Biochemistry Foundations Notes

The Foundations of Biochemistry

• Biochemistry describes the structures, mechanisms, and chemical processes shared by all organisms.

Life's Origins

• Life arose on Earth approximately 4 billion years ago.
• Simple microorganisms:
  • Extracted energy from chemical compounds and sunlight.
  • Used energy to make biomolecules from simple elements and compounds on Earth's surface.

Core Principles

• Principle 1: Cells as Fundamental Units

  • Cells are the fundamental unit of life.
  • They vary in complexity and can be highly specialized.
  • Share remarkable similarities.

• Principle 2: Carbon-Based Metabolites

  • Cells use a small set of carbon-based metabolites.
  • These create polymeric machines, supramolecular structures, and information repositories.
  • Chemical structure defines their function.
  • Molecule collection carries out a program for reproduction and self-perpetuation.

• Principle 3: Dynamic Steady State

  • Living organisms exist in a dynamic steady state, never at equilibrium with surroundings.
  • They extract energy from surroundings and use it to maintain homeostasis and do useful work.
  • Energy comes from electron flow, driven by sunlight or metabolic redox reactions.

• Principle 4: Self-Replication and Self-Assembly

  • Cells have the capacity for precise self-replication and self-assembly.
  • This uses chemical information stored in the genome.
  • Example: A single bacterial cell can give rise to a billion identical daughter cells in 24 hours.
  • Offspring resemble parents due to inheritance of parental genes.

• Principle 5: Gradual Evolution

  • Living organisms change over time through gradual evolution.
  • Evolution leads to diversity of life forms.
  • Shared ancestry is seen in molecular similarity of gene sequences and protein structures.

Cellular Foundations

• Cells Are the Structural and Functional Units of All Living Organisms
• Cells Include
  • Plasma membrane
  • Cytoplasm
  • Ribosomes
  • Nucleus (Eukaryotic Cells)
  • Nucleoid (Prokaryotic Cells)
  • Nuclear envelope (Eukaryotic Cells)
  • Membrane-bounded organelles (Eukaryotic Cells)

Plasma Membrane

• Defines the cell's periphery.
• Composed of lipid and protein molecules.
• Thin, flexible, hydrophobic barrier.
• Contains embedded transport proteins, receptor proteins, and membrane enzymes.

Cytoplasm

• Internal volume enclosed by the plasma membrane.
• Composed of:
  • Cytosol: aqueous solution.
  • Suspended particles: mitochondria, chloroplasts, ribosomes, proteasomes.

Cytosol

• Highly concentrated solution.
• Contains enzymes, RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions.

Nucleoid and Nucleus

• Genome: complete set of genes, composed of DNA.
• Prokaryotes (bacteria and archaea) store their genome in a nucleoid.
• Eukaryotes store their genome in a membrane-enclosed nucleus.

Cellular Dimensions

• Cells are microscopic:
  • Animal and plant cells: 5 to 100 $μm$ in diameter.
  • Unicellular microorganisms: 1 to 2 $μm$ long.
• Upper limit of cell size is likely set by transport rate and O2 delivery.
  • As size increases, surface-to-volume ratio decreases.

Three Domains of Life

• Bacteria:
  • Inhabit soils, surface waters, and tissues of other living or decaying organisms.
• Archaea:
  • Inhabit extreme environments.
• Eukarya:
  • All eukaryotic organisms.
  • More closely related to archaea than bacteria.

Archaea and Bacteria Habitats

• Aerobic: plentiful O2; organisms transfer electrons from fuel to O2 for energy.
• Anaerobic: devoid of O2; organisms transfer electrons to nitrate, sulfate, or CO2 for energy.
  • Obligate anaerobes: die when exposed to O2.
  • Facultative anaerobes: can live with or without O2.

Energy and Biosynthetic Precursors

• Phototrophs: trap and use sunlight.
• Chemotrophs: derive energy from oxidation of a chemical fuel.
• Autotrophs: synthesize all biomolecules directly from CO2.
• Heterotrophs: require preformed organic nutrients made by other organisms.

Bacterial and Archaeal Cells

• Cell envelope: composed of plasma membrane, outer membrane, and peptidoglycan.
• Gram-positive bacteria:
  • Colored by Gram's stain.
  • Thick peptidoglycan layer outside plasma membrane.
  • Lack an outer membrane.
• Gram-negative bacteria:
  • Outer membrane composed of a lipid bilayer.
• Archaea:
  • Layer of peptidoglycan or protein confers rigidity on their cell envelopes.

E. coli Cytoplasm

• Contains ribosomes, enzymes, metabolites, cofactors, and inorganic ions.
• The nucleoid contains a single, circular molecule of DNA.
• Plasmids: smaller, circular segments of DNA that confer resistance to toxins and antibiotics in the environment.

