Biochemistry of cell

• Atoms:

  • Smallest particles of elements
  • Composed of three types of subatomic particles: Protons, Neutrons, Electrons
• Molecules:

  • Formed by 2 or more atoms bonded together
• Elements:

  • Pure substances consisting only of atoms with the same number of protons
  • Organisms are primarily composed of 6 elements: C, H, N, O, P, S
• Compound:

  • A molecule made of atoms from different elements
  • Represented by a chemical formula like CO2, H2O, C6H12O6
• Chemical Bonding:

  • The attractive force that binds atoms together to form molecules
  • Types include Covalent Bond, Ionic Bond, Hydrogen Bond
• Covalent Bond:

  • Involves the "sharing" of electrons
  • Common in living things
• Ionic Bond:

  • Involves the transfer of electrons from one atom to another to form ions
  • Example: Formation of NaCl
• Hydrogen Bond:

  • Formed when hydrogen combines with oxygen or another electronegative atom
  • Weak and important in biological systems
• Water:

  • Polar molecule with O2 covalently bonded to two H+ atoms
  • Exhibits cohesion, adhesion, and thermal properties
• Physical and Chemical Properties of Water:

  • Includes high specific heat, thermal conductivity, and transparency to visible light
• Water as the Universal Solvent:

  • Due to its high polar character
  • Important for the uptake and distribution of substances within cells
• Water's Role in Macromolecules:

  • Forms hydrogen bonds with specific monomers of macromolecules
  • Maintains their structure and function
• Biomolecules:

  • Building blocks of living organisms
  • Include carbohydrates, lipids, proteins, nucleic acids
• Building Blocks of Biomolecules:

  • Include monosaccharides, amino acids, fatty acids, nucleotides
• Metabolites:

  • Low-molecular-weight precursors of biomolecules
  • Include vitamins, hormones, and metabolic waste products
• Molecules of Miscellaneous Function:

  • Include compounds formed along metabolic pathways
  • Serve various roles in cellular processes
• Carbohydrates:

  • Monosaccharides have a backbone of C atoms linked in a linear array by single bonds
  • Each C is linked to a single hydroxyl (--OH) group, except for one C that bears a carbonyl (C=O) group
  • Classes based on the nature of the carbonyl group: Aldose (carbonyl group at one end) and Ketose (carbonyl group at an internal position)
  • Classes based on the number of C atoms: Triose, Tetrose, Pentose, Hexose
• Stereoisomerism of Monosaccharides:

  • Describes the optical activity of C
  • Isomerism where molecules have the same molecular formula and atoms bonded the same way but differ in 3-D orientation
  • Chirality leads to enantiomers, mirror-image non-superimposable molecules
  • Enantiomers can be D (dextrorotatory) or L (levorotatory) forms
• Enantiomers of Monosaccharides:

  • D-form: -OH group projects to the right
  • L-form: -OH group projects to the left
  • For monosaccharides with more than 1 chiral C, the designation as D or L is based on the projection of the –OH group in the penultimate C
• Aldotetroses:

  • 4 stereoisomers
  • Mnemonic: All Altruists Gladly Make Gums In Gallon Tanks
  • -OH Pattern: C2: R/L/R/L/R/L/R/L, C3: 2R/2L/2R/2L, C4: 4R/4L, C5: 8R
• Disaccharides:

  • Two monosaccharides joined by a covalent glycosidic bond
  • Types: Maltose (glucose + glucose), Lactose (glucose + galactose), Sucrose (glucose + fructose)
• Oligosaccharides:

  • Monosaccharides linked together to form small chains
  • Composed of various sugar units
  • Found in glycolipids and glycoproteins of the plasma membrane, distinguishing cell types and mediating cell interactions
• Polysaccharides:

  • Composed of 10 to thousands of monosaccharides linked together
  • Classes: Homopolymer (1 sugar type) and Heteropolymer (multiple sugar types)
  • Types: Cellulose, Starch, Glycogen
• Lipids:

  • Fats are glycerol linked to 3 fatty acids (triacylglycerol)
  • Fatty acids are long, unbranched hydrophobic chains with a hydrophilic carboxyl group
  • Saturated fats have no double bonds and are solid at higher temperatures, while unsaturated fats have double bonds and are liquid at room temperature
• Hydrogenation:

  • Process to chemically reduce double bonds in unsaturated vegetable oils using hydrogen atoms to make margarine
• Steroids:

  • Lipid molecules with a characteristic 4-ringed hydrocarbon skeleton
  • Cholesterol is a major steroid, abundant in animal cell membranes and a precursor for steroid hormones
• Phospholipids:

  • Resemble triacylglycerols but have only 2 fatty acid chains
  • The third -OH of the glycerol backbone is covalently bonded to a phosphate group
• Phospholipids:

  • Resemble a TAG but have only 2 FA chains; known as a DAG
  • The third -OH of the glycerol backbone is covalently bonded to a phosphate group, which is then covalently bonded to a small polar group, giving the added hydrophilic character of the phospholipid
• Lipids:

  • Biomolecules that carry out virtually all cellular activities
  • Functions include acceleration of metabolic reactions, provision of mechanical support within and outside cells, regulation of cellular activities, regulation of entry and exit of materials, and allowing biological movement
• Proteins:

  • Perform varied functions due to a high degree of specificity brought about by the amino acid component, amino acid sequence, shape, and surface
• Proteins:

  • Amino acids:
  • 20 amino acids with a structure of a C atom with a carboxyl group (-COOH) and an amino group (-NH2)
  • All have a chiral C, except for glycine
  • The side chain or R group is highly variable, giving proteins diverse structures and activities
  • Peptide bond joins amino acids by linking the carboxyl group of one amino acid to the amino group of another to form a polypeptide chain
• Proteins:

  • Classification of amino acids based on their R groups
• Proteins:

  • Levels of protein structure organization:
  • Primary Structure:
  • Linear amino acid sequence of the polypeptide chain
  • Determines how a protein will fold into its higher structural forms
  • Secondary Structure:
  • Formed via non-covalent interactions between amino acids within the peptide backbone of the primary structure
  • Types include α-helix and β-pleated sheath
• Proteins:

  • Tertiary Structure:
  • 3-D structure of a polypeptide
  • Formed by non-covalent interactions between R groups of secondary structures
  • Hydrophobic interactions allow nonpolar R groups to constitute the inside of the resulting protein, while hydrophilic R groups are on the outside for interaction with water molecules
• Proteins:

  • Quaternary Structure:
  • Combination of two or more polypeptides to form a larger complex
  • Subunits form a complex by means of non-covalent interactions
  • Different types of complexes can be formed, such as dimers, trimers, tetramers, and multimers