Download Chemistry of Life

Entrance Quiz: Chapters 4 + 5
1. What are the 4 major macromolecules?
2. A short polymer and a monomer are linked, what is the
by-product and term for this process?
3. How many molecules of water are needed to completely
hydrolyze a polymer that is ten monomers long?
4. Why are human sex hormones considered lipids?
5. Identify the macromolecule
A
B
C
D
Entrance Quiz: Chapters 4 + 5
1. What are the 4 major macromolecules? LIPIDS,
NUCLEIC ACIDS, PROTEIN, CARBOHYDRATES
2. A short polymer and a monomer are linked, what is the
by-product and term for this process? WATER AND
DEHYDRATION
3. How many molecules of water are needed to completely
hydrolyze a polymer that is ten monomers long? 9
4. Why are human sex hormones considered lipids? THEY
ARE HYDROPHOBIC AND NONPOLAR
5. Identify the macromolecule
A
PROTEIN
B
NUCLEIC ACID
C
LIPID
D
CARBO
LIPIDS
FUNCTION: Lipids help to store energy, protects
organs, insulate the body, and form cell
membranes.
EXAMPLES: Lipids - include fats, phospholipids,
cholesterol and steroids.
FOOD SOURCE: Butter, cheese, meats, milk,
nuts, oils.
STRUCTURE: Monomer is a fatty acid and
glycerol. Polymer is a triglyceride
PROTEIN
FUNCTION: Proteins are used for muscle
movement, are part of the cell membrane and
are enzymes.
EXAMPLES: Amylase, Collagen
FOOD SOURCES: Dairy, eggs, fish, meat, nuts,
beans.
STRUCTURE: Monomer is an amino acid;
Polymer is protein in a polypeptide chain
Its structure is:
•
There are only 20 amino acids but a
million proteins
•
WHY?
1) Different lengths
2) Different combination
Carbohydrates
FUNCTION: Energy (for Mitochondria)
EXAMPLES: Glucose, Starch, Cellulose,
Chitin
FOOD SOURCES: Sugar, breads, cereal,
fruits, milk, pasta, vegetables, rice
STRUCTURE: Glucose (monosaccharide)
is the monomer. Polyssacharide is the
polymer
NUCLEIC ACIDS
FUNCTION: Transfers genetic information from one
generation to the next.
EXAMPLES: DNA and RNA
FOOD SOURCES: All foods from animals and plants have
DNA
STRUCTURE: Monomer is a nucleotide (P, S, and B)
Its structure is:
http://highered.mcgrawhill.com/sites/0072943696/studen
t_view0/chapter2/animation__pro
tein_denaturation.html
Make a model to show the
primary, secondary, tertiary, a
quarternary structure of a protein
Minimum 10 amino acids—pick
from each group
You must have the structure of
the amino acids
2nd
structure
of a
protein
H-bonds
R groups
are NOT
involved in
H-bonds
Tertiary
• Interactions with the aqueous solvent,
known as the hydrophobic effect results
in residues with non-polar side-chains
typically being buried in the interior of a
protein.
• Conversely, polar amino acid side-chains
tend to on the surface of a protein where
they are exposed to the aqueous milieu.
• http://bcs.whfreeman.com/thelifewire/conte
nt/chp03/0302002.html
Copy this:
“ If I am going to be absent on the day of a
test, I will contact Ms. Morris.”
TITLE page: Chemistry of Life
Chemistry of Life
Week 7-8
Overview
• Living organisms and the
world they live in are
subject to the basic laws
of physics and chemistry.
• Biology is a
multidisciplinary science,
drawing on insights from
other sciences.
• Life can be organized into
a hierarchy of structural
levels.
• At each successive level,
additional emergent
properties appear.
2.1 Matter consists of chemical elements in pure
form and in combinations called compounds.
• Organisms are composed of matter.
– Matter is anything that takes up space and has
mass.
– Matter is made up of elements.
2.1 Matter consists of chemical elements in pure
form and in combinations called compounds.
• An element is a pure
substance that cannot be
broken down into other
substances by chemical
reactions.
• There are 92 naturally
occurring elements.
• Each element has a
unique symbol, usually
the first one or two letters
of the name. Some of the
symbols are derived from
Latin or German names.
2.1 Matter consists of chemical elements in pure
form and in combinations called compounds.
