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Macromolecules and Prokaryotes: Lipids, Proteins, Nucleic Acids, and Bacterial Cell Structure

Lipids

  • Lipids are a diverse group of molecules with a common feature: they are hydrophobic (water-hating) and largely nonpolar.
  • Major roles/functions:
    • Fuel reserve (energy storage)
    • Components of cell membranes (phospholipids)
    • Insulation (in some organisms)
    • Lipid-based hormones (steroid hormones)
    • In bacteria, lipid content can influence cell envelope properties (e.g., waxy coatings in some organisms)
  • Major types discussed: triglycerides, phospholipids, waxes, sterols, terpenes
    • Waxes: example in respect to Mycobacterium tuberculosis, which has a waxy outer cell wall coating that can hinder penetration of some treatments.
    • Sterols: e.g., cholesterol; embedded in eukaryotic cell membranes but not typically in bacterial membranes (bacteria membranes are mainly phospholipids and proteins). Some wall-less bacteria may incorporate sterol-like compounds to stabilize membranes.
    • Terpenes: plant-based lipids (not covered in depth here).
  • Lipid composition: C, H, O; nonpolar or mostly nonpolar; insoluble in water; require organic solvents for solubilization.
  • Simple lipids vs. complex lipids:
    • Simple lipids include triglycerides (fat) and related forms.
    • Phospholipids are amphipathic (have both polar and nonpolar regions) and form the lipid bilayer of membranes.
  • Triglycerides (fats): structure and properties
    • Core structure: glycerol backbone with three fatty acid chains (esterified).
    • Fatty acid chains: typically even-numbered carbon chains.
    • Common chain lengths: from about 6–8 carbons up to 26–28; common length is 18–20 carbons.
    • Saturated vs. unsaturated fatty acids:
    • Saturated: maximum number of hydrogens; straight chains; pack tightly; solid at room temperature (e.g., butter when left at room temp, it remains a solid block though softer).
    • Unsaturated: have one or more double bonds causing kinks; less tight packing; typically liquid at room temperature (e.g., olive oil is monounsaturated; many vegetable oils are polyunsaturated).
    • Effect of saturation on membrane fluidity:
    • In warmer environments, bacteria tend to increase saturation to maintain membrane integrity (prevent leakage).
    • In cooler environments, bacteria tend to increase unsaturation to maintain fluidity.
  • Phospholipids: structure and role
    • Basic structure: glycerol backbone, two fatty acid tails, and a phosphate-containing head group.
    • Elements in heads: phosphorus, nitrogen, and sometimes sulfur-containing groups; overall molecule is amphipathic.
    • Role: primary building blocks of the cell membrane in bacteria and eukaryotes; form the lipid bilayer.
    • Amphipathic nature creates a hydrophobic interior and a polar (hydrophilic) head facing the aqueous environment.
  • Sterols
    • Example: cholesterol in eukaryotic membranes; not generally found in bacterial membranes.
    • Function: helps regulate membrane fluidity and stability in eukaryotes.
  • Waxes and other lipids
    • Waxes provide protective coatings in some organisms; discuss in relation to Mycobacterium tuberculosis waxy outer layer that can impede antibiotic penetration.
  • Monomers and polymers (lipids): discussion note
    • Lipids do not fit cleanly into a simple monomer–polymer model like carbohydrates, proteins, and nucleic acids. For educational purposes here, triglycerides (glycerol + 3 fatty acids) and phospholipids (glycerol + 2 fatty acids + phosphate) are treated as representative monomer/polymer concepts.
  • Quick recap of lipid concepts for exams
    • Lipids are nonpolar, hydrophobic molecules with diverse functions including energy storage, membrane structure, insulation, and signaling.
    • Key lipid types to know: triglycerides (energy storage), phospholipids (membranes), waxes (outer coatings in some organisms), sterols (cholesterol in membranes), terpenes (plant lipids).

