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Molecular Composition of

Cells
Molecular Composition of Cells
• One of the common features of organisms here on Earth is their
biochemical composition.
• All organisms contain a common set of chemicals, such as carbon,
oxygen, nitrogen, phosphorus, sulfur, and hydrogen, which build
larger and more complex molecules necessary in life.
• These large molecules—carbohydrates, lipids, proteins, and nucleic
acids—combine to produce different structures or substances that
perform specific functions in the cell.
Carbohydrates
Carbohydrates

• believed to be the most abundant


• more than 75% of the dry weight of
plants is carbohydrate in nature
• majority of carbohydrates have a
carbon-hydrogen-oxygen ratio of 1 :
2: 1
• include simple and complex sugars
• well-known as great sources of
energy
• provide structural support for
plants
Types and Functions of Carbohydrates
• Can be: monosaccharides,
disaccharides, and polysaccharides.
• Monosaccharides are called simple
sugars because they are monomers,
or the single structural units, of
some complex carbohydrates.
• Disaccharides are composed of two
monosaccharides joined together.
• Polysaccharides are composed of at
least three monosaccharides.
Monosaccharides
• Can be classified as aldose or ketose according to the placement of
chemicals in their structure.
• Aldoses: presence of an aldehyde (—CHO), usually at the terminal
atom.
• Ketoses: presence of ketone or a carbonyl group (C=O), usually at the
second atom of the molecule.
• When the carbonyl group is mixed with the hydroxyl group (—OH) in
an aqueous solution, the result is a cyclic compound (either
hemiacetal or hemiketal), which looks like a water-soluble crystalline
solid.
• A monosaccharide can also
be classified according to
the number of carbon
atoms it has.
• Can be: diose, triose,
tetrose, and so on.
• One familiar example is the
pentose which includes the
ribose found in RNA and
some vitamins.
• Some derivatives of
monosaccharides are also
important, such as ascorbic
acid, sorbitol, and mannitol.
• Monosaccharides provide
immediate energy to the
organism that takes them.
Disaccharides
• Composed of two monosaccharides
joined together through a process
called condensation reaction.
• In this process, dehydration synthesis
takes place, wherein water is
extracted upon combining the two
molecules.
• The result of the condensation
reaction is the formation of
glycosidic bond, a type of covalent
bond that links a carbohydrate
molecule to another molecule.
• Like monosaccharides, disaccharides are sweet and soluble in water.
• Sucrose comes from combining glucose and fructose.
• Lactose (milk sugar) is a combination of glucose and galactose. Whey,
a by-product of dairy production, contains lactose and is used in
making baked products.
• Maltose (beer sugar) comes from two glucose molecules. It is the
least sweet among the previously mentioned disaccharides. In making
beer, starches turn into maltose during the malting process.
Polysaccharides
• Composed of at least three
monosaccharides.
• Are not sweet and do not form
crystals when water molecules
are removed.
• The actual structure of certain
tissues or cellular parts may
depend on the polysaccharide’s
molecular structure, which is
either branched or linear.
• A linear polysaccharide
forms a rigid structure
and is insoluble in
water.
• A branched
polysaccharide is
soluble in water.
• Most polysaccharides are used for energy storage.
• Starch and glycogen are composed of chains of glucose molecules.
• In plants, energy storage is in the form of starch.
• In animals, energy storage is in the form of glycogen.
• Polysaccharides have many health benefits.
• Pectin is a soluble fiber.
• Found in apples, oranges,
grapefruits, bananas,
cabbages, and carrots.
• When extracted, pectin can
be sold commercially as
white or brown powder, and
can be used as a gelling
agent in jams or jellies.
• Chitin is found in the cell walls of
fungi and the exoskeletons of
some animals such as shrimp,
crab, krill, scorpion, and many
insects.
• Chitin has stronger hydrogen
bonds between bordering
polymers, which is why it is
harder and more stable than
cellulose.
• It also has antibacterial and
antiviral properties.
The Stereochemistry of
Carbohydrates
Stereochemistry /ˌsterēōˈkeməstrē,ˌstirēōˈkeməstrē/ noun. the branch of chemistry
concerned with the three-dimensional arrangement of atoms and molecules and
the effect of this on chemical reactions.
Stereoisomers
• Glyceraldehyde, the simplest carbohydrate, exists in two isomeric
forms that are mirror images of each other.