A compound is a pure substance consisting of two or more elements in a
fixed ratio.
• Table salt (sodium chloride or NaCl) is a compound with equal
numbers of atoms of the elements chlorine and sodium.
Reflect on
• Blue green magnets
• White-red magnets
Essential Elements of Life
• Essential elements
– Include carbon,
hydrogen, oxygen,
and nitrogen
– Make up 96% of
living matter
• A few other
elements
– Make up the
remaining 4% of
living matter
Trace elements
• Are required by an organism in only
minute quantities
– But the absence of trace element can have
deadly effects
Figure 2.3
(a) Nitrogen deficiency
(b) Iodine deficiency
Radioactive Isotopes
• Spontaneously give off particles and
energy
– Alpha, beta, gamma radiation
Biological Uses for Radioactive Isotopes
APPLICATION
Scientists use radioactive isotopes to label certain chemical substances, creating
tracers that can be used to follow a metabolic process or locate the substance within an organism.
In this example, radioactive tracers are being used to determine the effect of temperature on the
rate at which cells make copies of their DNA.
TECHNIQUE
Ingredients including
Radioactive tracer
(bright blue)
Incubators
1
2
3
10°C
15°C
20°C
4
5
6
Human cells
1
2
Ingredients for
making DNA are
added to human cells. One
ingredient is labeled with 3H, a
radioactive isotope of hydrogen. Nine dishes of
cells are incubated at different temperatures. The
cells make new DNA, incorporating the
radioactive tracer with 3H.
The cells are placed in test
tubes, their DNA is isolated,
and unused ingredients are
removed.
25°C
30°C
35°C
7
8
9
40°C
45°C
50°C
DNA (old and new)
1
2 3
4
5 6
7
8 9
3
A solution called scintillation fluid is
added to the test tubes and they
are placed in a scintillation counter.
As the 3H in the newly made DNA
decays, it emits radiation that
excites chemicals in the
scintillation fluid, causing them to
give off light. Flashes of light are
recorded by the scintillation
counter.
RESULTS The frequency of flashes, which is recorded as counts per minute, is proportional to
Counts per minute
(x 1,000)
the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment,
when the counts per minute are plotted against temperature, it is clear that temperature affects the
rate of DNA synthesis—the RESULTS
most DNA was made at 35°C.
30
20
Optimum
temperature
for DNA
synthesis
10
Figure 2.5
0
10
20
30
40
Temperature (°C)
50
PET
(positron-emission tomography)
Cancerous
throat tissue
Figure 2.4 Tagging the Brain
Covalent Bonds
Covalent bonds can be
• Single—sharing one pair of electrons
C H
• Double—sharing two pairs of electrons
C C
• Triple—sharing three pairs of electrons
N N
2.3 The formation and function of
molecules depend on chemical bonding
between the atoms.
Electronegativity: the
attractive force that an
atomic nucleus exerts
on electrons
Electronegativity depends on
the number of positive
charges (protons) and the
distance between the
nucleus and electrons.
Weak Chemical Bonds
Hydrogen bonds:
attraction between the δ– end
of one molecule and the δ+
hydrogen end of another
molecule
Hydrogen bonds form
between H and O and/or H
and N.
Important with
water
DNA
Proteins
Van der Waals Interactions
• Van der Waals interactions
– Occur when transiently positive and negative
regions of molecules attract each other
Structure and Function run from large scale body systems
through molecules and atoms.
Structure and function are what Enzymes are all about
Carbon
Nitrogen
Hydrogen
Sulfur
Oxygen
Natural
endorphin
Morphine
(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule
(left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine
molecule is a close match.
Natural
endorphin
Figure 2.17
Brain cell
Morphine
Endorphin
receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
Why do medics pump wounded soldiers with
morphine on the battlefield?
Concept 2.4: Chemical reactions
make and break chemical bonds
• Chemical reactions
– Convert reactants to products