Proteins

  • Core elements: Carbon, Hydrogen, Oxygen, Nitrogen; sometimes Sulfur (in some amino acids).
  • Essential roles: enzymes, transport, structural components, receptors, antibodies, regulatory functions, and more. Proteins are crucial for cell survival.
  • Amino acids (the monomers):
    • 20 naturally occurring amino acids; each has:
    • An amino group (–NH2)
    • A carboxyl group (–COOH)
    • A variable side chain (R group) that determines properties (polarity, charge, size)
    • Side chain properties determine whether an amino acid is polar, nonpolar, or charged and thus influence protein folding and function.
    • Examples: glycine (small, hydrogen side chain); proline (cyclic side chain that can disrupt regular secondary structure); cysteine (sulfhydryl –SH group capable of forming disulfide bonds).
  • Protein structure and folding (the central theme): four levels of organization
    • Primary structure: the linear sequence of amino acids in a polypeptide, held together by peptide bonds (formed by dehydration synthesis).
    • Secondary structure: localized shapes formed by hydrogen bonds between backbone atoms; common motifs are alpha helices and beta pleated sheets.
    • Tertiary structure: overall three-dimensional folding of a single polypeptide, driven by interactions among R groups (side chains):
    • Hydrophobic interactions drive nonpolar side chains to the interior.
    • Hydrogen bonds, ionic bonds, and disulfide bonds (between cysteines) stabilize the structure.
    • Quaternary structure: assembly of two or more polypeptide chains into a functional protein; held together by the same types of bonds as in the tertiary structure (hydrogen bonds, ionic bonds, disulfide bonds, hydrophobic interactions).
  • How proteins fold and why it matters
    • Each protein has a unique shape (conformation) essential for its function; misfolding leads to loss of function.
    • Example of functional importance: hemoglobin is a tetramer (four polypeptide chains) with heme groups that bind oxygen; four chains must assemble to be functional.
    • Sickle cell example: a single amino acid substitution in the hemoglobin chain can alter folding and function, impairing oxygen transport.
  • Protein synthesis and genetics (basic overview for context)
    • Primary structure is genetically determined: the DNA sequence dictates the order of amino acids through transcription and translation (DNA -> RNA -> protein).
    • Mutations can alter amino acid sequences; some mutations have little effect (e.g., substituting one hydrophobic amino acid for another) while others can dramatically affect folding and function.
  • Protein’s role in the cell membrane and transport
    • Many proteins are membrane-bound transporters, enabling molecules to enter and exit the cell.
  • Protein stability and denaturation
    • Proteins can denature (unfold) under certain conditions, losing function.
    • Denaturing factors include:
    • Heat (e.g., autoclaving denatures proteins to kill organisms)
    • pH changes (acidic or basic extremes)
    • Heavy metal salts
    • Alcohols
    • Denaturation disrupts noncovalent interactions; disulfide bonds can help some proteins retain structure but can be disrupted under harsh conditions.
  • Amino terminus and carboxyl terminus
    • Polypeptides have a starting amino (N) terminus and an ending carboxyl (C) terminus; numbering of residues proceeds from N-terminus to C-terminus.
    • This orientation is important for understanding active sites and protein processing.
  • Practical notes and exam strategy
    • Four key questions for each macromolecule: function, monomer, polymer, cellular location in bacteria.
    • For lipids, remember that there isn’t a clean monomer-polymer model like other macromolecules; focus on triglycerides and phospholipids as representative examples.
    • Be prepared to identify protein structure levels and how different bonds stabilize structures (hydrogen bonds in secondary, hydrophobic/ionic/disulfide in tertiary and quaternary).
    • Recognize the role of mutations (e.g., sickle cell) as demonstrations of how small sequence changes can alter function.

