Download Lecture 3 - Water and Carbon

Lecture 3: Water and carbon,
the secrets of life
In this lecture…
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Heat, temperature and energy
The four emergent properties of water
Acids and bases
Carbon skeletons
Hydrocarbons
Isomers
First, a little aside about heat and
energy
• Energy: the ability to do work
• Two main categories of energy: potential energy and
kinetic energy
• Energy cannot be created nor destroyed – 2nd law of
thermodynamics – it can only be converted
To transform one type of energy into another, you must input even more energy!
Potential energy is energy
that is not doing anything
right now, but has the
stored energy to be able to
do it in the future
Kinetic energy is the
energy in movement right
now
Chemical potential
energy is the
energy stored in
chemical bonds
Radiant energy is
in the form of
electromagnetic
radiation (light, UV,
gamma rays)
Gravitational
potential energy is
the ability of
something to fall
due to gravity
Thermal energy is
in the form of
molecules vibrating
Tracing energy transformations
Sunlight  Ancient ferns  Oil/Gas  Cars
Kinetic solar
energy in
photons
Potential chemical
energy in the bonds of
glucose
CO2 + H2O + photons
Potential
chemical
energy in the
bonds of oil
Kinetic
energy in
the car tires
moving
C8H12
CO2 + H2O
C6H12O6
Photosynthesis
Heat and
pressure
Chemical reaction
using the kinetic
energy in photons to
create potential
chemical energy
Chemical reaction
using earth’s heat
and pressure to
convert the chemical
energy of glucose
into the chemical
energy of oil
Spark plug
Combustion reaction
using electricity to
convert the chemical
energy of oil into the
kinetic energy of
moving tires
A little bit about heat and temperature…
• Heat is a measure of the total amount of kinetic
energy due to molecular motion
• Temperature measures the intensity of heat due
to the average kinetic energy of molecules
• A calorie (cal) is the amount of heat required to
raise the temperature of 1 g of water by 1°C
• The “calories” on food packages are actually
kilocalories (kcal), where 1 kcal = 1,000 cal
Water is crucial to life on Earth!!
Water is the biological medium on Earth
All living organisms require water more than any
other substance
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
Why water?
Four properties of water:
Water is a
versatile
solvent
Water sticks
to itself
(cohesion)
Water
moderates
temperature
Water
expands
upon
freezing
Water’s secret: Hydrogen bonding
• All of water’s properties come from the
fact that it:
– Is polar
– Can hydrogen bond because of its polarity
Water is a versatile solvent
• In chemistry, ‘like dissolves like’
• Water is a polar molecule
• Polar molecules can dissolve other polar
molecules
• Most molecules in biology are polar enough that
water can solvate them
A protein solvated by water
• A solution is a liquid that is a homogeneous
mixture of substances
• A solvent is the dissolving agent of a solution
• The solute is the substance that is dissolved
• An aqueous solution is one in which water is
the solvent
• Most biochemical reactions occur in water
• Chemical reactions depend on collisions of
molecules and therefore on the concentration of
solutes in an aqueous solution
Water and cohesion
• Collectively, hydrogen bonds hold water
molecules together, a phenomenon called
cohesion
• Cohesion helps the transport of water
against gravity in plants
• Surface tension is a measure of how
hard it is to break the surface of a liquid
• Surface tension is related to cohesion
Cohesion allows plants to ‘drink’
Water and temperature moderation
• 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
• The specific heat of a substance is the amount of heat
that must be absorbed or lost for 1 g of that substance to
change its temperature by 1ºC
• The specific heat of water is 1 cal/g/ºC
• Water resists changing its temperature because of its high
specific heat
• Water’s high specific heat can be traced to
hydrogen bonding
– Heat is absorbed when hydrogen bonds break
(thermal energy converted to chemical energy)
– Heat is released when hydrogen bonds form
(chemical potential energy converted into thermal energy)
• The high specific heat of water minimizes
temperature fluctuations to within limits that
permit life
Figure 3.5
Los Angeles
(Airport) 75°
70s (°F)
80s
San Bernardino
100°
Riverside 96°
Santa Ana
Palm Springs
84°
106°
Burbank
90°
Santa Barbara 73°
Pacific Ocean 68°
90s
100s
San Diego 72°
40 miles
Water and freezing
• Water’s hydrogen bonding forces it to create
orderly, angular bonds when it freezes
• These bonds force the water molecules further
apart than they are when liquid
• Ice floats in liquid water because it is less dense
– fewer water molecules/cm3
• Water reaches its greatest density at 4°C
• If ice sank, all bodies of water would eventually
freeze solid, making life impossible on Earth
Liquid water: transient
hydrogen bonds
Ice: stable hydrogen bonds
Shrimp??
• A hydrophilic substance is one that has an
affinity for water
– A hydrophilic molecule has lots of polar regions
• A hydrophobic substance is one that does not
have an affinity for water
– A hydrophobic molecule has lots of nonpolar regions
• (A colloid is a stable suspension of fine
particles in a liquid)
‘Hydrophilic’ and ‘hydrophobic’ are IMPORTANT VOCABULARY WORDS!!!!
