01: The Foundations of Biochemistry

Principles

  • cells are the fundamental unit of life

    • exceptions could be viruses or prions

  • cells use a relatively small set of carbon-based metabolites to create polymeric machines, supramolecular structures, and information repositories

    • why carbon??? maximum 4 bond/ can be double bond, triple bond, etc. (can provide very large flexibility structure for the type of molecule) longer life span??

  • living organisms exist in a dynamic steady state, never at equilibrium with their surroundings

    • cells are highly organized- to fight against entropy increment, energy is needed (entropy= how chaotic an environment is)

  • cells have the capacity for precise self-replication and self-assembly using chemical information stored in the genome

    • recall the central dogma of genetics (dna replication)

  • living organisms change over time by gradual evolution

    • have dinosaurs truly extinguished?

What is Biochemistry?

  • uses chemical approaches to describe the structures, functions, mechanisms, and chemical processes (metabolism= synthesis + breaking down) shared by all organisms

Plasma Membrane = defines the periphery of the cell

  • composed of lipid and protein molecules

  • thin, flexible, hydrophobic barrier around the cell

  • contains embedded transport proteins, receptor proteins, and membrane enzymes

  • compartments = different functions, different locations

Cytoplasm Contains Cytosol and Suspended Particles

  • cytoplasm= internal volume enclosed by the plasma membrane (everything in cell !!)

    • composed of the cytosol (an aqueous solution) and a variety of suspended particles (such as mitochondria, chloroplasts, ribosomes, and proteasomes)

  • cytosol = highly concentrated solution (soup)

    • contains enzymes, RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions

The Nucleoid or Nucleus of a Cell Stores the Genome

  • genome = complete set of genes, composed of DNA

    • bacteria and archaea (formally grouped as prokaryotes) store their genome in a nucleoid

    • eukaryotes store their genome in a membrane-enclosed nucleus

Cellular Dimensions are Limited by Diffusion

  • cells are microscopic:

    • animal and plant cells:

      • 5 to 100 um in diameter

      • unicellular microorganisms: 1 to 2 um long

  • upper limit of cell size is likely set by the rate of transport and the need to deliver O2 to all parts of the cell

    • as size increases, surface-to-volume ratio decreases

  • longest cell? biggest cell?

Archaea and Bacteria Subgroups are Distinguished by Their Habitats

  • aerobic = plentiful supply of O2; organisms transfer electrons from fuel to O2 for energy. die without oxygen

  • 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

Ex. Question

Which organelle is not membrane-bound?

a. lysosome

b. peroxisome

c. ribosome

d. the Golgi complex

The Cytoplasm is Organized by the Cytoskeleton and is Highly Dynamic

  • cytoskeleton = 3D network of protein filaments in eukaryotic cells

    • actin filaments

    • microtubules

    • intermediate filaments

  • filaments undergo constant disassembly into their protein subunits and reassembly into filaments

  • shape and morphology, matter transportation

Organisms Belong to Three Distinct Domains of Life

  • bacteria = inhabitat soils, surface waters, and the tissues of other living or decaying organisms

  • archaea = inhabit extreme environments

  • eukarya = all eukaryotic organisms

    • more closely related to archaea than bacteria

Phylogeny of the Three Domains of Life

Organisms Differ Widely in Their Sources of Energy and Biosynthetic Precursors

  • phototrophs = trap and use sunlight

  • chemotrophs = derive energy from oxidation of a chemical fuel

  • autotrophs = can synthesize all their biomolecules directly from CO2

  • heterotrophs = require some preformed organic nutrients made by other organisms

Classifying Organisms According to Their Source of Energy

Bacteria and Archaeal Cells Share Common Features but Differ in Important Ways

  • cell envelope = composed of plasma membrane, outer membrane, and peptidoglycan (high molecular weight polymer)