Nucleic Acids

  • Overview
    • The two main nucleic acids are DNA and RNA; they store and convey genetic information and are central to genetics and protein synthesis.
  • Nucleotides (monomers of nucleic acids)
    • Each nucleotide consists of:
    • Phosphate group
    • Sugar
    • Nitrogenous base
    • DNA nucleotide: deoxyribose sugar; bases = A, T, G, C; phosphate backbone; double-stranded structure with complementary base pairing.
    • RNA nucleotide: ribose sugar; bases = A, U, G, C; typically single-stranded; can fold into complex structures.
  • Base pairing and structure
    • Complementary base pairing in DNA:
    • Adenine pairs with Thymine (A-T) via two hydrogen bonds.
    • Guanine pairs with Cytosine (G-C) via three hydrogen bonds.
    • DNA structure: double helix, sugar-phosphate backbone on the outside, bases inside; strands are antiparallel (one runs 5'→3', the other 3'→5').
    • RNA structure: typically single-stranded; can form hairpins and folds to gain stability.
  • Antiparallel orientation in DNA
    • The two strands run in opposite directions: one 5'→3' and the other 3'→5'. This antiparallel arrangement is critical for replication and transcription.
  • Sugar differences
    • DNA uses deoxyribose; RNA uses ribose; the 2' carbon difference (hydroxyl group) contributes to RNA’s instability relative to DNA.
  • Nucleotides as energy currencies
    • ATP (adenosine triphosphate) is a nucleotide and a central energy currency in the cell.
    • Other nucleoside triphosphates can serve as energy sources in certain reactions, such as GTP (guanosine triphosphate) and UTP (uridine triphosphate).
    • In the ATP molecule: adenosine + ribose + three phosphate groups.
    • Energy from phosphate bond cleavage powers cellular reactions; typical representations include:
    • ATP hydrolysis: ext{ATP}
      ightarrow ext{ADP} + P_i
    • or cleavage of outer two phosphates: ext{ATP}
      ightarrow ext{AMP} + PP_i (this rate of energy release can drive various cellular processes depending on the reaction)
  • Nucleic acids and gene information
    • A single DNA molecule can contain thousands of genes; for example, E. coli has about 4,300 genes; humans have roughly 20,000–25,000 genes (numbers cited for context).
    • DNA and RNA are central to heredity and the control of cellular function through the processes of transcription and translation.
  • RNA types (brief overview)
    • Messenger RNA (mRNA): carries genetic information from DNA to ribosomes for protein synthesis.
    • Transfer RNA (tRNA): brings amino acids to ribosomes during translation.
    • Ribosomal RNA (rRNA): forms part of the ribosome and catalyzes protein synthesis.
    • There are other RNA types, but these three are the main ones involved in transcription and translation.
  • Nucleic acids in bacteria
    • Bacteria lack a nucleus; DNA is located in the nucleoid region within the cytoplasm.
    • The bacterial genome is typically a circular chromosome.
  • ATP, energy, and metabolism context
    • ATP provides the energy to drive cellular reactions; when ATP is depleted, cells trigger energy-producing pathways (e.g., glycolysis) to generate ATP again.
    • The energy stored in phosphoanhydride bonds enables endergonic reactions to proceed.

Protein folding and structure in context

  • Relationship to genetics and function
    • The sequence of amino acids (primary structure) determined by the DNA sequence dictates folding and final function.
    • A single change in the amino acid sequence can drastically alter structure and function, illustrating the precision of protein folding in biology.
  • Examples and analogies from the lecture
    • A telephone cord analogy was used to describe how a polypeptide chain begins straight and then folds into secondary and tertiary structures as it winds up.
    • Hemoglobin example illustrates quaternary structure and the importance of multiple polypeptide chains forming a functional protein.

Prokaryotes vs Eukaryotes (overview)

  • Shared features (common to all cellular life)
    • Cell membrane
    • DNA and RNA
    • Cytoplasm
    • Ribosomes
  • Key differences
    • Nucleus: Eukaryotes have a defined nucleus; prokaryotes have a nucleoid region without a membrane-bound nucleus.
    • Chromosomes: Prokaryotes typically have a single circular chromosome; eukaryotes have multiple linear chromosomes and are associated with histone proteins.
    • Organelles: Eukaryotes have membrane-bound organelles (e.g., mitochondria, Golgi); prokaryotes do not.
    • Cell wall composition: Bacteria have cell walls made of peptidoglycan; some organisms lack cell walls; plants/fungi/algae have cell walls with different compositions.
    • Membrane components: Eukaryotic membranes often contain sterols (e.g., cholesterol) that help regulate fluidity; bacterial membranes generally lack sterols (though some sterol-like compounds can be present in certain wall-less bacteria like Mycoplasma).
  • Prokaryotes of note
    • Do not have a nucleus; DNA resides in the nucleoid region.
    • Typically lack membrane-bound organelles; have a simpler internal organization.
    • Exhibit a variety of shapes and arrangements discussed below.

