Macromolecules #2 (Biology 31) - Vocabulary Flashcards

Carbohydrates

  • Overview
    • Living things are carbon-based because carbon has a prominent role in the chemistry of life. Carbon’s four covalent bonding positions allow a wide diversity of compounds with many functions.
    • Carbohydrates are a class of macromolecules important for energy, structural support, and cell recognition/reception on the surface.
  • Key concepts
    • Carbohydrates are classified by the number of monomer units they contain: monosaccharides, disaccharides, polysaccharides.
    • Primary functions include dietary energy, energy storage, and plant structural roles.
  • Monomer and bonds
    • Monomer: monosaccharide.
    • Monosaccharides link via glycosidic bonds to form disaccharides and polysaccharides.
    • General relation:
    • Monosaccharide → Disaccharide via a dehydration synthesis reaction (loss of water).
    • Monosaccharide + Monosaccharide → Disaccharide + H₂O
    • Example schematic (not shown in slide):
      extMonosaccharide<em>1+extMonosaccharide</em>2<br/>ightarrowextDisaccharide+H2Oext{Monosaccharide}<em>1 + ext{Monosaccharide}</em>2 <br /> ightarrow ext{Disaccharide} + H_2O
  • Functional implications
    • Structural roles (e.g., plant cell wall components like cellulose in some contexts; carbohydrates provide support in various organisms).
    • Surface receptors and cell recognition molecules help cells identify each other.
  • Connections to prior concepts
    • Builds on the idea of macromolecule diversity via carbon’s covalent bonding flexibility.
    • Relates to metabolism and energy pathways (carbohydrates as a primary energy source).
  • Quick takeaway
    • Carbohydrates = monosaccharides, disaccharides, polysaccharides; key roles in energy, structure, and recognition; glycosidic bonds link units.

Lipids

  • Overview
    • Lipids are nonpolar and hydrophobic, forming a diverse class including fats/oils, waxes, phospholipids, and steroids.
    • Major energy storage form includes fats and oils (triglycerides).
  • Monomer and polymer forms
    • Two primary monomers: glycerol and fatty acids.
    • Lipids as a group have monomeric units that can combine to form larger lipid structures; the most common storage lipids are triglycerides (three fatty acids linked to glycerol).
    • Ester linkages connect fatty acids to glycerol.
  • Types of lipids
    • Fats and oils (triglycerides): long-term energy storage.
    • Phospholipids: glycerol backbone, two fatty acid tails, and a phosphate group; form the phospholipid bilayer of cell membranes.
    • Sterols: cholesterol and steroid hormones (e.g., testosterone, estrogen).
  • Lipid structure details
    • Fatty acids: long hydrocarbon chains ending in a carboxyl group (COOH). The R group varies with different carbon chains.
    • Phospholipids: one fatty acid replaced by a phosphate group on the glycerol backbone, producing a amphipathic molecule suitable for membranes.
  • Lipid examples mentioned
    • Fats (triglycerides)
    • Steroids (testosterone, estrogen)
    • Cholesterol as a membrane component and precursor to other steroids.
  • Saturated vs. unsaturated fats
    • Saturated fatty acids: only single bonds between carbons; generally pack tightly and are solid at room temperature.
    • Unsaturated fatty acids: contain at least one double bond; kinks prevent tight packing, typically liquids at room temperature.
    • Visual/diagrams show hydrocarbon chains with single bonds (saturated) vs. double bonds (unsaturated).
  • Bonds and chemistry
    • Ester linkages connect fatty acids to glycerol in triglycerides.
    • Phospholipids form a bilayer due to their amphipathic nature (glycerol backbone + two fatty acid tails + phosphate group).
    • Phosphodiester bonds in nucleic acids (covered in Nucleic Acids) are a separate bond type from lipids.
  • Functional and real-world relevance
    • Lipids store energy efficiently and play crucial roles in membranes and signaling (steroids as hormones).
    • Saturation level of dietary fats is linked to heart health in public health discussions; unsaturated fats are generally considered healthier in moderation.
  • Connections to prior concepts
    • Illustrates how macromolecules differ chemistries (nonpolar vs polar, hydrophobic interactions) and how structure determines function (membrane formation, hormone signaling).
  • Quick takeaway
    • Lipids include triglycerides, phospholipids, and steroids; monomers glycerol + fatty acids; ester linkages; membranes rely on phospholipid bilayers; saturation affects state at room temperature.

