3/24/2016. Unit 2 From the Atom to the Cell. Organisms + Chemistry. What are Ions? Chemical Bonds Covalent. Chemical Bonds Ionic

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1 Organisms + Chemistry Organic chemistry: the study of carbon-containing compounds (help make up our bodies) Biochemistry: the study of chemical reactions that occur in living systems Unit 2 From the Atom to the Cell Elements are substances that cannot be broken down or converted into another substance...gold, carbon, oxygen, silver, etc. They are composed of atoms which are the smallest units of matter Atoms & Subatomic Particles An atom is composed of a nucleus, an electron cloud, and 3 subatomic particles: Electron cloud Protons (p + ) Neutrons (n 0 ) Nucleus Electrons (e - ) p+ Protons and neutrons are located in the nucleus of an atom and electrons in the electron cloud n 0 e- What are Ions? Ions are charged atoms that are made when an atom gains or loses one or more electrons Loss of electrons = cation Gain of electrons = anion Chemical Bonds Ionic Result from the attraction between ions with opposite charges Electrons are gained or lost Unstable bonds Example: NaCl Chemical Bonds Covalent Result from ions sharing electrons Equal sharing = nonpolar compounds Strong bonds; stable molecule Common in organic molecules Hydrogen, oxygen, carbon, & nitrogen commonly do this 1

2 Chemical Bonds Hydrogen Cellular Chemical Reactions Weak, numerous bonds; found in: DNA Protein folding Enzyme/substrate binding Makes H 2 0 a polar compound Catabolic (Decomposition) Bonds are broken Energy is released Ex. Breaking down food for energy Anabolic (Synthesis) Bonds are created Energy is required Ex. Making proteins The Importance of Water Water & Mixtures Water is a polar compound which means it can dissolve a lot of ionic compounds. Surface tension: how the surface of water acts as a thin, invisible, elastic membrane (keeps our membrane moist) High specific heat: can absorb or release large amounts of heat energy with little temp change Helps stabilize the temp of living organisms Acts as a medium for most chemical reactions Solutions: Composed of a solvent (liquid that dissolves) and a solute (particle being dissolved) Water is a universal solvent Glucose, CO 2, O 2, & small proteins are common solutes Colloids: when large particles aren t readily dissolved Ex. cytoplasm Acids & Bases ph Scale Every liquid you see will probably have either acidic or basic traits. Acid: a hydrogen ion (H+) donor In organisms, HCL ph scale: measures how acidic or basic (alkaline) something is ph 1-6: acidic; 7: neutral; 8-14:basic Base: a H+ acceptor or hydroxyl ion (OH-) donor In organisms, amino groups in proteins 2

3 Carbon & Organic Molecules Molecules are particles composed of atoms (from elements) held together by chemical bonds Classified as organic (contains carbon) and inorganic (doesn t contain carbon) Synthesizing Complex Organic Molecules Organic molecules are important because they are general types of molecules that all living organisms synthesize and use; they are essential for life Modular Approach Complex Organic Molecules The modular approach involves building organic molecules piece by piece (like a train with individual cars): Monomer: individual subunits (car) Polymer: long chains of monomers (train) Mono- means one Poly- means many Organic molecules: carbohydrates, lipids, proteins, & nucleic acids Molecule Monomer Polymer Carbohydrate Monosaccharide Polysaccharide Lipid Fatty acid Triacylglycerol Protein Amino Acid Proteins Nucleic Acid Nucleotide Nucleic Acid Carbohydrates-Sugars Carbohydrates Overall function: main source of energy for living things Monomer: monosaccharide Polymer: polysaccharide 1 sugar molecule (monomer) Function: mainly used to form polymers or for cell activities Most common: glucose C 6 H 12 O 6 Others: Fructose fruits Galactose lactose Ribose RNA Deoxyribose DNA 3

4 Lipids Lipids Overall function: help make up a cell & can be used for energy Monomer: fatty acid Polymer: triacylglycerol Types of lipids: - Fats - Phospholipids - Oils - Steroids - Waxes Triacylglycerol (formerly triglyceride): the chemical name of fats and oils; 1 glycerol + 3 fatty acids Amino Acids and Proteins Overall function: structural functions for cells, cell parts, and membranes or making enzymes Monomer: amino acids (AAs); there are 20 different AAs in all Polymer: protein (chains of AAs) Amino Acids and Proteins Bond between the AAs when they are making polymers is known as a peptide bond Peptide: short chains of AAs (2-49 AAs) Polypeptide: long chains, aka a protein (50 or more AAs) Protein Structure Primary structure (1 o )-the chain of AAs that make up the protein Secondary structure (2 o )- when the protein takes on a coiled or pleated shape Protein Structure Tertiary structure (3 o )-the 3-D shape a polypeptide becomes (like balling up a piece of paper) Primary Secondary Quaternary structure (4 o )-when polypeptide chains link together 4

