Transcript Medical Chemistry Lecture I

Chemistry
- science studying the properties and behavior of matter
Matter - physical material of the universe
- anything that has mass and occupies space
States of matter: 1) gas
(no fixed volume or shape)
2) liquid
(distinct volume but no specific shape)
3) solid
(both definite shape and volume)
Pure substance – matter that has fixed composition and
distinct properties (sodium chloride, water)
2 categories of substances:
Elements – cannot be decomposed by chemical methods
into simpler substances (carbon, oxygen, iron)
= consist of one kind of atoms
Compounds – contain two or more kinds of atoms
(water – H2O sodium chloride NaCl)
Structure of the atom
atom – the smallest particle of an element having
its chemical properties
("atomos" in old Greek language = "indivisible")
3 types of subatomic (elementary)
particles:
PROTONS
NEUTRONS
ELECTRONS
"nucleons"
Particle
Symbol
Relative charge
Relative mass
Proton
p
positive +1
1
Neutron
n
0
1
Electron
e
negative -1
negligible *
relative mass – expressed in „atomic mass units“
(relative atomic mass, relative molecular mass)
atomic mass unit = 1/12 of the mass of an atom of the carbon isotope 12C
(1.66 x 10-24 g)
* mass of the electron = only 1/1836 of the mass of the proton
Atoms have no overall charge
==>
number of protons = number of electrons
This number is different for every element !
= ATOMIC number ( Z )
Element = mixture of atoms with the same number of protons
(the atomic number)
The chemical properties of any given element are determined by
the arrangement of electrons around the nucleus.
Every atom is characterized by 2 numbers:
Atomic number (Z)
= number of protons
- it determines the element = symbol: C, N, Fe
Mass (nucleon) number (A)
= number of nucleons
(protons + neutrons)
mass number
atomic number
12
6
C
symbol of element
Nuclide - specific atomic number Z and mass number A
for example:
12
6C
238
92
U
- most elements are mixtures of different nuclides !
(same atomic number, different mass numbers)
= same number of protons, variation in number of neutrons
= ISOTOPES of an element
------------------------------------------------------------------Term "nuclide" - more general
- used: only one nucleus or several nuclei of different elements
Term "isotope" - used when referring to several different nuclides of the same
element
Isotopes of hydrogen
neutrons
proton
1
1
2
1
H
hydrogen
3
1
H
deuterium (D)
H
tritium (T)
The isotopes of an element have a different number of NEUTRONS
-identical chemical properties
water
H2O
"heavy water"
D2O
Isotopes of carbon
12
6
13
6
C
14
6
C
C
------------------------------------------------------------------------------------------------
Certain isotopes of some elements are radioactive !
Radioactive decay = unstable atomic nucleus "loses energy" by emitting:
particle
a
=
4
2
particle
b
=
0
-1
g
14
6
C
half life 5730 years
14
7
N
+
He
e
rays ( = high-energy photon)
0
-1
e
+ antineutrino
Electrons
- surround the nucleus in energy levels (shells, orbits)
1 electron
6 electrons
15 electrons
The chemical reactions = interaction of electrons
from the OUTERMOST orbit
Arrangement of electrons in the atom
4 quantum numbers:
1) n
principle quantum number
- determines energy level
- positive integral values 1, 2, 3, 4, ...
K, L, M, N, ...
2) l
orbital quantum number
- determines the shape of electron cloud
- values from 0 to (n-1) 0, 1, 2, 3, ...
s p d f
3) m
magnetic quantum number
- determines orientation of electron cloud
in space
- integral values from –l to +l
4) s
spin
- determines the intrinsic state of an electron
- only 2 possible values: +½ or -½
The s orbitals
orbital quantum number
l=0
magnetic quantum number m = 0 (only possib.)
in each s orbital can be only 2 electrons
(with different SPIN)
1s
1s1
1s
1s2
"spherical"
The p orbitals
"two lobes"
orbital quantum number
magnetic quantum number
l=1
m = -1
0
1
in each p orbitals can be 2 x 3 = 6 electrons
2p
2p2
2p
2p6
The d orbitals
orbital quantum number
magnetic quantum number
l=2
m = -2 -1
0
1
2
in each d orbitals can be 2 x 5 = 10 electrons
3d
3d7
Rules that must be respected
1) The lowest "energy levels" are
occupied first.
2) Hund‘s rule:
No electron pairing in p, d, f
orbitals until each orbital of given
set contains one electron.
