8
Macromolecules-Four classes
A/P Biology
Pages 44-92
Name: ____________________________ Date: ______________ Period(s): ________
Life on Earth revolves around carbon and water. “One of the tenets in the search
for life as we know it (the only kind we can meaningfully speculate about) is that it
requires water.” (Taken from: Discover Magazine, Cosmic Abodes of Life, by Adam
Frank. May, 2009) Yes, water is the basis of all life, but we have to consider carbon’s
versatility in creating many different kinds of bonds based on ability to arrange bond
angles of 109.5o AND its ability to create these bonds at temperature compatible with life
on Earth (and Earth’s “normal” temperature). The “allowable” angles of bonding (that is
the physical space that a molecule occupies and still not interfere with the spatial
relationship with the atom it is attaching to makes this an ideal molecule because of the
versatility it has in making single bonds, double bonds, and even triple bonds. The idea
is that silicon being a larger molecule (with an outer “unfilled” shell) needs (1) electrons
at a higher potential energy, and (2) has different chemical properties compared to carbon
(that is silicon’s ability to be part of certain
% of elements found
reactions are limited to the need for a higher
in human body
amount of heat or energy to get them to create a
bond). Both silicon and carbon can manage to
bond four other atoms!
So we realize that though carbon is fairly
limited in its abundance in the Earth’s crust
(0.03%) versus carbon per centage in the human
body at 18.5% (see Appendix 2). Carbon is ideal
for life because of its ability to form bonds with
four other molecules and form many different
high energy COVALENT compounds at temperatures that are close to the over-all
temperature of the Earth. The reason covalent bonds are so important is that these bonds
“hold” energy. When covalent bonds are broken in high energy compounds like fats,
sugars, and protein- they can release energy that can be “trapped” in small energy packets
called ATP (Adenosine triphosphate). All cells (as far as I know) use ATP to run the cell
machinery on a second by second basis! We will look at four DIFFERENT high energy
complex molecules or macromolecules: nucleic acids (DNA/RNA), proteins and
proteinaceous enzymes, lipids (fats), and carbohydrates (sugars).
(I will not go over so much what is explained in the book, rather, I will discuss
some things the text has not incorporated into its explanation(s). )
When we discuss macromolecules, we have to look how atoms become associated
with one another. Often molecules associate by forming bonds. We have read about and
briefly discussed some kinds of bonds. We will revisit this topic in more detail now.
Ionic Bonds
(Left) We see the basic idea behind the ionic
bond. To the right we see sodium chloride
and two other examples of the ionic bond
(magnesium oxide and calcium chloride).
Page 2 (Cont. #8 AP Biology)
Properties of an ionic bond:
(1) Opposite charges attract the ions together (like mini-magnets)
(2) Weak and easily broken
(3) Often form crystals that contain repeating orderly
arrangements of the two ions (see picture to right)
(4) May dissolve easily in water (example: table salt)
Covalent Bond
Above you see three different examples of
Covalent bonding.
(Above-2 Hydrogen atoms.)
Completing a covalent bond.
Instead of the electron being “given up”
(as in the ionic bond), in the covalent bond
the electron is shared with the other atoms
involved in the compound. Note:
only the OUTER electrons are
Molecules that contain covalent bonds are referred to as
involved in bonding!
Properties of covalent bonds: HIGH ENERGY bonds- release energy when broken!
(1) Electrons that are shared rotate around both (all) nuclei
(2) Very strong bonds (they are often high energy bonds (see sugar section))
(3) May be single, double, triple or four, depending on the number of pairs of
electrons involved.
(4) Most biological molecules use this type of bonding.
(5) Once all the shells have been satisfied (with electrons) they are no longer capable
of further interaction with other molecules (under “normal conditions”).
Page 3 (Cont.#8 AP Biology)
Hydrogen Bonding
Hydrogen bonding can occur between hydrogen and
any other molecule (that has a net charge that is
negative). Water forms hydrogen bonds readily
and THIS ACCOUNTS for waters ability to
absorb a lot of heat and hold heat even after a
heat source has been removed!
To the right you see
a number of
hydrogen bond
examples. The blue
lines indicate
hydrogen bonds
(attraction).