• These forms are stereoisomers of each other.


• Glyceraldehyde is a chiral molecule — it cannot be superimposed on
its mirror image.
Isomerism
• There are two types of isomerism: structural isomerism and
stereoisomerism.
• Structural isomerism is defined as isomers having identical molecular
formulas but differing in the order in which the individual atoms are
connected.
• In stereoisomerism,
the isomers have the
same molecular
formula and the same
structural formula but
differ in the spatial
arrangement of the
atoms in the molecule.
Chiral Carbons
• A molecule that is nonsuperimposable on its mirror-image is said to
be chiral.
• Achiral objects can be superimposed on the mirror images (ex.
drinking glasses, spheres, and cubes)
• Any carbon atom which is connected to four different groups will be
chiral and will have two nonsuperimposable mirror images; it is a
chiral carbon or a center of chirality.
• If any of the two groups on the carbon are the same, the carbon atom cannot
be chiral.
1. 2. 3. 4.
1. 2. 3.
1. 2. 3.
2 n Rule
• When a molecule has more than one chiral carbon, each carbon can
possibly be arranged in either the right-hand or left-hand form, thus if
there are n chiral carbons, there are 2n possible stereoisomers.
Fischer Projections
• Emil Fischer, a Nobel Prize winning German chemist, devised a simple
method to represent a three-dimensional molecule using a two-
dimensional drawing. This is called a Fischer Projection.
• When drawing Fischer projections, the molecule is drawn in the form
of a cross with the chiral carbon centered at the point of intersection.
• In writing the Fischer
projection of
carbohydrates, place
the carbonyl group at
or near the top and the
last achiral carbon
(CH2OH) at the bottom.
Naming
Stereoisomers

• When there is more than one


chiral center in a carbohydrate,
look at the chiral carbon farthest
from the carbonyl group: if the
hydroxy group points to right
when the carbonyl is “up” it is
the D-isomer, and when the
hydroxy group points to the left,
it is the L-isomer.
• L- is from the Latin levo meaning
left and D- is from the Latin
dextro meaning right.
• If there are two or more
chiral carbons in the
molecule, the chiral carbon
most distant from the
carbonyl group determines
the D- or L- isomers. This will
always be the second to the
last carbon in the Fischer
projection. Therefore, when
assigning D- or L- to more
complex isomers, focus only
on the second to the last
carbon.
Haworth Projections
• Experimental studies indicate that the dominant forms of
monosaccharides containing five or more carbons are cyclic
structures in aqueous solutions.
• The cyclic structure of monosaccharides is commonly represented
using Haworth projections, named after the English chemist Sir
Walter N. Haworth.
• The open-chain form of D-
glucose is converted to a cyclic
form through a ring closure
reaction involving the -OH
group on carbon five and the C-
1 carbonyl carbon.
• The carbonyl group at C-1
reacts with the hydroxyl group
at C-5 to give a six-membered
ring containing oxygen.
• The newly formed ring is a rigid
structure that has two planes,
one above the ring, the other
below.
• When the ring closes, the C-5 -
OH loses the hydrogen and the
oxygen is incorporated into the
ring.
• The C-1 carbonyl carbon loses
its double bond to oxygen and
becomes a single bond to -OH.
• The newly formed -OH at C-
1 (formerly the carbonyl
carbon) can be drawn above
or below the ring producing
two different isomers.
• These two isomers are
called anomers named α
(alpha) and β (beta)
anomers.
• In the α anomer, the C-1
hydroxyl group is below the
ring, in the β anomer, the C-
1 hydroxyl group is above
the ring.
Haworth Projection of Fructose

• Note the carbonyl carbon is carbon #2 in fructose. In the Haworth,


the carbonyl carbon will always be the carbon to the right of the
oxygen in the ring.
Biologically Important Disaccharides
• Two monosaccharides can react to form a disaccharide molecule in a
dehydration reaction.
Disaccarides

