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AP & Adv. Biology Honors
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Chapter 2: Basic Chemistry Highlites
Essential Elements of Life
About 25 of the 92 elements are essential to life
Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter
Most of the remaining 4% consists of calcium, phosphorus, potassium,
and sulfur
Trace elements are those required by an organism in minute quantities
CHNOPS
4/7/2016
4
Isotopes
• Atoms of an element have the same number of protons but may differ
in number of neutrons
• Isotopes are two atoms of an element that differ in number of neutrons
• Most isotopes are stable, but some are radioactive, giving off particles
and energy
• Some applications of radioactive isotopes in biological research:
– Dating fossils
– Tracing atoms through metabolic processes
– Diagnosing medical disorders
4/7/2016
5
LE 2-7b
Third energy level (shell)
Second energy level (shell)
Energy
absorbed
First energy level (shell)
Energy
lost
Atomic
nucleus
4/7/2016
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LE 2-12
–
O
H
+
4/7/2016
H
H2O
+
7
Chapter 3: Water and the Fitness of the Environment
– Water is the biological medium here on Earth
– All living organisms require water more than any other substance
•
Three-quarters of the Earth’s surface is submerged in water
•
The abundance of water is the main reason the Earth is habitable
Figure 3.1
• Concept 3.1: The polarity of water molecules results in hydrogen
bonding
• The water molecule is a polar molecule
•
The polarity of water molecules
–
Allows them to form hydrogen bonds with each other
–
Contributes to the various properties water exhibits
–
Hydrogen
bonds
+
H
+
Figure 3.2
–
–
+
H
+
–
Qualities of Water that are caused by its polarity and the biological
significance of those qualities
•
Water molecules exhibit cohesion: Water attracts to water as it
hydrogen bonds to itself
•
Biological Significance:
Qualities of Water that are caused by its polarity and the biological
significance of those qualities
•
Water has a high specific heat:
•
Biological Significance
–
Moderate Temperature
–
High Heat of Vaporization
–
Ice Floats
Qualities of Water that are caused by its polarity and the biological
significance of those qualities
Water is a versatile Solvent
•
Biological Significance
–
Reactions within and outside cells
–
Rings of Hydration
–
Interacts with Polar Molecules, such as some proteins
–
Hydrophilic Materials
–
Hydrophobic Materials
Qualities of Water that are caused by its polarity and the biological
significance of those qualities
• Dissociation of water molecules leads to acidic and basic conditions
that affect living organisms
•
Water can dissociate into hydronium ions (H3O)+ and hydroxide ions (OH-)
•
Changes in the concentration of these ions can have a great affect on living
organisms
–
+
H
H
H
H
Figure on p. 53 of water
dissociating
H
H
H
Hydronium
ion (H3O+)
Results in free H+ ions
+
H
Hydroxide
ion (OH–)
Qualities of Water that are caused by its polarity and the biological
significance of those qualities
•
Acids:
•
Bases:
•
The pH Scale
•
Biological Significance of Acids and Bases
–
Transport of hormones in plants
–
Alteration of protein structures for
•
Activation
•
Denaturing
•
If acids and bases are potentially harmful to cells and living things,
what prevents harm? Why can a person drink a quart of orange juice
without sustaining a lethal change in blood pH?
–
The Answer
–
Applications
•
Swansea Dam
•
Lungs and Small Intestine
Chapter 4
Carbon and the Molecular
Diversity of Life
•
•
Overview: Carbon—The Backbone of Biological Molecules
All living organisms
– Are made up of chemicals based mostly on the element carbon
•
Concept 4.1: Organic chemistry is
the study of carbon compounds
•
Organic compounds
–
Range from simple molecules
to colossal ones
Figure 4.1
• The concept of vitalism
– Is the idea that organic compounds arise only within living
organisms
– Was disproved when chemists synthesized the compounds in the
laboratory
EXPERIMENT
RESULTS
In 1953, Stanley Miller simulated what were thought to be
environmental conditions on the lifeless, primordial Earth. As
shown in this recreation, Miller used electrical discharges
(simulated lightning) to trigger reactions in a primitive
“atmosphere” of H2O, H2, NH3 (ammonia), and CH4 (methane)—
some of the gases released by volcanoes.