+
2 H2
Reactants
+
O2
Reaction
2 H2O
Product
Life is the result of Chemical
Reactions
• Photosynthesis
– Is an example of a chemical reaction
Figure 2.18
Chemical Equilibrium
• Chemical equilibrium
– Is reached when the forward and reverse
reaction rates are equal
Take out Water book
• Put notes and Hardy Weinberg lab in the
center of the table
• Make sure there is a post it at the
beginning of the lab
• If you want to go to a college talk and/or
assembly, you MUST have an A or B and
no Mi
Water: The Molecule That Supports
All of Life
• 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
3.1: The polarity of water molecules
results in hydrogen bonding
• The polarity of water molecules
– Allows them to form hydrogen bonds with each other
– Contributes to the various properties water exhibits
–
Hydrogen
bonds
+
H
+
–
–
+
H
+
–
3.2: Four emergent properties of water
contribute to Earth’s fitness for life
1. Cohesion
2. Moderation of
Temperature
3. Insulation of bodies of
water by floating ice
4. The solvent of life
(universal solvent)
1. Cohesion
• Cohesion – the hydrogen
bonds holding a substance
together. (water – water)
• Adhesion – the hydrogen
bonds holding one
substance to another.
(water – glass)
• Capillary Action – water
transport in plants. Uses
Cohesion and Adhesion
– Transpiration
• Surface tension –
measure of how difficult it
is to stretch or break the
surface of a liquid.
– Water has a greater surface
tensions than most liquids
2. Moderation of Temperature
• Kinetic Energy –
energy of motion
• Thermal Energy
(heat) – total energy
within a substance
– Calorie – amount of
heat energy to heat
1g water by 1°C
– Kcal – 1000c
• Temperature –
average kinetic
energy per molecule
(Celsius Scale)
2. Moderation of Temperature
• Specific heat – the
amount of heat
absorbed or loss for
1g of a substance to
change its
temperature by 1°C
– Water has high
specific heat capacity
compared to other
substances
– 1 cal/g/°C
2. Moderation of Temperature
• Evaporation
• Heat of vaporization –
the amount of heat 1g
of a liquid must absorb
to be converted to a
gas
• Evaporative cooling –
as a liquid evaporates
the surface of the
remaining liquid cools
– This occurs because the
“hottest” molecules
leave
3. Insulation of bodies of water by
floating ice
Hydrogen
bond
Ice
Liquid water
Hydrogen bonds are stable
Hydrogen bonds
constantly break and re-form
3. Insulation of bodies of water by
floating ice
4. Solvent of Life
• Water is claimed to be the
universal solvent.
– Solution – homogeneous
mixture of two or more
substances in the same phase
– Solute – substance which is
dissolved (in case of liquids,
substance with the least amount
– Solvent – substance which is
dissolving another
– Aqueous solution – solution
involving water
– Hydration shell – pocket formed
by water molecules in order to
dissolve a substance
4. Solvent of life
• Hydrophilic –
attracted to
water
– Can be dissolved
– Unless molecule
is too large
– Colloid –
stable
suspension of
fine molecules in
a liquid. (blood,
milk)
• Hydrophobic
– repel water
– Non-ionic, nonpolar, can’t form
H-bonds
4. Solvent of Life
• Solute
concentrations in
aqueous
solutions
– Concentration =
g solute / ml
solvent
– Molarity – moles
solute / Liter
solution
Acidic and Basic conditions affect
living organisms
• Water can dissociate
– Into hydronium ions and hydroxide ions
• H+ (hydrogen ion) is used to represent the hydronium ion
• Changes in the concentration of these ions
– Can have a great affect on living organisms
• Only 1 in 554 mil pure water molecules will diss.
–
+
H
H
H
H
Figure on p. 53 of water
dissociating
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
Acids and Bases
• Acids [H+]>[OH-]
• Bases [H+]<[OH-]
• When acids dissolve in water, they
release hydrogen ions—H+ (protons).
– H+ ions can attach to other molecules
and change their properties.
• Bases reduce H+ concentration by
accepting H+ ions and/or release
OH- ions
Strong Acid

