Download 1 Chapter 3: Chemistry of Water Polar covalent bonds within water

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Chapter 3:
Chemistry of Water
1. Polar covalent bonds within water
-Between slightly positive hydrogen atoms and slightly negative oxygen atom
2. Hydrogen bonds between water molecules
-Hydrogen bonds are electrical attractions between the hydrogen atom of one water
molecule and the oxygen atom of a nearby water molecule
-they create a structural organization of water that leads to its emergent properties
-weaker than polar covalent bonds
*One water molecule can form 4 hydrogen bonds
3. “Bent” geometry
O
H
H
4. Polar molecules
-Water molecules have a partial charge
-Oxygen has a partially negative charge (δ—) and hydrogen has a partially positive
charge (δ+) because oxygen is more electronegative (which means it attracts electrons
more)
δ+
INTER-molecular
INTRA-molecular
attractions
δ—
attractions
Polar Covalent bond
Hydrogen bond
-between hydrogen and
oxygen of the same atom
-between hydrogen
and oxygen of
different atoms
δ+
δ
δ+
—
= oxygen
= hydrogen
δ+
5. An attraction may exist between water molecules – depending on temperature
-At higher temperatures, molecules are farther apart
-When temperature decreases, kinetic energy and speed decrease, so entropy
decreases (which means molecules are more organized and closer together)
-As this happens, water goes from a gas to a liquid to a solid
Properties of Water
1) Cohesion/ Adhesion
2) Specific heat
3) Heat of vaporization
4) Less dense as a solid
5) Universal solvent
6) Neutral pH
*Explain each property of water and relate to its importance in biology
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Cohesion and Adhesion
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Cohesion- water molecules stick to each other
-They stick to each other due to the constant of forming and reforming of hydrogen
bonds that hold the molecules close together.
Adhesion- water molecules stick to other things
Capillary tubes:
-they have a tiny diameter: water molecules are smushed together in a small space 
they stick to each other better
-xylem = water conducting tissue
Importance in Biology:
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Cohesion and adhesion help transport water upward through plants (to the leaves)
-Water hits the ground and moves to the roots by diffusion
-Water moves up the roots and is pulled up through the stems to the leaves because of
their attractions to each other and the stem walls. This is called capillary action.
-This allows plants to produce glucose and oxygen in a process called photosynthesis.
Transpiration pull is the main way water travels to the leaves though.
-This process is: As water is lost in the stem, it’s pulled up through the roots. This allows
there to be a constant flow of water.
Cohesion and adhesion are the reason for water’s high surface tension
-benefits organisms who can walk on the surface of water
-soap breaks surface tension
Specific Heat and Heat of Vaporization
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Heat is a measure of the total amount of kinetic energy
Temperature measures the average amount of kinetic energy
-Temperature is measured using a Celsius scale
-Water boils at 100ºC and freezes at 0ºC
-A calorie (cal) is the amount of heat energy it takes to raise 1 g of water 1ºC
-1 Joule = .239 cal ; 1 cal = 4.184 J
-A kilocalorie (kcal) is 1,000 calories, the amount of heat energy it takes to raise 1 kg of
water 1ºC
Specific heat – amount of heat required to change the temperature of 1 gram of water by 1ºC
**Involves change in temperature
-It takes a lot of energy to change the temperature of water (exactly 1 cal)
Because a lot of energy must be absorbed to break hydrogen bonds, and a lot of
energy is released when forming hydrogen bonds
-Water’s specific heat is very HIGH  water is resistant to temperature change
Vaporization or evaporation occurs when molecules of a liquid with sufficient kinetic overcome
their attraction to other molecules and escape into the air as gas
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Heat of vaporization – amount of energy required to convert 1 gram of water to 1 gram of
water vapor
**Involves change in phase
-Takes a lot of energy to change phase (exactly 4.18 J/g/ ºC or 580 cal/g/ºC)
Because a lot of heat must be absorbed to break hydrogen bonds, allowing
water molecules to escape into the gas phase
-Water’s heat of vaporization is very HIGH  it’s very resistant to phase change
Importance in Biology:
 Specific heat moderates temperature:
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-In coastal areas, water and land temperatures are more moderate and mild than inland
areas
For aquatic organisms, water temperature is usually constant:
-they don’t have to adapt to wildly changing temperatures (like terrestrial animals do)
-they have less coping mechanisms
Evaporative cooling helps protect terrestrial organisms from overheating and contributes to the
stability of temperatures in lakes and ponds
-As a liquid vaporizes, the surface left behind loses the kinetic energy of the escaping
molecules, cooling it down
Water takes a long time to evaporate because of its high heat of vaporization
**Water-based organisms are resistant to evaporation
-Large bodies of water like the ocean do not evaporate
-When water finally does evaporate, it takes away heat from its surroundings;
conversely, when water condenses and it rains, it releases heat to its surroundings
Less Dense as a Solid
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As water freezes it expands  Hydrogen bonds pushed apart, creating a fixed crystalline
structure. The INTER-molecular attractions are stronger and more stable, creating more space.
