BES 107 Introduction to Cell Biology PDF

BES 107 Introduction to Cell Biology Part 1 – THE CHEMICAL CONTEXT FOR LIFE Campbell’s Biology Chapters 2 & 3 Winter 2025 Sophon Bailey All figures are from Campbell’s Bio...

BES 107 Introduction to Cell Biology Part 1 – THE CHEMICAL CONTEXT FOR LIFE Campbell’s Biology Chapters 2 & 3 Winter 2025 Sophon Bailey All figures are from Campbell’s Biology, © 2021 Pearson Press, unless otherwise attributed. Course content, digital or otherwise, created and/or used within the context of the course is to be used solely for personal study, and is not to be used or distributed for any other purpose without prior written consent from the content author(s). LEARNING OBJECTIVES Understand the hierarchical organization of life and the basis of cell theory Apply basic principles of chemistry to interpret the function of biomolecules › Understand how electron valence dictates the number and type of bonds formed by molecules › Identify the difference between polar and non-polar bonds Describe the molecular structure of water and how the properties of water emerge › Understand the four weak forces that govern the behaviour of biomolecules in water › Describe four emergent properties of water that are essential for life Discuss the ionization of water and how this gives rise to the properties of acids and bases 2  Organisms HIERARCHICAL ORGANIZATION Organs OF LIFE Tissues Individual components of biology are built of assemblies of smaller units CELLS With increasing complexity, properties cannot Organelles be easily predicted by the properties of the component units (emergence) Macromolecules Biochemistry focuses on the operations of molecules and macromolecules and how they Molecules affect higher order functions Atoms 3  CHEMICAL ELEMENTS OF LIFE 97% of biological mass comes from only 6 elements CHNOPS 5 ions form essential salts for all life Na+, K+, Mg 2+ , Ca2+, Cl- 18 various elements are found in biology typically as trace elements Principles of Biochemistry 5e, Moran et al, © 2012 Pearson 4 CHEMISTRY OF LIFE An element is a substance that cannot be broken down to other substances by chemical reactions › An atom is the smallest unit of matter that still retains the properties of an element A compound is a substance consisting of two or more elements in a fixed ratio Protons (+) › A compound has characteristics different from those Neutrons of its elements Electrons (—) Molecules are formed when two or more atoms are joined chemically 5 Campbell’s Biology © 2021 Pearson Press  WHAT IS THE DIFFERENCE BETWEEN A COMPOUND AND A MOLECULE? A molecule is formed when two or more atoms join together chemically A compound is a molecule that contains at least two different elements All compounds are molecules but not all molecules are compounds 6  Sodium (metal) Chlorine (gas) Sodium chloride (table salt) Campbell’s Biology © 2021 Pearson Press CHEMICAL Chemical elements combine in fixed ratios to form COMPOUNDS compounds 7  ELECTRON ENERGETICS A ball bouncing Third shell (highestenergy down a flight of level in this model) stairs provides an Second shell (higher Energy analogy for energy energy level) absorbed levels of electrons Electrons in higher First shell (lowest energy orbitals have level) greater potential Energy energy lost Atomic nucleus 8  Outermost electron shell (can hold 8 electrons) VALENCE Electron First electron shell (can hold 2 electrons) ELECTRONS Valence electrons are those in the outermost shell, or valenceshell The chemical behavior of an atom is mostly HYDROGEN (H) CARBON (C) NITROGEN (N) OXYGEN (O) determined by the Atomic number = 1 Atomic number = 6 Atomic number = 7 Atomic number = 8 valence electrons Elements with afull valence shell are chemically inert Campbell’s Biology © 2021 Pearson Press 9  ORBITALS Electron shells are spatially arranged as ‘clouds’ of probability with specific geometry Most organic molecules (CHNO) have valence electrons in a tetrahedral arrangement This arrangement defines the shapes, properties, and interactions of biomolecules https://chem.libretexts.org/Courses/Lumen_Learning/Book%3A_General_Chemistry Lecture_and_La b_(Lumen)/07%3A_Advanced_Theories_of_Covalent_Bonding/7.03%3A_Hybrid_Atomic_Orbitals 10  Name and Electron Lewis Dot Space- Molecular Formula Distribution Diagram Structure and Structural Formula Filling Model COVALENT (a) Hydrogen (H2) BONDING Some atoms share outer shell electrons with other atoms, (b) Oxygen (O2) forming covalent bonds › A covalent bond is the sharing of a pair of (c) Water (H2O) valence electrons by two atoms › In a covalent bond, the shared electrons count as part of each atom’s (d) Methane (CH4) valence shell 11  More electronegative (δ–) (δ–) ELECTRONEGATIVITY O Atoms in a molecule attract electrons to varying degrees based on their electronegativity H H › More electronegative atoms pull the electrons towards (δ +) Less electronegative themselves (δ +) Two equally electronegative atoms form nonpolar covalent bonds When one atom is more electronegative electrons are shared unequally forming a polar covalent bond Extremely electronegative atoms can strip an electronto form a charged ion Na Cl Na + Cl– Sodium atom Chlorine atom Sodium ion Chloride ion Sodium chloride (NaCl) 12 Campbell’s Biology © 2021 Pearson Press KEY POINTS Chemistry underpins the properties of life › Very few elements are required for life –mostly CHNOPS › Atoms combine to form compounds and molecules › Some atoms can strip electrons from other creating charged ions Covalent bonds form when two atoms share electrons › Electrons shared equally produce a non-polar molecule › Electrons share unevenly produce a polar molecule 13  WATER In a water molecule, H (δ–) (δ–) oxygen exerts a stronger pull on the shared electrons than O hydrogen O The oxygen end is H H slightly negative, while H