HCl  H  Cl

HCl is a strong acid—the
dissolution is complete.
Weak Acid
Organic acids have a carboxyl
group:

 COOH  COOH  H

Weak acids: not all the acid
molecules dissociate into ions.
Strong Base
NaOH is a strong base.

NaOH  Na  OH

The OH– absorbs H+ to form water.
Weak Bases
Weak bases:
• Bicarbonate ion


HCO3  H  H 2CO3
• Ammonia


NH3  H  NH4
• Compounds with amino groups


 NH2  H  NH3
Acids, Bases, pH
pH = negative log of the molar
concentration of H+ ions.
H+ concentration of pure water is
10–7 M, its pH = 7.
Lower pH numbers mean higher
H+ concentration, or greater
acidity.
Acids, Bases, buffers
• Living organisms
maintain constant
internal conditions,
including pH.
– Buffers help maintain
constant pH by accepting or
donating H+ ions.
– They are kept in excess in
systems
• A buffer is a weak
acid and its
corresponding base.

HCO3  H  H 2CO3
Figure 2.17 Buffers Minimize Changes in pH
2.4 What Properties of Water
Make It So Important in
Biology?
Buffers illustrate the law of mass
action: addition of reactant on
one side of a reversible
equation drives the system in
the direction that uses up that
compound.
2.4 What Properties of Water
Make It So Important in
Biology?
Life’s chemistry began in water.
Water and other chemicals may
have come to Earth on comets.
Water was an essential
condition for life to evolve.
FRQ
• The unique properties (characteristics) of
water make life possible on Earth. Select
three properties of water and:
a) for each property, identify and define the
property and explain it in terms of the
physical/chemical nature of water.
b) for each property, describe one example of
how the property affects the functioning of
living organisms.
Build a carbohydrate
• Carbon (black)=4 bonds
• Hydrogen (white)=1 bond
• Oxygen (red)= 2bonds
Pick up 2 FRQ
• Look at the FRQs from 2 sample students
• Write advice to each student
• Rewrite your FRQs—why
did you lose points?
Carbon
• Carbon atoms can form diverse molecules by
bonding to four other atoms
– Carbon has amazing ability to form molecules
because:
•
•
•
•
•
It has 4 valence electrons
It can form up to 4 covalent bonds
These can be single, double, or triple cov. Bonds
It can form large molecules.
These molecules can be chains, ring-shaped, or branched
– Isomers – are molecules that have the same
molecular formula, but different in their arrangement
of these atoms.
• This can result in different molecules with very different
activities.
Carbohydrates
Cells use
glucose
(monosacchar
ide) as an
energy
source.
Exists as a
straight chain
or ring form.
Ring is more
common—it is
more stable.
Glucose=C6H12O6
Carbon=black, Hydrogen=White, Oxygen=Red
• Carbohydrates: molecules in
which carbon is flanked by hydrogen
and hydroxyl groups.
H—C—OH
• Main Functions
– Energy source
– Carbon skeletons for many other
molecules
Carbohydrates
CH2O
Quick on Carbon
4.3 Characteristic chemical groups help
control how biological molecules function
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
Quick on Carbon
4.3 Characteristic chemical groups help
control how biological molecules function
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
5.1 Macromolecules are polymers
built from monomers.
• Monomer – smaller
repeating units of a polymer
• Polymer – large molecule
consisting of many similar or
identical building blocks
• Polymers with
molecular weights
>1000
• Polymerization – process of
joining monomers to form
polymers
The synthesis and breakdown of
polymers
• Dehydration
synthesis
(dehydration
reaction) –
synthesis reaction