So ice floats.
Importance in Biology

Floating ice insulates the liquid water below, preventing it from freezing and allowing life to
exist under the frozen surface.
COLD AIR
November
WARM AIR
Ice insulates the
pond, allowing life
to exist under the
surface.
COOL AIR
colder
warmer
October
Ice melts  Colder water sinks
and warmer water rises
colder
warmer
March
-This is called SPRING
OVERTURN. It recirculates nutrients.
The warm water at the surface becomes
colder and the bottom warms up  Colder
water sinks and warmer water rises
-This is called FALL OVERTURN. It
also re-circulates nutrients. ©SarahStudyGuides
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Change
in phase
Temperature
Change
in phase
ΔT
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Change in temperature = increases the average kinetic
energy of molecules (increases speed)
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Change in phase = disrupts hydrogen bonds
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But the structure of water never changes because
covalent bonds are very strong
ΔT
ΔT
Time
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Cellular Respiration:
C6H12C6 + O2  CO2 + H2O + ATP (energy)
-Fish get oxygen from underwater plants, not by breaking down water molecules.
Universal Solvent
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Water is the solvent in an aqueous solution
-A solution is a liquid homogeneous mixture of 2 or more substances
-The solvent is the dissolving agent and the solute is the substance that is dissolved
Hydration shell: the water molecules surround and break up the solute molecules
-This happens because the positive and negative regions of water molecules are
attracted to oppositely charged ions or partially charged regions of polar molecules
-for example: NaCl dissolves in water.
-Water molecules surround the NaCl molecules the slightly negative oxygen
atoms are attracted to the positive Na atoms, while the slightly positive hydrogen
atoms are attracted to the negative Cl atoms  this pulls the NaCl molecules apart
“Like dissolves like”
-Polar solvents dissolve polar solutes and ionic solutes
-Nonpolar solvents dissolve nonpolar solutes
-This is why oil (nonpolar) and water (polar) don’t mix
Hydrophilic = has an affinity for water due to electrical attractions and hydrogen bonding
-Polar and ionic substances are hydrophilic
-Large hydrophilic substances may not dissolve, but become suspended in an aqueous
solution forming a mixture called a colloid
Hydrophobic = does not easily mix with or dissolve in water
Importance in Biology
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Nonpolar and polar interactions help transport nutrients
-Nutrients diffuse across cell membranes
Neutral pH
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A water molecule can dissociate into a hydrogen ion, H+, and a hydroxide ion, OH–.
-In water, the concentrations of [H+] to [OH–] are the same = 1 x 10–7
When acids or bases dissolve in water, the H+ and OH– balance shifts.
-Acids donate H+ ions
-Bases accept H+ ions add OH– ions
An increase in [H+] results in a decrease in [OH–] (and vice versa)
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Water has a neutral pH and a pOH of 7
-Because cells are mostly water, most cells have an internal pH close to 7.
-The difference between each pH is a tenfold difference (For example: the difference
between 2 and 3 is 10 while the difference between 2 and 4 is 100)
Importance in Biology
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Keeps cells functioning at a neutral pH
-This is one of the reasons why most body fluids are around 7
Buffers are chemicals that prevent pH from changing too much
-Buffers may be acid-base pairs which accept excess H+ ions or donate H+ ions when H+
concentration decreases
-enzymes are very pH sensitive, so the pH must be constant
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Chapter 4
Organic chemistry is the study of carbon compounds.
