MCB 150 Lecture Notes

Lecture 2: Technology Intro; Domains of Life

• Announcements:
  • Lecture 3 pre-lecture assignment due 1:00 PM Monday.
  • Lecture 3 post-lecture available after class on Monday and due at 1:00 PM on Tuesday.
  • Send emails to mcb150@life.illinois.edu from your illinois.edu account.
  • Reminder to take other devices off the wireless network when doing iClicker questions.
• The Linnaean system of classification originated in the 1700s and was based on physical characteristics.
  • Considerations included: Does it make its own food? Does it move?
  • The Genus: species scheme is still used.
  • The original system with 2 kingdoms (animals & plants) wasn’t enough to explain fungi, microbes, etc.
• Technology advanced, allowing examination of individual cells, revealing two basic types:
  • Eukaryotes: Cells with a "kernel" (=karyon =nucleus).
  • Prokaryotes: Cells without a "kernel".
• Typical PROKARYOTIC cell:
  • Nucleoid: Contains usually a single chromosome and is not surrounded by a membrane.
  • Cytoplasmic membrane: Serves the role of cytoplasmic membrane and other internal membranes in eukaryotes.
  • Cell wall: Usually, but not always, present.
• Typical EUKARYOTIC cell (ANIMAL cell):
  • Organelles: Lysosome, Cytoplasmic membrane, Golgi Apparatus, Endoplasmic reticulum, Mitochondrion, Nucleus.
  • Plant cells have cell walls and chloroplasts.
  • The inside of the cell is separated into distinct compartments called organelles (representative, not exhaustive list).
• Until ~1977, organisms were thought to fall into 2 “superkingdoms”:
  • Prokaryotes: Without a nuclear membrane and membrane-bound organelles.
  • Eukaryotes: With a nuclear membrane and membrane-bound organelles.
• Physical/structural characteristics are useful for crude classifications.
• To understand true evolutionary relationships among organisms (to make a true "tree of life" and find a common ancestor), it’s necessary to look at their genomes and biochemical systems.
• In 1977, Carl Woese and co-workers at Illinois compared the sequences in different species of molecules (small subunit ribosomal RNAs) which are an essential component of every cell’s machinery for synthesizing proteins.
• Conclusion: "prokaryotes" are actually two distinct groups of organisms:
  • (EU)BACTERIA: true bacteria like E. coli; found everywhere.
  • ARCHAEA: "ancient" prokaryotes; frequently found in extreme habitats that resemble early Earth, such as extreme heat, pressure, acids, salts, gases, etc.
• That conclusion was based on the observation that archaeal rRNA sequences are more closely related to eukaryotic rRNA sequences than to bacterial rRNA sequences.
• Revised “Tree of Life” was created with 3 DOMAINS rather than 2 superkingdoms:
  • Bacteria.
  • Archaea.
  • Eukarya.
• Despite physically resembling bacteria (they are both prokaryotes), in most molecular processes, archaea are more similar to humans than they are to E. coli.
• Comparison of Bacteria, Archaea, and Eukarya:

• No two species are identical structurally and biochemically, but they are all made of one or more cells. Why?
• Life requires a structural compartment separate from the external environment in which molecules can perform unique functions in a relatively constant internal environment.
  • This “living compartment” is a cell.
• Basic tenets of the CELL THEORY:
  • Cells are the fundamental units of life.
  • All organisms are composed of (one or more) cells.
  • All cells come from preexisting cells.
• Why are cells so small and found in such a narrow size range?
  • As the size increases, the surface area-to-volume ratio decreases.
• Resolution: the ability to identify the separation of two objects that are close to each other.
  • Resolving power of light microscopes is ~0.2 microns (\(µ\)m; 10^{-6} m).
• What if we want to visualize sub-cellular objects?
  • Electron microscopy has resolution of ~0.5 nm (10^{-9} m).
  • Denser material affects electrons more and the sample appears darker.

Lecture 3: Overview of Cell Structure; Begin Carbohydrates

• Approaching a cell from the outside:
  • Some cells (plants, most prokaryotes) have a relatively rigid cell wall providing shape and protection.
  • Every cell is surrounded by a Plasma Membrane:
    • Allows cells to maintain a constant internal environment.
    • Acts as a selectively permeable barrier.
    • Is an interface for cells where information is received from adjacent cells and extracellular signals.
    • Has molecules that are responsible for binding and adhering to adjacent cells.

