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

Transcript of Physiology is an Integrated Science biology –molecular –cellular –organ and organism physics...

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