Properties of
Hydrogen Bonds:
(1) Because of the
polar nature of
their covalent
bonds, nearby
molecules of water
attract one another
(2) Many
biological
molecules form
hydrogen bonds
(3) These bonds
are VERY weak.
Hydrogen bonds are what hold the two strands of
DNA together!
This ThymineAdenine bond is an
example of DNA
hydrogen bonding
Page 4 (Cont. #8 A/P Biology)
Functional Groups and polymers: Many biological molecules are formed and broken
down by subtraction or addition of water molecules or carbon dioxide molecules. The
actual addition or subtraction of the water molecule involves functional group(s) attached
to molecules that are often composed of a carbon-based core.
“R” refers to groups of carbon
based molecules.
Acetyl-CoA is a
modified nucleotide
Page 5 (Cont.#8 A/P Biology)
When the cell creates (or synthesizes) a molecule by eliminating one hydrogen atom (H+)
and one hydroxyl atom (OH-), the reaction is called dehydration synthesis (that is water
is removed). This reaction invariably requires the input of energy-this reaction creates
water. When a molecule is broken down and requires that water be added (that is water
is broken- and part of water –OH is added to one part of the product, and H+ is added to
the other side of the product), this is called hydrolysis (-lysis means breaking down).
This reaction often yields energy.
Polymers
Polymers are long chains of repeating subunits that may be created or
broken down by chemical or physical means (such as enzymes, chemical treatment, or
heat)- not all polymers are able to be easily made nor broken down easily due to the
stability of their bond structure (examples of hard to break polymers; cellulose and
chitin...cellulose is found in plant cell walls where chitin is found in the exoskeletons of
insects and cell walls of fungi).
Examples: The cell often stores energy in high-energy bonds. To store a lot of
energy in an efficient way, the cell can store such high-energy bonds in carbohydrates or
lipids. Carbohydrates (often sugars) are often made into repeating units to be stored until
needed. Sugars are stored as polymers in animal cells as glycogen (a branched chain of
sugars). Sugars are stored as polymers in plant cells as starch (a straight chain of
sugars). This type of storage allows cells to access the energy stored in the polymers
rapidly in times of high energy demand (such as muscle contraction or growing larger).
By definition, carbohydrates are composed essentially of three different main
components:
1.) Carbon 2.) Hydrogen 3.) Oxygen
The molar ratio is usually 1:2:1
This means that for each
(1) Carbon atom, there are
(2) hydrogen atoms,
and (1) oxygen atom.
RING
STRUCTURE
In the case of glucose C6H12O6
Stereoisomers: A
stereoisomer is when the
chemical formula of two
molecules is exactly the
same, yet the orientation of
one functional group is a
mirror image of the other.
These stereoisomers do NOT
necessarily have the same
exact chemical properties.
LINEAR
STRUCTURE
Note: the functional group location (yellow
box) helps define the type of isomer
Page 6 (Cont. #8 A/P Biology)
Structural isomer: Structural isomers have the same exact chemical formula, yet a
functional group is moved to a different location. These structural isomers often do not
have the same chemical properties as each other.
It is important to realize that animal cells and plant cells must store energy in the
most efficient manner. That is to say that cells need to be able to access the high-energy
bonds in sugar quickly to maintain life. Cells can break down single molecules of sugar
(monosaccharides) very rapidly and use the energy to make high-energy compounds
(called ATP or Adenosine Triphosphate). Cells often transport sugars two at a time by
creating a disaccharide (that is two sugar molecules together). The disaccharides cannot
be used or broken down along the way without a special enzyme that will cleave the
disaccharide bond first. When animals store glucose they do so by forming long highly
branched chains called polysaccharides or glycogen (usually stored in the muscle tissue
and liver). On the other hand, plants that can make their own food (they are producers),
they store that food as a polysaccharide or starch (straight UNBRANCHED chain of
sugars). Plants also use glucose structurally. That is cellulose, a repeating glucose
polysaccharide, is used to build cell walls. The glycogen and starch are made of
repeating units of glucose, the difference lies in the type of bond that holds the repeating
units together. Bonds that hold the glycogen together require one type of enzyme to
break the polysaccharide bonds, bonds that hold the starch together require another type
of enzyme to break the polysaccharide bonds. As a side note, cellulose bonds CANNOT
be broken down by enzymes in most animals- so cellulose is indigestible/along with
lignin; and together is referred to as fiber (aka, good for digestion and elimination of
waste).