Eukaryotic Cells

• Membranous Organelles:
  • Mitochondria: site of energy-extracting reactions.
  • Endoplasmic reticulum and Golgi complexes: synthesis and processing of lipids and membrane proteins.
  • Peroxisomes: oxidation of very-long-chain fatty acids and detoxification of reactive oxygen species.
  • Lysosomes: filled with digestive enzymes.
  • Granules or droplets containing stored nutrients, such as starch and fat.
• Plant Cell Organelles:
  • Vacuoles: store large quantities of organic acids.
  • Chloroplasts: where sunlight drives the synthesis of ATP in photosynthesis.

Cytoskeleton

• Three-dimensional network of protein filaments in eukaryotic cells:
  • Actin filaments.
  • Microtubules.
  • Intermediate filaments.
• Filaments undergo constant disassembly into protein subunits and reassembly into filaments.

Structural Organization of Cytoplasm

• Endomembrane system: segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur.
• Exocytosis and endocytosis:
  • Mechanisms of transport (out of and into cells, respectively).
  • Involve membrane fusion and fission.
  • Provide paths between the cytoplasm and the surrounding medium.

Supramolecular Structures

• Held together by noncovalent interactions:
  • Hydrogen bonds.
  • Ionic interactions.
  • Van der Waals interactions.
  • Hydrophobic effect.

In Vitro vs. In Vivo Studies

• In vitro: "in glass".
• In vivo: "in the living".
• Molecules may behave differently in vivo and in vitro.

Chemical Foundations

Elements Essential to Animal Life and Health:

• Bulk elements: H, C, N, O, Na, Mg, P, S, Cl, K, Ca
• Trace elements: V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Se, I

Biomolecules

• Compounds of carbon with a variety of functional groups.
• Carbon can form covalent single, double, and triple bonds.

Geometry of Carbon Bonding

• Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds.
• Free rotation around each single bond.
• Limited rotation about the axis of a double bond.

Common Functional Groups of Biomolecules

• Methyl: $R-CH_3$
• Ethyl: $R-CH<em>2CH</em>3$
• Phenyl: $R-C<em>6H</em>5$
• Acetyl: $R-COCH_3$
• Carbonyl (aldehyde): $R-CHO$
• Carbonyl (ketone): $R-CO-R'$
• Carboxyl: $R-COOH$
• Hydroxyl (alcohol): $R-OH$
• Ether: $R<em>1-O-R</em>2$
• Ester: $R^1-COO-R^2$
• Anhydride: $R-CO-O-CO-R'$
• Thioester: $R^1-CO-S-R^2$
• Amino (protonated): $R-NH_3^+$
• Amido: $R-CO-NH_2$
• Phosphoryl: $R-OPO<em>3H</em>2$
• Phosphoanhydride $R-O-PO<em>2-O-PO</em>2-O-R2$
• Mixed anhydride: $R-CO-O-PO<em>3H</em>2$
• Guanidinium: $R-NH-C(NH<em>2)</em>2^+$
• Imidazole: $C<em>3H</em>4N_2$

Biomolecules

• Cells Contain a Universal Set of Small Molecules
  • Central metabolites:
    • Common amino acids
    • Nucleotides
    • Sugars and their phosphorylated derivatives
    • Mono-, di-, and tricarboxylic acids
• Secondary metabolites = specific to the organism
• Metabolome = entire collection of small molecules in a given cell under a specific set of conditions
• Metabolomics = the systematic characterization of the metabolome under very specific conditions

Macromolecules

• Macromolecules Are the Major Constituents of Cells
  • Macromolecules = polymers with molecular weights above ~5,000 that are assembled from relatively simple precursors
    • Proteins
    • Nucleic acids
    • Polysaccharides
• Oligomers = shorter polymers
• Informational macromolecules = name for proteins, nucleic acids, and some oligosaccharides, given their information-rich subunit sequences

Protein

• Protein Macromolecules
  • Proteins = long polymers of amino acids
    • Can function as enzymes, structural elements, signal receptors, transporters
• Proteome = sum of all the proteins functioning in a cell
• Proteomics = the systematic characterization of this protein complement under a specific set of conditions

Nucleic Acid

• Nucleic Acid Macromolecules
  • Nucleic acids = DNA and RNA = polymers of nucleotides
    • Store and transmit genetic information
    • Some RNA molecules have structural and catalytic roles in supramolecular complexes
• Genome = entire sequence of a cell’s DNA or RNA
• Genomics = the characterization of the structure, function, evolution, and mapping of genomes

