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![Page 1: LECTURE - 2 Water & Carbon. Quiz Answers The Carboxyl functional group: The most predominant color on a world map is blue. The Central dogma of.](https://reader035.fdocuments.us/reader035/viewer/2022081513/56649e0a5503460f94af2274/html5/thumbnails/1.jpg)
LECTURE - 2
Water & Carbon
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Quiz Answers
The Carboxyl functional group:
The most predominant color on a world map is blue. The Central dogma of Molecular Biology is:
DNA → RNA → PROTEIN
Epigenetics: The structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states.
The best part of California is the people!
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Outline
Water Structure Important properties
Carbon Structure Important properties Functional Groups
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Water
The molecule that supports all life (as we know it)
• It is the biological medium on Earth• All living organisms require water • Most cells are surrounded by water, and
cells themselves are about 70–95% water
• The abundance of water is the main reason the Earth is habitable
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Water is a polar molecule
Polar covalent bonds allow for extensive hydrogen bonding Polar – the opposite ends have opposite
charges
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Four Important Properties of Water
1. Cohesive behavior2. Ability to moderate temperature3. Expansion upon freezing4. Versatility as a solvent
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#1 - Cohesion
Cohesion Hydrogen bonds hold water molecules
together Adhesion
An attraction between different substances
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Water molecules bind together to form the water column (cohesion)
They also bind to the cell walls to help resist gravity (adhesion)
Example of Cohesion & Adhesion
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#1 - Cohesion
Surface tension Related to cohesion A measure of how hard it is to break the
surface of a liquid
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#2 – Moderation of Temperature Kinetic energy is the energy of motion Heat = the total amount of kinetic
energy due to molecular motion Temperature measures the intensity of
heat due to the average kinetic energy of molecules
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#2 – Moderation of Temperature Measuring temperature
Celsius scale to indicated temperature 0 degrees Celsius is freezing, 100 degrees is
boiling Room Temp is about 20 - 25 degrees Why would most biochemical experiments be
run at 37 degrees? Calorie
The amount of heat it takes to raise the temperature of 1g of water by 1 degree celcius
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#2 – Moderation of Temperature Specific Heat - The amount of heat that
must be absorbed or lost for 1g of substance to change its temperature 1 degree C.
Water has a high specific heat.
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#2 – Moderation of Temperature Water has a High Specific Heat
allows it to minimize temperature fluctuations
Heat is absorbed when hydrogen bonds break Example: Liquid water steam
Heat is released when hydrogen bonds form Water vapor in clouds raindrops Formation of raindrops or ice actually raises the
surrounding air temperature by a slight amount!
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#2 - Moderation of Temperature Oceans stabilize the temperature of the
air. Water absorbs heat from warmer air and
releases stored heat to cooler air Water can absorb or release a large
amount of heat with only a slight change in its own temperature
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#2 – Moderation of Temperature Oceans can absorb heat during the day
and release it back at night while the ocean temp remains relatively constant.
Santa Barbara 73°
Los Angeles(Airport) 75°
Pacific Ocean 68°
Santa Ana 84°
Burbank90°
San Bernardino100°
Palm Springs106°
Riverside 96°
San Diego 72° 40 miles
70s (°F)80s90s100s
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#2 – Moderation of Temperature Evaporation is transformation of a
substance from liquid to gas Heat of vaporization
The heat a liquid must absorb for 1 g to be converted to gas – water has a high heat of vaporization
As a liquid evaporates, its remaining surface cools, a process called evaporative cooling
Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water
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# 3 – Expansion Upon Freezing Ice Floats on Water
As H-bonds stabilize, the resulting crystal becomes less dense.
H-bonds are breaking and re-forming in liquid water, therefore there are more molecules per volume
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#3 – Expansion Upon Freezing
Hydrogen bond
Ice:Hydrogen bonds
are stable
Liquid water:Hydrogen bonds
break and re-form
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#3 – Expansion Upon Freezing Major benefit of Ice floating on water –
Insulation Insulates living organisms under ice pack in
lakes and frozen seas. Snow insulates seeds and roots under
ground in winter.
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#4 – Solvent Properties
Water is a versatile solvent due to its polarity It can easily for hydrogen bonds with other
molecules including ionic compoundsFigure 3.7
Cl Cl
Na
Na
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#4 – Solvent Properties
Large molecules such as proteins can dissolve in water if they have ionic and polar regionsFigure 3.8
+
+
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#4 – Solvent Properties
Hydrophilic - substance that has an affinity for water.
Hydrophobic – substance that does not have an affinity for water.
Some molecules are both.
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#4 – Solvent Properties
Water can disassociate into hydronium and hydroxide ions
2 H2O Hydroxideion (OH)
Hydroniumion (H3O
+)
+
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#4 Solvent Properties: Acids & Bases
The dissociation of water molecules has a great effect on organisms
Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell
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#4 Solvent Properties: Acids & Bases
Acid – donates a proton Increases the number of Hydronium Ions in
an aqueous solution Base –
Accepts a proton Reduces the number of Hydronium Ions in
an aqueous solution
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#4 – Solvent Properties: The pH scale
pH is a measure of the relative concentration of protons. 0 < pH < 7 is an Acid ([H30+] > 10-7M) 7 < pH < 14 is a Base ([H30+] < 10-7M) pH 7 is neutral ([H30+] = [OH-] = 10-7M)
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Figure 3.10pH Scale
Battery acid
Gastric juice, lemon juice
Vinegar, wine,cola
BeerTomato juice
Black coffee
Rainwater
Urine
SalivaPure waterHuman blood, tears
Seawater
Inside of small intestine
Milk of magnesia
Household ammonia
Householdbleach
Oven cleaner
Basicsolution
Neutralsolution
Acidicsolution
0
1
2
3
4
5
6
7
8
9
10
Neutral
[H+] = [OH]In
cre
asin
gly
Basic
[H+]
< [
OH
]
Incre
asin
gly
Acid
ic
[H+]
> [
OH
]
H+ H+
H+
H+H+
H+
H+
H+
OH
OH
H+
OH
H+
OH
OH
OHOH
H+H+
H+
H+
OHOH
OH
OH OHOH
OHH+
11
12
13
14
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#4 – Solvent Properties: Buffers
Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution. They resist a change in pH when a small
amount of acid or base is added to a solution.