Lecture 4: Continue Carbohydrates

• Monosaccharides are typically found with 3, 5, or 6 carbons.
  • Glucose (C6H{12}O_6).
• Circularization of Glucose: α-glucose vs. β-glucose.
• Some monosaccharides have identical formulas but different structures (called isomers).
  • Hexoses: 6-carbon sugars (C6H{12}O_6):
    • Glucose
    • Galactose
    • Fructose
• Other monosaccharides have similar (but not identical) formulas, similar structures, and related functions:
  • Deoxyribose
  • Ribose
• Pentoses: 5-carbon sugars (C5H{10}O_5):
  • Ribose
  • Ribulose
• Two monosaccharides can be brought together to form a very simple polysaccharide called a disaccharide via a covalent bond called a glycosidic linkage. Note that the glucose molecule contributing its C1 is an alpha glucose, making the resulting glycosidic linkage an α-1,4 glycosidic linkage. Cellobiose (not shown) is a disaccharide of beta glucose and another glucose connected via a β-1,4 glycosidic linkage.
• In maltose and cellobiose, both monosaccharides are glucose, but not all disaccharides have to be the same monomers:
  • Lactose (milk sugar) is a disaccharide of glucose and galactose.
  • Sucrose (table sugar) is a disaccharide of glucose and fructose.
• The chemical formula for a disaccharide of hexose sugars is C{12}H{22}O{11}. This differs from the general formula of (Cn(H2O)n) because a water molecule is removed during the condensation reaction.
• Some common terminology:
  • One monomer is a monosaccharide.
  • Two monomers are a disaccharide.
  • Several monomers are called an oligosaccharide (oligo = several).
  • Hundreds or thousands of monomers are a polysaccharide (poly = many).
• Carbohydrates can be modified:
  • Linkage of oligosaccharides to other macromolecules: When covalently linked to membrane proteins or lipids, carbohydrates act as identification and recognition molecules (chemical markers), as in blood typing.
  • Addition of chemical groups: Fructose-1,6-bisphosphate.
  • Addition of chemical groups: Glucosamine, Galactosamine.
• Polysaccharides serve as chemical sources of energy or structural compounds:
  • Cellulose.
  • Starches.
  • Glycogen.
• Cellulose:
  • The most abundant carbon-containing (i.e., organic) compound on Earth.
  • Found in plant cell walls.
  • Linear, unbranched polymer of glucose:
    • monomers covalently linked by β-1,4 glycosidic linkages
    • linear polymers held together by hydrogen bonding with neighboring strands.
• Starches:
  • Found chiefly in seeds, fruits, tubers, roots, and stems of plants for energy storage.
  • Helical, unbranched, or loosely branched polymers of glucose:
    • monomers within chains covalently linked by α-1,4 glycosidic linkages.
    • chains branch by connecting with other chains by α-1,6 glycosidic linkages.
• Glycogen:
  • Found in muscle and liver cells of animals for energy storage.
  • Helical, highly branched polymers of glucose:
    • monomers within chains covalently linked by α-1,4 glycosidic linkages.
    • chains branch by connecting with other chains by α-1,6 glycosidic linkages.

