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  1. 2A3 Essential knowledge 2.A.3: Organisms must exchange matter with theenvironment to grow, reproduce and maintain organization.

  2. Nature of Atoms • Matter has mass and occupies space • All matter is composed of atoms • Understanding the structure of atoms is critical to understanding the nature of biological molecules

  3. Electrons • Negatively charged particles located in orbitals • Neutral atoms have same number of electrons and protons • Ions are charged particles – unbalanced • Cation – more protons than electrons = net positive charge • Anion – fewer protons than electrons = net negative charge

  4. Isotopes • Atoms of a single element that possess different numbers of neutrons • Radioactive isotopes are unstable and emit radiation as the nucleus breaks up • Half-life – time it takes for one-half of the atoms in a sample to decay

  5. Electron arrangement • Key to the chemical behavior of an atom lies in the number and arrangement of its electrons in their orbitals • Bohr model – electrons in discrete orbits • Modern physics defines orbital as area around a nucleus where an electron is most likely to be found • No orbital can contain more than two electrons

  6. Atomic Structure

  7. Energy levels • Electrons have potential energy related to their position • Electrons farther from nucleus have more energy • Be careful not to confuse energy levels, which are drawn as rings to indicate an electron’s energy, with orbitals, which have a variety of three dimensional shapes and indicate an electron’s most likely location

  8. Atomic Structure

  9. Redox • During some chemical reactions, electrons can be transferred from one atom to another • Still retain the energy of their position in the atom • Oxidation = loss of an electron • Reduction = gain of an electron

  10. Extent of chemical reaction influenced by • Temperature • Concentration of reactants and products • Catalysts • Many reactions are reversible

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  12. Water • Life is inextricably tied to water • Single most outstanding chemical property of water is its ability to form hydrogen bonds • Weak chemical associations that form between the partially negative O atoms and the partially positive H atoms of two water molecules

  13. Polarity of water • Within a water molecule, the bonds between oxygen and hydrogen are highly polar • O is much more electronegative than H • Partial electrical charges develop • Oxygen is partially negative δ+ • Hydrogen is partially positive δ–

  14. Hydrogen bonds • Cohesion – polarity of water allows water molecules to be attracted to one another • Attraction produces hydrogen bonds • Each individual bond is weak and transitory • Cumulative effects are enormous • Responsible for many of water’s important physical properties

  15. Cohesion – water molecules stick to other water molecules by hydrogen bonding • Adhesion – water molecules stick to other polar molecules by hydrogen bonding

  16. Properties of water • Water has a high specific heat • A large amount of energy is required to change the temperature of water • Water has a high heat of vaporization • The evaporation of water from a surface causes cooling of that surface • Solid water is less dense than liquid water • Bodies of water freeze from the top down

  17. Water is a good solvent • Water dissolves polar molecules and ions • Water organizes nonpolar molecules • Hydrophilic “water-loving” • Hydrophobic “water-fearing” • Water causes hydrophobic molecules to aggregate or assume specific shapes 6. Water can form ions H2O  OH– + H+ hydroxide ion hydrogen ion

  18. Acids and bases • Pure water • [H+] of 10–7 mol/L • Considered to be neutral • Neither acidic nor basic • pH is the negative logarithm of hydrogen ion concentration of solution

  19. Acid • Any substance that dissociates in water to increase the [H+] (and lower the pH) • The stronger an acid is, the more hydrogen ions it produces and the lower its pH • Base • Substance that combines with H+ dissolved in water, and thus lowers the [H+]

  20. Buffers • Substance that resists changes in pH • Act by • Releasing hydrogen ions when a base is added • Absorbing hydrogen ions when acid is added • Overall effect of keeping [H+] relatively constant

  21. Most biological buffers consist of a pair of molecules, one an acid and one a base


  23. Cells • Cells were discovered in 1665 by Robert Hooke • Early studies of cells were conducted by • Mathias Schleiden (1838) • Theodor Schwann (1839) • Schleiden and Schwann proposed the Cell Theory

  24. Cell Theory • All organisms are composed of cells • Cells are the smallest living things • Cells arise only from pre-existing cells • All cells today represent a continuous line of descent from the first living cells

  25. Cell size is limited • Most cells are relatively small due reliance on diffusion of substances in and out of cells • Rate of diffusion affected by • Surface area available • Temperature • Concentration gradient • Distance

  26. Surface area-to-volume ratio • Organism made of many small cells has an advantage over an organism composed of fewer, larger cells • As a cell’s size increases, its volume increases much more rapidly than its surface area • Some cells overcome limitation by being long and skinny – like neurons


  28. Prokaryotic Cells • Simplest organisms • Lack a membrane-bound nucleus • DNA is present in the nucleoid • Cell wall outside of plasma membrane • Do contain ribosomes (not membrane-bound organelles) • Two domains of prokaryotes • Archaea • Bacteria

  29. Bacterial cell walls • Most bacterial cells are encased by a strong cell wall • composed of peptidoglycan • Cell walls of plants, fungi, and most protists different • Protect the cell, maintain its shape, and prevent excessive uptake or loss of water • Susceptibility of bacteria to antibiotics often depends on the structure of their cell walls • Archaea lack peptidoglycan

  30. Eukaryotic Cells • Possess a membrane-bound nucleus • More complex than prokaryotic cells • Hallmark is compartmentalization • Achieved through use of membrane-bound organelles and endomembrane system • Possess a cytoskeleton for support and to maintain cellular structure

  31. Nucleus • Repository of the genetic information • Most eukaryotic cells possess a single nucleus • Nucleolus – region where ribosomal RNA synthesis takes place • Nuclear envelope • 2 phospholipid bilayers • Nuclear pores – control passage in and out • In eukaryotes, the DNA is divided into multiple linear chromosomes • Chromatin is chromosomes plus protein

  32. Endomembrane System • Series of membranes throughout the cytoplasm • Divides cell into compartments where different cellular functions occur • One of the fundamental distinctions between eukaryotes and prokaryotes

  33. Golgi apparatus • Flattened stacks of interconnected membranes (Golgi bodies) • Functions in packaging and distribution of molecules synthesized at one location and used at another within the cell or even outside of it • Cis and trans faces • Vesicles transport molecules to destination

  34. Lysosomes • Membrane-bounded digestive vesicles • Arise from Golgi apparatus • Enzymes catalyze breakdown of macromolecules • Destroy cells or foreign matter that the cell has engulfed by phagocytosis

  35. Microbodies • Variety of enzyme-bearing, membrane-enclosed vesicles • Peroxisomes • Contain enzymes involved in the oxidation of fatty acids • H2O2 produced as by-product – rendered harmless by catalase

  36. Vacuoles • Membrane-bounded structures in plants • Various functions depending on the cell type • There are different types of vacuoles: • Central vacuole in plant cells • Contractile vacuole of some protists • Storage vacuoles

  37. Mitochondria • Found in all types of eukaryotic cells • Bound by membranes • Outer membrane • Intermembrane space • Inner membrane has cristae • Matrix • On the surface of the inner membrane, and also embedded within it, are proteins that carry out oxidative metabolism • Have their own DNA