Chapter 3 The Molecules of Cells

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Chapter 3 The Molecules of Cells
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3.1- This chapter starts off with a description
of what organic molecules are. The are carbon
containing compounds. Organic molecules such as
methane CH4, are hydrocarbons, they are made only
of carbon and hydrogen. Compounds that have the
same molecular formula, but have the atoms
arranged differently are called isomers.
Compounds that are mirror images of each other
are called sterioisomers.
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3.2- There is a table on page 35 that shows 4
functional groups found on organic molecules.
Learn these so that we can use this terminology
in the very near future. They may also show up
on the exam. They are hydroxyl groups, carbonyl
groups, carboxyl groups and amino groups. Also
know what makes a molecule an alcohol, an
aldehyde, a ketone, a carboxylic acid, or an
amine.
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3.3- The gist of how this material is being
handled becomes clear in this section. We
started with atoms which make molecules. We
considered functional groups and now we learn
that a cell makes or acquires precursors we call
monomers, and builds macromolecules from them.
In more cases than not, the monomers are combined
by a water molecule being pulled from them. We
call these reactions dehydration reactions. As
we will see later, polymers are broken down by
putting the water back in. We call that
hydrolysis.
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3.4- The first class of biomolecules considered
are the carbohydrates. The monomers are
monosaccharides. (Think of Saccharine to
remember the term.) Monosaccharides are simple
sugars and include glucose, fructose, ribose, and
many others.
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3.5- Two monosaccharides can be combined to form
a disaccharide. Two examples are sucrose (table
sugar), which is made of glucose and fructose,
and lactose (breast milk sugar), which is made of
glucose and galactose.
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3.7- Polysaccharides are long chains of
monosaccharides. Examples are starch, glycogen,
cellulose which are all polymers of glucose. So
what are the differences. Starch and glycogen
are similar except glycogen is a branched chain.
The differences between them and cellulose is in
the geometry of the bonds between the glucose
molecules. Our enzymes can hydrolyze the bonds
in starch and glycogen but not in cellulose. In
fact no animal, including termites, is able to
break down cellulose. So how does a termite eat
your house?
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3.8- Lipids. This section is concerned with
glycerides. As you are about to see there are
other types of lipids. Glycerides are a glycerol
molecules with one or more fatty acids attached.
(see the figure on page 40.) Fatty acids are
long chains of carbon and are very nonpolar or
hydrophobic. If the carbons have all the
possible hydrogens they are said to be
"saturated" with hydrogen. These are saturated
fats. If they do not have all the possible
hydrogens, there will be double bonds between
adjacent carbons. Double bond means the carbons
are sharing two pairs of electrons. These are
unsaturated fats. The more unsaturated the fatty
acid the more liquid it is. The more saturated
the fatty acid the more viscous (solid) it is. A
glycerol with a fatty acid on all three carbons
is a triglyceride. As you know they check the
triglyceride levels in your blood when they do
blood tests.
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3.9- Phospholipids and steroids. It is not
clear to me why they put these together.
Phospholipids are diglycerides with a phosphate
on the third carbon of the glycerol molecule.
Phospholipids make up most of the lipid bylayers
that make up membranes as we will discuss soon.
Steriods are complex organic molecules made up of
four rings as shown in the figure on page 41.
That figure shows cholesterol which is a steriod
you are no doubt familiar with. Steriods often
function in animals as hormones, which are
produced by certain tissues and secreted into the
blood stream. They then attach to the cell
surfaces in other tissues and induce changes in
gene expression or some other function of the
cell.
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3.10- Anabolic steroids are synthetic variants
of testosterone and induce the body to put on
muscle tissue. The problem with using these to
build muscle tissue is that they also can cause
violent mood swings, deep depression, and may
damage the liver leading to cancer. They may
also induce the body to reduce the production of
testosterone leading to impotence.
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3.11- Proteins are long chains of amino acids.
Proteins fall into seven classes that include
structural (hair), contractile (muscle), storage
(albumins), defensive (antibodies), transport
(hemoglobin), signal (hormones), and enzymes
(betagalactosidase).
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3.12- Figure A and B on page 42 show the basic
structure of an amino acid and three examples.
There are 20 different amino acids that are found
in protein, therefore there are 20 different R
groups.
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3.13- The figure at the top of page 43 shows the
dehydration reaction between the carboxyl group
of one amino acid and the amino group of another
that results in a peptide bond. We also call
proteins polypeptides because of the many peptide
bonds in the chain. A typical protein will have
around 300 amino acids in the chain, although
many are considerably smaller and others may be
considerably larger.
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3.14- It is the final three dimensional shape of
a protein, with certain amino acids located in
the "active site" that allows for the protein to
function properly. Any significant distortion of
that shape may distort the active site and result
in an inactive protein. The distortion is
referred to as denaturation. Heat and changes in
pH are factors that can denature a protein.
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3.15- Primary structure is the sequence of amino
acids in the chain. Primary structure determines
the other three levels of structure.
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3.16- Secondary structure occurs when a region
of the protein forms either a helix, the alpha
structure, or a fully extended form called the
beta structure. The fully extended form leads to
a structure called a pleated sheet when two or
more are aligned side by side in the protein.
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3.17- Tertiary structure occurs when the protein
folds up into its three dimensional shape. The
primary force that governs this folding is
hydrophilic/hydrophobic interactions. Some R
groups are hydrophobic (nonpolar) and will turn
toward the interior of the protein where they are
protected from the water in the cytoplasm.
Hydrophilic amino acids will turn toward the
surface of the protein where they are in contact
with the water in the cytoplasm.
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3.18- Some enzymes are made of two or more
proteins that come together to form a complex.
That is called quaternary structure.
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3.20- Nucleic acids are long (very long) chains
of nucleotides. These are the largest molecules
known. The two classes of nucleic acids are DNA
and RNA. A nucleotide consists of a sugar that
has attached to it a nitrogenous base and a
phosphate. The sugar in DNA is deoxyribose (that
is where the D comes from) and the sugar in RNA
is ribose (hence the R). In fact the only
correct answer to the question "What is the
difference between DNA and RNA?" is the sugar.
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The nucleotides are put together by attaching the
phosphate of one to the sugar of another (by
dehydration). This results in a sugar-phosphate
backbone with the bases sticking off
perpendicular to the chain. One chain is
referred to as a strand. Most DNA molecules are
"double stranded". Two strands are held together
by hydrogen bonding between the bases (shown in
figure c page 47). There are four bases found in
DNA, Adenine always base pairs with Thymine and
Guanine always base pairs with Cytosine. It is
this base pairing that allows nucleic acid to
serve as an information storing molecule and
therefore the genetic material! Double stranded
DNA forms a helix.
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