3) Pauli exclusion principle:
No TWO electrons in any given
atom can have exactly the same
set of all 4 quantum numbers.
Electron configuration of several elements
Electrons
Orbital diagram
1s2 2s1
1s2 2s2
1s2 2s2 2p1
1s2 2s2 2p2
1s2 2s2 2p3
1s2 2s2 2p6
1s2 2s2 2p6 3s1
The periodic properties of the elements
The elements with similar arrangement (configuration) of electrons
in the outer (superficial) shell have SIMILAR CHEMICAL PROPERTIES
Periodic table
Dmitri Mendeleyev (1869) - Russian chemist
- elements are listed in order of increasing atomic number
horizontal rows = PERIODS
vertical columns = GROUPS
elements in groups: the same number of electrons in outermost orbits
= similar chemical properties
Names for some of the groups
Group
Name
Elements
IA
Alkali metals
Li, Na, K, Rb, Cs, Fr
II A
Alkaline earth metals
Be, Mg, Ca, Sr, Ba, Ra
VI A
Chalcogens
O, S, Se, Te, Po
VII A
Halogens
F, Cl, Br, I
Noble (rare, inert) gases
He, Ne, Ar, Kr, Xe, Rn
VIII A (0)
Chemical bonding
Covalent bond
- sharing of one or more pairs of electrons
Coordinate covalent bond - both electrons of the bond belong to one
atom, the other has empty orbital
Ionic bond - big difference of electronegativities
- IONS attracted by electrostatic forces
Na+ Cl-
Hydrogen bonding
a weak electrostatic interaction between partly (+) charged hydrogen
atom and partly (-) charged another atom (O, N, F)
R
N
R
H bonds
(+)
(-)
H ............. O
R
C
vodíkový můstek
R
important in stabilizing the structures of: PROTEINS
NUCLEIC ACIDS
The EARTH
Core (inner, outer)
Mantle
Crust
Crust
Lithosphere
Hydrosphere
Atmosphere
Biosphere
93 %
7%
0.03 %
0.001 %
The elementary composition (%)
Earth crust
Human body
O
49.5
62.4
Si
25.7
-
Al
7.5
-
Fe
4.7
0.005
H
0.9
9.8
P
0.12
1.0
C
0.09
21.1
S
0.06
0.16
N
0.03
3.1
- elementary composition of the human body is very different
from that of lithosphere
Specific selection of some elements for the biological uses
% in human body
% in the Earth crust
C
243
N
103
H
11
P
8
S
2.7
O
1.26
Fe
0.001
Al
0.000 13
Si
0.000 04
- some chemical elements (C, H, N, O, ...) are "better" than
others to make up molecules of living organisms
- most abundant elements of the Earth core:
Fe, Ni
- most abundant elements of the Earth crust:
O, Si, Al, Fe
- most abundant elements in living organisms:
O, C, H, N
- oxygen is the most abundant element both on the Earth surface
and in human body
The atmosphere of the Earth
Composition of the AIR
Water vapour
1-4%
The dry air (by volume)
Nitrogen
Oxygen
Argon
Carbon dioxide
All others
78 %
21 %
0.93 %
0.038 %
only trace amounts
The geological development of the atmosphere
• the loss of very light gases ( H2
• the increase of O2
20th centrury - slight increase of CO2
burning of coal, gas, oil
destruction of forests and phytoplankton
current levels
0.0296 %
0.0385 %
CH4 )
(photolysis of water by the green plants)
• fixation of CO2 by photosynthesis
1900
He
296 ppm
385 ppm
The greenhouse effect
CO2 is a "greenhouse gas" - global warming
The oxygen cycle
O2
Animals, plants
RESPIRATION
CO2
H2O
We need per day:
air
water
food
Plants
PHOTOLYSIS of H2O
PHOTOSYNTHESIS
15 000 l [ 13.5 kg ]
2 kg
1.2 kg
Comparison of inspired and expired air
Inspired
Expired
O2
21 %
15 %
CO2
0.03 %
5%
N2
78 %
78 %
CO2 is a waste product
of respiration
Air pollution
Emissions = the pollutants released into the environment
Pollution
natural
industrial
Natural sources
Volcano eruptions
Dust storms
Fires
Lightnings
Biological decomposition
dust
dust
dust
NO
CO2
ash
SO2
ash CO2 CO
NO2
H2S NH3 CH4
Dust particles  water condensation  CLOUDS, RAIN
Impact of big meteor  heavy dust pollution of atmosphere
 climate changes
( extinction of giant reptiles in mesozoic era ? )
Industrial sources
The progress of civilization  global air pollution
(overcharging of the natural cycles of regeneration and detoxication)
1)
2)
3)
4)
5)
6)
dust – ashes
Sulphur dioxide ( SO2 )
Nitrogen oxides ( NOx )
Carbon oxides ( CO2 CO )
Toxic metals
Organic compounds
Particulate matter - dust, ashes
complex mixture of extremely small particles and liquid droplets
sources: power plants, industrial and agriculture processes, transport, home
effects: irritation of respiratory system
contains adsorbed number of components: toxic metals, SO2
cancerogenic hydrocarbons
the size of particles is directly linked to their potential for causing
health problems - smaller than 10 mm pass through the airways
and enter the lung !
