the chemical context of life chemical basis of biology
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The Chemical Context of Life
Chemical Basis of Biology
Elements :
Matter : made up of elements, substances that cannot be broken down to other substances by chemical reactions
Compounds
Molecular
Atom
• Each element
– Consists of a certain kind of atom that is different from those of other elements
• An atom
– Is the smallest unit of matter that still retains the properties of an element
• The atomic number of an element– Is the number of protons– Is unique to each element
Secondshell
Helium
2He
Firstshell
Thirdshell
Hydrogen
1H
2He
4.00Atomic mass
Atomic number
Element symbol
Electron-shelldiagram
Lithium
3LiBeryllium
4BeBoron
3BCarbon
6CNitrogen
7NOxygen
8OFluorine
9FNeon
10Ne
Sodium
11NaMagnesium
12MgAluminum
13AlSilicon
14SiPhosphorus
15PSulfur
16SChlorine
17ClArgon
18Ar
The periodic table of the elements
• A few other elements
– Make up the remaining 4%
of living matter
• major elements
Essential Elements of Life (25/92)
O, C, H, N (96%)
• Trace elements (<0.01%)
(a) Nitrogen deficiency (b) Iodine deficiency
The effects of essential element deficiencies
0.15mg/per day
Neutrons: no electrical charge
Protons: positively charged
Electrons: negatively charged
Atoms
Nucleus
Cloud of negativecharge (2 electrons)
Electrons
orbital
Valence electrons
Are those in the outermost, or valence shell
Determine the chemical behavior of an atom
Isotopes
• Isotopes
differ in the number of neutrons
same number of protons
• Radioactive isotopes
– Spontaneously give off particles and energy
32P 3H 14C
Incubators
Human cells
1 2 3
4 5 6
987
10°C 15°C 20°C
25°C 30°C 35°C
40°C 45°C 50°C
DNA (old and new)
1 2 3 4 5 6 7 8 9
Radioactive isotopesIngredients includingRadioactive tracer (bright blue)
3H
scintillation fluid
Whether temperature affects the rate of DNA synthesis?
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
O
HRNA
DNA-OH
32P 3H 14C
Temperature (°C)
10 20 30 40 50
Optimumtemperaturefor DNAsynthesis
30
20
10
0
Cou
nts
per
min
ute
(x 1
,000
)
scintillation counter
*DNA (3H)
Temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.
– Can be used in biology
Cancerous throat tissue
Radioactive isotopes
*glucose
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Isotopes
12C 13C 14C
stable stable radioactive
Proton number Neutron number
6 6 6
e- number
6 7 8 6 6 6
Chemical properties: the samePhysical properties: different
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
How atom combine to form molecular and ionic compounds?
Covalent bond
Ionic bond
2 or more atoms
2 or more atoms
molecular
Ionic compoundsor salts
Strong chemical bonds:
Sodium Chloride (Cl) Sodium Chloride
+
• ionic compounds (or salts)
– two or more elements combined in a fixed ratio
– In nature as crystals of various shape and size
(see fig2.14)
NaCl
(Na)
–characteristics different from those of its elements
–
Na NaCl Cl
+
Cl–
Chloride ion(an anion)Na
Sodium atomCl
Chlorine atom
Na+
Sodium on(a cation)
Sodium chloride (NaCl)
– an attraction between anions and cations
– Environment affects the strength of ionic bonds
ionic bond in compound
An anion: negatively charged ions
A cation: positively charged ion
(c)
Methane (CH4).
Water (H2O).
(d)
HO
H
H H
H
H
C
Covalent bond in compounds
-sharing of a pair of valence electrons
• In a nonpolar covalent bond
– The atoms have similar electronegativities
– Share the electron equally
Hydrogen (H2).
Oxygen (O2).
H H
O O
• Electronegativity
– Is the attraction of a particular kind of atom for the electrons in a covalent bond
• The more electronegative an atom
– The more strongly it pulls shared electrons toward itself
O2The most electronegative of the 92 elements:
H2O
–
O
H H+ +
In a polar covalent bond
The atoms have differing electronegativities
Share the electrons unequally
( O>H )
Delta minus
Delta plus
Partial negative
Partial positive
Weak chemical bonds are important in living systems
Hydrogen Bonds
Van der Waals Interactions
ReversibilityInter-molecular interaction:
Intra-molecular interaction in the large biological molecular
ex. Protein
Ionic bond
(3D structure)
Hydrogen Bonds
– +
+
Water(H2O)
Ammonia(NH3)
OH
H
+
–
N
HH H
+ d+
When a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom
Partial positive charge
Partial negative charge
H…..OH…..N
Insects walk on water.
Van der Waals Interactions
Help molecules adhere to each other
•Weak•Occur only when atom and molecular are very close together•Occur when transiently positive and negative regions of molecules attract each other
Gecko lizard
Tiny hairsIncrease surface area
Molecular Shape and Function
• The precise shape of a molecule
– Is usually very important to its function in the living cell
– Is determined by the positions of its atoms’ valence orbitals
Electron Orbitals• An orbital
– Is the three-dimensional space where an electron is found 90% of the time
• Each electron shell– Consists of a specific number of orbitals
1s orbital 2s orbital Three 2p orbitals1s, 2s, and 2p orbitals
(a) First shell (maximum 2 electrons)
(b) Second shell (maximum 8 electrons)
(c) Neon, with two filled shells (10 electrons)
x
Z
Y
s orbital
ZThree p orbitals
X
Y
Four hybrid orbitals
Tetrahedron
In a covalent bond
The s and p orbitals may hybridize, creating specific molecular shapes
Molecular Shape and Function
determined by the positions of its atoms’ valence orbitals
Space-fillingmodel
Hybrid-orbital model(with ball-and-stick
model superimposed)UnbondedElectron pair
104.5°
O
HWater (H2O)
Methane (CH4)
H
H H
H
C
O
H
H
H
C
Ball-and-stickmodel
H H
H
H
The positions of the hybrid orbital determine the shapes of the molecules
Morphine
Carbon
Hydrogen
Nitrogen
Sulfur
OxygenNaturalendorphin
Naturalendorphin
Endorphinreceptors
Morphine
Brain cell
specificity
Structures of endorphin and morphine
drugs
Molecular Shape and Function
Reactants
Reaction
Product
2 H2 O2 2 H2O
+
+
– Convert reactants to products
Reactants
– making and breaking of chemical bonds
– changes in the composition of matter
A chemical reaction
Photosynthesis
6CO2+ 6H2O C6H12O6 + O2
glucose
Sunlight
the forward and reverse reaction rates are equal
Chemical equilibrium
dynamic process
3H2+ N22NH3
reversible
Relative concentration of product and reactants stop to change