Download Homework set 1: Biological Molecules

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Homework set 1: Biological Molecules
Molecules found in cells most frequently are organic, made up of primarily chains or groups of carbon atoms.
These include carbohydrates, sugars and lipids. Carbon is a versatile element because it easily forms 4
covalent bonds. Carbons may bond or share electrons with other carbons as well as other elements to form
chain or ring structures. In the following exercises, draw the molecules. Remember from chemistry that a line
between the two elemental symbols illustrates a single bond between 2 atoms. For example, a carbon-carbon
single bond is shown as C-C. A double bond is shown by 2 lines: C=C.
1. How is a triple bond represented?
2. Draw an atomic model (showing subatomic particles, in this case you can just write #C’s and #n’s, but show
all the valence electrons) containing two carbons sharing one pair of electrons: (note: although it does not
exist in nature, do not draw any other atoms, just the carbon atoms)
3. Now draw an atomic model containing two carbons sharing two pairs (4) of electrons between two carbons:
(note: although it does not exist in nature, do not draw any other atoms)
Hydrogen is most stable when it has two electrons in its outermost electron shell. A carbon sharing 4 electrons
with hydrogen forms a stable molecule methane.
4. Using chemical symbols (shows elements and bonds), draw a methane molecule:
Oxygen forms 2 bonds. If it is found within a carbon chain, it is called an ether (R-O-R: where R stands for one
or more carbon atoms). If Oxygen is bonded to a carbon with a double bond, it forms a ketone.
5. Using chemical symbols (DO NOT USE R), draw a simple ketone.
If oxygen is bonded to a carbon chain at the end of the molecule, it results in an aldehyde.
6. Using chemical symbols, draw an aldehyde.
When oxygen is double bonded to a carbon in either of the above forms, it is known as a carbonyl group. So
while a ketone or an aldehyde is a carbonyl, a carbonyl is not necessarily a ketone or an aldehyde.
Other bonds where oxygen is involved include alcohols and carboxylic acids.
7. Using chemical symbols, draw each of these functional groups and a simple example of each. (note: you are
not required to name them)
a. Alcohol
b. Carboxy groupl
Nitrogen has a valence of three and in
biological molecules is usually bonded to a
carbon skeleton of some kind:
(an amino group)
8. Draw a carbonyl using generic terms as shown above for an amino group?
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9. How many bonds does carbon form? Nitrogen? Ionic Nitrogen? Oxygen? Ionic Oxygen?
If an atom forms either more bonds or fewer bonds than it needs to in order to be a neutral
molecule, it will take on a charge. It is common for Nitrogen to form 4 bonds because it is so
electronegative. For example, instead of forming NH3 (ammonia), it will form NH4+ (ammoniumion). Thus, in aqueous solution, the nitrogen end of a molecule almost always carries a positive
charge.
Macro Molecules
With our knowledge of the bonding properties of C, H, O, and N, we can construct more
complex organic molecules. Please take time to learn each of these complex molecules
thoroughly.
You will be expected to tell the differences between each of them and understand their
functions in organisms.
CARBOHYDRATES:
Major functions in the body include:
1) Being broken down to form energy with a release of CO2 and water,
2) A storage form of energy,
3) Forming biological structures — most notable the cell wall of plants and receptor
molecules on the cell membrane.
The simplest type of sugar is a monosaccharide.
Monosaccharides have multiple hydroxyl groups and a carbonyl group (aldehyde or ketone
group) in their molecular structure.
10. Draw monosaccharides, glucose and fructose, in the chain form (not ring form):
11. Write the chemical formula for both glucose and fructose:
12. What molecular similarities, in structure, are there between the glucose and fructose
molecules?
13. What are the differences?
14. What are these two molecules called in relation to one another (when molecules have the
same atoms but in a different arrangement)?
The differences in these molecules, even though it is just the rearrangement of the atoms,
result in different physical properties such as
melting point, solubility, etc.
Even the taste of a particular sugar can be
different based on the fact
that it has a different structure, though the
molecular formula is the same.
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There are 5 carbon sugars such as ribose:
Five carbon sugars are not used for energy, but are used within the structure of DNA and RNA.
The carbohydrates shown above are drawn in what is known as the "chain form" of these
monosaccharides. In solution (which is where we find them in living cells) the chain form of
these monosaccharides exists only in small amounts. Most often, they exist in a "ring form"
which is considerably more stable. (Principles: p 40, Ch 8 Fig 2 / Campbell Biology p 71). If we
use glucose as an example as in your book, in a ring form, the aldehyde group on the end of the
sugar swings around and forms a bond with one of the carbons further along the chain (see
Figure 5, Campbell 9th edition). In the case of a 6-carbon sugar, this will occur with carbon #5.
The double bond between the Oxygen and the Carbon is broken and the oxygen forms a bond
with hydrogen as this occurs. As this reaction occurs randomly in a solution, depending on the
position of the aldehyde when the ring closes, the new –OH group may end up on either the top
or the bottom of the ring structure. If it is on the bottom, we call it an alpha glucose (α-glucose).