Another polymer, chitin (n-acetyl glucosamine), is made of a modified polysaccharide
used in the formation of exoskeletons of some invertebrates (example- lobsters, insects).
Few organisms are able to break down or digest chitin (and for that matter,
cellulose) because they lack the specific enzymes to break it down. As mentioned before,
we make n-acetyl glucosamine (mucous),
but not in the polymer form- so it can
remain moist or in liquid form easier.
Lipids: Fats are simply long chains of
hydrocarbons (simply stated- long chains
of carbon molecules that have hydrogen
attached). Fats are non-polar (and
therefore cannot form hydrogen bonds
like simple carbohydrates). A typical fat
is made up of three fatty acids and a glycerol (called a triglyceride).
The glycerol portion of the triglyceride consists of
the three carbons connected by covalent bonds (blue lines).
You can have saturated fats (where there are no double
bonds in the chain of hydrocarbons) or you can have an
unsaturated fat (where there are one or more double
bonds in the chain of hydrocarbons).
Page 7 (Cont. #8 A/P Biology)
Proteins: Proteins are made up of two or more amino acids. Amino acids are
compounds primarily composed of carbon, nitrogen, oxygen, hydrogen and sulfur. (It is
important to note that DNA and RNA have a similar
elemental composition compared to proteinEXCEPT for Sulfur. Sulfur is found in protein,
phosphorous is found in DNA and RNA. This proves
to be a tool scientists have used to be able to
examine how these different macromolecules work.)
Amino Acids have the basic structure shown:
The “R” group refers to a set of functional side
group that helps define the protein made.
There are 20 COMMON amino acids.
Amino acids are roughly divided into four groups:
1.) non-polar
a.) alanine (Ala, A)
b.) Valine (Val, V)
c.) Leucine (Leu, L)
d.) Isoleucine (Ile, I)
e.) Proline (Pro, P)
f.) Phenylalanine (Phe, F)
g.) Tryptophan (Trp, W)
h.) Methionine (Met, M)
2.) uncharged polar
a.) Glycine (Gly, G)
b.) Serine (Ser, S)
c.) Threonine (Thr, T)
d.) Cysteine (Cys, C)
e.) Tyrosine (Tyr, Y)
f.) Asparagine (Asn, N)
g.) Glutamine (Glu, Q)
3.) negatively charged (acidic)
a.) Aspartic acid (Asp, D)
b.) Glutamic Acid (Glu, E)
The names of ALL the common amino acids
4.) positively charged (basic)
are listed to the left and their abbreviations
a.) Lysine (Lys, K)
are listed. The actual structures of the amino
b.) Arginine (Arg, R)
acids and “R” groups can be visualized in
c.) Histidine (His, H)
your text books.
Amino acids can be arranged in groups depending on their “R” groups (See Appendix 1).
When amino acids are linked to one another they form a special bond. This special bond
was even given a special name: the Peptide Bond. See formation of peptide bond, pg.8.
Page 8 (Cont. #8 A/P Biology)
The formation of a peptide bond
is an example of “dehydration
synthesis”. That is the reaction
forms water and is an ENERGYREQUIRING PROCESS!
The proteins formed by amino
acids coming together in long
chains are called a polymer or
commonly called polypeptide.
Protein polymers have four different levels of structure.
This reaction
REQUIRES
energy- because it
makes water…
1.) Primary structure: The specific amino acid sequence of a protein is its “primary
structure”. It is erroneous to think that the “R” groups play no role in the peptide
backbone of proteins. The “R” groups HAVE a spatial and in some cases charged
qualities that will not allow certain amino acids to be packed together in certain
sequences.
