BIOCHEMISTRY REVIEWER

CHEM POINTERS: MOLECULAR COMPOSITION OF CELL

➢ CELL
➢ Organic vs Inorganic
Compounds Water accounts for about 70-75% of the
➢ Carbohydrates weight of the cell.
➢ Lipids
Organic compounds accounts for 25-30% of
CELL
the cell weight.

They are nucleic acids, proteins,

Biochemistry explores molecular mechanisms
polysaccharides (carbohydrates) and lipids.
of normal cellular processes as well as
diseases. Inorganic compounds account for the rest of
the cell weight.
All higher living organisms including humans
are made up of cells. EUKARYOTIC CELL
Two major classes:

➢ Prokaryotes Eukaryotic cells have a membrane-bound

nucleus and a number of other membrane-
➢ Eukaryotes
bound subcellular (internal) organelles, each
HISTORICAL NOTES of which has a specific function.

PLASMA MEMBRANE
Robert Hooke was the first person to use the
term “cell”. He referred to the small empty
chambers in the structure of cork as cells. Structure: Phospholipid bilayer containing
cholesterol and proteins and some
Matthias Schleiden and Theodor Schwann
carbohydrates; forms a selectively permeable
concluded that all plant and animal tissues
boundary of the cell.
were composed of cells.
Functions: Acts as a physical barrier to
Rudolf Virchow proposed the theory of
enclose cell contents; regulates material
biogenesis where cells only arise from pre-
movement into and out of the cell; functions
existing cells.
in cell communication
Cell theory

NUCLEUS
A cell is the basic structural and functional
unit of living organisms.
Structure: It is enclosed within a double
The activity of an organism depends on the membrane called nuclear envelope; contains
collective activities of its cells. nucleolus

According to the principle of Nucleolus: It consists of RNA and proteins

complementarity, the activities of cells are
dictated by their structure (anatomy), which
determines function (physiology).
EUKARYOTIC CELL vs. PROKARYOTIC CELL
which functions in ribosomal unit assembly.
Nucleoplasm: It surrounds the chromatin and
the nucleoli.
Function: It contains the DNA that serves as
the genetic material for directing protein
synthesis.

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CYTOPLASM
Structure: This can be seen between the
plasma membrane and the nucleus where the
other cellular elements are embedded.
Organelles are membrane-bound structures
which carry out specific metabolic activities of
the cell.
Cytosol provides support for organelles and
serves as the viscous fluid medium.
Function: It is responsible for various cellular
processes.
MITOCHONDRIA
Structure: Double-membrane-bound
organelles containing a circular strand of DNA
Outer membrane is highly permeable to small
molecules, due to the presence of a pore-
forming protein called porin.
Intermembrane contains many proteins that
participate in oxidative phosphorylation.
Inner membrane has multiple folds projecting
inwards, called cristae.
Function: It is responsible for the production
of energy in the form of ATP.
LYSOSOMES
Structure: Spherical shaped membrane bound
organelles formed from the golgi apparatus;
contain digestive enzymes
The fluid inside lysosomes is much more
acidic, at about pH 4.8, than the normal pH of
about 7.0–7.3.
Function: Digest microbes or materials by the
cell
ENDOPLASMIC RETICULUM
It is further subdivided into:
Rough endoplasmic reticulum
Structure: Extensive interconnected
membrane network that varies in shape;
ribosomes attached on the cytoplasmic
surfaces
Ribosomes are involved in the protein
synthesis.
Functions: Modifies, transports, and stores
proteins produces by attached ribosomes
Smooth endoplasmic reticulum
Structure: Extensive interconnected
membrane network lacking ribosomes
GOLGI APPARATUS
Structure: Series of several elongated,
flattened saclike membranous structures.
Functions: Modifies, packages, and sorts
materials, that arrive from the endoplasmic
reticulum in transport vesicles
Vesicles transport cellular material. Mature
vesicles are called secretory vesicles.
PEROXISOMES
Structure: smaller, spherical membrane
bound organelles formed from the
endoplasmic reticulum.
Functions: Detoxify specific harmful
substances either produced by the cell or
taken into the cell
CYTOSKELETON
Cytoskeleton
Structure: Organized network of protein
filaments
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Function: Maintains integral structural
support and organization of cells
Microfilaments maintain cell shape.
Intermediate filaments give mechanical
support to structures like nucleus and plasma
membrane.
Microtubules provides structural support.
IMPORTANT NOTES IN PROKARYOTIC CELL
Prokaryotes (Eubacteria and Archaebacteria)
are the most abundant organisms on earth.
A prokaryotic cell does not contain a
membrane-bound nucleus.
Each prokaryotic cell is surrounded by a
plasma membrane.
The cell has no subcellular organelles, only
infoldings of the plasma membrane called
mesosomes.
The deoxyribonucleic acid (DNA) is condensed
within the cytosol to form the nucleoid.
Some prokaryotes have tail-like flagella.
CELL MEMBRANE TRANSPORT
Passive Transport Process
Diffusion is the movement of a substance
from an area of its higher concentration to an
area of its lower concentration.
Simple diffusion is the type of diffusion of
dissolved solutes through the plasma
membrane
Facilitated Diffusion is the type of diffusion
that requires a protein carrier.
Osmosis is the diffusion of water point across
a selectively permeable membrane.
CELL MEMBRANE TRANSPORT
Active Transport Process
This type of cell membrane transport uses
energy (ATP) provided by the cell.
For example, cell has low intracellular
sodium; but concentration of potassium
inside the cell is very high. This is maintained
by the sodium–potassium activated ATPase,
generally called as sodium pump.
Exocytosis refers to bulk movement of
substance out of the cell by fusion of
secretory vesicles with the plasma membrane.
Endocytosis refers to bulk movement of
substance into the cells by vesicles forming at
the plasma membrane.
ACTIVE TRANSPORT
ENDOCYTOSIS and EXOCYTOSIS
CEL LIFE CYCLE
Interphase
It is the longer phase of the cell cycle where
the cell is active and preparing for cell
division.
The DNA molecule is duplicated exactly in a
process called DNA replication which occurs
toward the end of the interphase.
Cell Division
Cells arise from the division of other cells.
Mitosis consists of four stages-prophase,
metaphase, anaphase, and telophase. The
result is two daughter nuclei, each identical to
the mother nucleus.
Prophase- each chromosome consists of two
chromatids joined at the centromere.
Metaphase- chromosomes align at the center
of the cell
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Anaphase- chromatids separate at the
centromere and migrate to opposite poles.
Halogen-Containing Compunds
Telophase- two new nuclei assume their
normal structure, and cell division is
completed, producing two new daughter
cells.