Proteins

  • Overview
    • Proteins are polymers made from amino acid monomers; they represent a large fraction (more than 5050) of the dry weight of most cells and perform a wide range of cellular functions.
  • Functions (five major roles)
    • Structural proteins: provide support.
    • Storage proteins: supply amino acids for growth.
    • Contractile proteins: enable movement.
    • Transport proteins: assist in moving substances.
    • Enzymes: catalyze chemical reactions.
  • Amino acids (monomers)
    • There are 2020 standard amino acids.
    • Each amino acid has:
    • A central carbon (alpha carbon)
    • An amino group (–NH₃⁺)
    • A carboxyl group (–COOH)
    • A variable side group (R group) that determines properties (hydrophobic vs hydrophilic).
    • General structure (illustrated in slides): amino group, carboxyl group, and a side chain attached to the central carbon.
  • Polymers and synthesis
    • Amino acids link via dehydration reactions to form peptide bonds, creating polypeptide chains.
    • Dehydration reaction (condensation):
      extAminoAcid<em>1+extAminoAcid</em>2<br/>ightarrowextDipeptide+H2Oext{AminoAcid}<em>1 + ext{AminoAcid}</em>2 <br /> ightarrow ext{Dipeptide} + H_2O
    • The sequence of amino acids in a protein is its primary structure.
  • Protein structure levels
    • Primary structure: linear sequence of amino acids.
    • Secondary structure: due to hydrogen bonds, proteins form alpha helices or beta-pleated sheets (pleated sheet) (presence of alpha-helix or beta-sheets).
    • Tertiary structure: overall 3D folding driven by side chain interactions (hydrophobic/hydrophilic interactions, hydrogen bonds, ionic interactions, disulfide bridges, van der Waals).
    • Quaternary structure: two or more polypeptide subunits assemble into a functional protein.
  • Determinants of shape and stability
    • Protein shape depends on the environment: pH, salt concentration, temperature.
    • Denaturation occurs when a protein loses its native shape due to unfavorable conditions (e.g., high temperature; fever can denature proteins).
    • Misfolded proteins are implicated in diseases such as Alzheimer's, mad cow disease, and Parkinson's; often linked to mutations (DNA changes).
  • Structural details and terminology
    • Disulfide bridges (–S–S–) contribute to stabilizing tertiary and quaternary structures.
    • Hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces all contribute to folding and stability.
    • The protein’s three-dimensional shape enables specific molecular recognition and function within cells.
  • Examples of amino acid properties
    • Leucine: hydrophobic side chain.
    • Serine: hydrophilic side chain.
  • Quick takeaway
    • Proteins are versatile polymers whose function is determined by sequence (primary structure) and higher-order folding (secondary, tertiary, quaternary); environment and mutations can alter function dramatically.

Nucleic Acids

  • Overview
    • Nucleic acids are polymers composed of nucleotides; they direct cellular activities such as cell division and protein synthesis.
    • They serve as genetic information carriers and are the templates for protein production.
  • Monomer: nucleotide
    • Each nucleotide consists of three parts:
    • A phosphate group
    • A five-carbon sugar
    • A nitrogen-containing base
  • Types and sugars
    • Two main nucleic acids:
    • DNA (deoxyribonucleic acid): uses deoxyribose as the sugar.
    • RNA (ribonucleic acid): uses ribose as the sugar.
    • Nucleobases: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T) in DNA; Adenine (A), Guanine (G), Cytosine (C), and Uracil (U) in RNA.
  • Polymers and structure
    • Nucleic acids are polynucleotides formed by phosphodiester linkages between nucleotides.
    • RNA is typically single-stranded; DNA is typically double-stranded.
    • Base pairing in DNA: A−TA-T and C−GC-G; in RNA, A−UA-U can pair with C−GC-G in folded structures.
  • Central role in biology
    • Genes store information encoded in DNA.
    • Central dogma: DNA → RNA → Protein (conversion of genetic information into functional products).
  • Key terms and visuals
    • Nucleotides serve as the building blocks for DNA and RNA.
    • The backbone of nucleic acids consists of sugar-phosphate linkages, with bases projecting to the interior (for DNA) or participating in structure and function (for RNA).
  • Quick takeaway
    • Nucleic acids are the genetic material and the templates for protein synthesis; monomers are nucleotides, and polymerization occurs via phosphodiester bonds forming polynucleotides.

Connections and overarching themes

  • Carbon versatility and structure-function relationships
    • The four macromolecule classes demonstrate how carbon’s tetravalence enables complex, diverse structures that drive function in biology.
  • Structure determines function across macromolecules
    • Carbohydrates: structure and recognition; Lipids: membrane formation; Proteins: structure to catalysis and transport; Nucleic Acids: information storage and flow to protein synthesis.
  • Environmental sensitivity and health implications
    • Protein folding is sensitive to pH, temperature, and salts; misfolding links to neurodegenerative diseases.
    • Lipid saturation affects health outcomes and physical states of fats.
  • Foundational links to prior and real-world knowledge
    • Macromolecular structure underpins metabolism, signaling, genetics, and disease;
    • Dehydration synthesis is a common theme in forming macromolecules (peptide bonds in proteins, ester linkages in lipids).
    • Phosphodiester bonds in nucleic acids form the backbone of DNA/RNA and enable genetic information transfer.
  • Summary equations and key formulas
    • Protein synthesis (dehydration):
      extAminoAcid<em>1+extAminoAcid</em>2<br/>ightarrowextDipeptide+H2Oext{AminoAcid}<em>1 + ext{AminoAcid}</em>2 <br /> ightarrow ext{Dipeptide} + H_2O
    • Triglyceride formation (lipids):
      extGlycerol+3extFattyAcids<br/>ightarrowextTriglyceride+3H2Oext{Glycerol} + 3 ext{ Fatty Acids} <br /> ightarrow ext{Triglyceride} + 3 H_2O
    • Nucleic acid backbone linkage (backbone): phosphodiester bond along sugar-phosphate chain; base pairing rules: A−Text(DNA), A−Uext(RNA), C−Gext(both)A-T ext{ (DNA)},\, A-U ext{ (RNA)},\ C-G ext{ (both)}
  • Key terms to memorize
    • Monomer types: monosaccharides, amino acids, nucleotides, fatty acids/glycerol.
    • Bond types: glycosidic bonds (carbohydrates), peptide bonds (proteins), ester linkages (lipids), phosphodiester bonds (nucleic acids).
    • Protein structure levels: 44 levels: primary, secondary, tertiary, quaternary.
    • Standard amino acids: 2020 common amino acids.
    • Nucleic acid sugar distinctions: deoxyribosedeoxyribose (DNA) vs riboseribose (RNA).