If the –OH group is on the top, we call it beta glucose (β-glucose) (Principles: Fig 8.2 / Campbel
Fig 5.7). This is important as bonds between beta glucose molecules cannot be broken down by
most organisms (think about the differences between starch and cellulose).
15. Draw the formation of α-glucose and a β-glucose starting from the chain form using your
book as a guide.
Disaccharides are formed when glycosidic links (glyco- = sugar, -ic = pertaining to) between 2
monosaccharides will be in the ring form when this occurs. This reaction involves the loss of a
molecule of water and so is called dehydration synthesis. It is a common way to form biological
polymers. If the two sugars involved are in the α form, the resulting bond is called an α-1.4
glycosidic bond. This is because the #1 carbon of one sugar with an α-OH group becomes
bonded to the #4 carbon of the other sugar.
16. Use your text to find and draw this reaction (in the form of chemical equation, reactants and
products) forming an α-1,4 glycosidic bond (chemical symbols, DON’T use chemical formula
format which just show elements in their ratios, ex: NOT C5H10H5):
On the other hand, if two β-glucoses form a covalent bond, the result is a β-1,4 glycosidic link.
17. Draw the reaction (using chemical symbols)::
Although α-1,4 links are easily broken down by the chemical catalysts (enzymes) in our body, β1,4 links are not.
18. Would you guess cellulose (which most animals cannot break sown) consists of alpha or
beta links?
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LIPIDS:
Lipids are a diverse group of molecules. The main characteristic they share is insolubility in
water because they are nonpolar molecules. (If you are unsure what a nonpolar molecule is,
please ask before you go on!) The basic types of lipids we will be concerned with are
triglycerides or triacylglycerides (which we call fats), steroids (molecules that are based on
cholesterol) and phospholipids (which make up the majority of cell membranes), terpenes
(including chlorophyll) and prostaglandins (which act as hormones in animals)
Steroids are molecules that are based on cholesterol. Below is an “abbreviated” structure of
cholesterol. Each "line" of the carbon rings represents a bond while a carbon atom is assumed
to be at the angle between any two bonds. Even though they may not be drawn in, hydrogen
atoms are assumed to be present in order to fulfill the requirement of each carbon having 4
bonds. Thus a carbon at one angle of the ring structure will have 2 hydrogens attached as well.
19. Given and abbreviated form of a molecule of
cholesterol below, draw an “unabbreviated”
molecule of cholesterol.
Triacylglycerides are made up of one molecule of glycerol (which is basically three carbons
attached to 3 hydroxyl groups) bonded to 3 fatty acids (a chain of carbons and hydrogens with a
carboxyl group on the end).
H
R-C-OH
|
II
H-C-OH
O
|
H-C-OH
|
H-C-OH
|
H
Fatty acid
Glycerol
20. What kind of organic compound is glycerol? (Hint: look at the functional groups present)
21. Construct a monoglyceride from this molecule of glycerol + a fatty acid (make the fatty acids
up) via dehydration synthesis: (be sure to show the reaction, use chemical symbol format)
22. How many reactions are required to make a triglyceride?
Fatty acids are found in nature in both saturated and unsaturated forms.
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23. Which kind did you draw? What different physical properties occur as a result of being
saturated or unsaturated?
Make sure you can recognize a glycerol molecule and both saturated and unsaturated fats.
Phospholipids are amphipathic molecules. They have one end that is polar, and one end that is
nonpolar. Due to the interactions each end prefers they have the unique property of being able
to form a stable bilayer in a water environment.
24. Look in your text in Principles p 45, ch 9 fig 5 or in Campbell p 76. Explain why phospholipids
would form a bilayer in water and not just a single layer.
Terpenes have a fundamental building block called the isoprene unit, C5H8.
isoprene
head
tail
Terpenes commonly occur in the oils that give plants their fragrance, they occur as components
of many biologically important pigments, such as the photosynthetic pigment chlorophyll in
plants and the visual pigment retinal in vertebrate eyes. Rubber is also a terpene. The larger
structures are "assembled"from several isoprene units, usually by "head-to-tail" linked isoprene
units.
myrcene
Terpenes can be cyclic or acyclic, with a large range of structural variations. A few examples are
given below. More than 23,000 terpene systems are known. Monoterpenes are based on two
isoprene units and so have the molecular formula C10H16
Other terpenes have multiples of the isoprene C5 units such as: C15, C20, C25, C30 etc.
