KP

bio bio molecules

Dehydration Synthesis and Hydrolysis

  • Anabolic reactions build larger molecules from smaller units; dehydration synthesis is the process of linking monomers by removing a water molecule, forming a covalent bond.
  • Dehydration synthesis results in a dehydrated product; hydrolysis is the reverse, where water is added to break bonds.
  • Characteristic memory aid:
    • Dehydration → product is "dehydrated" (loses water).
    • Hydrolysis → product is hydrated (gains water).
  • Role of enzymes:
    • Dehydration synthesis is catalyzed by a polymerase enzyme (e.g., DNA polymerase is a common example in biochemistry contexts).
    • Hydrolysis is catalyzed by a hydrolase enzyme.

Macromolecules, Monomers, and Polymers

  • Most biological molecules are large and built from small units called monomers to form long chains called polymers or macromolecules.
  • A process of linking monomers is dehydration synthesis (loss of water); the reverse process is hydrolysis (addition of water).
  • Visual cue: generic monomers with OH groups can link to form polymers via dehydration synthesis; water is released in the process.
  • Important distinction for biochemistry vs general biology: some naming conventions and enzyme specifics can be nuanced; enzymes may be more specific in vivo.

Carbohydrates: Monosaccharides, Polysaccharides, and Bonds

  • Monosaccharides: simple sugars, typically with a general formula of ext{(CH}2 ext{O)}n; many variations exist (e.g., glucose is a key sugar).
  • Glucose is particularly important as an energy source for brains, organs, tissues, and cells.
  • When monosaccharides join, they form disaccharides (two units) or polysaccharides (many units).
  • Linkages between monosaccharides are called glycosidic linkages (a type of covalent bond).
  • The dehydration reaction forms these bonds and releases water:
    • Example general representation: ext{Monomer}1- ext{OH} + ext{Monomer}2- ext{H}
      ightarrow ext{Bond} + ext{H}_2 ext{O}
  • Do not memorize every end-group detail for this course; focus on the concept that sugars form larger carbohydrates via dehydration and are broken down by hydrolysis.

Amino Acids, Peptides, and Proteins

  • Amino acid structure:
    • Each amino acid has a central (alpha) carbon with four groups:
    • An amino group (–NH₂)
    • A carboxyl group (–COOH)
    • A hydrogen atom (–H)
    • An R group (side chain) that determines the amino acid’s properties (polarity, charge, size).
  • R group diversity:
    • Polar (hydrophilic) side chains
    • Electrically charged side chains: acidic (negative) or basic (positive)
    • Some are acidic or basic, affecting interactions and folding in water.
  • Sequence and structure:
    • The sequence of amino acids determines how a polypeptide folds into a functional protein.
    • When amino acids join, they form peptide bonds (a covalent bond) between the carboxyl of one amino acid and the amino group of the next.
    • A chain of amino acids is a polypeptide; when it folds and achieves function, it is a protein.
  • Amino acid supplements:
    • Some people take free amino acids as supplements instead of whole protein for faster absorption.
    • Whole protein must be digested first; amino acids can be absorbed more quickly, bypassing digestion.
    • Practical context: athletes sometimes consider amino acid supplements to support rapid availability, especially around workouts.

Nucleotides, Nucleosides, and Nucleic Acids

  • Nucleotide structure: three parts
    • Phosphate group
    • Sugar (ribose in RNA, deoxyribose in DNA)
    • Nitrogenous base (purine or pyrimidine)
  • Nucleoside vs nucleotide:
    • A nucleoside is a sugar attached to a nitrogenous base.
    • A nucleotide is a nucleoside with one or more phosphate groups.
  • Polynucleotides:
    • Bases along a sugar-phosphate backbone give rise to nucleic acids like DNA and RNA.
  • DNA vs RNA sugars:
    • DNA contains deoxyribose
    • RNA contains ribose
  • Base types:
    • Purines: Adenine (A) and Guanine (G)
    • Pyrimidines: Cytosine (C) and either Thymine (T) in DNA or Uracil (U) in RNA
  • Backbones and linkages:
    • Nucleotides are linked by phosphodiester bonds, forming a sugar-phosphate backbone.
    • The backbone is negatively charged due to phosphate groups.
  • Antiparallel strands:
    • DNA consists of two polynucleotide strands running in opposite directions (5'→3' on one strand and 3'→5' on the other).
  • Base pairing rules (Chargaff):
    • Cytosine pairs with Guanine (C≡G) via three hydrogen bonds.
    • Adenine pairs with Thymine (A=T) in DNA via two hydrogen bonds; in RNA, Adenine pairs with Uracil (A=U).
  • Base pairing visual (conceptual):
    • The bases form rungs of a ladder between the two antiparallel strands.
  • Key memory aid (Chargaff’s rule):
    • A and T pair, G and C pair; in any double-stranded DNA, %A ≈ %T and %G ≈ %C.

DNA Structure and Function Basics

  • Overall DNA form: double helix with two antiparallel polymer strands; bases stack inside the helix like steps on a ladder.
  • Bases and information storage: the sequence of bases encodes genetic information.
  • Evidence of the backbone’s charge: the phosphate groups confer a negative charge to the backbone, influencing electrophoresis and molecular biology techniques.
  • Schematic