A variety of organic compounds that play key roles in living cells were
synthesized in Miller’s apparatus.
Organic compounds may have been synthesized abiotically on the
CONCLUSION early Earth, setting the stage for the origin of life. (We will explore
Figure 4.2
this hypothesis in more detail in Chapter 26.)
•
Concept 4.2: Carbon atoms can form diverse molecules by bonding to four
other atoms
•
Carbon has four valence electrons
•
This allows it to form four covalent bonds with a variety of atoms
• The bonding versatility of carbon
– Allows it to form many diverse molecules,
including carbon skeletons
Name and
Comments
Molecular Structural
Formula
Formula
H
(a) Methane
CH4
H C
H
H
(b) Ethane
H H
C2H
H C C H
6
(c) Ethene
Figure 4.3 A-C (ethylene)
H H
H
C2H4
H
C C
H
H
Ball-andStick Model
SpaceFilling
Model
• The electron configuration of carbon
– Gives it covalent compatibility with many
different elements: i.e., it can bond covalently
with many other kinds of atoms.
Figure 4.4
Hydrogen
Oxygen
Nitrogen
Carbon
(valence = 1)
(valence = 2)
(valence = 3)
(valence = 4)
H
O
N
C
Molecular Diversity Arising from Carbon Skeleton
Variation
• Carbon chains
– Form the skeletons of most organic molecules
– Vary in length and shape
H H H
H C C C H
H H H
Propane
H
H C H
H
H
H H H H
(b) Branching
H C C C C H
H C C C H
H H H
H H H H
2-methylpropane
Butane
(commonly called isobutane)
H H H H
H H H H
(c) Double bonds H
H C C C C H
C C C C H
H
H
H H
1-Butene
2-Butene
H
H
H
H
C
H
H
C C H
C H
(d) Rings
H C
C
H
H C
C
H
H
C
C
C
(a) Length
Figure 4.5 A-D
H H
H C C H
H H
Ethane
Cyclohexane
Benzene
Hydrocarbons
•
Hydrocarbons Are molecules consisting of only carbon and hydrogen
– Are found as parts of many of life’s vital organic molecules
Fat droplets (stained red)
Figure 4.6 A, B
(a) A fat molecule
100 µm
(b) Mammalian adipose cells
Concept 4.3: Functional groups are the parts of molecules involved in chemical
reactions
– Are the chemically reactive groups of atoms within an organic molecule
– Give organic molecules distinct properties.
Estradiol
OH
CH3
HO
Female lion
OH
CH3
CH3
O
Figure 4.9
Male lion
Testosterone
• Some important functional groups of organic
compounds
FUNCTIONAL
GROUP
HYDROXYL
CARBONYL
CARBOXYL
O
OH
(may be written HO
C
C
OH
)
STRUCTURE In a hydroxyl group (—OH),
a hydrogen atom is bonded
to an oxygen atom, which in
turn is bonded to the carbon
skeleton of the organic
molecule. (Do not confuse
this functional group with the
hydroxide ion, OH–.)
Figure 4.10
O
The carbonyl group
( CO) consists of a
carbon atom joined to
an oxygen atom by a
double bond.
When an oxygen atom is doublebonded to a carbon atom that is
also bonded to a hydroxyl group,
the entire assembly of atoms is
called a carboxyl group (—
COOH).
• Some important functional groups of organic
compounds
NAME OF
COMPOUNDS
Alcohols (their specific
names usually end in -ol)
EXAMPLE
H
H
H
C
C
H
H
Ketones if the carbonyl group is Carboxylic acids, or organic
within a carbon skeleton
acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
H
OH
H
C
H
C
H
H
Ethanol, the alcohol
present in alcoholic
beverages
H
O
C
H
C
OH
H
H
Acetone, the simplest ketone
H
Figure 4.10
C
O
H
H
C
C
H
H
O
C
Propanal, an aldehyde
H
Acetic acid, which gives vinegar
its sour tatste
• Some important functional groups of organic
compounds
AMINO
SULFHYDRYL
H
N
H
Figure 4.10
O
SH
(may be written HS
The amino group (—NH2)
consists of a nitrogen atom
bonded to two hydrogen
atoms and to the carbon
skeleton.