• Disaccharides are joined


through an “oxygen bridge”.
The carbon-oxygen bonds
are called glycosidic bonds.
• The most common
disaccharides are sucrose,
lactose, and maltose.
Sucrose
• Sucrose (table sugar) is the most abundant disaccharide in the
biological world. Sucrose contains an α-D-glucose unit and a β-D-
fructose unit joined by α , β (1 → 2) glycosidic linkage.
Lactose
• Lactose (milk sugar) is made up of a β-D-galactose unit and a D-
glucose unit joined by a β (1 → 4) glycosidic linkage.
Maltose
• Maltose (malt sugar) is made up of two D-glucose units. The
glycosidic linkage between two glucose units is an α (1 → 4) linkage.
Polysaccharides
• Polysaccharides consist of a large number of bound monosaccharide
units.
• Three very important polysaccharides are starch, glycogen, and
cellulose. They all contain only glucose units and are differentiated by
the type of glycosidic bonds and the degree of branching in the
molecule.
Starch

• Starch is the primary storage


polysaccharide in plants. The
most common forms of starch
are amylose and amylopectin.
• Most starches contain 20 to
25% amylose and 75 to 80%
amylopectin. Complete
hydrolysis (breakdown) of
both amylose and
amylopectin produces only D-
glucose. This Photo by Unknown Author is licensed under CC BY-SA
Amylose
• Amylose molecules are continuous chains of D-glucose units joined
by α-1,4-glycosidic linkage. There are no branch points in the
molecule which may contain of as many as 4,000 D-glucose units.
Amylopectin
• Amylopectin is a branched-
chain polysaccharide much
larger than amylose.
Amylopectin molecules, on the
average, consist of several
thousand α-D-glucose units
joined by α-1,4-glycosidic
linkage. The molecular masses
routinely approach 1 million or
more.
• Major sources of starch are rice,
corn, potatoes, and wheat.

This Photo by Unknown Author is licensed under CC BY-SA


Glycogen

• Glycogen is the major


glucose storage molecule in
animals. Structurally,
glycogen is very similar to
amylopectin (α-D-glucose
units joined by α-1,4-
glycosidic linkages), but
glycogen is more highly
branched.
Cellulose

• Cellulose is the most


abundant organic molecule
found in nature.
Structurally, cellulose is a
long, unbranched, D-glucose
polymer in which the
glucose units are linked by β
(1 → 4) glycosidic bonds.
• Cellulose in our diet is
referred to as fiber and, in
contrast to glycogen,
amylose, and amylopectin,
it cannot be digested. This is
because our digestive
system does not have the
enzymes to catalyze the
hydrolysis of β-glycosidic
bonds.

This Photo by Unknown Author is licensed under CC BY-SA


Lipids
Lipids

• Lipids area biomolecules


containing chains of
hydrocarbons.
• Hydrocarbons are organic
compounds that are made up
of carbon and hydrogen, and
are insoluble in water.
• When lipids are metabolized,
they release large amounts of
energy, and thus they are
useful to organisms.
This Photo by Unknown Author is licensed under CC BY-SA
• Aside from functioning as long-
term energy storage, they also
serve as insulation. Therefore,
organisms with more lipids in
the body can keep themselves
warmer.
• Animals that live in the polar
regions, such as polar bears,
reindeer, and penguins, have
bodies with thick fat layers as
their form of adaptation to the
freezing temperature.
• Lipids come in different types:
triglycerides, phospholipids,
steroids, and waxes.
This Photo by Unknown Author is licensed under CC BY-SA-NC
Triglycerides

• Generally known as fats,


triglycerides contain a
glycerol attached to three
fatty acids.
• A fatty acid is composed of
a long chain of carbon
atoms connected to a This Photo by Unknown Author is licensed under CC BY-SA-NC

carboxylic acid (−COOH).


