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August 25-27, 2010 9:00a.m Bisc 160
cjackson@olemiss.edu Shoemaker 506 Monday 11-12 & Tuesday 8-
Monday thru Thurs Stockard-Martin classroom (just off of the lobby) Nicole Davidson
CHAPTER 2
What chemicals make up living things?
1) Elements are the fundamental substances
a) H2O 2H+O
2) The most common elements in organisms are:
a) Carbon Hydrogen Oxygen Nitrogen > 96% of living organisms
3) What elements are made of
a) All elements are made of atoms
4) Atoms consist of:
a) PROTONS (+)
b) NEUTRONS(n)
c) ELECTRONS (-) nucleus
Bohr Diagram consists of nucleus electrons in the clouds. SIMPLIST DRAWING
Helium (2e-, 2protons, and 2neutrons) e- means electron
Carbon (6e-, 6 protons, and 6neutrons)
ELEMENTS ARE NEUTRAL
Oxygen (8e-, 8p, and 8n)
Neutrons change. Ex: Hydrogen (1e-, 1p) H+
No. of protons ALWAYS = NUMBER OF E-
How do we classify elements and atoms?
Atomic number= number of protons
Atomic mass= number of protons+ number of neutrons
What does atomic mass mean?
=Number of protons + number of neutrons
Mole Abundance of a substance (how many elements/ atoms)
1 mole of C weighs =12g 1 mole of O weighs= 16g .5 moles of C= 6g
1) Carbon
a) 6p 6n 6e- Carbon 12
i) Sometimes 6p 7n 6e- Carbon 13
(1) Or 6p 8n 6e- Carbon 14
Isotopes (atoms of one element wit different numbers of neutrons *same atomic number, different
atomic mass*)
What is the importance of electrons?
1) Electrons
a) small, negative charge, orbit around nucleus
b) Electrons orbit in (energy levels/ electron shells)
i) First energy level max. 2
ii) Second energy level max. 8
Oxygen has 8e- 2, 6z
Phosphorus 15e- 2, 8, 5
Potassium 19e- 2, 8, 8, 1
In what order do electrons fill energy levels?
Each energy level consists of orbitals
o 1 st^ 1 orbital (S)
o 2 nd^ 1s + 3p orbitals 4 total orbitals
o 3 rd^ 1s + 3p + 5d 9 total orbitals
Each orbital can hold two electrons
Orbitals fill with single electrons, then pairs
August 27, 2010
Energy level
Ion can form crystal lattices Opposites attract
Na+ Cl- Na+
Cl- Na+ Cl-
Na+ Cl- Na+
Cl- Na+ Cl-
Covalent Bonds
o Two or more atoms share electrons
E.g. Hydrogen gas (H2)
Electrons are shared part of both atoms (H2)
E.g. Oxygen gas (O2)
Two sets of shared pares of electrons (O2)
O=O
August 30, 2010
Methane (CH4)
How can we keep track of how an atom shares or exchanges electrons?
Oxidation Number Charge it would have to have for a full electron level
o Sodium (Na) 11 2,8,1 loose one to gain a +1 chargeloose one to gain a +1 chargeloose one to gain a +1 charge
o Chlorine (Cl) 17 2,8,7 loose one to gain a +1 chargegain one to gain a -1 chargeloose one to gain a +1 charge
o Oxygen (O) 8 2,6 loose one to gain a +1 chargegain two to make a -2 chargeloose one to gain a +1 charge o Hydrogen (H) 1 1 loose one to gain a +1 chargeloose one to make a +1 chargeloose one to gain a +1 charge o Carbon (C) 6 2,4 loose one to gain a +1 chargegain or lose 4 to make +4 or -4loose one to gain a +1 charge Water (H2O) o Since the electrons are being pulled to the oxygen the Hydrogens become slightly more positive due to the lack of electrons. Known as Polar Positive ends (H) attract to the negative ends (O) of other water molecules. Known as Hydrogen Bonds (interaction of a hydrogen atom with an electronegative atom) Some atoms have a greater tendency to attract electrons than other atoms o (electro negativity) e.g. Oxygen, Nitrogen Ionic compounds dissolve in water What are the important properties of water (H20)? Hydrogen bonds Cohesion o Surface Tension (bugs running on water) Adhesion o Capillary Action (how plants get water through water roots) High Specific Heat o (energy to raise temperature of 1g by 1 degree Celsius) Organisms hold temperature High Heat of Vaporization o Energy to change 1g liquid to gas Sweating 1 evaporation removes heat Solid water is less dense than liquid water o Ice floats, water freezes from the top down Solvent o Polar chemicals dissolve in water (Hydrophilic) o Non-Polar chemicals separate from water (Hydrophobic) Water can separate into ions o H2O OH- loose one to gain a +1 chargehydroxylloose one to gain a +1 charge + H+ loose one to gain a +1 chargeprotonloose one to gain a +1 charge o pH= -log [H+] (low pH means more H+) What are the typical values of pH? 0 14 Acids < 7 Neutral = 7 Alkalis (Bases) > Wednesday, September 01, 2010 Organisms generally maintain a constant pH HOMEOSTASIS