the hydrogen end is (δ +) (δ +) slightly positive Water is a polar molecule –has a permanent dipole Principles of Biochemistry 5e, Moran et al, © 2012 Pearson 14  HYDROGEN BONDING The opposite dipoles of water create a weak attractive force Each oxygen (2δ—) can interact with one hydrogen (δ+) to form a hydrogen bond Hydrogen bonds are weaker than covalent bonds but are one of the strongest non- covalent bonds Principles of Biochemistry 5e, Moran et al, © 2012 Pearson 15 THE 4 WEAK FORCES Electrostatic interactions –non-covalent attractive forces between charged ions (opposites attract) › Charge-charge interactions e.g. forms the crystal structure of NaCl (Na+ : Cl-) › Water disrupts electrostatic interactions to dissolve many salts Hydrogen bonding –non-covalent attractive forces between molecules with polar dipoles (δ—/δ+) › H-bonds form between any 2 polar molecules –one acts as a H-donor, one is H-acceptor Van der Waals forces –weak attractive forces between non-polar molecules due to random fluctuations in electron charge › Weak individually, but strong when many combine Hydrophobic effects –weak repulsive force that drives non-polar molecules to segregate from polar molecules › Drives separation of hydrophobic and hydrophilic molecules (oil & water) 16 H-BONDS IN WATER − + Hydrogen bond Polar covalent − bonds A water molecule can form up to four + − + hydrogen bonds + − › H-bonds ideally positioned into a tetrahedral arrangement Water acts as a solvent to dissolve polar and ionized solutes into an aqueous solution 17 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson EMERGENT PROPERTIES OF WATER ESSENTIALFOR LIFE 1. Cohesion & adhesion –water is ‘sticky’ 2. Moderation of temperature –high specific heat capacity 3. Density & insulation of ice –liquid water is more dense than ice 4. The solvent of life –dissolves both ionic and polar molecules 18  COHESION & ADHESION H-bonds make water sticky › H-bonds within water gives it cohesion and a high surface tension › H-bonds between water and other surfaces gives it adhesion Water and nutrient transport through plants depends on cohesion and adhesion Campbell’s Biology © 2021 Pearson Press 19  SPECIFIC HEAT CAPACITY Moderation of body temperature by evaporative Each H-bond has cooling ~5% of the energy of a covalent O-H bond Breaking H-bonds is https://commons.wikimedia.org/w/index.php?curid=20511008 required to heat water or for phase change H-bonds give water Moderation of temperature by an unusually high proximity to specific heat water bodies capacity Campbell’s Biology © 2021 Pearson Press 20  CRYSTAL STRUCTURE Ice forms when water H-bonds into an ordered tetrahedral lattice Liquid water has fewer, transient H- bonds, and a collapsed irregular lattice 21 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson  INSULATION AND DENSITY Ice is less dense than liquid water › Bodies of water freeze from the top down › Ice layers insulate the underlying water › Aquatic plant and animal life is protected from weather extremes 22 Campbell’s Biology © 2021 Pearson Press  SOLVENT PROPERTIES A solution is a homogeneous mixture of substances › Solvent is the dissolving agent (found in excess) › Solute is the substance dissolved Water is polarand can disrupt electrostatic interactions of crystals › Water that interacts with solutes is less able to H-bond to itself Hydrophilic(water loving) substances dissolve easily Hydrophobic (water fearing) substances do not 23 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson KEY POINTS Water is polar due to uneven sharing of electrons across O-H bonds › Water has a permanent dipole and can form H-bonds with itself and other polar molecules 4 weak forces contribute to chemistry of life › Electrostatic forces –between ions › H-bonds –between polar, H-containing molecules › van der Waals forces –spontaneous forces between non-polar molecules › Hydrophobic effects – weak repulsion of non-polar molecules from water 4 effects of water are essential for life › Cohesion and adhesion –e.g. transport of water in plants › Specific heat capacity –e.g. moderation of climate, moderation of body temperature › Density of ice and water –e.g. insulates water to allow aquatic life to survive › Solvent properties –readily dissolves ions and polar molecules 24  Campbell’s Biology © 2021 Pearson Press The hydrogen atom involved in H-bonds can occasionally be captured by the H-bond acceptor This creates two charged ions of water –H 3 O + (hydronium) and OH- (hydroxide) This occurs continuously in a dynamic equilibrium 25 ACIDS AND BASES Ionization of water has a huge effect of biochemistry › Water can accept or donate a proton (H+) making it both an acid and base › In pure water [OH-] = [H3O+] = 10-7 M Substances that can donate or accept protons will form acidic or basic solutions in water › pH measures acidity as pH = -log[H 3 O + ] 26 Campbell’s Biology © 2021 Pearson Press PH BUFFERING Substances that are weak acids or bases can accept or donate protons in response to changing pH This decreases the pH change and allows pH to remain stable Body fluids moderate pH using bicarbonate from dissolved CO2 27 Campbell’s Biology © 2021 Pearson Press IMPACT: ACIDIFICATION CO2 absorbed into bodies of water decreases the pH (increases [H3O+]) Like blood, ocean pH is somewhat moderated by bicarbonate Acidification removes carbonate (buffering) which blocks calcification (CaCO3 production) by shellfish and corals 28 Campbell’s Biology © 2021 Pearson Press KEY POINTS Water can spontaneously ionize to OH- and H 3 O + › Dynamic equilibrium –some small amount of water is always ionized Solutes that can donate or accept protons can make acidic or basic solutions in water Changes in pH can be moderated by buffers (e.g. CO2, bicarbonate) › Changes in CO2 levels can cause solutions to become basic or acidic 29