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Compounds on can either be inorganic or organic. If it’s organic, it contains carbon and involves
living things and often H and O as well.
Before, chemists couldn’t synthesize the complex molecules found in living organisms, so they
believed that life did not involve physical and chemical laws, a belief called vitalism.
Mechanism, which organic chemistry is based on, holds that physical and chemical explanations
account for all natural life.
The Miller Urey Experiment
-It was designed to test the Halding hypothesis (Halding’s hypothesis: the atmosphere
contains hydrogen, not oxygen)
-They found that you can take inorganic molecules and get organic molecules (contain
H, C, O, and N)
-This is an example of molecular evolution, science as a process, and science,
technology, and science
Chemistry of Carbon
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Has 4 valence electrons (=outermost energy level)
.
.C. .
Its electron configuration:
1s22s22p2
This electron
configuration allows
LIKE:
carbon to form 4
bonds with other
atoms. This is called
carbon’s tetravelence.
H
H C H
H
Methane:
4 single nonpolar
covalent bonds,
symmetrical,
tetrahedral shape
It exists as a gas
because it’s not
attracted to itself.
Carbon atoms can form diverse molecules by bonding to four other atoms.
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Carbon has 4 valence electrons, so it can form at most 4 covalent bonds. This tetravalence
allows the formation of large, complex, diverse molecules.
Carbon can form single, double, or triple covalent bonds.
-4 single bonds around carbon creates a tetrahedral shape.
-A double bond between carbons leads to a flat molecule.
Carbon can bond with other elements and other carbons  forms short or long chains,
branches, and rings
Carbon skeletons can vary in:
1) Length
2) Branching
3) Placement of double bonds
4) Location of atoms of other elements
Molecular Diversity Arising from Carbon Skeleton Variation
Hydrocarbons
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Hydrocarbons consist of only carbon and hydrogen
The nonpolar C – H bonds in hydrocarbon chains result in their hydrophobic properties
-Many cells have hydrocarbon regions, like the hydrophobic fatty acid tails
Hydrocarbons can undergo reactions that release a large amount of energy.
-In fats, hydrocarbons help cells store fat molecules as a reserve. The fat tails can be
broken down to provide energy.
Isomers
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Isomers are compounds with the same molecular formula but different structures and
properties
Structural isomers have different covalent arrangements of their atoms
-For example: C6H12O6 is the molecular formula for glucose, fructose, and galactose.
Glucose and galactose are hexagons, but fructose is a pentagon and is sweeter than the others.
Geometric isomers have the same covalent arrangements but differ in spacial arrangements around a
Carbon-Carbon double bond
-Always around a C = C bond
-A cis isomer has the same atoms attached to double-bonded carbons on the same side of the
double bond (see figure 4.7 in the book)
-A trans isomer has these atoms on opposite sides of the double bond.
Enantiomers are isomers that are mirror images of each other around an asymmetrical carbon
-An asymmetrical carbon is a carbon that is covalently bonded to four kinds of atoms or groups
of atoms, whose arrangement can result in mirror images
-They’re left and right handed versions of each other and can differ greatly in their biological
activity
-For example: Our hands are mirror images of each other.2 isomers are designated the L and D
isomers L for the left hand, D for the right hand. Enantiomers can’t be superimposed on each
other.
Characteristic chemical groups help control how biological molecules function
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In an organic molecule, the chemical groups that attach to the carbon skeleton are essential to
the distinctive properties of the molecule
The Chemical Groups Most Important in the Process of Life
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Different chemical groups affect the molecules shape  This affects function!!
*So these important chemical groups are called functional groups
For example: sex hormones are similar in shape, but different in function.
-Both are steroids, organic molecules in the form of 4 fused rings.
-They only differ in the chemical groups attached to the rings.
-The body takes in cholesterol, which binds to the hormones.
Other examples = enzymes and antibodies. Their shape is essential because they have to fit into
special binding spots.
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The 7 most important chemical groups are listed below. The 1st 6 act as functional groups and
are hydrophilic, increasing solubility of compounds in water. But methyl is unreactive.