The structure of vegetable oil
Oil molecules are hydrophobic because they have mostly
nonpolar bonds
Acids, bases, and life
• An acid is any substance that increases the H+
concentration of a solution, or reduces the OHconcentration
– Another definition: acids accept electron pairs
• A base is any substance that reduces the H+
concentration of a solution, or increases the OHconcentration
– Bases donate electron pairs
H+ means hydrogen
ion, a hydrogen
minus its electron
H+ is therefore just a
single proton! ‘H+’ is
interchangeable with
‘proton’
The pH scale
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The pH scale goes from 1-14
Acidic solutions have pH values less than 7
Basic solutions have pH values greater than 7
Pure water has a value of 7
Most biological fluids have pH values in the
range of 6 to 8
– Stomach acid is at pH 2
– Humans can’t tolerate large changes in pH, but some
plants and bacteria can!
Buffers
• The internal pH of most living cells must
remain close to pH 7
• Buffers are substances that minimize
changes in concentrations of H+ and OH–
in a solution
• Most buffers consist of an acid-base pair
that reversibly combines with H+
Figure 3.10
H+
H+
 H+
H+ OH
+

OH H H+
+
H H+
Acidic
solution
Increasingly Acidic
[H+] > [OH]
pH Scale
0
1
Battery acid
2
Gastric juice, lemon juice
3
Vinegar, wine,
cola
4
Tomato juice
Beer
Black coffee
5
6
Neutral
solution
OH
OH
OH H+ OH

OH OH
OH
+
H
Basic
solution
Neutral
[H+] = [OH]
7
8
Increasingly Basic
[H+] < [OH]
OH
OH
H+ H+ OH

OH OH +
H+ H+ H
Rainwater
Urine
Saliva
Pure water
Human blood, tears
Seawater
Inside of small intestine
9
10
Milk of magnesia
11
Household ammonia
12
13
Household
bleach
Oven cleaner
14
Acidification: A Threat to Water Quality
• Human activities such as burning fossil
fuels threaten water quality
• CO2 is the main product of fossil fuel
combustion
• About 25% of human-generated CO2 is
absorbed by the oceans
• CO2 dissolved in sea water forms carbonic
acid; this process is called ocean
acidification
Figure 3.11
CO2
CO2 + H2O
H2CO3
H2CO3
H+ + HCO3
H+ + CO32
CO32 + Ca2+
HCO3
CaCO3
Figure 3.12
• As seawater acidifies, H+ ions combine with carbonate
ions to produce bicarbonate
• Carbonate is required for calcification (production of
calcium carbonate) by many marine organisms,
including reef-building corals
• The burning of fossil fuels is also a major source of sulfur
oxides and nitrogen oxides
• These compounds react with water in the air to form
strong acids that fall in rain or snow
• Acid precipitation is rain, fog, or snow with a pH lower
than 5.2
• Acid precipitation damages life in lakes and streams and
changes soil chemistry on land
Vocabulary
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Hydrophilic, hydrophobic
Potential energy, kinetic energy
Buffer
Acid, base
Heat, temperature
Calorie, kilocalorie
Astrobiology
Carbon: the backbone of life
• Living things are composed largely of carbon
• Proteins, DNA, and carbohydrates all use
carbon as their base
• Organic chemistry (o-chem) is the study of the
chemistry of carbon
– An organic molecule contains carbon
– Most organic molecules have hydrogen as well as
carbon
The chemistry of carbon
• Carbon has four valence electrons, and so can
have up to four bonds
• Carbon can have single bonds, double bonds, etc.
