabolites sciences to understand how life works at the smallest level. - These precursors transform into metabolites, which are Biochemistry is divided into three intermediates in energy main areas: production and biosynthesis. 1. Structural Biochemistry Building Blocks Study of molecular structures. 2. Metabolism - Metabolites build essential Study of how the body uses energy. molecules like amino acids, 3. Molecular Genetics sugars, nucleotides, fatty acids, Study of how genes work at the and glycerol. molecular level. Macromolecules Living things differentiation: - These building blocks combine Are made of complex, tiny parts. via covalent bonds to form proteins, polysaccharides, nucleic Can take in and use energy. acids, and lipids. Have different parts with special Supramolecular Complexes jobs that work together. - Macromolecules interact through Can sense and react to their noncovalent forces to form surroundings. structures like enzyme Can make copies of themselves. complexes, ribosomes, and cytoskeletons. Can change and evolve over time. Organelles Organic Chemistry Methods - In eukaryotes, organelles - Reactions between biomolecules (membrane-bound structures) are studied using organic perform specific functions within chemistry techniques, which cells. involve classifying compounds based on their functional groups. Chemical Foundations Chemical Bonding and Molecular Organic Chemistry Interaction - Focuses on carbon and - Occurs when atoms interact to hydrogen compounds and their achieve stability. derivatives. Biomolecules are a - Types of Bonds: key part of this because living o Covalent Bonds: Atoms organisms are made of carbon- share electrons to form based compounds. molecules. Friedrich Wöhler’s Experiment (1828) o Ionic Bonds: Atoms transfer electrons, creating - Wöhler synthesized urea from charged ions that attract ammonium cyanate, showing that each other. Common organic compounds could be between metals and made from nonliving materials. nonmetals. This disproved vitalism and o Hydrogen Bonds: Weak advanced our understanding of bonds between a organic chemistry. hydrogen atom in one Vitalism molecule and an electronegative atom in - Before the 19th century, it was another. believed that living things had a unique “vital force” making them Bonding in organic compounds fundamentally different from Organic Compounds nonliving things. This idea suggested that compounds in - Primarily consist of carbon, along living organisms couldn't be with hydrogen, oxygen, nitrogen, made from nonliving materials in sulfur, and halogens. a lab. Non-Metal Interaction - These elements are non-metals and form covalent bonds.  Octet Rule 3. Ethers: Contain an oxygen atom between two alkyl or aryl groups - Atoms aim to achieve stability by 4. Aldehydes: Contain a carbonyl having 8 electrons in their group (C=O) bonded to a valence shell. hydrogen atom Key functional groups of biochemical 5. Ketones: Contain a carbonyl importance: group (C=O) bonded to two carbon atoms. 1. Hydroxyl Group (-OH) 6. Carboxylic Acids: Contain a 2. Carbonyl Group (C=O): carboxyl group (-COOH) 3. Aldehyde: R-CHO 7. Esters: Derived from carboxylic 4. Ketone: R-CO-R' acids and alcohols 5. Carboxyl Group (-COOH) 8. Amines: Contain nitrogen atoms 6. Amino Group (-NH₂) bonded to carbon atoms 7. Sulfhydryl Group (-SH) 9. Amides: Contain a carbonyl 8. Phosphate Group (-PO₄³⁻) group bonded to a nitrogen atom 9. Methyl Group (-CH₃) 10. Nitriles: Contain a cyano group Main classes of organic compounds: (C≡N) 11. Thiol: Contain a sulfhydryl group 1. Hydrocarbons: (-SH) Alkanes: Single bonds 12. Phosphates: Contain a phosphate group (PO₄³⁻) Alkenes: Double bonds Alkynes: Triple bonds Aromatic Hydrocarbons: Rings with alternating double bonds 2. Alcohols: Primary Alcohols: -OH attached to a carbon with two hydrogens. Secondary Alcohols: -OH attached to a carbon with one hydrogen. Tertiary Alcohols: -OH attached to a carbon with no hydrogens. CARBOHYDRATES 2. Type of carbonyl group (Aldose and Ketose) - Most abundant biomolecule in EXAMPLE: nature - Contains: Carbon, hydrogen and oxygen Main functions: - Metabolic precursors ALDOHEXOSE - Provides energy Aldoses - Components of cell walls and extracellular structures - Recognition between cell types or the recognition of cellular structures by other molecules. Structural Definition - Known as polyhydroxy aldehydes and ketones Classification: 1. Monosaccharides Ketoses 2. Disaccharides 3. Oligosaccharides 4. Polysaccharides MONOSACCHARIDES - Smallest unit of sugars - Mostly contain 3-6 C atoms Classified by: 1. Number of carbon atoms 2 – di 3 – tri 4 – tetra 5 – penta 6 - hexa Stereochemistry - Epimers o Differ in position of only on - Study of different spatial -OH group arrangements of atoms in molecules Isomers Structural isomers stereoisomers: - Enantiomers - Diastereomers - Cis-trans isomers - Constitutional Isomers o Same formula but different Monosaccharide Isomers functional group - Molecules having same molecular formula but different arrangement, connectivity and orientation in space - Diastereomers o Not mirror images of each other - Stereoisomers o Same molecular formula and functional group but different orientation of atoms § Enantiomers Non- superimposa ble mirror images of each other § D and L notation Determined based on chiral carbon (farthest) from group.