Structure
Name of Compound
Hydroxyl
Oxygen and hydrogen (–OH )
Alcohols (names usually end in –ol)
Carbonyl
Carbon double bonded to an oxygen
Aldehyde if carbonyl group is at the
end of the skeleton
CO
Ketone if it’s in the middle
Carboxyl
Carbon double bonded to an oxygen
and bonded to an –OH group
–COOH
Amino
Sulfhydrl
A nitrogen atom bonded to 2
hydrogens
Carboxylic acids or organic acids
They tend to release H+, becoming
a carboxylate ion (–COO- )
Amines
–NH2
Can act as bases, picking up a
hydrogen ion becoming –NH3 +
A sulfur atom bonded to a hydrogen
Thiols
–SH
Phosphate
A phosphorus atom is bonded to 4
oxygen atoms: on oxygen is bonded to
the carbon skeleton, 2 oxygens carry
negative charges
Organic phosphates
–OPO3 2-Methyl
A carbon bonded to three hydrogens
–CH3
Methylated compounds may have
their function modified due to the
addition of the methyl group
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Chapter 5
Organic compounds:
1)
2)
3)
4)
Carbohydrates
Lipids
Proteins
Nucleic acids
Macromolecules
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Carbohydrates, proteins, and nucleic acids are all macromolecules
Polymers are chain-like molecules formed from the linking together of many similar or identical
small molecules called monomers.
Monomers are the repeating units that serve as the building blocks of a polymer.
The Synthesis and Breakdown of Polymers
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Condensation/dehydration reaction: the reaction in which 2 molecules are covalently bonded to
each other through loss of a water molecule
-monomers are connected through dehydration reactions
-One monomer contributes a hydroxyl group (—OH) and the other provides a hydrogen (—H)
-Enzymes are specialized macromolecules that catalyze both dehydration reactions and
hydrolysis.
Hydrolysis: a process that breaks bond between monomers by adding a water molecule
-it’s the reverse of dehydration reactions
-A hydrogen from the water molecule attaches to one monomer, and the hydroxyl group
attaches to the other monomer
-For example: digestion
-organic material in our food is broken down, with the help of enzymes, through
hydrolysis
Carbohydrates
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Functions of carbohydrates:
1) Quick energy (4-5 calories per gram)
2) Structure and support (cellulose and chitin)
Empirical formula for all carbohydrates= CH2O
-literally a carbon + a water molecule  a hydrated carbon molecule  a carbohydrate
-All carbohydrates contain C, H, and O
Sugars may be aldoses or ketoses, depending on the location of the carbonyl group.
-Aldoses = aldehyde sugars = carbonyl group on the end of the molecule
-example: glucose and galactose
-Ketoses = ketone sugars = carbonyl group in the middle of the molecule
-example: fructose
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Sugars many also be classified according to the length of their carbon skeletons.
-The size of the carbon skeleton ranges from 3 to 7 sugars, with hexoses (C6H12O6 = glucose,
fructose, galactose), trioses, and pentoses found most commonly.
-Even though a fructose molecule has 5 sides, it is still a hexose because it has 6 carbons
Sugar molecules may be enantiomers due to the spatial arrangements of parts around asymmetrical
carbons (like glucose and galactose- see figure 5.3)
Most carbons form rings because it’s the most stable configuration
-Carbons are numbered 1 through 6: these numbers refer to their location
1) Monosaccharides
C6H12O6
o
Glucose
o
Fructose
o
Galactose
*galactose is never found by itself
-Same molecular formula, but different structural formulas  they’re structural isomers
-Glucose= major source of nutrition for cells
-It is broken down to yield energy in cellular respiration
2) Disaccharides
C12H22O11
o Maltose = glucose + glucose
o Sucrose = glucose + fructose
o Lactose = glucose + galactose
*Condensation/ Dehydration reactions:
-A glycoside linkage is a covalent bond between any 2 monosaccharides.
