CHEMISTRY element substance with unique identity atom single
CHEMISTRY
• element substance with unique identity • atom single unit of element • molecule 2 + atoms • compound molecules of different atoms
elements H 2 O
more elements
atom charge mass + 1 none 1 - none
Periodic table • atomic number # protons identity
electrons electron shells can hold: 1 st 2 2 nd 8 3 rd 8 4 th 8 outer electrons = valence electrons
only the outer shell electron shells can hold: 1 st 2 2 nd 8 3 rd 8 4 th 8 outer electrons = valence electrons
• rows • columns # electron shells 1 2 + # electron shells # valence electrons ~ behavior # electrons (valence) in outer shell 3 4 5 6 7 8 -
Nature’s rules • nature is lazy • nature wants equilibrium • equal concentrations • equal charges • equal pressure • nature wants a full outer shell entropy opposites attract octet rule
Biology rule • rule of living things: • You can break these 3 rules briefly, if: • you pay the price energy • it aids survival
Ions • nature wants a full outer shell • atoms gain/lose electron • ion = charged atom or molecule • cation = + charged • anion = - charged octet rule
which atoms form ions # electron shells 1 2 + # electrons (valence) in outer shell 3 4 5 6 7 8 -
physiology requires ions • • • Sodium Potassium Calcium Phosphates Iron Copper Chlorine Bicarbonate Na+ K+ Ca++ PO 4 --Fe++ Cu++ Cl. HCO 3 - see table 2. 1
• many physiologic functions are merely molecules seeking to have equal charges – molecules will move toward opposite charge – molecules will move away from like charge – molecules will change their shape to get equal charge
Nature’s rules - bonding • Chemical bonds are the result of nature’s desire for : – a full outer shell – – equal charges octet rule
types of bonds • ionic • covalent – di-sulfide • hydrogen
ionic bonds • ions with full outer shell • ions with + / - charge nature happy? • opposites attract ionic bond ions = ionic bond
salts • • • = ionic compound cation + anion Na. Cl KCl Ca. PO 4 • dissociation • electrolytes not H+ = or OH- breaks into ions easily ions in water
covalent bond • too many electrons to gain or lose • nature still wants ? • shared electrons • neutral atoms
covalent bond • octet rule? is nature happy? • neutral charge? is nature happy?
What element can form the most covalent bonds ? # electron shells 1 2 # electrons (valence) in outer shell 3 4 5 6 7 8
polar covalent • nonpolar – electrons shared equally • polar – electrons shared unequally – have + and - ends
hydrogen bonds • H tends to be + • attracted to - end of other molecules (eg. O ) • water • 3 D shape of proteins
hydrogen bonds - Water
water • universal solvent polarity • reactivity – makes bond – breaks bonds dehydration synthesis hydrolysis
acid – base • water dissociates H 2 O H+ + OH- • p. H = -log 10[H+] • p. H = 7 (neutral) • acids increase H+ p. H < 7 • base decrease H+ p. H > 7
p. H • p. H = parts Hydrogen • acidity • alkalinity • danger ? Figure 2. 13
chemical reactions • anabolic make bonds • A + B AB • builds large biochemicals = synthesis • catabolic break bonds • AB A + B • breaks apart biochemicals = decomposition
Biochemistry • molecules of life • based on Carbon • • carbohydrates lipids proteins nucleic acids
carbohydrates • Carbon + hydrates (water) • C + H 2 O • functions: – store energy – DNA – antigens – structural CHO C H 2 O C 2 H 4 O 2 C 6 H 12 O 6
carbohydrates • polymers of sugars see p 44 -45 Figure 2. 14 a, b
carbohydrates • polymers of sugars Figure 2. 14 a, b
lipids • fats • mostly C and H (little O) • functions: • hydrophobic energy storage insulation cell membranes hormones
triglycerides • glycerol + 3 fatty acids
phospholipds • 2 fatty acids + phosphate group • cell membranes hydrophilic hydrophobic
steroids • • • made from Cholesterol cell membranes hormones Vitamin D bile
also: Estrogen ; Progesterone
amino acids
Proteins • polymers of amino acids • diverse molecules – different order of AA • genes control AA order 20 diff AA - different protein
Protein functions Table 2. 3. 1
Protein functions Table 2. 3. 2
Proteins • functions based on 3 D structure • 3 D shape based on AA order – di-S bonds – H bonds in molecule in water
H-Bonds
Fig. 2. 27 tertiary
3 D shape dictates function
what changes 3 D ? • other molecules • ions • change AA order • heat • p. H covers some AA change charge genes damage
Physiology and protein 3 D • function ~ change protein 3 D • examples: – open / close channels – enzyme functions – receptors – immunity
cells as chemical soup • many chemicals in cell • chemical reactions are too slow • helpers = catalyst • cell’s reactions depend on what “helpers” are present
Enzymes • catalyst made of protein • name = ______ase – lipase – lactase – hydrolase – phosphatase – protein kinase – DNA synthase
enzyme properties • specific for one reaction • 3 D active site • activation energy • rate of reaction • same total energy
Enzymes and 3 D • change 3 D of enzyme • turns enzyme on/off • destroys – heat – p. H – ions – other enzymes
optimum temperature • heat increases energy • heat changes 3 D shape
optimum p. H • p. H changes 3 D shape ( correct 3 D shape at that p. H)
enzymes and cell specialization • cells differ by their chemical reactions • cells differ by their enzymes • to control what chem rxn and when : – make specific enzyme gene – activate enzymes present hormone
Nucleic Acids • DNA • RNA genetic code protein synthesis • gene code for protein code for AA order
genes and cells • • all cells have all genes cells differ by their active genes cells differ by their proteins different proteins - different physiology
ATP • adenosine triphosphate • storage for energy • ability to do work » change protein 3 D » shorten muscle » activate enzymes
• Physiology is what happens when chemicals do what chemicals do !
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