SMOG [ smoke + fog ]
"London smog"
HELP: industry, power plants - electrostatic precipitation
home - no burning of coal and peat
- using gas or oil, solar energy
Sulphur dioxide
SO2
main source: burning of soft coal ( 1 % S as sulphides of Fe )
Europe 1980: 40 000 000 tons of SO2
( ¾ bound to fly ash )
irritation of respiratory system, rhinitis, laryngitis
SO2 + H2O  H2SO3
SO2

SO3 + H2O  H2SO4
sulphurous acid (weak acid)
sulphuric acid
(strong acid)
ACID RAIN
pH ~ 4
 acidification of soil  solution of minerals  Al3+ Pb2+ Cu2+ ...
 intoxication of plants and animals
green plants: CO2 x SO2 competition  destruction of photosynthetic enzymes
(damage of pine forests)
Sulphur dioxide
SO2
HELP: Power plants: soft coal + CaCO3
 CaSO4 ("gypsum")
OR
SO2
+ Ca(OH)2  CaSO4
Acid soil: + CaCO3
+ Ca(OH)2
("limestone")
("lime water")
Nitrogen oxides
NO
NOx
limit: 0.1 mg / m3
NO2
brown haze
sources: motor vehicles, power plants, chemical industry
secondary pollutants:
OZONE ( O3 )
PAN = peroxyacylnitrates
sun light
NO2
NO + O
Photochemical smog
( "Los Angeles – type" smog )
O2 + O
 O3
O3 + hydrocarbons

aldehydes
(car exhausts)
+ NO2
PAN
very irritating to eyes
and respiratory system
"London – type" smog
combustion of coal
= smoke + fog
 emission of sulphur dioxide ( SO2 ) and dust
+ mixed with FOG
"Los Angeles – type" smog
dry air + sunny days
+ NOx
+ volatile organic gases
(emitted by automobiles)
= photochemical smog
Carbon dioxide CO2
colorless, odorless gas
"overproduction" sources: burning of fossil fuels
air: 0.038 %
higher levels stimulate breathing
long time respiration of 5 % CO2  respiration troubles
> 15 %  DEATH
Danger: old mines, caves, wine cellars
(heavier than air  it tends to go down)
Carbon monoxide CO
colorless, odorless gas
sources: car exhausts, incomplete burning (smouldering)
local street pollution – dangerous level: 10 ppm / 8 hours
TOXIC: very high affinity to HEMOGLOBIN
35 ppm / 1 hour
 carbonylhemoglobin
 impaired ability of the blood to transport O2  oxygen deprivation
drowsiness  unconsciousness  DEATH
Toxic heavy metals
Lead
Pb
- tetraethyllead was used as antiknock agent in gasoline
(organometallic compound)
Pb (CH2CH3)4
neurotoxic

PbO (lead oxide aerosol)
deposition in the vicinity of highways
toxic effects of inorganic lead compounds: impaired heme synthesis  anemia
Toxic metals aerosol As, Pb, Cd, Hg, ... oxides bound to ash particulate matter
- source: power plants ( COAL ! ), smelters
- general toxicity – decrease of vitality
Organic compounds
Hydrocarbons – motor vehicles, industry, cigarette smoke ( TAR )
- carcinogens, precursors to PAN
Freons - hydrocarbons with hydrogen atoms substituated by F, Cl
= chlorofluorocarbons ( CFCs )
- in older refrigeration and air-conditioning systems
- effect: destroying the ozone layer in the stratosphere
Indoor air pollution
Respiration  CO2
( H2O)
Digestion (intestinal bacteria)  H2S
Gas stove  CO2
CO
indole
( H2O)
Tobacco smoke  TAR (cancerogens)
Formaldehyde
Radon
Rn
HCHO
nicotine
- released from foamed insulation
tapestry
plywood adhesives
- radioactive gas
- radon from natural sources can accumulate in buildings
222
86
Rn 
4
2 He
+
218
84
Po
Water
non-bonding electron pairs
O
H2O
H
105o
H
bent molecule
d-
polar character
O
H
d+
-
H
+
d+
electrical dipole
Hydrogen bonding
-
attractions between water molecules
+
+

+
-
+
-
+
0 oC
3.6
/ H2O
HIGH melting point
boiling point
specific heat
heat of vaporization
surface tension
H bonds - much weaker than covalent bonds !