Bacterial shapes and arrangements (visual overview from slides)

  • Three common shapes:
    • Bacillus (rods): individual rods or short chains; chains can be called streptobacilli when they form long chains.
    • Cocci (spheres): can be found alone or in arrangements; examples include:
    • Diplococcus: two cocci together (e.g., Neisseria gonorrhoeae).
    • Streptococcus: chains of cocci (e.g., Streptococcus pyogenes, cause of strep throat).
    • Tetrads: four cocci in a square arrangement (less common).
    • Staphylococcus: irregular grape-like clusters.
    • Spirals: several types including:
    • Vibrios: curved rods (comma-shaped), e.g., Vibrio cholerae.
    • Spirilla: rigid corkscrew-shaped spirals.
    • Spirochetes: flexible corkscrew-shaped spirals, e.g., Treponema pallidum (syphilis).
  • Observations from slides and lab practice
    • Staining and microscopy reveal these shapes and arrangements; slides may show rods, spheres, and spirals in various configurations.
    • Stain patterns and morphology are often used for preliminary bacterial identification in education settings.
  • Lab and exam context
    • The upcoming exam focuses on the three groups of slides shown in class (the three bacterial morphology groups).

Practical and exam-oriented notes

  • To study effectively for exams, consider building a concise table that covers:
    • Macromolecule: function
    • Monomer: polymer relationship
    • Polymers (or representative polymers)
    • Location in bacterial cells (where they are typically found)
  • Example entries (based on content above):
    • Lipids: function = energy storage, membrane structure, signaling; monomer/polymer = no simple monomer/polymer model; common examples = triglycerides (glycerol + 3 fatty acids), phospholipids (glycerol + 2 fatty acids + phosphate); location = cell membrane for phospholipids; bacterial relevance = membrane composition and permeability; note about waxes and sterols.
    • Proteins: function = enzymes, transport, structure, signaling, antibodies; monomer = amino acids; polymers = polypeptide chains; location = throughout the cell (membrane proteins, enzymes, cytosol, etc.); notable concepts = primary/secondary/tertiary/quaternary structure; folding determines function; mutations can alter function; denaturation factors.
    • Nucleic acids: function = store and transmit genetic information; monomer = nucleotides; polymers = DNA and RNA; location = DNA in nucleoid (bacteria); RNA transcription and translation machinery; energy currency = ATP/ GTP/ UTP; antiparallel strands in DNA; base pairing A-T and G-C.
    • Prokaryotes vs Eukaryotes: similarities (cell membrane, DNA/RNA, ribosomes) and differences (nucleus vs nucleoid, histones vs non-histone proteins, organelles, cell wall composition).
  • Real-world relevance and implications
    • Antibiotic strategies often target differences in cell membranes, cell walls (peptidoglycan), or protein synthesis machinery. The waxy outer layer in some bacteria can impede antibiotic penetration, illustrating how membrane composition affects treatment options.
    • Protein folding is central to function; misfolding can cause disease (e.g., sickle cell disease demonstrates how a single amino acid change affects hemoglobin function).
    • Understanding nucleic acids is foundational for genetics, biotechnology, and medicine; DNA replication, transcription, and translation are core processes in all cellular life.

Quick reference and recap

  • Lipids: triglycerides, phospholipids; saturated vs. unsaturated fatty acids; amphipathic phospholipids; sterols in eukaryotes; waxes in some bacteria; membrane fluidity adaptation.
  • Proteins: 20 amino acids; peptide bonds; primary, secondary, tertiary, and quaternary structures; folding and function; disulfide bonds; denaturation factors; proteins as enzymes and transporters.
  • Nucleic acids: DNA and RNA; nucleotides; base pairing; antiparallel strands; RNA types; energy currencies (ATP, GTP, UTP).
  • Prokaryotes vs Eukaryotes: nucleus, organelles, cell walls; similarities in fundamental molecular components; bacterial shapes and arrangements.
  • Exam strategy reminder: build a single-page study guide linking functions, monomers, polymers, and cellular locations; focus on how this information connects to bacterial cells and cellular processes.