Chapter 2 Chemistry
Physiology is an Integrated Science
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Biology
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molecular
cellular
organ systems
Physics
Chemistry
we are made of the stuff of the universe
we follow the rules of the universe
Chemistry
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element
substance with unique identity
atom
single unit of element
molecule
2 + atoms
compound
molecules of different atoms
elements – table 2.1
Periodic table
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# protons
identity
# electrons
behavior
atomic number
Nature’s rules
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nature is lazy
entropy
nature wants equilibrium
• equal concentrations
• equal electric charges
• equal pressure
nature wants a full outer shell
opposites attract
octet rule
Biology’s rule of living things
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You can break nature’s 3 rules briefly, if:
• you supply energy
• it aids survival
breaking the rules requires energy :
molecules are organized
gradients require work
these store energy
what is life ?
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Living things take energy from the environment and use it to break nature’s rules.
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build molecules
change molecules
maintain gradients
what is energy ?
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it is the stuff that does work
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holds molecules and atoms together
prevents equilibrium
• maintains concentration gradients
• maintains electrical gradients
breaks chemical bonds
Ions
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ion = charged atom or molecule
• cation
• anion
= + charged
= - charged
nature wants a full outer shell
octet rule
atoms gain/lose electron
common ions
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Sodium
Na+
Potassium
K+
Calcium
Ca++
Chlorine
Cl-
Phosphates
PO4---
Iron
Fe++
Copper
Cu++
Bicarbonate
HCO3-
see table 2.1
ions and physiology
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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
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Chemical bonds depend on nature’s desire for :
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a full outer shell
equal charges
chemical bonds store energy
decreases entropy
types of chemical bonds
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ionic
covalent
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di-sulfide
hydrogen
ionic bonds
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ions with full outer shell
nature happy?
ions with + / - charge
nature happy?
opposites attract
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ionic bond
covalent bond
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too many electrons to gain or lose
nature still wants ?
shared electrons
neutral atoms
polar covalent
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nonpolar
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electrons shared equally
polar
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electrons shared unequally
have + and - ends
hydrogen bonds
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H tends to be +
attracted to - end of other molecules (eg . O )
water
3D shape of proteins
Polarity - ions in water
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universal solvent
ions (salts) dissolve in water
acid – base
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pH = parts Hydrogen
pH = 7
(neutral)
acidity
increase H+
neutral
pH < 7
pH = 7
decrease H+
alkalinity
pH > 7
Biochemistry
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biomolecules molecules of life
based on Carbon
specific functions
store energy
carbohydrates
lipids
nucleic acids
proteins
carbohydrates
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Carbon + hydrates (water)
C
+

H2O
CHO
C H2O
C2 H4O2
C6 H12O6
functions:
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energy source
glucose
energy storage
glycogen
DNA
antigens
lipids
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fats
mostly C and H
functions:
(little O)
energy storage
insulation
cell membranes
hormones
triglycerides
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phospholipids
cholesterol
hydrophobic
triglycerides
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glycerol + 3 fatty acids
phospholipids
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2 fatty acids + phosphate group
cell membranes
steroids
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made from Cholesterol
cell membranes
hormones
Vitamin D
bile
Nucleic Acids
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DNA genetic code
RNA protein synthesis
gene code for protein
code for AA order
other nucleic acids
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ATP
adenosine triphosphate
ADP
adenosine diphosphate
cAMP
cyclic AMP
GTP
guanosine triphosphate
NAD
nicotinamide adenine dinucleotide
FAD
flavin adenine dinucleotide
amino acids
Proteins
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polymers of amino acids
20 diff AA
diverse molecules
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different order of AA
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different protein
genes control AA order
Protein functions
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see table 2.3
Proteins and 3D shape
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3D shape based on AA order
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di-S bonds
H bonds
in molecule
in water
functions based on
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3D structure
change in 3D structure
what changes 3D ?
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other molecules
covers some AA
ions
change charge
ATP
phosphorylation
change AA order
genes
damage
heat
pH
Physiology and protein shape
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function ~ CHANGE PROTEIN 3D SHAPE
examples:
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open / close channels
receptors
hormone actions
transcription factors
enzyme functions and activation
immunity
chemical reactions
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anabolic
make bonds
• A + B  AB
• builds large biochemicals
• require energy
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catabolic
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synthesis
endergonic
break bonds
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decomposition
• AB  A + B
• breaks apart biochemicals
• release energy =
exergonic
exergonic reaction need help
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exergonic reactions release energy
but are very slow
need energy to get started
activation energy
enzymes lower activation energy
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solutions:
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provide energy
heat
lower activation E
chemical helpers
chemical helpers
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catalyst
catalyst made of protein =
enzyme
enzyme properties
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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
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change 3D can turn enzyme on/off
change 3D by:
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heat
pH
ATP
ions
other enzymes
enzymes and cell specialization
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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
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hormone
other enzyme
ATP
Enzyme names tell what they do
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name = ______ase
hydrolysis – dehydration
protease , lipase
hydrolase
build molecule (via ATP)
synthetase
exchange phosphate
kinase
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add phosphate
phosphorylase
subtract phosphate
phosphatase
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redox
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exchange AA
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lose elose H+
oxidase
dehydrogenase
transaminase
add AA
aminase
subtract AA
deaminase
endergonic reactions require energy
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2nd Law of Thermodynamics
anabolic reactions require E
energy – from chemical bonds (glucose)
coupled reactions: transfer E from exergonic to endergonic rxn
we need a transfer molecule
ATP
ATP
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adenosine triphosphate
energy transfer molecule
ADP + ~P + energy 
ATP
ability to do work
» change protein 3D
» activate enzymes
» anabolic synthesis
coupling reactions
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glucose
 CO2 + H2O
ADP + P  ATP
exergonic
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 the sun
cell respiration
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main exergonic reaction of the body
catabolism of energy sources
 6CO2 + 6H2O + E
C6H12O6
3 steps:
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glycolysis
Kreb’s cycle
electron transport chain / oxidative phosphorylation
oxidative phosphorylation
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main endergonic reaction of the body
tranfers E to ATP
ADP + P + E  ATP
put ‘em together
cell respiration – to release energy to run phosphorylation of ATP
energy sources
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glucose
liver, food
glycogen
liver
lipids
adipose, food
amino acids
muscle
lactic acid
muscle
Where do these molecules get their energy ?
plants vs animals
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animals
E from biomolecules
plants
E from sun
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of other animals and plants
we are mainly cell respirators
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most of our A&P performs or supports cell respiration
food gathering
digestion, absorption, respiration
transport
control systems
cell physiology
energy, chemistry, and physiology
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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:
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we make and break chemical bonds
we change protein shapes
we create gradients
Physiology uses the natural behavior of matter:
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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