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

elements – table 2.1

H2O

more elements

atom = protons + electrons

charge mass

+ 1

none 1

- none

Periodic table• # protons identity atomic number• # electrons behavior

electrons

electron shells can hold:

1st 2

2nd 8

3rd 8

4th 8

outer electrons =

valence electrons

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

electron shells hold Energy

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

which atoms form ions

# electron

shells

# electrons (valence) in outer shell

1 2 3 4 5 6 7 8

+ -

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

types of chemical bonds

• ionic• covalent

– di-sulfide• hydrogen

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

• octet rule? is nature happy?

• neutral charge? is nature happy?

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

hydrogen bonds - Water

Polarity - ions in water

• universal solvent ions (salts) dissolve in water

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

Figure 2.14a, b

•

Figure 2.14a, b

lipids

• fats• mostly C and H (little O)

• functions: energy storage triglyceridesinsulation “cell membranes phospholipidshormones cholesterol

• hydrophobic

triglycerides• glycerol + 3 fatty acids

• unsaturated FA• saturated FA• trans fats

phospholipids

• 2 fatty acids + phosphate group• cell membranes

hydrophilic hydrophobic

steroids

• made from Cholesterol• cell membranes• hormones• Vitamin D• bile

Cholesterol, other Steroids

also: Estrogen ; Progesterone

Nucleic Acids

• DNA genetic code• RNA protein synthesis

• gene code for protein code for AA order

other nucleic Acids

• ATP adenosine triphosphate• ADP adenosine diphosphate

• cAMP cyclic adenosine monophosphate •

• NAD nicotinamide adenine dinucleotide• FAD flavin adenine dinucleotide

• GTP

amino acids• building blocks of proteins

Proteins

• polymers of amino acids 20 diff AA

• diverse molecules– different order of AA - different protein

• genes control AA order

Protein functions

Table 2.3.1

Protein functions

Table 2.3.2

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

H-Bonds

Fig. 2.27

tertiary

3D shape dictates function

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

enzyme-substrate complex

• 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

p 957

energy sources• glucose liver, food• glycogen liver• lipids adipose, food• amino acids muscle• lactic acid muscle

• Where do these molecules get their energy ?

p 969 interaction of biochemicals

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

• Physiology is what happens when chemicals do what chemicals do !

Professor Gary Covitt, D.C. 2004