biol 210 general biology 1
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Biol 210 General Biology 1. Lecture 2 Review Chemical Bonds. Atomic Structure. Nucleus Protons, mass = 1, charge = +1 Neutrons, mass = 1, charge = 0 Electrons Mass = negligible Charge = -1 # e – = # protons Outer shell (most energenic) e – ’ s form chemical bonds. Isotopes. - PowerPoint PPT PresentationTRANSCRIPT
Biol 210 General Biology 1
Lecture 2
Review
Chemical Bonds
Atomic Structure
• Nucleus– Protons, mass = 1, charge = +1
– Neutrons, mass = 1, charge = 0
• Electrons– Mass = negligible
– Charge = -1
– # e– = # protons
– Outer shell (most energenic) e–’s form chemical bonds
Isotopes
• Some isotopes are stable, such as 1H2
• Other isotopes are unstable, such as 1H3.
• When tritium decays, it gives off particle.
• Because the mass of an element includes the average isotope abundance, the mass and the atomic weight differ slightly
• Helium, He, atomic number 4, mass 4.003
Important Elements• C HOPKINS CaFe Mg
– C = carbon– H = hydrogen– O = oxygen– P = phosphorous– K = potassium– I = iodine– N = nitrogen– S = sulfur– Ca = calcium– Fe = iron– Mg = magnesium
Na = sodiumCl = chloride
•Every atom has a characteristic total number of covalent bonds that it can form = an atom’s valence.
•The valence of hydrogen is 1.
•Oxygen is 2.
•Nitrogen is 3.
•Carbon is 4.
•Phosphorus should have a valence of 3, based on its three unpaired electrons, but in biological molecules it generally has a valence of 5, forming three single covalent bonds and one double bond.
Chemical Bonds
• Two atoms share one or more pairs of valence electrons
• Four kinds of chemical bonds– Covalent– Hydrogen– Ionic– Van der Waals
• You must know the first 3 kinds
Covalent Bonds
• Two atoms share one or more pairs of electrons
Covalent Bonds
• Two atoms share one or more pairs of electrons
• Strongest chemical bond
Covalent Bonds
• Two atoms share one or more pairs of electrons
• Strongest chemical bond
• 50-110 kcal/mol
Hydrogen molecule
• Hydrogen atoms have one valence electron each
• Innermost shell can accommodate two electrons
• Each atom contributes an electron
• Electrons effectively fill valence shell for both atoms
Oxygen
• Oxygen has 2 valence electrons• Can share two pairs of electrons• Two O atoms can form 2 covalent bonds
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond• O must bond two H atoms
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond• O must bond two H atoms• H2O = water
Carbon
• Carbon has a valence of 4 electrons
Carbon
• Carbon has a valence of 4 electrons• Can form 4 covalent bonds
Carbon
• Carbon has a valence of 4 electrons• Can form 4 covalent bonds• Biological molecules are largely carbon-
containing molecules
Carbon
• Carbon has 4 valence electrons• Can form 4 covalent bonds• Biological molecules are largely carbon-containing
molecules• Organic = derived from organisms
s orbital
ZThree p orbitals
X
Y
Four hybrid orbitals
(a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink).
Tetrahedron
Figure 2.16 (a)
H—H
O=O
H—O—H
CH4
Morphine
Carbon
Hydrogen
Nitrogen
Sulfur
OxygenNaturalendorphin
(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.
Naturalendorphin
Endorphinreceptors
Morphine
Brain cell
Ionic Bond
• Covalent bonds result from two atoms sharing electrons
Ionic Bond
• Covalent bonds result from two atoms sharing electrons
• Sometimes one atom “takes” the electron from another atom.