Polysaccharides

• Polysaccharide Macromolecules
  • Polysaccharides = polymers of simple sugars
    • Energy-rich fuel stores
    • Rigid structural components of cell walls (in plants and bacteria)
    • Extracellular recognition elements that bind to proteins on other cells
• Glycome = entire complement of carbohydrate-containing molecules

Lipid

• Lipid Molecules
  • Lipids = water-insoluble hydrocarbon derivatives
    • Structural components of membranes
    • Energy-rich fuel stores
    • Pigments
    • Intracellular signals
• Lipidome = the lipid containing molecules in a cell

3D Structure

• Three-Dimensional Structure Is Described by Configuration and Conformation
  • Configuration = the fixed spatial arrangement of atoms
  • Stereoisomers = molecules with the same chemical bonds and same chemical formula
  • Stereospecific = requiring specific conformations in the interacting molecules
    • Describes typical interactions between biomolecules
      * Geometric Isomers: differ in the arrangement of substituent groups with respect to the double bond * Chiral and Achiral Molecules = asymmetric carbons
• A molecule can have $2^n$ stereoisomers, where n is the number of chiral carbons
  • Enantiomers = stereoisomers that are mirror images of each other
  • Diastereomers = stereoisomers that are not mirror images of each other
  • Enantiomers have nearly identical chemical reactivities, but differ in optical activity
  • A racemic mixture (equimolar solution of two enantiomers) shows no optical rotation

RS System

• Naming Stereoisomers Using the RS System

  • Each group attached to a chiral carbon is assigned a priority, where: —OCH3 > —OH > —NH2 > —COOH > —CHO > —CH2OH > —CH3 > —H

• Molecular Conformation

  • Conformation = the spatial arrangement of substituent groups that are free to assume different positions in space

• Are Stereospecific

Living Organisms

• Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings
  • Small molecules, macromolecules, and supramolecular complexes are continuously synthesized and broken down
  • Living cells maintain themselves in a dynamic steady state distant from equilibrium
  • Maintaining steady state requires the constant investment of energy
• Organisms Transform Energy and Matter from Their Surroundings
  • System = all the constituent reactants and products, the solvent that contains them, and the immediate atmosphere
  • Universe = system and its surroundings
    • Types of systems:
      • Isolated = system exchanges neither matter nor energy with its surroundings
      • Closed system = system exchanges energy but not matter with its surroundings
      • Open system = system exchanges both energy and matter with its surroundings

Thermodynamics

• Energy Transformation in Living Organisms
  • First law of thermodynamics: in any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change
• Creating and Maintaining Order Requires Work and Energy
  • Second law of thermodynamics: randomness in the universe is constantly increasing
  • Entropy, S = represents the randomness or disorder of the components of a chemical system
  • Enthalpy, H = heat content, roughly reflecting the number and kinds of bonds
  • Free energy, G, of a closed system = $H – TS$, where H represents enthalpy, T represents absolute temperature, and S represents entropy
  • Free-Energy Change, \[Delta]G = \[Delta]H − T\\[Delta]S where \[Delta]H is negative for a reaction that releases heat, and \[Delta]S is positive for a reaction that increases the system’s randomness
  • Spontaneous reactions occur when \[Delta]G is negative

Reactions and Energy

• Coupling Reactions

  • Energy-requiring (endergonic) reactions are often coupled to reactions that release free energy (exergonic)
  • The breakage of phosphoanhydride bonds in ATP is highly exergonic

• Energy Coupling Links Reactions in Biology

  • Free-energy change, \[Delta]G = amount of energy available to do work
    • Always less than the theoretical amount of energy released
  • In closed systems, chemical reactions proceed spontaneously until equilibrium is reached

• Keq and \[Delta]G° Are Measures of a Reaction’s Tendency to Proceed Spontaneously For the reaction,

• The equilibrium constant, Keq, is given by
  Where [A]eq is the concentration of A, [B]eq the concentration of B, and so on, when the system has reached equilibrium.

• Mass-Action Ratio, Q

  • Mass-action ratio, Q = ratio of product concentrations to reactant concentrations at a given time
    • Can be calculated to determine how far the reaction is from equilibrium

• = the actual free-energy change) for any chemical reaction is a function of the standard free-energy change
  where [A]i is the initial concentration of A, and so forth; R is the gas constant; and T is the absolute temperature. For the reaction,
  Reactions Can Do No Work at Equilibrium
  at equilibrium, \[Delta]G = 0
  and
  thus,

Reactions Can Do No Work at Equilibrium
at equilibrium, \[Delta]G = 0

Reaction Coordinate Diagrams

• Reaction coordinate diagrams = illustrates how exergonic reactions can be coupled to endergonic reactions
  • reaction 1: endergonic; \[Delta]G1 is positive
  • reaction 2: exergonic; \[Delta]G2 is negative
  • reaction 3: \[Delta]G3 is negative