PHOSPHATE
)
O P OH
OH
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
In a phosphate group, a
phosphorus atom is bonded to four
oxygen atoms; one oxygen is
bonded to the carbon skeleton; two
oxygens carry negative charges;
abbreviated P . The phosphate
group (—OPO32–) is an ionized
form of a phosphoric acid group (—
OPO3H2; note the two hydrogens).
• Some important functional groups of organic
compounds
H
O
C
HO
C
H
H
N
H
H
Glycine
Figure 4.10
H
H
C
C
H
H
OH OH H
SH
H
C
C
C
H
H
H
O
O
P O
O
Ethanethiol
Because it also has a carboxyl
group, glycine is both an amine
and a carboxylic acid;
compounds with both groups
are called amino acids.
Glycerol phosphate
Chapter 5
The Structure and Function of
Macromolecules
•
Macromolecules
–
Are large molecules composed of smaller molecules (polymers)
–
Are complex in their structures
Concept 5.1: Most macromolecules are polymers, built by
joining identical or similar monomers into long chains.
Three of the classes of life’s organic
molecules are polymers
–
Carbohydrates: Sugars, Starch
Figure 5.1
–
Proteins
–
Nucleic acids: DNA, RNA
The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by condensation
reactions called dehydration reactions
HO
1
3
2
H
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
Figure 5.2A
1
2
H
HO
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
• Polymers can disassemble by
– Hydrolysis
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
H
Figure 5.2B (b) Hydrolysis of a polymer
H
H2O
HO
H
Sugars
Monosaccharides
– Are the simplest sugars
– Can be used for fuel
– Can be converted into other
organic molecules
– Can be combined into
polymers
Triose sugars Pentose sugars
(C3H6O3)
(C5H10O5)
H
O
H
Aldoses
C
O
H
H
O
C
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
HO
C
H
C
OH
H
H
C
OH
H
H
H
H
C
H
C
OH
H
HO
C
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
H
Glucose
Galactose
H
C OH
H
C
O
H
C OH
H
C OH
C
O
O
C OH
H
C OH
HO
H
H
C OH
H
C OH
Dihydroxyacetone
H
C OH
H
C OH
H
H
C OH
H
Ribulose
O
C
H
Ribose
Figure 5.3
Hexose sugars
(C6H12O6)
C
Glyceraldehyde
Ketoses
•
C H
H
Fructose
• Monosaccharides
– May be linear
– Can form rings (about 65% of the time)
O
H
1C
H
HO
2
3
C
6CH OH
2
OH
H
C
H
4
H
H
H
C
5
5C
6
C
H
OH
4C
OH
OH
OH
O
5C
H
H
OH
C
6CH OH
2
3
C
H
2C
O
H
H
4C
1C
CH2OH
O
OH
H
OH
3C
6
H
1C
H
2C
4
HO
H
OH
3
OH
H
H
1
2
OH
OH
H
H
O
5
OH
OH
H
Figure 5.4 (a) Linear and ring forms. Chemical equilibrium between the linear and ring
structures greatly favors the formation of rings. To form the glucose ring,
carbon 1 bonds to the oxygen attached to carbon 5.
• Disaccharides
– Consist of two monosaccharides
– Are joined by a glycosidic linkage
• Examples of disaccharides
(a) Dehydration reaction
in the synthesis of
maltose. The bonding
of two glucose units
forms maltose. The
glycosidic link joins
the number 1 carbon
of one glucose to the
number 4 carbon of
the second glucose.
Joining the glucose
monomers in a
different way would
result in a different
disaccharide.
CH2OH
CH2OH
H
O
H
OH H
OH
HO
H
H
H
HO
H
OH
H
OH
H
H
OHOH
H
O
H
OH H
CH2OH
H
1–4
1 glycosidic
linkage
HO
4
O
H
H
OH H
OH
O
H
OH
H
H
OH
OH
H2O
Glucose
Glucose
CH2OH
H
(b) Dehydration reaction
in the synthesis of
HO
sucrose. Sucrose is
a disaccharide formed
from glucose and fructose.