-Glycoside linkages form through dehydration reactions, when a water molecule is
removed (hydroxyl group is removed from one monosaccharide and a hydrogen is
removed from the other)
-Glycoside linkages form between different carbons depending on the monosaccharide:
-Glucose + glucose forms 1-4 glycoside linkages. (This means that Carbon 1 from
the 1st glucose is bonded to Carbon 4 from the other)
-Fructose + glucose forms 1-2 glycoside linkages
3) Polysaccharides
Polysaccharides are storage or structural macromolecules made from a few hundred to a few
thousand monosaccharides. They’re polymers of glucose.
a. Starch = amylose
-unbranched
*found in plants
-1-4 alpha linkages: bonds are below the plane of the molecule
-We have enzymes that can digest alpha linkages
-These linkages give starch a helical shape
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-Starch doesn’t dissolve in water. When you cook potatoes or pasta, they get soft
because you’re breaking glycoside bonds and getting the molecules to uncoil.
b. Cellulose
-1-4 beta linkages: bonds are alternative above the plane of the molecule
-So 1-4 linkages in amylose and cellulose have the same composition, but the
configuration of the ring form of glucose and the resulting geometry of the
glycosidic bonds are different
*We cannot digest cellulose because we do not have the enzymes needed to break
down cellulose
-Enzymes must fit their substrate, so different enzymes break down starch and
cellulose. We don’t have enzymes that can break down beta linkages.
-Only a few organisms (some microbes and fungi) have enzymes that can digest
cellulose.
-Cows have enzymes from prokaryotes and bacteria that help them digest
cellulose. Bacteria make vitamin K that helps break it down.
-Foods with cellulose include fruits and vegetables – have natural sugars,
provide fiber in our diet, and fill you up more with fewer calories.
*Cellulose is the major component plant cell walls.
-Hydrogen bonds between hydroxyl groups hold parallel cellulose molecules
together to form strong microfibrils.
-It’s the most abundant organic compound on Earth
c. Glycogen
-highly branched and complex
-Found in animals (often called animal starch)
-it’s stored in liver and muscle tissue as quick energy that’s readily available
*Short term energy storage
d. Amylopectin
-branched form of starch
-found in plants
-it has alpha linkages – we can digest it
e. Chitin
-structural polysaccharide formed from glucose monomers with a nitrogencontaining group
-provides structure and support
-forms the exoskeleton of arthropods and the cell walls of many fungi
-We can’t break it down or get nutrients from it because it also has beta linkages
Lipids
-All lipids are hydrophobic
-long term storage of energy
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-Lipids are a more condensed and packed way to store energy, and they have more categories
 important to animals who are always on the move
-provides 9-10 cal per gram
-has the elements C, H, and O
-mostly consist of hydrocarbons
1) Triglycerides
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Glycerol + 3 Fatty acids  Triglyceride + 3H2O
-3 ester linkages = bond between glycerol and fatty acid
-This is a dehydration reaction: loss of a water molecule
-The carbonoxyl end of the fatty acid loses an – OH. The glycerol loses an – H.
-Fatty acids- consists of a long hydrocarbon chain with a carboxyl group at one end
Fats are hydrophobic because the fatty acid chains are nonpolar
-The nonpolar hydrocarbons make it nonpolar
Unsaturated fats:
-has double bonds
-fewer hydrogens per carbon
-healthy
-liquids at room temperature
-the cis double bonds create a kink in the hydrocarbon chain and prevents fat
molecules that contain unsaturated fatty acids from packing closely together
and becoming solidified and fixed
-The fats of fish and plants are generally unsaturated and are called oils
-examples: vegetable, olive, peanut, sunflower, and corn oils
Saturated fats:
-only have single bonds
-unhealthy
-increases blood pressure and leads to heart disease
-solids at room temperature
-from animals
o Trans fats are made in the process of hydrogenation: converting from unsaturated to
saturated fats to make the molecules solid
-extremely unhealthy and leads to heart disease
-example: oreos
Functions of fats:
1) Excellent energy storage molecules
-Contains 2x the energy reserves of carbohydrates
2) Cushions organs and insulates the body
-example: adipose tissue, which is made of fat storage cells
2) Phospholipids
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Phospholipids consist of a glycerol linked to 2 fatty acids and a negatively charged phosphate
group, to which other small molecules are attached.
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Insoluble in water:
-phosphate head = polar
-phosphate group
-carries a large negative charge
-hydrophilic
-fatty acid tails tails = nonpolar
-fatty acids
-hydrophobic
 Function: STRUCTURE- they are the primary component in cell membranes:
-form the phospholipid bilayer
-regulates the types of material that move in and out of cells
-keeps animal cells flexible
Extacellular fluid =H20 outside of cell
nucleus
cell membrane
Phospholipid
Bilayer
cytoplasm
Hydrophilic head
Hydrophobic tails
Cell cytoplasm = H20 inside of cell
The hydrophilic head turns outward towards
water. The hydrophobic tails turn inward
away from water.