bond energy of H-bonds in liquid water: about 19 kJ/mol
( covalent H – O bond in water: 460 kJ/mol )
water is most dense at 3.98 °C !!!
(when freezing, ice will form first on the surface)
WATER - very good solvent !
Attraction between
water dipoles and ions
"hydrated ions"
Dispersing "amphipathic" molecules
"micelles"
"Amphipathic" molecules – contain both highly hydrophobic
and highly polar groups
palmitic acid
non-polar chain = hydrophobic
polar group = hydrophilic
(water-fearing)
(water-loving)
Phospholipids
phosphatidylcholine
(lecithin)
polar groups
Water in human body
~ 60 % of the body weight
intracellular ~ 40 %
extracellular ~ 20 %
PLASMA
5%
interstitial fluid 15 %
- a very complex solution of inorganic & organic components
Phosphates
Proteins
K+
Na+ Mg2+
Na+
Cl-
Na+
K+
Ca2+
HCO3-
Mg2+
Phosphates
K+
Na+/K+ pump
( = Na+/K+ -ATPase )
Blood plasma
( extracellular fluid )
Cell fluid (cytosol)
( intracellular fluid )
Human blood plasma
mmol/l
Na+
132 – 145
K+
3.8 - 5.2
Ca*
2.1 – 2.6
Mg2+
0.8 – 1.1
Cl-
97 – 108
HCO3-
22 – 26
Phosphates
HPO42- + H2PO4-
0.6 – 1.6
pH = 7.36 – 7.44
* Ca "total Ca"
Ca2+ "ionized" is about ½ of "total" ~ 1.2 mmol/l
Colligative properties of solutions
- dependent on the number of solute particles
the same effect
Effects of a solute on a solvent:
depression of the freezing point
elevation of the boiling point
depression of the vapour pressure
osmotic pressure
osmolality = moles of solute particles dissolved in 1 kg of solvent
( osmolality of blood plasma: 285 mmol/kg )
Water balance
Intake: ~ 1.5 - 2.0 l / day
metabolic water (produced in human body by oxidation of food) 0.3 – 0.5 l /day
Resorption: stomach, small intestine, LARGE INTESTINE
Secretion:
Excretion:
Saliva
Stomach
Bile
Pancreas
Small intestine
1 500 ml / day
2 500
500
700
3 000
Urine 60 %
Skin
20 % (perspiration)
Lungs 15 %
Faeces 5 %
8 200 ml /day
Water in nature
Hardness of water:
technical problems – deposits after boiling
Temporary hardness: cause = Ca(HCO3)2
Boiling:
Ca(HCO3)2
soluble in water
CaCO3 + CO2
+ H2O
Softening water in water stations:
Ca(HCO3)2 + Ca(OH)2
2 CaCO3 + 2 H2O
Permanent hardness: cause = CaCl2 CaSO4 ...
softening: CaSO4 + Na2CO3
CaCO3 + Na2SO4
Biological pollution of water
urine, excrements, dead bodies
BACTERIAL decomposition (most efficiently by aerobic bacteria)
I. organic compounds: UREA, proteins, peptides
II. NH3
III. NO2-
markers of
RECENT pollution
ammonia
NO3-
- final decomposition products
- good for plant nutrition
EUTROPHICATION of water
- fertilizers, phosphates
(compounds of N, P)
The bioelements (summary)
1)
Principal bioelements:
O, C, N, H, P, S
(biomolecules: proteins, nucleic acids, lipids, saccharides)
2)
Water and ions ( H2O ) Na+, K+, Mg2+, Ca2+, Cl-, ( HCO3- , phosphates)
3)
Mineral constituents of bones and teeth Ca (Mg, Na)
PO43- CO32- ( F- Cl- )
4)
Microelements (trace elements)
Fe, Cu, Co, Zn, I, F, Se, ...
--------------------------------------------------------
5)
Contamination (intoxication):
Hg, Al, ...