Notice that fructose,
though a hexose like
glucose, forms a
five-sided ring.
Figure 5.5
O
CH2OH
O
H
OH
H
H
CH2OH
H
OH
HO
CH2OH
O
H
H
H
HO
CH2OH
OH
OH
Maltose
H
O
H
OH
H
1–2
glycosidic
1
linkage
H
Fructose
2
H
H
CH2OH
OH H
OH
Sucrose
H
HO
O
HO
H2O
Glucose
CH2OH
O
Polysaccharides
• Polysaccharides Are polymers of sugars
– Serve many roles in organisms
•
Starch Is a polymer consisting
Chloroplast
Starch
entirely of glucose monomers
–
In plants, the starch is
amylose or amylopectin,
such as in potatoes.
–
In animals, the starch is
glycogen, stored in the liver
and muscles.
1 m
Amylose
Amylopectin
Figure 5.6 (a) Starch: a plant polysaccharide
• Glycogen
– Consists of glucose monomers
– Is the major storage form of glucose in animals
Mitochondria
Glycogen
granules
0.5 m
Glycogen
Figure 5.6 (b) Glycogen: an animal polysaccharide
Structural Polysaccharides
•
Cellulose Is a polymer of beta glucose
H
CH2O
H
O
H
OH H
H
4
H
OH
HO
H
O
CH2O
H
H
O OH
H
4
1
OH H
HO
H
C
OH
 glucose
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
OH
 glucose
(a)  and  glucose ring structures
CH2O
H
O
CH2O
H
O
HO
4
1
OH
O
1
OH
4
O
1
OH
OH
OH
CH2O
H
O
CH2O
H
O
O
4
1
OH
O
OH
OH
(b) Starch: 1– 4 linkage of  glucose monomers
CH2O
H
O
HO
Figure 5.7 A–C
OH
CH2O
H
O
OH
O
1
4
OH
O
OH
OH
O
OH
O
O
CH2O
CH2O
OH
OH
H
H
(c) Cellulose: 1– 4 linkage of  glucose monomers
OH
– Is a major component of the tough walls that
enclose plant cells
Cell walls
Cellulose microfibrils
in a plant cell wall
Microfibril
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
0.5 m
Plant cells
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
Figure 5.8
OH CH2OH
OH
CH2OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH2OH
2
H
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH CH2OH
2
H
CH2OH
OH
OH CH2OH
O O
O O
OH
OH
OH O
O OH
O O
O
O CH OH
OH CH2OH
2
H
 Glucose
monomer
Cellulose
molecules
A cellulose molecule
is an unbranched 
glucose polymer.
• Cellulose is difficult to digest
– Cows (and termites) have microbes in their
stomachs to facilitate this process
Figure 5.9
An Animal Structural Polysaccharide
• Chitin, is an important structural polysaccharide in animals
– Is found in the exoskeleton of arthropods
– Can be used as surgical thread
CH2O
H
O OH
H
H
OH H
OH
H
H
NH
C
O
CH3
(a) The structure of the (b) Chitin forms the exoskeleton
of arthropods. This cicada
chitin monomer.
is molting, shedding its old
exoskeleton and emerging
Figure 5.10 A–C
in adult form.
(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.
Carbohydrates Review
Lipids: Fats, Waxes, Oils
• Concept 5.3: Lipids are a diverse group of hydrophobic molecules
• Lipids Are the one class of large biological molecules that do not
consist of polymers
– Share the common trait of being hydrophobic
•
Fats
–
Are constructed from two types of smaller molecules, a single glycerol
and usually three fatty acids
Fats
H
H
C
O
C
OH
HO
H
C
OH
H
C
OH
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
Fatty acid
(palmitic acid)
H
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
O
H
H
C
O
C
H
C
H
O
H
C
O
C
O
H
C
H
Figure 5.11
O
C
H
C
H
H
C
H
C
H
H
H
C
H
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
(b) Fat molecule (triacylglycerol)
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
H
H
H
C
H
H
H
C
H
H
• Fatty acids Vary in the length and number and locations of double
bonds they contain
•
Saturated fatty acids Have the maximum number of hydrogen atoms
possible: Have no double bonds
Stearic acid
Figure 5.12 (a) Saturated fat and fatty acid
• Unsaturated fatty acids Have one or more double bonds
– Can be converted to saturated via hydrogenation (pump-in
hydrogens), forming trans-fats, or trans-fatty acids.