Most buffers consist of an acid-base pair that reversibly combines with H+
Buffers work within a specific pH range.
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#4 – Solvent Properties: Buffers Carbonic Acid – contributes to pH
stability in blood and other biological solutions.
H2CO3 is formed when CO2 reacts with water.
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Carbon
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Carbon
The backbone of life Living organisms consist
mostly of carbon-based compounds.
Really good at forming large, complex, and diverse molecules.
Proteins, DNA, carbohydrates, and other molecules - all composed of carbon compounds.
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Carbon
Electron configuration determines the kinds and number of bonds an atom will form with other atoms
Four valence electrons – Four covalent
Allows for the formation of large, complex molecules possible
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Figure 4.3
Name andComment
MolecularFormula
(a) Methane
(b) Ethane
CH4
Ball-and-Stick Model
Space-FillingModel
(c) Ethene (ethylene)
C2H6
C2H4
StructuralFormula
Carbon bonds determine molecular shape
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Diversity of carbon molecules Carbon chains form the skeletons of most organic
molecules Carbon chains vary in length and shapeFigure 4.5
(a) Length
Ethane 1-Butene
(c) Double bond position
2-ButenePropane
(b) Branching (d) Presence of rings
Butane 2-Methylpropane(isobutane)
Cyclohexane Benzene
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Valence Electrons
The electron configuration of carbon gives it covalent compatibility with many different elements
The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules
Figure 4.4
Hydrogen(valence 1)
Oxygen(valence 2)
Nitrogen(valence 3)
Carbon(valence 4)
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Isomers
Compounds with the same molecular formula but different structures and properties
Structural isomers have different covalent arrangements of their atoms (constitutional)
Cis-trans isomers have the same covalent bonds but differ in spatial arrangements
Enantiomers are isomers that are mirror images of each other (they are chiral)
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Isomers – Three typesFigure 4.7 (a) Structural isomers
(b) Cis-trans isomers
(c) Enantiomers
cis isomer: The two Xsare on the same side.
trans isomer: The two Xsare on opposite sides.
CO2HCO2H
CH3
H NH2
L isomer
NH2
CH3
H
D isomer
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Isomers - EnatomersFigure 4.8
Drug
Ibuprofen
Albuterol
Condition EffectiveEnantiomer
IneffectiveEnantiomer
Pain;inflammation
Asthma
S-Ibuprofen R-Ibuprofen
R-Albuterol S-Albuterol
http://www.youtube.com/watch?v=L5QbBYj_zVs
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Functional Groups
The components of organic molecules that are most commonly involved in chemical reactions
The number and arrangement of functional groups give each molecule its unique properties
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The importance of functional groups
CH3
OH
HO
O
CH3
CH3
OH
Estradiol
Testosterone
Female lion
Male lion
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7 most biologically important functional groups
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Figure 4.9a
STRUCTURE
EXAMPLE
Alcohols(Their specificnames usuallyend in -ol.)
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
(may be written HO—)
Ethanol
• Is polar as a resultof the electronsspending moretime near theelectronegativeoxygen atom.
• Can form hydrogenbonds with watermolecules, helpingdissolve organiccompounds suchas sugars.
Hydroxyl
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Figure 4.9b
Carbonyl
STRUCTURE
EXAMPLE
Ketones if the carbonylgroup is within acarbon skeleton
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Aldehydes if the carbonylgroup is at the end of thecarbon skeleton
• A ketone and analdehyde may bestructural isomerswith different properties,as is the case foracetone and propanal.
Acetone
Propanal
• Ketone and aldehydegroups are also foundin sugars, giving riseto two major groupsof sugars: ketoses(containing ketonegroups) and aldoses(containing aldehydegroups).
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Carboxyl
STRUCTURE
EXAMPLE
Carboxylic acids, or organicacids
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Acetic acid
Polar; can form H-bonds
Weak acids; reversible dissociation in H2O
• Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion.
Nonionized Ionized
Figure 4.9c
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Amino
Amines
Glycine
STRUCTURE
EXAMPLE • Acts as a base; canpick up an H+ from thesurrounding solution(water, in livingorganisms):
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
• Found in cells in theionized form with acharge of 1.
Nonionized Ionized
Figure 4.9d
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Sulfhydryl
Thiols
(may bewritten HS—)
STRUCTURE
EXAMPLE • Two sulfhydryl groups canreact, forming a covalentbond. This “cross-linking”helps stabilize proteinstructure.
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
• Cross-linking of cysteinesin hair proteins maintainsthe curliness or straightnessof hair. Straight hair can be“permanently” curled byshaping it around curlersand then breaking andre-forming the cross-linkingbonds.
Cysteine
Figure 4.9e
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Figure 4.9f
Phosphate
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Organic phosphates
Glycerol phosphate
• Contributes negativecharge to the moleculeof which it is a part(2– when at the end ofa molecule, as at left;1– when locatedinternally in a chain ofphosphates).
• Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.
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Figure 4.9g
Methyl
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Methylated compounds
5-Methyl cytidine
• Addition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.
• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.