Lecture 5: Lipids and Biomembranes Part 1

• Lipids:
  • Defined by a physical property, not a chemical structure.
  • Vary widely in structure.
  • Functions: Energy Storage, Biomembrane Composition, Chemical Signaling.
  • Types: Triglycerides, Phospholipids & Glycolipids, Steroids.
• The monomers of (biological membrane) lipids: Glycerol and Fatty Acids.
• 3 Fatty Acids + Glycerol = Triglyceride.
• 2 Fatty Acids + Glycerol + Phosphate = Phospholipid
• Variety in Phospholipid polar head groups.
• Fatty acid tails in phospholipids can also vary in length and degree of saturation.
• Phospholipids are Amphipathic.
• Phospholipids in water will spontaneously form micelles or bilayers.
• Bilayers have exposed edges and will fold into liposomes.
• Artificial bilayers can be used to study lipid properties.
• Exclusion of water at the bilayer interface is a key property of lipid bilayers.
• Some membrane lipids are Glycolipids.
• Steroids:
  • Can be used as circulating hormones like estrogen and testosterone or as membrane components.
  • Animal cells have cholesterol in their biomembranes.
  • Plants & fungi: different steroids; bacteria: none.
• Biomembranes are Asymmetrical.
• Biomembranes have associated Proteins: Transmembrane, Membrane-associated, Lipid-linked, Peripheral.
• Proteins in biomembranes serve a variety of functions:
  • Transport.
  • Enzymatic activity.
  • Signal transduction.
  • Cell-cell recognition.
  • Intercellular joining.
  • Attachment to the cytoskeleton and extracellular matrix (ECM).
• Not everything can cross a lipid bilayer (selective permeability).

Lecture 6: Lipids and Biomembranes Part 2; Nucleic Acids

• Biological membranes are fluid.
• Lipids can move around within the membrane in various ways.
• Membrane fluidity is temperature-dependent.
• The cell can regulate membrane fluidity by changing:
  • The number of unsaturated fatty acids: High level +, Low level –.
  • The tail length of fatty acids: Short chains +, Long chains –.
  • The number of cholesterol molecules (at low temperatures): High level +, Low level –.
• Nucleic Acids:
  • Two types: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA).
  • Serve an information storage role in a cell.
  • The monomers of Nucleic Acids are Nucleotides: Base, Sugar, Phosphate.
• Numbering, labeling, and naming conventions:
  • Base + Sugar = Nucleoside
  • Nucleoside + 1 Phosphate = nucleoside monophosphate
  • Nucleoside + 2 Phosphates = nucleoside diphosphate
  • Nucleoside + 3 Phosphates = nucleoside triphosphate
• The nucleotides of DNA and RNA differ in two important ways:
  • Which nitrogenous bases are found in each nucleic acid?
    • RNA: Uracil, Cytosine, Adenine, Guanine
    • DNA: Cytosine, Thymine, Adenine, Guanine
  • Which 5-carbon sugar is found in each nucleic acid?
    • DNA = Deoxyribose.
    • RNA = Ribose.
• Nucleotide nomenclature: A, G, C, U, or T depends on which base it contains.
• Summarizing Nucleic Acid Properties (DNA):
  • Deoxyribose sugar (H at 2' carbon).
  • Pyrimidine bases are Cytosine (C) and Thymine (T).
  • Purine bases are Adenine (A) and Guanine (G).
  • DNA monomers are called deoxyribonucleotides (or deoxyribonucleoside triphosphates, or dNTPs).
  • Usually double-stranded.
• Summarizing Nucleic Acid Properties (RNA):
  • Ribose sugar (OH at 2' carbon).
  • Pyrimidine bases are Cytosine (C) and Uracil (U).
  • Purine bases are Adenine (A) and Guanine (G).
  • RNA monomers are called ribonucleotides (or ribonucleoside triphosphates, or NTPs).
  • Usually single-stranded.
• Polymerization of Nucleic Acid.