• Fatty acids have two
different types: saturated
fats and unsaturated fats.
Saturated fats

• Saturated fats contain only


single bonds in the fatty
acid chain.
• Because of this, they are
normally solid at room
temperature.
Unsaturated fats

• Unsaturated fats, mostly


known as oils, contain one
or more double bonds in the
fatty acid chain.
• Because of this, they are
normally liquid at room
temperature.
Hydrogenation
In hydrogenation reactions, alkenes are converted into alkanes with
hydrogen gas (H2) and a catalyst (Pt, Ni, or some other metal). This
process is used to convert unsaturated vegetable oils, which are liquids
at room temp., to saturated fats, which are solids at room temp.
(shortening, etc.).
In partially hydrogenated vegetable oils, not all of the double bonds are
saturated, allowing the texture of the product to be controlled. In the
process, this twists some of the naturally-occurring cis double bonds
into trans isomers (trans fats).
Hydrolysis of
Triglycerides

Triglycerides can be broken


apart with water and an acid
catalyst (hydrolysis), or by
digestive enzymes called
lipases:
Saponification of
Triglycerides

In saponification reactions,
triglycerides react with strong
bases (NaOH or KOH) to form
the carboxylate salts of the
fatty acids, called soaps:
Soaps
• NaOH produces a “hard” soap, commonly found in bar soaps; KOH
produces a “soft” soap, such as those in shaving creams and liquid
soaps.
• These salts combine two solubility characteristics:
• a long, nonpolar, water-insoluble (hydrophobic) hydrocarbon “tail.”
• a charged, water-soluble (hydrophilic) “head.”
• In water, the “tails” become
tangled, leaving the charged
heads sticking out into the
solution, forming a structure
called a micelle.
Activity: Reactions of
Triglycerides
Write the products of the following reactions
Phospholipids
• Phospholipids are lipids with a phosphate
group.
• They have a structure similar to fats, but with
additional properties.
• Attached on one side of the glycerol
backbone are the hydrophobic or nonpolar
“tails,” which are composed of two chains of
fatty acids.
• Attached on the other side of the glycerol
backbone is the hydrophilic or polar “head,”
which is composed of a phosphate group.

This Photo by Unknown Author is licensed under CC BY-SA


Steroids
• Steroids have four fused carbon
rings.
• There are different types of
steroids according to the
functional group attached to
their carbon skeleton.
• In general, steroids help in
regulating metabolism, immune
response, reproduction, and
other essential biological
processes.

This Photo by Unknown Author is licensed under CC BY-SA


Cholesterol
• Cholesterol is a sterol (steroid
alcohol), one of the most
common steroid forms.
• Cholesterol formation usually
happens in major organs such as
the brain and blood vessels,
where it gets deposited on the
walls and linings of these
organs.

This Photo by Unknown Author is licensed under CC BY-SA


Waxes
• Waxes are esters (carboxylic acid derivatives), which are combined
from certain alcohols and fatty acids.
• Because of the long hydrocarbon chains, waxes are extremely
hydrophobic.
• Aside from waterproofing functions, waxes are also used for
protection. Cerumen, the earwax, prevents the entry of some
materials into the ear canal.
• Aside from being
hydrophobic, waxes are
also transparent, less
viscous, and have high
melting points (usually
about 48℃ and above).
• Because of these
properties, waxes have
been synthesized to form
a variety of products used
in cosmetics, lubricants,
insecticides, UV
protection materials, and
even food.
Proteins
Proteins
• Proteins are recognized as the most diverse among the biomolecules.
• They are believed to be the central compound necessary for life,
which is why they are also called life’s “building blocks.”
• Sometimes, our body parts can be characterized by the proteins they
contain or produce. For example, muscle cells contain large amounts
of actin and myosin proteins for contraction. Also, ligaments and
tendons contain collagen proteins to maintain their toughness
• Proteins also play major roles as antibodies, enzymes, hormones, and
other substances involved with digestion, respiration, reproduction,
and even normal vision.
• Proteins are composed of
chains of amino acids.
Amino acids contain an
amino group (-NH2) and an
acid group (-COOH). The
third group is called an R
group, which helps
distinguish the amino acids
from others, because its
specific name and function
in the body will depend on
the sets of chemicals that
are in this group.
• The R group ranges from
the polar to the nonpolar
side chains.
This Photo by Unknown Author is licensed under CC BY-SA
• The amino acid requirements of humans are classified into three
groups. The essential amino acids are those that cannot be produced
by our bodies. The nonessential amino acids are those that can be
produced by our bodies. Finally, the conditional amino acids are not
vital but may become urgent during health crisis or stress.
Peptide bond