Enzymes Promote Sequences of Chemical Reactions

• Enzymes = greatly enhance reaction rates of specific chemical reactions without being consumed in the process
  Transition state = higher free energy than reactant or product
• Activation energy, = difference in energy between the reactant in its ground state and its transition state
  Catabolism and Anabolism
• Pathways = sequences of consecutive reactions in which the product of one reaction becomes the reactant in the next
  Catabolism = degradative, free- energy-yielding reactions
  *Drives ATP synthesis
  *Produces the reduced electron carriers NAD(P)H
  *Anabolism = synthetic pathways that require the input of energy

Metabolism

• Metabolism = overall network of enzyme-catalyzed pathways, both catabolic and anabolic
• Unity of life = pathways of enzyme-catalyzed reactions that act on the main constituents of cells—proteins, fats, sugars, and nucleic acids—are nearly identical in all living organisms
• Metabolism Is Regulated to Achieve Balance and Economy
  • Feedback inhibition = keeps the production and utilization of each metabolic intermediate in balance
  • Systems biology = tasked with understanding complex interactions among intermediates and pathways in quantitative terms

Genetic Information Is Encoded in DNA

• Deoxyribonucleic acid, DNA = sequence of the monomeric subunits (deoxyribonucleotides)
  • Encode the instructions for forming all other cellular components
    Provide a template to produce identical DNA molecules
• Genetic Continuity Is Vested in Single DNA Molecules
  DNA of an E. coli cell is a single molecule containing 4.64 million nucleotide pairs
  *Must be replicated perfectly to give rise to identical progeny by cell division
  The Structure of DNA Allows Its Replication and Repair with Near-Perfect Fidelity
  Deoxyribonucleotides = monomeric subunit that make up the DNA polymer
  *Each deoxyribonucleotide in one strand pairs specifically with a complementary deoxyribonucleotide in the opposite strand
  *Strands are held together by hydrogen bonds
  The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures
  Native conformation = precise three-dimensional structure of a protein
  Crucial to protein function

Changes in the Hereditary Instructions Allow Evolution

• Mutation = changes in the nucleotide sequence of DNA
  Changes the instructions for a cellular component
• Can be beneficial
  Wild type = unmutated cells

Biomolecules First Arose by Chemical Evolution

• Miller and Urey experiments found that biomolecules may have been produced near hydrothermal vents at the bottom of the sea or by the action of lightning and high temperature on gaseous mixtures
  The Role of RNA in Prebiotic Evolution
• RNA (ribonucleic acid) = can act as catalysts in biologically significant reactions
  • Likely played a crucial role in prebiotic evolution, both as catalyst and as information repository

RNA or Related Precursors May Have Been the First Genes and Catalysts

• RNA or similar molecule may have been the first gene and the first catalyst
• Alternatively, simple metabolic pathways may have evolved first, perhaps at the hot vents in the ocean floor
• Biological Evolution Began More Than Three and a Half Billion Years Ago
• Lipid vesicles containing organic compounds and self-replicating RNA gave rise to protocells
  *Protocells with the greatest capacity for self-replication became more numerous
  The First Cell Probably Used Inorganic Fuels
• Earliest cells probably obtained energy from inorganic fuels, such as ferrous sulfide and ferrous carbonate
• Photosynthetic processes:
  Arose from evolution
  *Pigments capture energy of light from the sun and reduce CO2 to organic compounds
  *Atmosphere became richer in O2 with the rise of O2- producing photosynthetic bacteria

Eukaryotic Cells Evolved from Simpler Precursors in Several Stages

• Three major changes led to the evolution of eukaryotes:
  • Evolution of the chromosome
  • Evolution of the nucleus
  • Formation of endosymbiotic associations between early eukaryotic cells and aerobic or photosynthetic bacteria
• In multicellular organisms, differentiated cell types specialize in functions essential to the organism’s survival
• Molecular Anatomy Reveals Evolutionary Relationships
• Homologs = proteins encoded by genes that share ready detectable sequence similarities
• Gene or protein sequence similarities between organisms can determine phylogenetic relationships
• Functional Genomics Shows the Allocations of Genes to Specific Cellular Processes
  *Genes can be grouped according to the specific process in which they function
• Can approximate the proportion of the genome dedicated to a specific process
  *Genes involved in regulation of cellular processes tend to increase with organism complexity
  *Housekeeping genes = expressed under all conditions, not subject to much regulation
  Genomic Comparisons Have Increasing Importance in Medicine
• Large-scale sequencing studies have identified many genes in which mutations correlate with a medical condition
  *The proteins these genes encode might become the target for drugs to treat a given condition