• Carbon’s ability to have four bonds lets it create
large, complex molecules
• The four bonds have very exact angles and
positions
• Carbon most frequently bonds with hydrogen,
nitrogen, oxygen, and itself
Missing four of
the eight
electrons it
needs to be
‘happy’
Figure 4.3
Name and
Comment
Molecular
Formula
(a) Methane
CH4
(b) Ethane
C2H6
(c) Ethene
(ethylene)
C2H4
Structural
Formula
Ball-andStick Model
Space-Filling
Model
Figure 4.5
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
Hydrocarbons
• Hydrocarbons are organic molecules consisting
of only carbon and hydrogen
• Many organic molecules, such as fats and oil
have hydrocarbon components
• Hydrocarbons can undergo reactions that
release a large amount of energy
• Gasoline is a hydrocarbon
Figure 4.6
Hydrocarbons in human fat
Nucleus
Fat droplets
10 m
(a) Part of a human adipose cell
(b) A fat molecule
• Isomers are compounds with the same
molecular formula but different structures and
properties
– Structural isomers have different covalent
arrangements of their atoms
– Cis-trans isomers have the same covalent
bonds but differ in spatial arrangements
– Enantiomers are isomers that are mirror
images of each other
Figure 4.7
(a) Structural isomers
(b) Cis-trans isomers
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
(c) Enantiomers
CO2H
CO2H
H
NH2
CH3
L isomer
NH2
H
CH3
D isomer
Enantiomers and pharmaceuticals
• Enantiomers are important in the pharmaceutical
industry
• Two enantiomers of a drug may have different effects
• Usually only one isomer is biologically active
• Differing effects of enantiomers demonstrate that
organisms are sensitive to even subtle variations in
molecules
Figure 4.8
Drug
Condition
Ibuprofen
Pain;
inflammation
Albuterol
Effective
Enantiomer
Ineffective
Enantiomer
S-Ibuprofen
R-Ibuprofen
R-Albuterol
S-Albuterol
Asthma
Functional Groups
• In the place of hydrogen, distinct chemical
functional groups groups can bond carbon
• The properties of an organic molecule depends
on the carbon skeleton and its functional groups
– Functional groups are 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
Figure 4.UN02
The same carbon skeleton, different functional groups, very
different effects
Methyl group
Estradiol
Testosterone
Hydroxyl group
Carbonyl group
There are only seven main functional
groups:
• The seven functional groups that are most
important in the chemistry of life:
–
–
–
–
–
–
–
Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
Methyl group
Figure 4.9a
Hydroxyl
STRUCTURE
(may be written
HO—)
EXAMPLE
Ethanol
Alcohols
(Their specific
names usually
end in -ol.)
NAME OF
COMPOUND
• Is polar as a result
of the electrons
spending more
time near the
electronegative
oxygen atom.
FUNCTIONAL
PROPERTIES
• Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.
Figure 4.9b
Carbonyl
STRUCTURE
Ketones if the carbonyl
group is within a
carbon skeleton
NAME OF
COMPOUND
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton
EXAMPLE
Acetone
Propanal
• A ketone and an
aldehyde may be
structural isomers
with different properties,
as is the case for
acetone and propanal.
• Ketone and aldehyde
groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
groups).
FUNCTIONAL
PROPERTIES
Figure 4.9c
Carboxyl
STRUCTURE
Carboxylic acids, or organic
acids
NAME OF
COMPOUND
EXAMPLE
• Acts as an acid; can
FUNCTIONAL
PROPERTIES
donate an H+ because the
covalent bond between
oxygen and hydrogen is so
polar:
Acetic acid
Nonionized
Ionized
• Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion.
Figure 4.9d
Amino
STRUCTURE
Amines
NAME OF
COMPOUND
EXAMPLE
•
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
Glycine
Nonionized
•
Ionized
Found in cells in the
ionized form with a
charge of 1.
Figure 4.9e
Sulfhydryl
STRUCTURE
Thiols
NAME OF
COMPOUND
•
Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
FUNCTIONAL
PROPERTIES
•
Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
(may be
written HS—)
EXAMPLE
Cysteine
Figure 4.9f
Phosphate
STRUCTURE
Organic phosphates
EXAMPLE
•
FUNCTIONAL
Contributes negative
charge to the molecule PROPERTIES
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
•
Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.
Glycerol phosphate
NAME OF
COMPOUND
Figure 4.9g
Methyl
STRUCTURE
Methylated compounds
EXAMPLE
•
Addition of a methyl group FUNCTIONAL
PROPERTIES
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
•
Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine
NAME OF
COMPOUND
ATP, the (potential chemical) energy
of the cell
• One phosphate molecule, adenosine triphosphate
(ATP), is the primary energy-transferring molecule in
the cell
• ATP consists of an organic molecule called
adenosine attached to a string of three phosphate
groups
A closer look at ATP
High-energy phosphate bonds
ATP’s chemical energy
• ATP is hydrolyzed to break off a phosphate
functional group
• The potential energy stored in the chemical
bond of the phosphate can be coupled to other
chemical reactions
– This chemical energy acts as the catalyst in other
biochemical reactions
The 3D shape of organic molecules
• The 3D shape of
organic molecules
determines their
ultimate function
• A molecule’s shape
is determined by
the positions of its
atoms’ valence
orbitals
Biological molecules and shape
• Biological molecules recognize and
interact with each other with a specificity
based on molecular shape
• ‘Lock and key’ model
– A lock will only take a key of a specific shape
• Molecules with similar shapes can have
similar biological effects
Astrobiology: The study of life on other
planets
• Can carbon be replaced?
– Silicon has a similar reactivity to carbon
• Have difficulty forming double and triple bonds
– Phosphorus can also form long-chain
molecules
• Unstable and easily break apart
• Can water be replaced?
– Liquid methane and liquid ammonia are also
candidates to support life
Organic molecules on other planets
• Organic molecules commonly form in the
dust and gas clouds that form planets
• Complex molecules form as functional
groups bond together
Ethyl formate (C2H5OCHO).
n-Propyl cyanide (C3H7CN
Vocabulary
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Organic molecule
Enantiomer
Isomer
Structural Isomer
Geometric isomer
Functional group
Hydrocarbon
ATP
Questions??