3) Steroids
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4 fused carbon rings with attached groups
-Have a totally different structure – they’re only classified as lipids because of their
insolubility
-Typically come from animals
Function: Many are hormones or pre-cursors to hormones
Examples: cholesterol is an important steroid that is a common component of animal cell
membranes.
-It is a pre-cursor for other steroids, including estrogen and testosterone. Cholesterol
molecules are modified to form sex hormones and can act as signaling molecules.
-Heart disease: too much cholesterol can lead to narrowed arteries and blocked blood
vessels, increasing blood pressure  This causes heart disease and atherosclerosis
-Structure: cholesterol increases the fluidity of cell membranes
Are found in:
-Cholesterol - cell membranes
-Hormones – reproductive organs
Proteins
-Contain carbon, hydrogen, oxygen, and nitrogen (*carbs and lipids don’t have nitrogen)
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Variety of Functions
1) Structural – provides structure and support.
-Keratin is the protein of hair, fur, claws, beak, nails.
-Actin and myosin are the proteins of muscle tissue, and are responsible for muscle
movement.
2) Enzymes – catalyze reactions
-Digestive enzymes like amylase catalyze the hydrolysis of polymers in food.
-break down (catabolism) or build up molecules (anabolism)
3) Transport – across cell membranes
-In red blood cells, hemoglobin transports oxygen from the lungs to other parts of the
body
4) Defense – protection against disease
-antibodies – combat bacteria and viruses
5) Storage – store energy
-Proteins in meat, egg white (protein = albumin), legumes, milk (protein =casein)
-provide 4-5 cal per gram of energy
6) Information receptors – response of cell to chemical stimuli
-Receptors on the cell surface of a nerve cell detect chemical signals released by other
nerve cells.
7) Hormones – signaling molecules that help with the coordination of an organism’s activities
-Insulin regulates concentration of sugar. Somatotropin is the protein in HGH (human
growth hormones).
Polypeptides
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A polypeptide is a polymer of amino acids.
A peptide bond is a bond between amino acids.
-links the carboxyl group of one amino acid with the amino group of another
A protein consists of one or more polypeptide chains folded into a specific 3-D shape
Amino Acid Structure:
amino
group
H
H
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variable group
R
O
N–C–C
OH
H
carboxylic acid
group
**Composed of an asymmetric carbon (called
the alpha carbon) bonded to a hydrogen, a
carboxyl group, an amino group, and a
variable side chain called the R group**
At the pH in a cell, the amino and carboxyl groups are usually ionized.
The R group is the variable group and it differs in different kinds of amino acids.
-It confers the unique physical and chemical properties of each amino acid.
-There are 20 different R groups.
-Side chains may be either nonpolar and hydrophobic, or polar and charged (acidic or basic) and
hydrophilic.
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Amino acids usually end in –ine
20 different amino acids
Polypeptide chains are several amino acids linked by peptide bonds. Polypeptide chains have an
amino end (N-terminus) with a free amino group, and a carboxyl end (C-terminus) with a free
carboxyl group.