HO-MON-OH HO-MON-OH
loose one to gain a +1 chargewhen monomers join to join polymers a condensation reaction (release water/dehydration reaction)loose one to gain a +1 charge HO-MON-O-MON-OH How do polymers break down into monomers? HO-Mon-O-MON-o-mon-oh o Add water (Hydrolysis Reaction) to break these bonds HO-MON-O-MON-OH HO-MON-OH o Condensation reactions join monomers o Hydrolysis reactions break polymers What are carbohydrates? Used for energy, storage, structure o Monosaccharide- simply sugars Eg. Glucose, Fructose o Disaccharides- two monosaccharaides (glycosidic bond) Eg. Sucrose o Polysaccharides- long chains of monosaccharides Eg. Starch, cellulose, glycogen All carbohydrates are (CH2O0 n What are important monosaccharides? Hexose (6C) C6H12O o Glucose loose one to gain a +1 chargeForms a ring in solution What are other important monosaccharides? Pentose (5C) Ribose loose one to gain a +1 chargeremove bottom right it makes dioxiriboseloose one to gain a +1 charge What are important disaccharides? Glucose + Galactose Lactose Glucose + Fructose Sucrose
September 3, 2010
Glycosidic bond- when two sugars are bound together What are important polysaccharides? Starch- polymer of a-glucose –energy storage in plants Cellulose- polymer of B-glucose-structure of plant cell walls When the OH group is on the bottom of glucose it is an Alpha glucose when it’s on the top, its Beta glucose. Body can only digest Alpha glucose, where as Beta glucose is not broken down What is the structure of starch? Long branched chains of a-glucose
o Starch asl has alpha1,6 linkage What is the structure of cellulose? Long unbranched chains of B-glucose What polysaccharides exist in other organisms? Glycogen –polymer of a-glucose –energy storage in animals o –similar to starch but longer chains and more branched Chitin- polymer of N-aceytylglucosamine –cell walls of fungi, exoskeleton of arthropods What are nucleic acids? Used to store and carry information Deoxyribonucleic acid (DNA) Stores genetic information Ribonucleic acid (RNA) Carry genetic information used in protein synthesis o Messenger RNA (mRNA) o Ribosomal RNA (rRNA) o Transfer RNA (tRNA) What is the structure of a nucleic acid? Long chins of NUCLEOTIDES Each nucleotide is made of: o Pentose sugar Ribose Deoxyribose What are the nitrogenous bases? Pyrimidines –single CN ring o Cytosine (C) DNA + RNA o Thymine (T) DNA o Uracil (U) RNA Purines- double CN ring o Adenine (A) DNA+RNA o Guanine (G) DNA+RNA How do nucleotides join together? The Phosphodiester linkage brings them together The bond is a covalent bond by an Oxygen Add other molecules onto the number three end Sugar Phosphate backbone RNA (-Single strand of nucleotides with A, C, G, U bases) What is the structure of DNA? Tow strands of nucleotides wound as a helix (Double Helix)
Eukaryotic o DNA is in a membrane; nucleus o Internal membranes divide cell into compartments (organelles) o Larger, 10 – 100 um (micrometers) Prokaryotic o DNA is not in a membrane; nucleoid o No internal membranes o Smaller, 1 – 10 um (micrometers) How are prokaryotic and eukaryotic cells similar Cell is surrounded by plasma membrane Both have DNA in one area (eukaryotic has a membrane around DNA) Full of cytoplasm made of a gel (cytosol) with other components Contains ribosomes for protein synthesis
What do eukaryotic cells look like? Animal Cell Plant Cell Nucleus o Nuclear envelope (double phospholipid bilayer) Nuclear pores DNA as chromosomes o With protein o Chromatin Nucleolus makes o rNA o makes ribosomes Rough Endoplasmic Reticulum o Folded membrane sacs o Connects to nuclear envelope o Ribosomes on surface Protein Synthesis Ribosomes o Protein synthesis o Small & Large subunit RNA + Protein o Free or on rough er Golgi Apparatus o Stacks of flattened membrane sacs o Processes proteins, packages them into membrane sacs Vesicles o Produces Lysosomes Contains digestive enzymes (low pH loose one to gain a +1 chargeslightly acidicloose one to gain a +1 charge) Can digest food inside the cell Digest/Destroy old cell components Smooth ER o Membranous tubes o Makes lipids (membranes) o Detoxifications o Stores Ca (calcium)