5 Protein Disruption Nucleic Acids Denaturation: disruption of the 2 o, 3 o, or 4 o structures caused by extreme heat or chemicals. This is why cultures are autoclaved before disposal Main reason why chemicals used as antimicrobial agents work Overall function: stores the genetic material of an organism which contains the directions for protein synthesis Monomers: nucleotides Polymers: nucleic acids (NAs) Adenosine triphosphate (ATP): main energy storing molecule in organisms Types of Nucleic Acids Nucleotides are made of 3 parts: a nitrogenous base, a sugar, and one or more phosphate groups Prokaryotic Cells 2 types of nucleic acids: DNA-deoxyribonucleic acid (2 strands) RNA-ribonucleic acid (1 strand) Sugars: deoxyribose (DNA) and ribose (RNA) Bacterial cell (prokaryotic) Comparing & Contrasting the Cell Types Protists, Fungi, & Animal cells (eukaryotic) Prokaryotic (Bacteria) Both Eukaryotic (Protist, Fungi, & Animal) -ALWAYS unicellular - smaller cells - less complex (simple) - Do not have a nucleus - Genetic material (RNA, DNA) is found free within the cytoplasm - Organelles do not have membranes (ribosomes, vacuoles) - Have genetic material - Has a plasma/ cell membrane - Have organelles - Have cell walls -larger cells - more complex - have a nucleus and nuclear envelope that contains the genetic material (RNA, DNA) - most organelles have membranes (mitochondria) 5

6 Prokaryotic Size, Shape, & Arrangement Size Prokaryotic cells are among the smallest organisms Ex. Most range from mm Human RBCs are 7.5 mm Prokaryotic Shapes Prokaryotic Size, Shape, & Arrangement Prokaryotic Size, Shape, & Arrangement Shape 1. Coccus/cocci (spherical): 4. Spirillum/spiralla (rigid, wavy spiral): - Ex. Streptococcus & Staphylococcus - Ex. Spirillum minus 2. Bacillus/bacilli (rod): 5. Spirochete (corkscrew spiral): - Ex. E.coli -Ex. Treponema pallidum 3. Vibrio (comma shaped spiral) - Ex. Vibrio cholerae **Pleomorphism: how the same bacteria can vary in shape within a single culture Arrangements (usually only cocci & bacilli) Diplo- Pairs Strepto- Chains Staphylo- Clusters Tetrads 4 cells in a cube Sarcinae 8 cells in a cube Typical Prokaryotic Cell Bacterial cells have the following: 1. A cell membrane 2. Internal cytoplasm with ribosomes, a nuclear region, and sometimes vesicles 3. A variety of external structures such as capsules, pili, and flagella Cell Wall Outside the cell membrane in nearly all bacteria; semi-rigid and porous (things can enter it) Function: 1. maintain cell shape 2. prevent the cell from bursting if it takes in too much water via osmosis 6

7 Cell Wall Components Peptidoglycan (also called murein): a structural polymer that forms a supporting net; most important component; in Gram positive cells, it is accompanied by teichoic acid Outer Membrane: selectively permeable; has receptors and binding sites for certain molecules; found mainly in Gram-negative cells Cell Wall Components Lipolysaccharide A (LPS) (also called endotoxin): part of the cell wall in Gram-negative cells ONLY; Lipid A/endotoxin is released when cells are dying so it can make infections worst if treated late; helps identify different Gram-negative bacteria Periplasmic space: active site of cell metabolism; gap between the cell wall and membrane; contains peptidoglycan, digestive enzymes, & transport proteins Distinguishing Bacteria by Cell Walls: Gram Staining Gram Positive & Gram Negative Gram positive Cell wall has thick layer of peptidoglycan & teichoic acid Less complex colors purple Gram Negative Cell wall has a thin layer of peptidoglycan & LPS More complex colors pink Distinguishing Bacteria by Cell Walls Brain Check Acid-Fast Bacteria: Mycobacteria: Cell wall is thick, but mostly lipid based and only a small percentage of peptidoglycan Use carbolfuschin as a dye for a red staining Will stain as Gram-positive first 1. What is peptidoglycan? Where is it found? 2. What takes place in the periplasmic space? Which organisms have such a space? 3. Compare the cell walls of Gram-positive, Gram-neagtive, and acidfast bacteria. 7