Beta-Pleated Sheet
2.) Secondary structure: The primary structure helps to dictate
the ultimate shape of the protein. The “R” groups interact with
each other, with water around it, with other polar molecules, and
with non-polar molecules. As the protein is synthesized (at the
mRNA/rRNA, and tRNA site) it begins to fold. Some scientists
believe that this folding is spontaneous based only on the
primary sequence. Other scientists believe that folding is a result
of the primary amino acid sequence and specific factors found
surrounding the synthesis site and/or the canal within the
endoplasmic reticulum with the assistance of chaperone
molecules and chelating
molecules such as Zinc and/or
Calcium. The ability of
proteins to fold into special 3-D
structures allow them to be
used for very strong structures
like keratin (hair, nails, claws),
tubulins (cytoskeletons),
collagen (connective tissue holding muscle to bone),
and even spider “silk” is made from various
combinations of 20 different amino acids. Secondary
structures that include hydrogen bonding, create pleated sheets and/or -helix structures.
Alpha-helix
Page 9 (Cont. #8 A/P Biology)
So the take home message is that the secondary structure consists of the folding of the
protein molecule where hydrogen bonds form to hold the different parts of the protein
strands (polypeptides) together. These multiple hydrogen bonds can be fairly strong and
flexible (see examples: hair for strong and flexible- claws for strong).
3.) Tertiary structure: The final folded shape of a protein that allows the protein to have
the most stable conformation for its environment, can be referred to as the tertiary
structure. Certain amino acids (cysteine and methionine) form covalent bonds (usually a
sulfur-sulfur bond) to allow the protein to fold back on itself. In short, the tertiary
structure is a combination of covalent bonds (sulfur-sulfur), the interaction of all the “R”
groups to form non-polar areas, and polar areas that MUST fit together in precise
manners to afford the protein a proper spatial configuration to do its job. The interaction
of non-polar “R” groups within the interior of a protein molecule forms a weak attraction
called van der Waal’s forces (these attractions are individually weak, but many of these
forces can form attractions that are quite strong when added together).
4.) Quaternary structure: This is the interaction of two or more protein strands. All the
different attractive forces are in play in this kind of protein chain association. Each chain
is referred to as a sub-unit. The sub-units need not be the same, nor do they have to be
anywhere near the same size. Example of replicated sub-units interacting would be
hemoglobin. Look this up on the Internet!)
Certain protein structures are known to be extremely versatile in their ability to
withstand high pressure, high temperatures, very low temperatures, and other drastic or
extreme conditions. At the same time, proteins can lose their ability to perform a specific
task (such as structural or enzymatic) if the conditions for that particular protein change.
In other words, most proteins work best at a specific pH, temperature, and pressure. If
any of these conditions change, the protein may lose some or all of its ability to function.
This is called denaturation! When the conditions return to
their original parameters, the protein MAY revert back (this
is called annealing) to its original shape and function. If the
conditions are so harsh that the protein cannot return to its
original configuration, the protein has been irreversibly
denatured (example egg “whites” - they look clear when you first crack open the eggthen they turn white when you heat the proteins- white protein is irreversibly denatured
and cannot turn back to clear once heat has been removed..
Proteins can also be altered by small changes in the amino acid sequence. As we
have mentioned before, one amino acid difference in the hemoglobin molecule can cause
the entire red blood cell to “sickle” (see above).
Nucleic acids are macromolecules that store genetic
information for each and every living organism on
Earth. Moreover, individual nucleic acids are also used
as the main source of energy (as in energy packets called
ATP-Adenosine Triphosphate). To a lesser extent some
nucleic acids are used in structural capacities as well as
specialized enzymes.
The nucleotide is made up of three parts:
Page 10 (Cont. #8 A/P Biology)
There are two CLASSES of nucleic acids:
PURINES
PYRIMIDINES
It is not important to know the actual structure of these
molecules, rather it IS important that you know
purines from pyrimidines and that:
#1
Adenine is abbreviated
“A”
Guanine is abbreviated
“G”
Cytosine is abbreviated
“C”
Thymine is abbreviated
“T”
Uracil is abbreviated
“U”
Page 11 (Cont. #8 A/P Biology)
#2
AGTC is found in DNA and that “A” binds with “T” -using 2 hydrogen bonds to hold
these together- and “G” binds with “C” using 3 hydrogen bonds to hold these
together.