Lecture 7: Proteins, Part 1

• Proteins:
  • We are the product of our proteins and protein activity.
  • The study of proteins and protein activity: Proteomics.
  • Proteins account for most of the dry weight in the cell.
• Proteins are involved in nearly all categories of cellular function:
  • Movement (Actin/Myosin).
  • Defense (Antibodies).
  • Structure (Keratin).
  • Transport (Hemoglobin).
  • Signaling (Glucagon).
  • Catalysis/Regulation/Metabolism.
• Most of our (useful) genetic information instructs the cell on how to build proteins or regulates that process.
• Amino Acids are the monomers of Proteins:
  • Basic structure of an amino acid (ionized form): Carboxyl (or C) Terminus, Amino (or N) Terminus, Side Chain, or R-Group.
  • The R group—the only part that differs—is what makes one amino acid different from another.
• Peptide bond formation: Condensation/ Dehydration.
• During protein synthesis, ribosomes link amino acids by constructing covalent PEPTIDE BONDS that join the NH2 (or NH3+) group of the incoming amino acid to the COOH (or COO-) group of what was already there in the N→C direction.
• Some common (and familiar) terminology:
  • Two amino acids = DIPEPTIDE.
  • A few amino acids = OLIGOPEPTIDE.
  • A long chain of amino acids = POLYPEPTIDE.
  • A polypeptide with a purpose = PROTEIN.
• 20 different amino acids commonly found in proteins:
  • differ only in R groups, which confer distinct properties to that amino acid.
  • large number of amino acids makes possible a huge number of different amino acid sequences:
  • 20^2 (=400) possibilities for dipeptides.
  • 20^3 (=8,000) possibilities for tripeptides.
  • 20^5 (=3,200,000) possibilities for pentapeptides.
  • most proteins are >100 amino acids!!
• Amino acid R-groups (4 classes based on charge):
  • Uncharged, but polar.
  • Uncharged and non-polar (hydrophobic).
  • Positively-charged (basic).
  • Negatively-charged (acidic).
• Proteins exist in a virtually infinite number of 3-dimensional conformations:
  • That conformation is critical to the functioning of each protein.
  • The consequence of folding improperly is usually very significant: Alzheimer’s, CF, Parkinson’s, Mad Cow –– all caused by errors in protein folding → accumulation of toxic insoluble “gunk” (e.g. “plaques” in Alzheimer’s).
• To describe how linear protein chains fold into their 3-D conformations, protein structure is organized into 4 different categories:
  • 1° (pronounced ‘primary’)
  • 2° (pronounced ‘secondary’)
  • 3° (pronounced ‘tertiary’)
  • 4° (pronounced ‘quaternary’)
• Primary structure (1°, or primary sequence):
  • Linear sequence of amino acids from N → C (“beads on a string”).
  • All proteins have a UNIQUE primary structure.
• Secondary Structure (2°):
  • First level of folding.
  • Stabilized by (relatively weak) hydrogen bonds between peptide linkages:
    • Peptide backbone is polar (N-H is partially +, C=O is partially –).
  • Independent of R groups, so found in most proteins.
  • α-helix and β-pleated sheet are 2 major types.

Lecture 8: Proteins, Part 2; Begin Energy & Enzymes

• Hair protein (keratin) is very rich in α-helical structures.
  • Hair stretches because it is easy to break the H-bonds that stabilize α-helices.
• Prions:
  • Misfolded proteins which somehow induce normal versions of that protein to fold the same (incorrect) way.
  • Misfolded protein comes out of solution, creates plaques.
  • Causes a family of diseases called spongiform encephalopathies like Mad Cow, Scrapies, and Creutzfeldt-Jakob.
• Tertiary Structure (3°):
  • Unique 3D folded structure.
  • Final conformation of some proteins.
  • Due to interactions between R-groups with each other and with backbone.
  • Stabilized by:
    • H-bonds between polar (or charged) side chains.
    • H-bonds between hydrophilic side chains and backbone.
    • Ionic bonds between acidic and basic amino acids.
    • Hydrophobic clustering of non-polar side chains.
    • Van der Waals forces.
    • Disulfide linkages.
  • Thousands of water molecules surround a protein, contorting the protein so that its hydrophilic R groups are on the outside and hydrophobic R groups are on the inside.
  • Line up sites for functional activity of that protein.
• Quaternary Structure (4°):
  • Found in proteins with multiple polypeptide chains (subunits).
  • Subunits can be same or different:
    • 2 identical subunits = homodimer.
    • 2 different subunits = heterodimer.
    • Ferritin (iron storage protein) has 24 identical subunits.
  • Hemoglobin (Hb):
    • 4 separate polypeptides (2 α and 2 β chains).
    • Sickle Cell mutation:
      • changes a Glu (HydroPHILIC) to a Val (HydroPHOBIC).
      • affected amino acid is on the outside of the protein.
      • Hb molecules stick together to “hide” Val from water.
      • oxygen levels fall, Hb precipitates, distorts RBC.
• Relative stabilities of biomolecular forces:
  • Disulfide linkages → Covalent.
  • Ionic bonds → Easily made and broken.
  • Hydrogen bonds.
  • Hydrophobic clusters.
  • Van der Waals forces.
• Does the information for how a protein will fold lie in its primary structure?
  • How could we determine this?
    • Removal or inactivation of stabilizing forces unfolds (denatures) the protein to 1° structure, but no peptide bonds are broken.
    • All 2° and 3° structure is lost.
    • Almost always leads to loss of function.
    • Acids/bases, heat, detergents.
  • If denaturing agent is removed, some proteins will resume properly folded 3D structure.
    • “instructions” are in 1° structure.
• Many proteins are enzymes: biological catalysts; they facilitate biological reactions.
  • This is necessary because most cellular reactions proceed at a very slow rate.
  • Two broad categories of cellular reactions based on change in energy level (E):
    • Reactions that require an input of energy.
    • Reactions that release energy upon completion.
• Reactions that require energy are called biosynthetic or anabolic.
  • Linking together of smaller molecules into larger ones, such as condensation reactions of monomers to macromolecules
• Reactions that release energy are called catabolic.
  • Break down larger molecules into smaller ones, such as the hydrolysis reactions of macromolecules to monomers.
  • Also referred to as spontaneous reactions.
• Two different meanings for the word spontaneous:
  • Typical meaning: happens automatically.
  • Biology meaning: a reaction that releases energy, much of which is lost as heat.
• Catabolic (E–releasing) reactions require a certain amount of energy to get started.
  • Energy of Activation, or Ea.
  • Could come from heat.

