physiology is an integrated science biology –molecular –cellular –organ and organism physics...
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Physiology is an Integrated Science
• biology– molecular– cellular– organ and organism
• physics• chemistry
• we are made of stuff of universe• we follow rules of the universe
chemistry basics
• element substance with unique identity
• atom single unit of element
• molecule 2 + atoms
• compound molecules of different atoms
only the outer shell matters
electron shells can hold:
1st 2
2nd 8
3rd 8
4th 8
outer electrons =
valence electrons
Nature’s rules• nature is lazy entropy
• nature wants equilibrium• equal concentrations• equal electric charges opposites
attract• equal pressure
• nature wants a full outer shell octet rule
Biology’s rule of living things• You can break nature’s 3 rules , if:
• you supply energy• it aids survival
• breaking the rules requires energy :– molecules are organized– gradients require work– these store energy
what is life ?
• Living things take energy from the environment• Living things use energy to break nature’s rules.
– build molecules– change molecules– maintain gradients
what is energy ?
• it is the stuff that does work– holds molecules and atoms together– prevents equilibrium
• maintains concentration gradients• maintains electrical gradients
– breaks chemical bonds
Ions
• ion = charged atom or molecule• cation = + charged• anion = - charged
• nature wants a full outer shell octet rule• atoms gain/lose electron
common ions
• Sodium Na+
• Potassium K+ • Calcium Ca++
• Chlorine Cl-
• Phosphates PO4---
• Iron Fe++
• Copper Cu++
• Bicarbonate HCO3-
• see table 2.1
ions and physiology• 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 depend on nature’s desire for :– a full outer shell– equal charges
• chemical bonds store energy decreases entropy
ionic bonds
• ions with full outer shell nature happy?• ions with + / - charge nature happy?
• opposites attract = ionic bond
ions ionic bond
covalent bond
• too many electrons to gain or lose• nature still wants ?
• shared electrons• neutral atoms
What element can form the most covalent bonds ?
# electron
shells
# electrons (valence) in outer shell
1 2 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
• 3D shape of proteins
acid – base
• pH = parts Hydrogen
• acidity• increase H+ pH < 7
• neutral pH = 7
• alkalinity • decrease H+ pH > 7
Figure 2.13
Biochemistry
• biomolecules molecules of life• based on Carbon• specific functions• store energy
• carbohydrates• lipids• nucleic acids • proteins
carbohydrates
• Carbon + hydrates (water) CHO
• C + H2O C H2OC2 H4O2
C6 H12O6
• functions:– energy source glucose– store energy glycogen– DNA– antigens
lipids
• fats• mostly C and H (little O)
• functions: energy storage triglyceridesinsulation “cell membranes phospholipidshormones cholesterol
• hydrophobic
other nucleic Acids
• ATP adenosine triphosphate• ADP adenosine diphosphate
• cAMP cyclic adenosine monophosphate •
• NAD nicotinamide adenine dinucleotide• FAD flavin adenine dinucleotide
• GTP
Proteins
• polymers of amino acids 20 diff AA
• diverse molecules– different order of AA - different protein
• genes control AA order
Proteins and 3D shape• 3D shape based on AA order
– di-S bonds– H bonds in molecule
in water• functions based on
– 3D structure– change in 3D structure
what changes 3D ?
• other molecules covers some AA• ions change charge• ATP phosphorylation• change AA order genes
damage• heat • pH
Physiology and protein shape
• function ~ CHANGE PROTEIN 3D SHAPE
• examples:– open / close channels– receptors– hormone actions– transcription factors– enzyme functions and activation– immunity
chemical reactions• anabolic make bonds = synthesis
• A + B AB• builds large biochemicals• require energy = endergonic
• catabolic break bonds = decomposition• AB A + B• breaks apart biochemicals• release energy = exergonic
exergonic reactions need help
• exergonic reactions release energy• but are very slow• need energy to get started activation energy
enzymes lower activation energy• solutions:
– provide energy heat– lower activation E chemical helpers
• chemical helpers = catalyst• catalyst made of protein = enzyme
enzyme properties• increase the rate of reaction• specific for one reaction ; substrates
• 3D active site
• increase contacts• strain bonds
• induced fit
• enzymes have optimum temperature
• enzymes have optimum pH
• change temp , pH changes 3D of enzyme
• end-product inhibition
Enzymes have specific 3D
• change 3D can turn enzyme on/off• change 3D by:
– heat– pH– ATP– ions– other enzymes
enzymes and cell specialization
• cells differ by their chemical reactions• cells differ by their enzymes
• to control a cell’s chemical reactions:• control which enzymes are present gene• control which enzyme is active modulator
– hormone– other enzyme– ATP
Enzyme names tell what they do
• name = ______ase• hydrolysis – dehydration hydrolase
protease , lipase• build molecule (via ATP) synthetase • exchange phosphate kinase
– add phosphate phosphorylase– subtract phosphate phosphatase
• redox lose e- oxidaselose H+ dehydrogenase
• exchange AA transaminase– add AA aminase– subtract AA deaminase
endergonic reactions require energy• 2nd Law of Thermodynamics • anabolic reactions require energy• Energy from chemical bonds (glucose)
• coupled rxn: transfer E from exergonic to endergonic rxn
• we need a transfer molecule ATP
ATP• adenosine triphosphate• energy transfer molecule• ADP + ~P + energy ATP• ability to do work
» change protein 3D
» activate enzymes
» anabolic synthesis
coupling reactions
• glucose CO2 + H2O exergonic
• ADP + P ATP endergonic
• ATP ADP + P exergonic• A + B AB endergonic
• ATP transfers E from glucose to AB
• E to build AB from glucose• E in glucose from sun
cell respiration• main exergonic reaction of the body• catabolism of energy sources
• C6H12O6 6CO2 + 6H2O + E
• 3 steps:– glycolysis– Kreb’s cycle– electron transport chain
oxidative phosphorylation• main endergonic reaction of the body• transfers E to ATP
• ADP + P + E ATP
put ‘em together• all cell resp just to release E to run this anabolic rxn
• C6H12O6 6CO2 + 6H2O + E exergonic
• ADP + P ATP endergonic
energy sources• glucose liver, food• glycogen liver• lipids adipose, food• amino acids muscle• lactic acid muscle
• Where do these molecules get their energy ?
plants vs animals• animals E from biomolecules
– eat molecules of other animals– eat molecules of plants
• plants E from sun
we are mainly cell respirators• most of our A&P performs or supports cell respiration
• food gathering• digestion, absorption, respiration• transport• control systems• cell physiology
energy, chemistry, and physiology
• We are an organized sack of chemicals• Keeping that order requires energy (work)• That energy comes from the environment – chemical bonds• Physiology uses energy to do our work:
– we make and break chemical bonds– we change protein shapes– we create gradients
• Physiology uses the natural behavior of matter:– move toward chemical equilibrium– move towards electrical equilibrium– move towards pressure equilibrium