AGCU is found in RNA and that “A” binds with “U” and “G” binds with “C”. (when
a strand of DNA and a strand of RNA are "together" (as in transcription), the "T"
in the DNA binds with the "A" in RNA)
#3
There are three important differences between DNA and RNAa.) DNA contains Thymine and RNA contains Uracil
b.) DNA contains deoxyribose as a sugar, RNA contains ribose as a sugar
c.) DNA is “normally” a double stranded helix and RNA is “normally” a single
stranded molecule.
Page 12 (Cont. Macromolecules A/P Biology)
We have several chemical tests that can help us determine if certain macromolecules are
present. If we have an unknown compound, we may want to determine if it has sugar,
starch, glycogen, protein or lipid . Macromolecules can be detected with certain chemical
solutions.
Macromolecule Tests
Iodine- detects the presence of plant starch (long chains of sugar
molecules/polysaccharides) by turning dark blue or purple and animal glycogen by
turning purple/brown color. The actual chemical interaction of Iodine with
polysaccharides is complex, suffice it say that the interaction produces a dark purple
color.
Benedict’s Solution- detects the presence of simple sugars by turning green, orange, or
brown when the indicator and testing solution is heated for 3 minutes in boiling water.
Biuret Solution- detects the presence of protein by turning a light purple.
Sudan Black III- detects the presence of fats or lipids and long chain fatty acids by
turning bright red. There is also the “Paper Test” for lipids that is far less technical, yet
is quite effective in that lipids applied to paper turns paper translucent.
Answer the following questions here and on your scan-tron.
_____ 1.) An ionic bond is
a.) only when one elements gives up an electron to satisfy the outer shell of another
element
b.) only when one element shares an electron to satisfy the outer shell of another
element
c.) only when an oxidation reduction reaction is occurring
d.) all of the above are correct
_____ 2.) All covalent bonds
a.) involve the last two shells of electrons in the elements that are reacting
b.) involve only the last shell of electrons in the elements reacting
c.) involve only one pair of electrons
d.) are the same as Van der Waal’s forces
_____ 3.) (T/F) Elements that form ionic bonds can form crystals.
_____ 4.) (T/F) Most biological molecules use covalent bonding.
_____ 5.) (T/F) Hydrogen bonds are only formed when there is water present.
_____ 6.) (T/F) Hydrogen bonds hold DNA together.
_____ 7.) (T/F) Iodine can test for both starch and glycogen.
_____ 8.) (T/F) Egg albumin (look this up) will test positive with Benedict’s solution.
Page 13 (Cont. #8 A/P Biology)
_____ 9.) Carbohydrates contain:
a.) nitrogen, hydrogen, carbon and oxygen in a 1:2:1:1 ratio
b.) hydrogen and carbon in a 1:1 ratio
c.) carbon, hydrogen, and oxygen in a 1:2:1 ratio
d.) carbon, hydrogen and oxygen in a 1:3:1 ratio
e.) carbon, hydrogen and oxygen in a 1:1:1 ratio
_____ 10.) The molecules to the right represent:
a.) structural isomers
b.) the exact same molecule
c.) two totally unrelated molecules
d.) stereoisomers
_____ 11.) A typical polymer of sugar in plants can be called:
a.) a monosaccharide b.) a disaccharide c.) glycogen d.) starch
_____ 12.) A positive Biuret test means:
a.) protein is present b.) carbohydrates are present c.) nucleic acids are present
_____ 13.) Which indicator would be used to detect stearic acid? (look this up!)
a.) Biuret solution b.) Sudan Black 3 c.) Iodine d.) Benedict’s solution
_____ 14.) What macromolecule is egg white or egg albumin made up of?
a.) sugar b.) starch c.) protein d.) nucleic acids e.) glycogen
_____ 15.) Which indicator would give a positive test for butter?
a.) Benedict's b.) Biuret c.) Iodine d.) Sudan Black 3
Answer the following questions on this handout ONLY!