8 Cell Membrane aka Plasma Membrane Cell Membrane aka Plasma Membrane Fluid-mosaic model: Fluid: means that the membrane is flexible Mosaic: means that proteins are embedded in the membrane and form a pattern Polar Head-water loving or hydrophilic The Cell Membrane-- also called a Phospholipid Bilayer: a flexible boundary between the cell and its environment; it s selectively permeable b/c it only allows certain things in or out Non polar tail- made of fat so it s water fearing or hydrophobic Internal Structures of the Cell Organelles: internal structures within cells that have specific functions to help maintain the cell ( little organs ) Internal cytoplasm with ribosomes, a nuclear region, and sometimes vesicles Internal Structures Cytoplasm: site of protein synthesis, suspends all of the organelles ; semifluid substance Nuclear region or Nucleoid: location of DNA, RNA, & some protein; some bacteria have circular DNA called plasmids Ribosomes: make proteins Internal Structures Chromatophores: contain pigments to capture light; found only in photosynthetic bacteria or cyanobacteria Vacuoles: small bodies called granules or vesicles Internal Structures Endospores (Bacillus or Clostridium): Found in stasis (resting state) versus vegetative state (metabolizing nutrients) Medically significant genera: tough to kill Granules: stores glycogen for energy or polyphosphate for metabolic processes; no membrane Vesicles: stores substances like gas or lipid deposits that help bacterial cells float or store energy Resistances: to heat, drying, ph, certain disinfectants, & radiation Contain dipicolinic acid: helps with heat resistance 8

9 Flagella: aid in locomotion; long, whip-like External Structures External Structures Cilia: aid in locomotion; short, hair-like Why Move? Chemotaxis: movement from or to substances in the environment Positive: to the substance Negative: away from the substance Phototaxis: movement from or to light in the environment Positive: to the light Negative: away from the light Pili (pilus): not used for movement; tiny, hollow projections Conjugative pili: allow the transfer of DNA between bacteria, in the process of bacterial conjugation. Attachment pili: attach bacteria to surfaces; also called fimbriae; contribute to pathogenicity External Structures Glycocalyx: coating that covers prokaryotic cells the outside of many Movement Across the Membranes Capsule: protective structure outside the cell wall; prevents host cell defense mechanisms from destroying it (phagocytosis); not every bacteria secretes it; unique to the strain making it Slime layer: protects the cell against drying, helps trap nutrients, sometimes binds cells together, helps bacteria attach to surfaces as a biofilm; less tightly bound to the cell wall Passive Transport Passive Transport molecules moving from a high to low concentration & this DOES NOT REQUIRE ENERGY Passive Transport: Diffusion and Osmosis 1) Diffusion: molecules moving from a high to low concentration 2) Facilitated diffusion: molecules move from high to low concentrations, but need transport proteins in the cell membrane to help them 3) Osmosis: the diffusion of water across a selectively permeable membrane 9

10 Osmosis Why do we need to regulate osmosis? To maintain homeostasis because the plasma membrane is NATURALLY permeable to water How long does water diffuse in a solution? - Until it is evenly distribution, or causes solutes to reach equilibrium High concentration of sugar molecules Low concentration Osmosis in Microbes Bacterial cells have cell walls that prevent them from bursting or shrinking in different watery environments. ISO means EQUAL SOLUTE: equal inside & outside the cell WATER: moves equally in both directions Isotonic Solution Animal cell Protists have contractile vacuoles that will expel the water. ANIMAL CELLS: stays the same BACTERIAL CELLS: slightly firm WHICH CELL LIKES IT BEST: ANIMAL Bacterial cell HYPO means LESS Hypotonic Solutions HYPER means MORE Hypertonic Solution SOLUTE: more inside the cell SOLUTE: more outside the cell WATER: enters the cell Animal cell WATER: leaves the cell Animal cell ANIMAL CELLS: swells ANIMAL CELLS: shrinks BACTERIAL CELLS: very firm WHICH CELL LIKES IT BEST: BACTERIAL Bacterial cell BACTERIAL CELLS: shrinks WHICH CELL LIKES IT BEST: both HATE it!!!!!!! Bacterial cell 10

11 Active Transport: Requires Energy Active Transport molecules moving from a LOW to HIGH concentration & this requires energy Active Transport & Energy 2 reasons we need active transport: 1. To move large molecules 2. When a high concentration of molecules are needed and there are already enough there Active Transport & Energy Types of Active Transport The mitochondria is the organelle that makes the energy for active transport; in bacterial cells, there are high energy molecules that provide energy Endocytosis- cell membranes making vesicles to absorb molecules; endo = enter Types of Active Transport Types of Active Transport Phagocytosis- the engulfing and ingesting of solid molecules- cell eating Very important in microbiology Pinocytosis- the ingestion of fluid into a cell- cell drinking 11

12 Types of Active Transport Exocytosis- the expulsion or release of materials from a cell; exo = exit 12