Oleic acid
Figure 5.12
(b) Unsaturated fat and fatty acid
cis double bond
causes bending
Phospholipids
•
Phospholipids Have only two fatty acids Have a phosphate group instead of
a third
fatty acid
•
Phospholipid structure Consists of a hydrophilic “head” and hydrophobic
“tails”
CH2
+
N(CH )
3 3
Choline
CH2
O
O
P
O–
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Figure 5.13
(a) Structural formula
(b) Space-filling model
(c) Phospholipid
symbol
The structure of phospholipids
– Results in a bilayer arrangement found in cell membranes. They
will spontaneously form into this structure when placed in water.
• This happens because water is excluded from the hydrophobic
regions and attracted to the hydrophilic.
WATER
Hydrophilic
head
WATER
Hydrophobic
tail
Figure 5.14
Steroids: A type of Lipid (guaranteed answer on
this year’s AP Exam!!)
• Steroids Are lipids characterized by a carbon skeleton consisting of
four fused rings
•
One steroid, cholesterol Is found in cell membranes
–
Is a precursor for some hormones
H3C
CH3
CH3
Figure 5.15
HO
CH3
CH3
• Concept 5.4: Proteins have many structures,
resulting in a wide range of functions
– Proteins
• Have many roles inside the cell
–
–
–
–
–
Enzymes
Channels, gates, receptors in membranes
Signals (protein kinases)
Transcription Factors
And More!!
• An overview of protein functions
Table 5.1
• Enzymes
– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
Figure 5.16
3 Substrate is converted
to products.
Polypeptides
• Polypeptides Are polymers of amino acids
• A protein Consists of one or more polypeptides
•
Amino acids Are organic molecules possessing both carboxyl and
amino groups
–
Differ in their properties due to differing side chains, called R
groups
• 20 different amino acids make up proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N+
C
H
Alanine (Ala)
O–
CH
CH3
CH3
O
C
CH2
CH2
O
H3N+
C
H
Valine (Val)
CH3
CH3
O–
C
O
H3N+
C
H
Leucine (Leu)
H3C
O–
CH
C
O
C
O–
H
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
H3N+
C
O–
Methionine (Met)
Figure 5.17
CH2
O
C
H
CH2
O
H3 N+
C
C
O–
Phenylalanine (Phe)
H
O
H2C
CH2
H2N
C
O
C
O–
H
C
O–
Tryptophan (Trp)
Proline (Pro)
OH
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
Serine (Ser)
C
CH2
O
H3N+
C
O–
H
C
CH2
O
C
H
O–
H3N+
C
O
H3N+
C
O–
H
Electrically
charged
H3N+
CH2
C
H3N+
O–
C
NH3+
O
C
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
CH2
C
O–
H
H3N+
C
O
CH2
C
H
O–
H3N+
C
H
O–
H
Glutamic acid
(Glu)
NH+
C
O–
Lysine (Lys)
NH2+
H3N+
CH2
O
CH2
H3N+
C
H
Aspartic acid
(Asp)
O
C
Glutamine
(Gln)
NH2
C
C
C
Basic
O–
O
O
Asparagine
(Asn)
Acidic
–O
CH2
CH2
H
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
NH
CH2
O
C
C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
Peptide
bond
OH
CH2
SH
CH2
H
N
H
OH
CH2
H
C C
H
N C C OH H N C
H O
H O
H
(a)
C OH
O DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
SH
OH
Peptide
CH2 bond CH2
CH2
H
H N C C
H O
Figure 5.18
(b)
Amino end
(N-terminus)
H
H
N C C
H O
N C C OH
H O
Carboxyl end
(C-terminus)
Side
chains
Backbone
Determining the Amino Acid Sequence of a Polypeptide
• The amino acid sequences of polypeptides is CRITICAL!!