_____ 16.) (T/F) The chemical properties of isotopes are exactly the same. (Internet)
_____ 17.) The primary structure of a protein consists of…
a.) the specific folding structure
b.) the sequence of amino acids
c.) interaction of 2 chains of protein
d.) ability to form hydrogen bonds
_____ 18.) Secondary protein structures are: (Mark all that apply.)
a.) sequence of amino acids
b.) alpha helix
c.) pleated sheets
d.) interaction of protein folding back upon itself
e.) interaction of two different chains of proteins
Page 14 (Cont. Handout #8 AP Biology)
_____ 19.) Sickle celled hemoglobin is caused by…
a.) a single amino acid change in the hemoglobin molecule
b.) a poor diet
c.) a disease given to you by an infected mosquito
d.) a carcinogen
e.) all of the above are correct
_____ 20.) A peptide bond…
a.) is formed by dehydration synthesis
b.) requires an input of energy
c.) cause the production of a water molecule
d.) is unique to proteins
e.) all of the above are correct
Answer the following question on this handout.
21.) Explain how plants can “get away” with making long chains of polysaccharides (that
require many molecules of glucose that “could” be used for energy) for structural
purposes?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
22.) List those amino acids (inside a protein molecule that would most likely be involved
in Van der Waal’s forces of attraction. (Hint- see Handout #7)
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
23.) Using your book for specific structures of the amino acids below, draw the peptide
bond between: (see page 7 of this handout and page 41 of text)
A and Q
N and H
Page 15 (Cont. Handout #8 AP Biology)
24.) Explain what a nucleotide and a nucleoside are.
25.) In question 14, what OTHER molecules/organelles are present in egg whites of a
freshly broken egg?
25.) List the three main differences between RNA and DNA.
26.) What are Chargaff’s Rules and how did this help solve the structure of the DNA
molecule?
27.) Speculate which molecule came first in history, the RNA molecule or the DNA.
You must support your answer with solid reasoning.
28.) For the following DNA SINGLE STRAND Sequence… What would be its
complement (in other words, what nucleotides would match up-look at handout!)
(The first one is done for you…)
A-T-T-C-G-A-T-A-T-T-A
TFor the following DNA Single strand sequence, what would the complement mRNA
sequence?
A-T-T-C-G-A-T-A-T-T-A
U-
Appendix 1 (Handout #8)
Appendix 2 (for handout #8)
Element
Symbol
Atomic
#
8
Approx.
% of Earth’s
Crust by
Weight
46.6
% of
human
body by
Weight
65.0
Oxygen
O
Silicon
Aluminum
Iron
Si
Al
Fe
14
13
26
27.7
6.5
5.0
Trace
Trace
Trace
Calcium
Ca
20
3.6
1.5
Sodium
Na
11
2.8
0.2
Potassium
K
19
2.6
0.4
Magnesium
Mg
12
2.1
0.1
Hydrogen
H
1
0.14
9.5
Manganese
Fluorine
Phosphorous
Mn
F
P
25
9
15
0.1
0.07
0.07
Trace
Trace
1.0
Carbon
Sulfur
Chlorine
C
S
Cl
6
16
17
0.03
0.03
0.01
18.5
0.3
0.2
Vanadium
Chromium
Copper
Nitrogen
V
Cr
Cu
N
23
24
29
7
0.01
0.01
0.01
Trace
Trace
Trace
Trace
3.3
Boron
Cobalt
Zinc
Selenium
Molybdenum
Tin
Iodine
B
Co
Zn
Se
Mo
Sn
I
5
27
30
34
42
50
53
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Trace
Importance or Function
Required for cellular respiration,
Component of water
Critical component of human
blood
Components of bones and teeth;
triggers muscle contraction
Principal positive ion outside
cells; important to nerve function
Principal positive ion inside
cells; important in nerve function
Critical component of many
energy transferring reactions
Electron carrier; component of
water and most organic
molecules
Backbone of nucleic acids;
important in energy transfer
Backbone of organic molecules
Component of most proteins
Principal negative ion outside
cells
Component of proteins and
nucleic acids
Key component in enzymes
Key component in enzymes
Component of thyroid hormone
Date: __________________
Lesson Plan for Handout #8
A/P Biology
Objective: TLWD ability to identify biological macromolecules, explain how they are
used in the cell and body, determine how to detect specific macromolecules with
indicator solutions, explain what are functional groups, stereo isomers, structural isomers,
and determine the chemical and physical properties of each macromolecule when given
handout #8.
Content: Biological macromolecules, structure, function
Method: Power point, white board, discussion and demonstration of indicators.
Homework: Complete #8
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