o Movement of the cell o Can move the cell of move things outside of the cell around the cell Made of 9 + 2 set of microtubules o 9 pairs of microtubules around the perimeter of the inside o 2 more microtubules in the center Attach to cell by basal body (centriole) Euglena uses flagellum Paramecium surrounded by cilia Cilialed epithelium tissue line breathing passages to catch dirt What is outside of the plasma membrane? Some cells have a rigid cell wall o Plants, some protists – cellulose o Fungi – chitin Animal cells often have an extracellular matrix o Glycoproteins, fibers o Connects to cell (integrins) Friday, September 17, 2010 What is the structure of the plasma membrane? Composed of phospholipids (Glycerol, a phosphate and a fatty acid) o Glycerol Hydrophilic head Hydrophobic tail (fatty acid) Phospholipids are in a bilayer. Hydrophobic tails group together (inside) while the hydrophilic heads are on the outside Proteins in the cell membrane (attached to the cell membrane) o Sometimes completely through the bilayer sometimes connected to the inside or the inside Phospholipids are fluid (like oil) loose one to gain a +1 chargeoily membraneloose one to gain a +1 charge o Proteins can move through the oily membrane Fluid mosaic structure o Things embed in the membrane and can move through What other things does the fluid nature allow? Flexible (can move twist bend) Can seal itself if a hole is punctured Portions can pinch off (like oil in water ) o To form vesicles Vesicles can fuse with another membrane Side Notes: Proteins in phospholipid bilayer o If it goes all the way through it has hydrophilic and phobic parts, just like the membrane (so it can stay in the membrane) Glycoprotein (protein with a carbohydrate attached to it) o Cells have a lot of these Integral proteins (proteins that go all the way through the membrane) Peripheral protein (sits on one side of the membrane (either inside or outside))
Cholesterol – important in the cell membrane (attached to some phospholipids) helps to keep the membrane fluid and helps to keep it organize (helps things enter and leave the cell and helps to prevent shape loss)
o Does not require energy, it just happens. Cells don’t try to make this happen, Just how the universe makes things happen Simple diffusion (when high moves to low) Facilitated Diffusion (only happens cause the protein allows it to) loose one to gain a +1 chargeTRANSPORT PROTEINloose one to gain a +1 charge o Polar molecules cant move through phospholibid bilayer but can come through the transport protein Does water move through diffusion? OSMOSIS o Diffusion of water through a selectively permeable membrane is OSMOSIS Solute ( what’s dissolved in the solvent) If the membrane gets too much water inside it starts to swell (osmotic pressure) o More water inside Higher the pressure (cell can actually burst) Monday, September 20, 2010 Solute (chemical dissolved in the water) Higher concentration of solute = lower concentration of water (Solvent) How cells respond to different solutions? Isotonic - equal solute concentration o No net movement of H2O Hypertonic - higher [Solute] outside than inside loose one to gain a +1 chargelower [H2O]loose one to gain a +1 charge o Net loss of H2O from cell cell shrinks Hypotonic - lower [solute] outside than inside o Net flow of H2O into cell cell swells How do plant cells respond to osmotic pressure? Vacuole stores water nutrients and sugars Cell wall (thick and rigid) not flexible Hypotonic – cell is swollen (TURGID) o Turgor pressure – cell membrane pushes against cell wall Hypertonic - cell shrinks and pulls on cell wall loose one to gain a +1 chargeplasmolysisloose one to gain a +1 charge plant wilts Can cells transport substances across the membrane against a concentration gradient? Requires energy, ACTIVE TRANSPORT Cell uses ATP o Bonds between the phosphate is most important. (loose one to gain a +1 chargeHigh Energyloose one to gain a +1 charge) o ATP ADP + P + ENERGY How does active transport work? Change ATP ADP and uses energy to bring stuff in against diffusion Active protein loose one to gain a +1 chargePumps chemical into cell loose one to gain a +1 charge Transports against a concentration gradient What is an example of active transport? Sodium-potassium pump o Pumps sodium out and Potassium into the cell 3Na out 2K in