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Limonene
Menthol
Camphor
(Found in skin
of citrus fruits)
vitamin A
(involved in the chemistry of vision)
citral
(lemon grass)
β-carotene
(in carrots and other vegetables, enzymes convert it to vitamin A)
Prostaglandins are a group of about 20 lipids that are modified fatty acids, with two nonpolar
"tails" attached to a five-carbon ring. Prostaglandins occur in many vertebrate tissues, where
they appear to act as local chemical messengers. The name is derived from the fact that the
original members of the series were derived from the prostate gland (in sheep). Structurally,
they are a C20 system containing a cyclopentane unit, a carboxylic acid functional group and OH groups at C11 and C15. They are divided into series A, B, C, D, E and F depending on the
cyclopentane substituents. Aspirin is known to inhibit an enzyme involved in prostaglandin
biosynthesis so lowering the prostaglandin levels in the body and as a result, lowering pain and
inflammation.
Prostaglandin E1 (PGE1)
Prostaglandin F2α (PGF2α )
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PROTEINS are very large and complex molecules. They are polymers (many units) of repeating
smaller molecules collectively called amino acids. Today we will focus on amino acids and their
structure; we will take a look at examples of protein structures later. Proteins serve two basic
functions in the body: they give cells structure and are found between cells providing structure,
and they are our biological catalysts — enzymes.
Let's start at the beginning, though. When looking at an organic acid, it consists of an "R" group
(usually a carbon skeleton) attached to a carboxyl group.
25. Write down the chemical formula for a carboxyl group:
If the carbon directly adjacent to the carboxyl group has an amino group attached to it, this
gives us an amino acid.
26. On the standard format of an amino acid below, circle the amino group and put a square
around the carboxyl group.
In living systems there are approximately 20 amino acids that commonly occur. Although all
amino acids have an amino group and a carboxyl group, the R group will vary. Two of the
simplest amino acids are:
Glvcine
Alanine
27. What are the functional [R] groups (aka side chain) for these amino acids? (Hint: the R
group is what makes one amino acid different from the others)
Proteins are very long polymers of different amino acids. A protein may contain anywhere from
8 to 100,000 amino acids. The resulting long chain may fold back and forth on itself and have
virtually any imaginable pattern.
The bonds between amino acids are called peptide bonds and are covalent bonds formed when
a molecule of water is removed from two adjacent amino acids.
28. This type of synthesis in forming any large biological molecule is called:
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The formation of a peptide bond results from the loss of the —OH from the carboxyl group and
the loss of one —H from the amino group. The resulting peptide bond is formed between the
carbon of the carboxyl group and the nitrogen of the amino group. NOTE that the "R" groups
are not affected in the formation of a peptide bond. Their structure is preserved and will
ultimately decide the characteristics of the protein being made.
29. Draw a molecule of a dipeptide consisting of glycine and alanine.
Solubility. Water is called the universal solvent. It is the liquid upon which life is based. The
solubility of biological molecules in water in many ways determines where in a cell those
molecules will be found and what their job will be. Predicting the solubility of, say, a protein will
tell us whether that protein will be found in the cytosol of the cell (the liquid form), or within
the cell membrane.
In general, solubility is based on the fact that water is polar. Other like substances that are
either polar or charged will also dissolve in water. It is clear that NaCl, for example, will dissolve
in water. However, what about biological molecules?
30. Predict the solubility of the functional groups.
Hydroxyl groups
Soluble
Methyl
Soluble
Ketones
Soluble
Amino groups
Soluble
Carboxyl groups
Soluble
Aldehyde groups
Soluble
Insoluble
Insoluble
Insoluble
Insoluble
Insoluble
Insoluble
On what chemical basis are you making your judgments for these functional groups? Let's make
sure you understand the concepts. It turns out that some molecules with these groups are
soluble in water and others are not. Why the difference? Let's look at some examples.
An —OH group will increase the solubility of a molecule. This is because the large polar oxygen
atom attracts the hydrogens of water molecules. The more hydroxyl groups a molecule has, the
more soluble it will be. On the other hand, if a molecule is a long chain of carbons (forming a
nonpolar molecule) with just one hydroxyl group on the end, that hydroxyl group will not be
enough to make the molecule soluble in water. The same is true for ketones and carboxylic
acids. If the molecule has just one ketone or carboxyl group, it will be soluble if it is small. If
they are attached to a large nonpolar carbon chain, however, the molecule will not be soluble.
What about amino acids? Individual amino acids are soluble in water. The carboxyl and amino
group will lose a hydrogen ion and the amino group will pick up a hydrogen ion. However, when
these amino acids are placed into a polypeptide, the carboxyl and amino groups are now tied
up in peptide bonds between the amino acids. They can no longer ionize. Thus, it will be the R
groups of the individual amino acids, which will determine the solubility of the molecule. In
general, a benzene or carbon ring, or a chain of carbon molecules with just hydrogens attached
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will decrease solubility. Having electronegative atoms such as nitrogen, oxygen (especially
double bonded so it "sticks out") or sulfur will increase solubility.
Suggested Practice:
Using your text on page 79 and the blank area below, take turns with your lab partners drawing
out amino acids for each other. Quiz each other on whether the amino acid would be soluble or
not (just consider the R groups). You do not have to memorize each amino acid, just be able to
predict its solubility. (NOT TO TURN IN)