biol 210 general biology 1
DESCRIPTION
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
![Page 1: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/1.jpg)
Biol 210 General Biology 1
Lecture 2
Review
Chemical Bonds
![Page 2: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/2.jpg)
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
![Page 3: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/3.jpg)
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
![Page 4: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/4.jpg)
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
![Page 5: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/5.jpg)
•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.
![Page 6: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/6.jpg)
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
![Page 7: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/7.jpg)
Covalent Bonds
• Two atoms share one or more pairs of electrons
![Page 8: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/8.jpg)
Covalent Bonds
• Two atoms share one or more pairs of electrons
• Strongest chemical bond
![Page 9: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/9.jpg)
Covalent Bonds
• Two atoms share one or more pairs of electrons
• Strongest chemical bond
• 50-110 kcal/mol
![Page 10: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/10.jpg)
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
![Page 11: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/11.jpg)
Oxygen
• Oxygen has 2 valence electrons• Can share two pairs of electrons• Two O atoms can form 2 covalent bonds
![Page 12: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/12.jpg)
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms
![Page 13: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/13.jpg)
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond
![Page 14: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/14.jpg)
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond• O must bond two H atoms
![Page 15: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/15.jpg)
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
![Page 16: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/16.jpg)
Carbon
• Carbon has a valence of 4 electrons
![Page 17: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/17.jpg)
Carbon
• Carbon has a valence of 4 electrons• Can form 4 covalent bonds
![Page 18: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/18.jpg)
Carbon
• Carbon has a valence of 4 electrons• Can form 4 covalent bonds• Biological molecules are largely carbon-
containing molecules
![Page 19: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/19.jpg)
Carbon
• Carbon has 4 valence electrons• Can form 4 covalent bonds• Biological molecules are largely carbon-containing
molecules• Organic = derived from organisms
![Page 20: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/20.jpg)
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)
![Page 21: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/21.jpg)
H—H
O=O
H—O—H
CH4
![Page 22: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/22.jpg)
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
![Page 23: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/23.jpg)
Ionic Bond
• Covalent bonds result from two atoms sharing electrons
![Page 24: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/24.jpg)
Ionic Bond
• Covalent bonds result from two atoms sharing electrons
• Sometimes one atom “takes” the electron from another atom.
![Page 25: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/25.jpg)
Ionic Bond
• One atom has more protons than electrons = +1
![Page 26: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/26.jpg)
Ionic Bond
• One atom has more protons than electrons = +1• Other atom has one more electron than protons = -
1
![Page 27: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/27.jpg)
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)
![Page 28: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/28.jpg)
Hydrogen Bond
• We have studied two bonding extremes
![Page 29: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/29.jpg)
Hydrogen Bond
• We have studied two bonding extremes• Covalent bond = atoms share electrons
![Page 30: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/30.jpg)
Hydrogen Bond
• We have studied two bonding extremes• Covalent bond = atoms share electrons• Ionic bond = one atom “take”s electrons
![Page 31: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/31.jpg)
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule
![Page 32: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/32.jpg)
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons
![Page 33: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/33.jpg)
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons • Hydrogen nucleus less attractive
![Page 34: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/34.jpg)
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
![Page 35: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/35.jpg)
Hydrogen Bond
• Water = polar molecule
![Page 36: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/36.jpg)
Hydrogen Bond
• Water = polar molecule• Can interact weakly with other polar molecules
![Page 37: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/37.jpg)
Hydrogen Bond
• Water = polar molecule• Can interact weakly with other polar molecules• H-bond 3-7 kcal/mol
![Page 38: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/38.jpg)
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
![Page 39: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/39.jpg)
Predicted BP for water = -76°C
![Page 40: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/40.jpg)
Predicted BP for water = -76°CPredicted MP for water = -87°C
![Page 41: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/41.jpg)
Predicted BP for water = -76°CPredicted MP for water = -87°CTemp. range for liquid water = 11°
![Page 42: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/42.jpg)
Predicted BP for water = -76°CPredicted MP for water = -87°CPredicted temp. range for liquid water = 11°Actual: 0–100°C
![Page 43: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/43.jpg)
Predicted BP for water = -76°CPredicted MP for water = -87°CPredicted temp. range for liquid water = 11°Actual: 0–100°CRationale: H-bonds
![Page 44: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/44.jpg)
Hydrogenbonds
+
+
H
H+
+
–
–
– –
Figure 3.2
•The polarity of water molecules
![Page 45: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/45.jpg)
Hydrogenbonds
+
+
H
H+
+
–
–
– –
Figure 3.2
•The polarity of water molecules
–Allows them to form hydrogen bonds with each other
![Page 46: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/46.jpg)
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
![Page 47: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/47.jpg)
• 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
![Page 48: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/48.jpg)
• 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
![Page 49: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/49.jpg)
• 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
![Page 50: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/50.jpg)
• 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
![Page 51: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/51.jpg)
pH
• Water can dissociate
H
Hydroniumion (H3O+)
H
Hydroxideion (OH–)
H
H
H
H
H
H
+ –
+
Figure on p. 53 of water dissociating
![Page 52: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/52.jpg)
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
![Page 53: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/53.jpg)
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
![Page 54: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/54.jpg)
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
![Page 55: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/55.jpg)
• 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
![Page 56: Biol 210 General Biology 1](https://reader036.vdocument.in/reader036/viewer/2022062308/568132aa550346895d9951ae/html5/thumbnails/56.jpg)
• 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