Ionic Bond
• One atom has more protons than electrons = +1
Ionic Bond
• One atom has more protons than electrons = +1• Other atom has one more electron than protons = -
1
Ionic Bond
• One atom has more protons than electrons = +1• Other atom has one more electron than protons = -
1• Opposite charges attract weakly (3-7 kcal/mol)
Hydrogen Bond
• We have studied two bonding extremes
Hydrogen Bond
• We have studied two bonding extremes• Covalent bond = atoms share electrons
Hydrogen Bond
• We have studied two bonding extremes• Covalent bond = atoms share electrons• Ionic bond = one atom “take”s electrons
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons • Hydrogen nucleus less attractive
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons • Hydrogen nucleus less attractive• Partial charges, O more neg, H more pos
Hydrogen Bond
• Water = polar molecule
Hydrogen Bond
• Water = polar molecule• Can interact weakly with other polar molecules
Hydrogen Bond
• Water = polar molecule• Can interact weakly with other polar molecules• H-bond 3-7 kcal/mol
Comparative Bond Strength
• Covalent bond = 50-110 kcal/mol
• Ionic bond = 3-7 kcal/mol
• H-bond = 3-7 kcal/mol
• van der Waals bond = ~1 kcal/mol
Predicted BP for water = -76°C
Predicted BP for water = -76°CPredicted MP for water = -87°C
Predicted BP for water = -76°CPredicted MP for water = -87°CTemp. range for liquid water = 11°
Predicted BP for water = -76°CPredicted MP for water = -87°CPredicted temp. range for liquid water = 11°Actual: 0–100°C
Predicted BP for water = -76°CPredicted MP for water = -87°CPredicted temp. range for liquid water = 11°Actual: 0–100°CRationale: H-bonds
Hydrogenbonds
+
+
H
H+
+
–
–
– –
Figure 3.2
•The polarity of water molecules
Hydrogenbonds
+
+
H
H+
+
–
–
– –
Figure 3.2
•The polarity of water molecules
–Allows them to form hydrogen bonds with each other
Hydrogenbonds
+
+
H
H+
+
–
–
– –
Figure 3.2
•The polarity of water molecules
–Allows them to form hydrogen bonds with each other
–Contributes to the various properties water exhibits
• The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them
+
+
+
+Cl –
–
–
–
–
Na+
++
+
+
–
–
–
–
–
–Na+
Cl–
Figure 3.6
• The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them
Negative
oxygen regions
of polar water molecules
are attracted to sodium
cations (Na+).
+
+
+
+Cl –
–
–
–
–
Na+
++
+
+
–
–
–
–
–
–Na+
Cl–
Figure 3.6
• The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them
Negative
oxygen regions
of polar water molecules
are attracted to sodium
cations (Na+).
+
+
+
+Cl –
–
–
–
–
Na+Positive hydrogen regions
of water molecules cling to chloride anions
(Cl–).
++
+
+
–
–
–
–
–
–Na+
Cl–
Figure 3.6
• Water can also interact with polar molecules such as proteins
This oxygen is
attracted to a slight
positive charge on
the lysozyme
molecule.
This oxygen is attracted to a slight
negative charge on the lysozyme
molecule.
(a) Lysozyme molecule
in a nonaqueous
environment
(b) Lysozyme molecule (purple)
in an aqueous environment
such as tears or saliva
(c) Ionic and polar regions on the protein’s
Surface attract water molecules.
+
–
Figure 3.7
pH
• Water can dissociate
H
Hydroniumion (H3O+)
H
Hydroxideion (OH–)
H
H
H
H
H
H
+ –
+
Figure on p. 53 of water dissociating
pH
• Water can dissociate– Into hydronium ions and hydroxide ions
H
Hydroniumion (H3O+)
H
Hydroxideion (OH–)
H
H
H
H
H
H
+ –
+
Figure on p. 53 of water dissociating
pH
• Water can dissociate– Into hydronium ions and hydroxide ions
• Changes in the concentration of these ions
H
Hydroniumion (H3O+)
H
Hydroxideion (OH–)
H
H
H
H
H
H
+ –
+
Figure on p. 53 of water dissociating
pH
• Water can dissociate– Into hydronium ions and hydroxide ions
• Changes in the concentration of these ions– Can have a great affect on living organisms
H
Hydroniumion (H3O+)
H
Hydroxideion (OH–)
H
H
H
H
H
H
+ –
+
Figure on p. 53 of water dissociating
• The pH scale and pH values of various aqueous solutions
Incr
easi
ngly
Aci
dic
[H+]
> [
OH
–]
Incr
easi
ngly
Bas
ic[H
+]
< [
OH
–]
Neutral[H+] = [OH–]
Oven cleaner
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
pH Scale
Battery acid
Digestive (stomach) juice, lemon juiceVinegar, beer, wine,colaTomato juice
Black coffee RainwaterUrine
Pure waterHuman blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
Figure 3.8
• The pH scale and pH values of various aqueous solutions
Incr
easi
ngly
Aci
dic
[H+]
> [
OH
–]
Incr
easi
ngly
Bas
ic[H
+]
< [
OH
–]
Neutral[H+] = [OH–]
Oven cleaner
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
pH Scale
Battery acid
Digestive (stomach) juice, lemon juiceVinegar, beer, wine,colaTomato juice
Black coffee RainwaterUrine
Pure waterHuman blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
Figure 3.8
—pH 7.4