– Were first determined using chemical means
– Can now be determined by automated machines
•
A protein’s specific conformation
–
Determines how it functions
• Two models of protein conformation
Groove
(a) A ribbon model
Groove
Figure 5.19
(b) A space-filling model
Four Levels of Protein Structure
• Primary structure
– Is the unique sequence of amino acids in a
polypeptide
+H N
3
Amino
end
GlyProThrGly
Thr
Gly
Glu
CysLysSeu
LeuPro
Met
Val
Lys
Val
Leu
Asp
AlaValArgGly
Ser
Pro
Ala
GluLle Asp
Thr
Lys
Ser
Tyr
Trp
Lys
LeuAla
Gly
lle
Ser
ProPheHis
GluHis
Ala
Glu
Val
AlaThrPheVal
Asn
lle
Thr Ala
Asp
ArgTyr
Ser
Ala
Arg
GlyPro
Leu
Leu
Ser
Pro
SerTyr
Tyr
Ser
Thr
Thr
Ala
Val
Val
Glu
ThrAsnProLys
o
c –
o
Figure 5.20
Carboxyl end
Amino
acid
subunits
• Secondary structure
– Is the folding or coiling of the polypeptide into a
repeating configuration
– Includes the  helix and the  pleated sheet
 pleated sheet
O H H
C C N
Amino acid
subunits
C N
H
R
R
O H H
C C N
C C N
O H H
R
R
O H H
C C N
C C N
OH H
R
R
R
O
R
C
H
H
R
O C
O C
N H
N H
N H
O C
O C
H C R H C R
H C R H C
R
N H O C
N H
O C
O C
H
C
O
N H
N
C
C
H
R
H
R
N
Figure 5.20
C
C
H
H
 helix
O H H
C C N
C C N
OH H
R
O
C
H
H
H C N HC
C N HC N
C
N
H
H
C
O
C
C
O
R
R
O
R
O
C
H
H
NH C N
C
H
O C
R
C C
O
R
R
H
C
N HC N
H
O C
• Tertiary structure
– Is the overall three-dimensional shape of a
polypeptide
– Results from interactions between amino acids
and R groups
Hyrdogen
bond
CH22
CH
O
H
O
CH
H3C
CH3
H3C
CH3
CH
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
• Quaternary structure
– Is the overall protein structure that results from
the aggregation of two or more polypeptide
subunits
But What Holds all this
Together??
Polypeptide
chain
Peptide Bonds
Sulf-hydryl groups form disulfide bridges
Hydrogen bonds
If you remove all but
the peptides, you lose
the 2’, 3’, and 4’.
Remove the peptides,
lose it all.
Collagen
 Chains
Van der Waals forces
Iron
Heme
Hydrophobic interactions
 Chains
Hemoglobin
Sickle-Cell Disease: A Simple Change in
Primary Structure
Primary
structure
Normal hemoglobin
Val
His Leu Thr
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Figure 5.21
Val
His
Leu Thr


Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Pro
Val Glu
...
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Pro Glul Glu
Sickle-cell hemoglobin
. . . Primary
Quaternary
structure
 subunit




Function
10 m
10 m
Red blood
cell shape
Exposed
hydrophobic
region
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
What Determines Protein Conformation?
• Protein conformation Depends on the physical and chemical
conditions of the protein’s environment
•
Denaturation Is when a protein unravels and loses its native conformation
(notice the improper usage in this phrase? Good to avoid it).
Denaturation
Normal protein
Figure 5.22
Denatured protein
Renaturation
The Protein-Folding Problem
• Most proteins Probably go through several intermediate states on
their way to a stable conformation
•
Chaperonins Are protein molecules that assist in the proper folding of other
proteins
Polypeptide
Cap
Correctly
folded
protein
Hollow
cylinder
Chaperonin
(fully assembled)
Figure 5.23
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from one end.
2 The cap attaches, causing
3 The cap comes
the cylinder to change shape in off, and the properly
such a way that it creates a
folded protein is
hydrophilic environment for the released.
folding of the polypeptide.