  • 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

The 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 environments

Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study

  • mitochondria = the site of most of the energy-extracting reactions of the cell

  • endoplasmic reticulum and golgi complexes = play central roles in the synthesis and processing of lipids and membrane proteins

  • peroxisomes = site of the 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 (adenosine triphosphate) in the process of photosynthesis

Eukaryotic Cell Structure

Subcellular Fractionation of Tissue

  • first step = gently disrupt cells or tissues by physical shear to rupture the plasma membrane

  • second step = centrifuge the homogenate

  • organelles differ in size and sediment at different rates

Cytoskeletal Filaments

The Structural Organization of the 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

Cells Build Supramolecular Structures

  • held together by noncovalent interactions (hydrogen bonds, ionic interactions, van der waals interactions, and the hydrophobic effect)

  • why noncovalent??

In Vitro Studies May Overlook Important Interactions Among Molecules

  • in vitro = ‘in glass’

  • in vivo = ‘in the living'

  • molecules may behave differently in vivo and in vitro

1.2 Chemical Foundations

Biomolecules are Compounds of Carbon with a Variety of Functional Groups

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

Additional Functional Groups of Biomolecules

Many Biomolecules are Polyfunctional

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 are the Major Constituents of Cells

  • macromolecules = polymers with molecular weights above ~5000 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 sequences

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 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

  • genomes = entire sequence of a cell’s DNA or RNA

  • genomics = the characterization of the structure, function, evolution, and mapping of genomes

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 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

Building Blocks of Biochemistry

Major Classes of Biomolecules in E. coli Cells

3 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

Configurations of Geometric Isomers

  • geometric isomers, or cis-trans isomers = differ in the arrangement of substituent groups with respect to the double bond

Chiral and Achiral Molecules

  • chiral centers = asymmetric carbons

  • a molecule can have 2n stereoisomers, where n is the number of chiral carbons

Enantiomers and Diastereomers

  • enantiomers = stereoisomers that are mirror images of each other

  • diastereomers = stereoisomers that are not mirror images of each other

Optical Activity of Enantiomers

  • enantiomers have nearly identical chemical reactivities, but differ in optical activity

  • a racemic mixture (equimolar solution of two enantiomers) show no optical rotation

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

Interactions between Biomolecules are Stereospecific

Biological Systems can Distinguish Stereoisomers

  • stereospecificity = the ability to distinguish between stereoisomers

1.3 Physical Foundations

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

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

Extracting Energy from the Surroundings

  • photoautotrophs:

  • chemotrophs

Oxidation-Reduction Reactions

  • autotrophs and heterotrophs participate in global cycles of O2 and CO2, driven by sunlight, making these 2 groups interdependent

  • oxidation-reduction reactions = one reactant is oxidized (loses electrons) as another is reduced (gains electrons)

    • describes reactions involved in electron flow

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

Free Energy, G

  • 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, △G

  • △G = △H - T△S

    • where △H is negative for a reaction that releases heat, and △S is positive for a reaction that increases the system’s randomness

  • spontaneous reactions occur when △G is negative

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, △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 △Gº are Measures of a Reaction’s Tendency to Proceed Spontaneously

  • for the reaction,

  • the equilibrium constant, Keq is given by,

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

Standard Free-Energy Change, △Gº

  • △G (the actual free-energy change) for any chemical reaction is a function of the standard free-energy change, △Gº

Reactions Can Do No Work at Equilibrium

Reaction Coordinate Diagrams

  • reaction coordinate diagrams = illustrates how exergonic reactions can be coupled to endergonic reactions

    • reaction 1: endergonic; △G1 is positive

    • reaction 2: exergonic; △G2 is negative

    • reaction 3: △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, △G = 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 prodicy 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

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 acods- 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

1.4 Genetic Foundations

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 3D structure of a protein

    • crucial to protein function

1.5 Evolutionary Foundations

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

  • 3 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

Evolution of Eukaryotes through Endosymbiosis

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