Protein Structure and function
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A protein has a unique 3-dimensional shape, or structure, created by the twisting or folding of
one or more polypeptide chains
Protein structure depends on the interactions between the amino acids that make up the
polypeptide chain and usually arises spontaneously as the protein is synthesized in the cell
The unique structure of a protein enables it to recognize and bind to other molecules
4 Levels of Protein Structure
1) Primary Structure
-The unique, genetically coded sequence of amino acids within a protein
-DNA encodes the sequence and determines how amino acids are put together
2) Secondary Structure
-Involves the coiling and folding of the polypeptide backbone
-An alpha helix = coils
-produced by hydrogen bonding between every 4th amino acids
-A beta pleated sheet = folds
-is also held by repeated hydrogen bonds along regions of polypeptide backbone lying
parallel to each other
-pleated sheets make up the core of many globular proteins
-This is stabilized by hydrogen bonds between the repeating constituent amino acids of the
polypeptide backbone
-Hydrogen bonds form between the electronegative oxygen of one peptide bond and
the weakly positive hydrogen attached to the nitrogen of another peptide bond
-The cell cytoplasm is made of water, so:
-The hydrophilic parts of the polypeptide chain turn outward
-The hydrophobic parts turn inward
3) Tertiary Structure
-Tertiary structure result from interactions between the various side chains (R groups) of the
constituent amino acids
-These interactions include:
-Hydrophobic interactions between nonpolar side groups clumped in the center of the
molecule due to their repulsion by water
-Van der Waals interactions among those nonpolar side chains (very weak)
-Hydrogen bonds between polar side chains
-Ionic bonds between negatively and positively charged side chains
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*These interactions produce the stable and unique shape of the protein
-Strong covalent bonds, called disulfide bridges, may reinforce the protein’s structure
-may occur between the sulfhydryl side groups of cysteine monomers that have been
brought closer together by the folding of the polypeptide
4) Quaternary structure
-2 or more polypeptide subunits combine and interact with each other
-occurs in proteins that are composed of more than one polypeptide chain
-the individual polypeptide subunits are held together in a precise structural arrangement
-For example: In hemoglobin proteins, each subunit has a nonpolypetpide component
called a heme, with an iron atom that binds oxygen
Proteins can change shape
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Folding of polypeptides normally occurs as the protein is being synthesized within the cell. However,
protein conformation also depends on the physical and chemical conditions of the protein’s
environment.
Denaturation is a change in original protein shape, usually resulting from a change in the pH,
temperature, salt concentration, or exposure to chemicals
-Because it is misshapen, the denatured protein is biologically inactive
-Most proteins become denatured if they’re transferred form an aqueous environment to an
organic solvent.
If a denatured protein remains dissolved, it can often renature when the chemical and physical
aspects of its environment are restored to normal
Defective Proteins
-a problem with encoding DNA can have serious effects on protein shape and function
Sickle cell anemia
-Results from a simple change in the primary level in 1 amino acid
-called a point mutation, resulting from substitution
-This changes the shape of the secondary and tertiary levels too  the hemoglobin protein is misshapen
Muscular dystrophy
-defective protein within muscle (actin/myosin)
Tay-Sachs
-enzymes are defective
Hemophilia
-clotting protein is defective
Cystic fibrosis
-transmembrane protein is defective (Cl—ions)
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Nucleic Acids
-information molecules that carry genetic code
DNA
-is inherited from one generation to the next and is copied whenever a cell divides so that all cells of an
organism contain its DNA
-polymer of nucleotides
-nucleotide:
1. 5-carbon sugar (deoxyribose)
2. Phosphate group
3. Nitrogenous base
-Adenine
-Thymine (*Only in DNA)
-Guanine
-Cytosine
-found in the nucleus in chromosomes
RNA
-directs protein synthesis
-polymer of nucleotides
-nucleotide:
1. 5-carbon sugar (ribose)
2. Phosphate group
3. Nitrogenous base
-Adenine
-Uracil (*Only in RNA)
-Guanine
-Cytosine
-found throughout the cell
-in the nucleus (mRNA), in ribosomes (rRNA), and as transport (tRNA)
Structure of Nucleic Acids
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Polynucleotides are polymers of nucleotides—monomers that consist of a pentose (5-carbon
sugar), a phosphate group, and a nitrogenous base
A monomer without the phosphate group is called a nucleoside
There are 2 types of nitrogenous bases:
1. Pyrimidines= 6-membered rings of carbon and nitrogen
-cytosine (C), thymine (T), and uracil (U)
2. Purines = add a 5-membered ring of carbon and nitrogen to the pyrimidines ring
-adenine (A) and guanine (G)
Covalent bonds between sugar, phosphate and the base
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Hydrogen bonds between nitrogenous bases
-Easily broken
Phosphodiester linkages = covalent bonds between nucleotides
-Between the sugar of one nucleotide and the phosphate of the next
-This bonding results in a sugar-phosphate backbone with repeating sugar and phosphate units
The polymer has 2 distinct ends: a 5’ end with a phosphate attached to a 5’carbon of a sugar and a
3’ end with a hydroxyl group on a 3’ sugar
-The nitrogenous bases extend from this backbone of repeating sugar-phosphate units
-The unique sequence of bases in a gene codes for the specific amino acid sequence of a protein
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