How are particles transported across the plasma membrane? Vesicles merge with the plasma membrane to release chemicals o EXOCYTOSIS loose one to gain a +1 chargeexo (release)loose one to gain a +1 charge Releases materials from the cell Increases area of membrane o Phagocytosis (endocytosis) When exocytosis is reversed it makes vacuoles (larger than vesicles) Does endocytosis of liquids occur? Pinocytosis o Microvilli = made of folds (absorbs) usually found in intestines Makes vesicles Then vesicles are opened and liquid is released How do cells transport materials across the plasma membrane? Simple diffusion Facilitated diffusion Active transport Exocytosis Endocytosis o Phagocytosis o Pinocytosis How do cells connect together? Intercellular junctions What types of cell junctions are there? Anchoring Junctions cadherens connect the two cells together (desmosome) loose one to gain a +1 chargein skin and musclesloose one to gain a +1 charge Tight Junctions loose one to gain a +1 chargetotally seals space between cellsloose one to gain a +1 charge (intestine and blood brain barrier) Do any junctions allow cells to exchange materials? Gap junctions Can pass particles, materials and electrical charges from one cell to another through the gap in the connections loose one to gain a +1 chargelike a tubular connectionsloose one to gain a +1 charge Connexon loose one to gain a +1 chargesix proteinsloose one to gain a +1 charge tubular and can transport from one cell to another o Proteins can open or close more according to the cell in a twisting manner Found in Heart, nervous tissue and brain) Chapter 7 Wednesday, September 22, 2010 What do we mean by energy? Energy is the capacity to do work Measured in kilojoules (kJ) o Also look at as calories=energy from food o 1 kilocalorie = 4.1854 kJ Kilocalorie is measure of heat energy What forms of energy exist?
ADP TO ATP + “delta G” gains exergonic energy from another reaction ATP TO ADP – “delta G” releases energy and this energy is used for endergonic reactions Friday, September 24, 2010 How do exergonic and endergonic reactions match to metabolism? Catabolism- Breakdown of large molecules into smaller ones. o Exergonic (release of energy) e.x. starch glucose CO Anabolism – Synthesis of large molecules from smaller ones o Endergonic (requires energy) e.x. amino acids protein muscle What other types of reactions do cells use to generate energy? Oxidation-Reduction reactions (REDOX) o Reactons involving the exchange of electrons What happens during redox reactions? See note# What is an example of an electron carrier? Nicotinamide adenine dinucleotide (NAD+) o Accepts electrons as part of H atoms See note NADP+ works the same way o loose one to gain a +1 chargehow plants use energy in photosynthesisloose one to gain a +1 charge How do cells control reactions? See note# What controls activation energy? Catalyst – lowers the activation energy (with a specific action without being changed) o Cells packed with catalysts (loose one to gain a +1 chargeEnzymeloose one to gain a +1 charge)- biological catalyst
Enzymes allow reactions to happen by lowering the activation energy (Most are proteins)
o Catalysts are not used during the reaction loose one to gain a +1 chargenot a reactant or substrateloose one to gain a +1 charge 90% of the time, Cells produce enzymes to lower the activation energy of specific reactions o Makes reaction more likely to happen (easier to happen) o Increases rate of reaction (faster) How do enzymes function? See note # What is the structure of an enzyme? Proteins Tertiary (quaternary) gives the enzyme activity o Where the enzyme connects with the substrate is Active Site o Rest of the enzyme is the allosteric site/region/part (substrate doesn’t bond) Non-catalyctic site (not involved in speeding up the rate of reaction)