• A peptide bond is a
chemical bond formed
between two molecules
when the carboxyl group of
one molecule reacts with
the amino group of the
other molecule, releasing a
molecule of water (H2O).
• This is a dehydration
synthesis reaction
Shapes of Proteins
• Whether hydrophilic or hydrophobic, the peptide’s R groups will help
determine the structure of the protein. The structures of a protein
and its corresponding function makes it unique.
• Peptide chains eventually twist and fold into their specialized shape,
forming the protein. Within the geometry of proteins are several
bonds that stabilize their structure and help them adapt to their
specific functions.
Primary Proteins
• The simplest structure of all proteins, this is composed only of a linear
sequence of amino acids in a peptide chain.

This Photo by Unknown Author is licensed under CC BY-SA


Secondary Proteins
• This is a three-dimensional
shape created by several
hydrogen bonds. The first
two patterns of the
secondary structure were
first predicted by Linus
Pauling and Robert Corey in
1951. They called the coiling
structure as alpha (𝛼) helix
because it was the first
pattern they had discovered.
The second shape was called
beta (𝛽) pleated sheet, which
is wavelike in appearance.
Tertiary Proteins
• This refers to the three-dimensional shape of a
peptide, which can either be fibrous or globular
in structure. The tertiary structure is determined
by the interactions of the side chains of the
different amino acids in the peptide.
• Most substances that take on the tertiary
structure are the nonstructural proteins such as
enzymes.
Quaternary Proteins
• This happens when proteins have more than one polypeptide. Often,
the polypeptide chains will create hydrogen bonds with one another
in unique patterns to achieve the desired protein configuration.
Nucleic Acids
Nucleic Acids
• Nucleic acids are the largest
molecules among the organic
compounds, being composed of
several nucleotide subunits.
• Each nucleotide is composed of a
nitrogenous base, a pentose sugar,
and at least one phosphate group.
The importance of nucleic acids lies
in their capacity to store vital
information about the cell.
DNA and RNA
• One important type of nucleic acid is the deoxyribonucleic acid
(DNA). It is a long molecule that contains coded instructions for
cellular activities such as growth, reproduction, death, and
production and acceptance of certain substances.
• Another important type of nucleic acid is ribonucleic acid (RNA). Just
like DNA, RNA is active in the acquisition of traits. However, the uses
of RNA may range from encoding to decoding and regulating the
expression of genes, depending on the type of RNA present.
• Messenger RNA (mRNA) serves as a temporary copy of a gene in the
DNA that directs the sequence of amino acids during protein
synthesis.
• Transfer RNA (tRNA) translates the sequence of nucleic acids in a
gene to create the correct sequence of amino acids during protein
synthesis.
• Ribosomal RNA (rRNA) forms the peptide bonds between amino acids
in a polypeptide.
Composition of DNA
and RNA
• A nucleotide contains three
different types of molecules: sugar,
phosphate group, and nitrogenous
base. From this composition alone,
DNA can already be distinguished
from RNA. DNA has a pentose
sugar called deoxyribose, whereas
RNA has a pentose sugar called
ribose.
• Both DNA and RNA have four
nucleotides with a single-base ring
called pyramidine and a double-
ring called purine. The difference
lies in one type of pyrimidine – the
uracil in RNA is the counterpart for
thymine in DNA. The purines for
both nucleic acids contain adenine
and guanine.
Adenosine
Triphosphate (ATP)

• Adenosine triphosphate,
also called ATP, is another
special nucleotide that is
incorporated in the nucleic
acid. Its structure shows the
presence of an adenine and
three phosphate groups all
attached to the ribose.

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