forming a
byproduct of water
• Hydrolysis –
degradation of
a molecule
using water to
break down
bonds
– These processes
are often aided by
enzymes
Dehydration Synthesis
Demonstrate
• Dehydration
• All the names for a polymer of glucose +
glucose
The Diversity of Polymers
• Each cell has thousands of
different kinds of
macromolecules.
– The inherent different between
human siblings reflect the
variations in polymers:
• Especially DNA and proteins
• There are four major classes
of biological macromolecules
–
–
–
–
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbohydrates
• Monosaccharides:
simple sugars
• Disaccharides: two
simple sugars linked
by covalent bonds
• Oligosaccharides:
three to 20
monosaccharides
• Polysaccharides:
hundreds or
thousands of
monosaccharides—
starch, glycogen,
cellulose
Carbohydrates
• Monosaccharides
have different
numbers of
carbons.
– Trioses: three
carbons– structural
isomers glyceraldehyde
– Hexoses: six
carbons—structural
isomers
– Pentoses: five
carbons
Carbohydrates
• Monosaccharides bind together in
condensation reactions to form glycosidic
linkages.
• Glycosidic linkages can be
α or β.
Beta – glycosidic linkage
Alpha – glycosidic linkage
Carbohydrates
• Oligosaccharides
may include other
functional groups.
• Often covalently
bonded to proteins
and lipids on cell
surfaces and act
as recognition
signals.
• ABO blood groups
Carbohydrates
• Starch: storage of
glucose in plants
– 1-4 glycosydic linkages
between alpha glucose
• Cellulose: very stable,
good for structural
components (cell walls
of plants
– 1-4 glycosydic linkages
between beta glucose
• Glycogen: storage of
glucose in animals
– 1-4 glycosydic linkages
between alpha glucose
• with branching
Chitin
• Chitin, another important structural
polysaccharide
– Is found in the exoskeleton of arthropods
CH O
– Can
be used as surgical thread
H
2
O OH
H
OH H
OH
H
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.
5.3 Lipids are a diverse group of
hydrophobic molecules
Lipids are nonpolar
hydrocarbons:
•
•
•
•
Fats and oils—energy storage
Phospholipids—cell membranes
Steroids
Carotenoids
Fats serve as insulation in animals,
lipid nerve coatings act as
electrical insulation, oils and
waxes repel water, prevent
drying.
Lipids
Fats and oils are
triglycerides—
simple lipids—
made of three fatty
acids and 1
glycerol.
Glycerol: 3 —OH
groups—an alcohol
Fatty acid: nonpolar
hydrocarbon with a
polar carboxyl
group—carboxyl
bonds with
hydroxyls of
glycerol in an ester
linkage.
Lipids
• Saturated fatty acids:
no double bonds
between carbons—it is
saturated with hydrogen
atoms.
• Unsaturated fatty acids:
some double bonds in
carbon chain.
– monounsaturated: one
double bond
– polyunsaturated: more
than one
Lipids
Animal fats tend to be saturated—packed together tightly—solid at
room temperature.
Plant oils tend to be unsaturated—the “kinks” prevent packing—
liquid at room temperature.
Lipids
Phospholipids:
fatty acids bound
to glycerol, a
phosphate group
replaces one fatty
acid.
Phosphate group is
hydrophilic—the
“head”
“Tails” are fatty acid
chains—
hydrophobic
Lipid (phospholipid bilayer)
Lipid (Steroids)
• Steroids
– Are lipids
characterized by a
carbon skeleton
consisting of four
fused rings
– Many hormones,
including vertebrate
sex hormones, are
steroids produced
from cholesterol
– Steroids play a role
in regulating cell
activities
Lipids (carotenoids)
Carotenoids: light-absorbing pigments
5.4 Proteins have many structures,
resulting in a wide range of functions
Functions of proteins:
• Structural support