Lecture 9: Continue Energy & Enzymes

• Catabolic (E–releasing) reactions require a certain amount of energy to get started.
  • Instead, comes from Enzymes.
• Standard Activation Energy Diagram:
  • [S] = energy level of substrate (reactants).
  • [P] = energy level of products.
  • Ea = activation energy, which converts substrates into unstable transition states
  • ΔG = Free Energy of Reaction: difference in E between reactants & products.
• Enzymes do not cause reactions to occur that would not eventually occur anyway; only speed up existing reactions.
  • Many enzymes ↑ reaction rates by several million times.
  • Some enzymes ↑ reaction rates by several trillion times.
  • Example of enzyme catalyzed reaction:
    • 2H2O2 ↔ 2H2O + O2
      • platinum (inorganic catalyst) decreases Ea by 1/3rd.
      • catalase (enzyme) decreases Ea by almost 90%!
• Enzymes bind substrates with extremely high specificity into their active sites (usually just a few amino acids).
  • Enzymes will most likely cause some conformational change in the substrate molecule(s), but they themselves usually change shape upon binding substrate.
  • Called induced fit.
• How does substrate binding to active site decrease Ea?
  • Acting as a template for substrate orientation.
  • Stressing the substrate(s) and stabilizing the transition state.
  • Providing a favorable microenvironment.
  • Participating directly in the catalytic reaction.
• Very Important Point:
  • If an enzyme accepts a group from a substrate, it must, in turn, donate that group to help form the product.
  • ENZYMES ARE (ultimately) UNCHANGED BY THE REACTIONS THEY CATALYZE.
• ENZYMES DO NOT CHANGE THE EQUILIBRIUM OF REACTIONS, they only make it easier (and therefore faster) to reach that equilibrium.
  • Enzymes decrease E_a by the same amount in both directions Exergonic Endergonic.
• Because most enzymes are proteins, it follows that conditions that affect protein stability also affect enzyme activity.
  • Enzymes have temperature and pH optimums.
  • Most tend to be near body temperature (37 °C) and neutral pH (7.0).
• Enzyme Inhibition:
  • E + S −−> [ES] −−> E + P
  • E + I −−> [EI] −−//−−>
  • Can be either reversible or irreversible.
    • Reversible inhibition can be competitive or noncompetitive.
• Irreversible Inhibitors:
  • Permanently bind to or modify active site; changing concentration of natural substrate or inhibitor has no effect.
    • Nerve agents like sarin gas are irreversible inhibitors of acetylcholinesterase, which catalyzes the termination of nerve impulses.
  • Tend to be molecules not typically encountered by that particular cell.
  • Irreversible inhibition is a demonstration of the important point that enzymes must ultimately be unchanged if they are to be used over and over.
• In competitive inhibition, the inhibitor molecule physically resembles the natural substrate and occupies the active site:
  • enzyme can’t use inhibitor as substrate - no products are formed.
  • can be