Some Uses of Proteins
•
•
•
•
•
•
•
•
Antibodies
Enzymes
Contractile Proteins
Gene Regulation
Receptor Proteins
Sensory Proteins
Signal Proteins
Transport Proteins
• Concept 5.5: Nucleic acids store and
transmit hereditary information
• Genes
– Are the units of inheritance
– Program the amino acid sequence of
polypeptides
– Are made of nucleic acids
The Roles of Nucleic Acids
• There are two types of nucleic
acids
– Deoxyribonucleic acid (DNA)
• Stores information for the
synthesis of specific
proteins
• Directs RNA synthesis
• Directs protein synthesis
through RNA
– Ribonucleic acid (RNA)
DNA
1 Synthesis of
mRNA in the nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
3 Synthesis
of protein
Figure 5.25
Polypeptide
Amino
acids
The Structure of Nucleic Acids
• Nucleic acids Exist as polymers called polynucleotides
•Each polynucleotide Consists of monomers called nucleotides
5’ end
Nucleoside
5’C
O
Nitrogenous
base
3’C
O
5’C
O

O
P
O
Phosphate
group
O
Figure 5.26
3’C
OH
Figure 5.26
O
O
O
5’C
CH2
(b) Nucleotide
3’ end
(a) Polynucleotide,
or nucleic acid
3’C
Pentose
sugar
Nucleotide Monomers
• Nucleotide monomers
– Are made up of nucleosides and phosphate
groups
Nitrogenous bases
Pyrimidines
NH2
O
O
C
C
CH
C
3
N
CH
C
CH HN
HN
CH
C
CH
C
C
CH
N
N
O
N
O
O
H
H
H
Cytosine Thymine (in DNA) Uracil
(in
RNA)
Uracil (in RNA)
U
C
U
T
Purines
O
NH2
N C C
N CC
NH
N
HC
HC
C
CH
N C
N
NH2
N
N
H
H
Adenine
Guanine
A
G
5”
Pentose sugars
HOCH2 O OH
4’
H H
1’
5”
HOCH2 O OH
4’
H H
1’
H
H
H 3’ 2’ H
3’ 2’
OH H
OH OH
Deoxyribose (in DNA) Ribose (in RNA)
Figure 5.26
(c) Nucleoside components
Nucleotide Polymers
• Nucleotide polymers
Are made up of nucleotides linked by the–OH
group on the 3´ carbon of one nucleotide
and the phosphate on the 5´ carbon on the
next
5’ end
3’ end
Sugar-phosphate
backbone
The sequence of bases along a
nucleotide polymer Is unique for
each gene
Base pair (joined by
hydrogen bonding)
Old strands
•Cellular DNA molecules Have two
polynucleotides that spiral around an
imaginary axis and Forms a double
helix
A 3’ end
Nucleotide
about to be
added to a
new strand
5’ end
•
The DNA double helix
–
Consists of two
antiparallel nucleotide
strands
3’ end
5’ end
New
strands
3’ end
Itinerary For The Week
• Tues., Wed, Fri. (9/10 – 9/13): Notes: Ch. 2-5
• Thurs-Fri: DO?
• Fri: Thornton Wilder
“It is a far, far better thing that I do, than I have
ever done; it is a far, far better rest that I go
to than I have ever known.”
• Readings:
–
–
–
–
P. 27: Familiarize
51 – 56
63 – 66
68 – 89 (as needed; should be very little)
73
Itinerary For The Day
• Sidney Carton, as he comforted a young lady as
they both were carted to the guillotine.
• He saved Charles Darnay for Lucy.
• Author????:
4/7/2016
74
Extra Help, Lab Time, Advisory
Date
Day of Week
Day of
Rotation
Times
9/6
Friday
7
9:15 – 1:30
Notes
Note: Whenever possible, get a pass the day BEFORE coming,
and in ANY case, get a pass. Can’t make one of those times,
please see me and we’ll work something out.
Assignments, Tests, and Due Dates
Assignment
Due
Date
Agar Lab
9/6
Test: Ch. 2-5
??