• Protection
• Transport
• Catalysis
• Defense
• Regulation
• Movement
Proteins
• Proteins are made
from 20 different
amino acids
(monomeric units)
• Polypeptide chain:
single, unbranched
chain of amino acids
– The chains are folded
into specific three
dimensional shapes.
– Proteins can consist of
more than one type of
polypeptide chain.
Protein (polypeptide)
The composition of a
protein: relative
amounts of each
amino acid present
The sequence of
amino acids in the
chain determines
the protein structure
and function.
Proteins
• Amino acids have
carboxyl and amino
groups—they
function as both
acid and base.
Functional Group
– The α carbon atom
is asymmetrical.
– Amino acids exist in
two isomeric forms:
• D-amino acids
(dextro, “right”)
• L-amino acids
(levo, “left”)—
this form is
found in
organisms
Proteins (amino acids are grouped
by characteristics)
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
O–
H
Glycine (Gly)
C
H
H3N+
C
O–
CH
CH3
CH3
O
C
H
H3N+
C
CH2
CH2
O
C
O–
Valine (Val)
Alanine (Ala)
CH3
CH3
H
O
H3C
H3N+
C
C
O
C
O–
O–
Leucine (Leu)
CH
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)
Proteins (amino acids are grouped
by characteristics)
OH
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
C
CH2
O
H3N+
C
O–
H
C
CH2
O
C
H
Serine (Ser) Threonine (Thr)
O–
H3N+
C
O
H3N+
C
O–
H
Electrically
charged
C
CH2
H3N+
C
O
H
H3N+
NH3+
O
CH2
C
H3N+
–
O
C
C
H
O
C
O–
H
C
CH2
CH2
CH2
CH2
CH2
C
O
CH2
C
O–
H3N+
C
H
Glutamic acid
(Glu)
NH+
NH2
CH2
H
Aspartic acid
(Asp)
O
C
CH2
C
O–
CH2
Basic
O–
O
CH2
Asparagine Glutamine
(Gln)
(Asn)
Tyrosine
(Tyr)
Cysteine
(Cys)
Acidic
–O
C
NH2 O
C
SH
CH3
OH
NH2 O
C
Lysine (Lys)
H3N+
CH2
O
O–
NH2+
CH2
H3N+
C
H
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg) Histidine (His)
Proteins
• Amino acids
bond together
covalently by
peptide
bonds to form
the
polypeptide
chain.
– Dehydration
synthesis
Proteins
A polypeptide chain is
like a sentence:
• The “capital letter” is
the amino group of
the first amino acid—
the N terminus.
• The “period” is the
carboxyl group of the
last amino acid—the
C terminus.
Proteins
The primary structure of a
protein is the sequence of
amino acids.
The sequence determines
secondary and tertiary
structure—how the
protein is folded.
The number of different
proteins that can be
made from 20 amino
acids is enormous!
• Protein structure
–Primary
–Secondary
–Tertiary
–Quartinary
Proteins (primary structure)
Proteins (secondary structure)
Secondary structure:
• α helix—right-handed coil resulting from hydrogen
bonding; common in fibrous structural proteins
• β pleated sheet—two or more polypeptide chains are
aligned
Proteins (tertiary structure)
Tertiary structure: Bending and folding results in a
macromolecule with specific three-dimensional shape.
The outer surfaces present functional groups that can
interact with other molecules.
Proteins (tertiary structure)
Tertiary structure
is determined
by interactions
of R-groups:
• Disulfide bonds
• Aggregation of
hydrophobic
side chains
• van der Waals
forces
• Ionic bonds
• Hydrogen
bonds
•
Proteins (Quartinary
structure)
Quaternary
structure
results from
the
interaction of
subunits by:
–
hydrophobic
interactions
– van der
Waals
forces
– ionic bonds
– hydrogen
bonds.
Proteins (Sickle-cell Disease)
– Results from a single
amino acid
substitution in the
protein hemoglobin
Hemoglobin structure and
sickle-cell disease
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
structure 1 2 3 4
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Sickle-cell hemoglobin
Pro
GlulGlu . . . Primary


Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Quaternary
structure
...
Val
5 6 7
Pro
 subunit




Function
10 m
10 m
Red blood
cell shape
Exposed
hydrophobic
region
Glu
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of abnormal
hemoglobin
deform cell into
sickle shape.
EnzymeSubstrate
Complex
Proteins (Denaturing)
• Conditions that affect
secondary and tertiary
structure:
• High temperature
• pH changes
• High concentrations of
polar molecules
• Denaturation: loss of 3dimensional structure
and thus function of the
protein
Proteins (folding)
• Proteins can sometimes fold incorrectly and bind to the wrong ligands.
• Chaperonins are proteins that help prevent this.
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.
5.5 Nucleic acids store and
transmit hereditary information
Nucleic acids: DNA—
(deoxyribonucleic
acid) and RNA—
(ribonucleic acid)
Polymers
(polynucleotides) —
made of the
monomeric units are
nucleotides.
Nucleotides consist of a
pentose sugar, a
phosphate group, and
a nitrogen-containing
base.
5.5 Nucleic acids store and transmit
hereditary information
DNA—deoxyribose
RNA—ribose
5.5 Nucleic acids store and transmit
hereditary information
The “backbone” of DNA
and RNA consists of the
sugars and phosphate
groups, bonded by
phosphodiester
linkages.
The phosphate groups link
carbon 3′ in one sugar to
carbon 5′ in another
sugar.
Antiparallel The two
strands of DNA run in
opposite directions.
5.5 Nucleic acids store and transmit
hereditary information
DNA bases: adenine
(A), cytosine (C),
guanine (G), and
thymine (T)
Complementary
base pairing:
A—T
C—G
Purines pair with
pyrimidines by
hydrogen bonding.
•
A particular small polypeptide is nine amino acids long.
Using three different enzymes to hydrolyze the
polypeptide at various sites, we obtain the following five
fragments (N denotes the amino end of the chain):
Ala-Leu-Asp-Tyr-Val-Leu
Tyr-Val-Leu
N-Gly-Pro-Leu
Asp-Tyr-Val-Leu
N-Gly-Pro-Leu-Ala-Leu
Determine the primary structure of this polypeptide.
–
–
–
–
N-Gly-Pro-Leu-Ala-Leu-Asp-Tyr-Val-Leu
Asp-Tyr-Val-Leu-Gly-Pro-Leu-Ala-Leu
N-Gly-Pro-Leu-Ala-Leu-Ala-Leu-Asp-Tyr-Val-Leu
N-Gly-Pro-Leu-Asp-Tyr-Val-Leu-Tyr-Val-Leu
• (a) You are studying a cellular enzyme involved in
breaking down fatty acids for energy. Looking at
the
R groups of the amino acids in the following
figures, what amino acids would you predict to
occur in the parts of the enzyme that interact with
the fatty acids? *
–
–
–
–
–
non-polar
polar
electrically charged
polar and electrically charged
all of these
The 20 Amino Acids of Proteins
The 20 Amino Acids of Proteins
(cont.)
• (b) You are studying a cellular enzyme
involved in breaking down fatty acids for
energy. Where would you predict to find the
amino acids in the parts of the enzyme that
interact with the fatty acids?
– On the exterior surface of the enzyme
– Sequestered in a pocket in the interior of the
enzyme
– Randomly dispersed throughout the enzyme
• The R group or side chain of the amino acid
serine is –CH2 –OH. The R group or side chain of
the amino acid alanine is –CH3. Where would you
expect to find these amino acids in globular
protein in aqueous solution?
– Serine would be in the interior, and alanine would be
on the exterior of the globular protein.
– Alanine would be in the interior, and serine would be
on the exterior of the globular protein.
– Both serine and alanine would be in the interior of the
globular protein.
– Both serine and alanine would be on the exterior of
the globular protein.
– Both serine and alanine would be in the interior and
on the exterior of the globular protein.
• (a) The sequence of amino acids of the
enzyme lysozyme is known. Following is a
list of amino acids and the number of each
in the lysozyme molecule. Based on this
list and the structures of the amino acids
how many S-S bonds are possible in
lysozyme?
–
–
–
–
–
0
2
4
6
8
Amino Acids in the Lysozyme
Type
Number
in
Type
Number in
Molecule
Lysozyme
Lysozyme
Alanine
Arginine
Asparagine
Aspartic acid
12
11
13
8
8
2
Leucine
Lysine
Methionine
Phenylalanin
e
Proline
Serine
Cysteine
Glutamic
acid
Glutamine
Glycine
Histidine
8
6
2
3
2
10
3
12
1
Threonine
Tryptophan
Tyrosine
7
6
3
The 20 Amino Acids of Proteins
The 20 Amino Acids of Proteins
(cont.)
• (b) The sequence of amino acids of the
enzyme lysozyme is known. Following is a
list of amino acids and the number of each
in the lysozyme molecule. Based on this
list and the structures of the amino acids is
the net charge on lysozyme positive or
negative?
– positive
– negative
Amino Acids in the Lysozyme
Type
Number
in
Type
Number in
Molecule
Lysozyme
Lysozyme
Alanine
Arginine
Asparagine
Aspartic acid
12
11
13
8
8
2
Leucine
Lysine
Methionine
Phenylalanin
e
Proline
Serine
Cysteine
Glutamic
acid
Glutamine
Glycine
Histidine
8
6
2
3
2
10
3
12
1
Threonine
Tryptophan
Tyrosine
7
6
3
The 20 Amino Acids of Proteins
The 20 Amino Acids of Proteins
(cont.)
• Polymers of glucose units are used as
temporary food storage in both plant and
animal cells. Glucose units are connected to
one another by 1, 4-linkages to make a
linear polymer and by 1, 6-linkages to make
branch points.
• (cont.) Polysaccharides of glucose units
vary in size. The three most commonly
Type of
Cell Type
Polymer
Average
encountered
are:
Starch
Size
Amylopectin Plant
Number of
1,4-Bonds
Between
Branches
100,000,000 24 to 30
Amylos
Glycogen
500,000
3,000,000
Plant
Animal
Linear
8 to 12
• (cont.) When each polymer bond is made, a
water molecule is released and becomes part
of the cell water. How many water molecules
were released during formation of each of the
Glycogen?
–
–
–
–
–
1,000,000
2,000,000
2,666,666
3,000,000
3,300,000