Organic vs Inorganic Compounds

Organic chemistry: Study of hydrocarbons

(only carbon and hydrogen atoms) and their
various derivatives. Oxygen-Containing Compounds
Inorganic chemistry: Study of all substances
other than hydrocarbons and their
derivatives.

Bonding Characteristics of Carbon Atom

C-atom always makes total of 4 Bonds

The sharing of four valance electrons requires

the formation of four covalent bonds which
are represented by four lines.

Functional Groups

Are groups of atoms in organic molecules that

are responsible for the characteristics,
chemical reactions of those molecules.

Simple molecules that contain the same

functional group in their structure can be
expected to react in similar ways.
Carboxylic Acid Derivatives
More complicated chemical molecules may
contain more than one functional group
within their structure.

Hydrocarbons

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 component of the plants, starch the energy
reservoir in plants and
Nitrogen-Containing Compounds
glycogen (animal starch) found in animal
tissues and human body in

smaller quantities.

Plant products are the major source of

carbohydrates and average

human diet contains 2/3 of carbohydrates.

Recommended percents in the daily diet:

Recommended carbohydrates ~ 60 %
Recommended sucrose less than 10%

Carbohydrates
Importance of Carbohydrates
Carbohydrates
Carbohydrates are polyhydroxy aldehydes or
ketones, or substances that yield such
compounds on hydrolysis

Carbohydrates are compounds of tremendous

biological importance:

they provide energy through

oxidation
they supply carbon for the synthesis
of cell components
they serve as a form of stored
chemical energy
they form part of the structures of Classes of Carbohydrates
some cells and tissues

Carbohydrates, along with lipids, proteins,

nucleic acids, and other compounds are
known as biomolecules because they are
closely associated with living organisms.

Occurrence of Carbohydrates

Almost 75% of dry plant material is produced

by photosynthesis.

Most of the matter in plants, except water,

are carbohydrate material.

Examples of carbohydrates are cellulose

which are structural

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 Stereochemistry of Carbohydrates Many organic compounds, including
carbohydrates, contain more than
one chiral carbon.
Glyceraldehyde, the simplest carbohydrate,
exists in two isomeric forms that are mirror
images of each other:

Fischer Projections

These forms are stereoisomers of each other.

Glyceraldehyde is a chiral molecule
it cannot be superimposed on its mirror
image. The two mirror image forms of
glyceraldehyde are enantiomers of each
other.
Chirality
Fischer projections are a convenient way
to represent mirror images in two
dimensions.
Place the carbonyl group at or near the
top and the last achiral CH2OH at the
bottom.

Chiral molecules have the same relationship

to each other that your left

and right hands have when reflected in a

mirror.

Achiral objects can be superimposed on the

mirror images — for example,

drinking glasses, spheres, and cubes.

Any carbon atom which is connected
to four different groups will be chiral,
and will have two nonsuperimposable Naming isomers
mirror images; it is a chiral carbon or
a
When there is more than one chiral center in
Center of chirality.
a carbohydrate, look at the chiral carbon
if any of the two groups on the carbon farthest from the carbonyl group: if the
are the same, the carbon atom hydroxy group points to right when the
cannot be chiral. carbonyl is “up” it is the D-isomer, and when

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the hydroxy group points to the left, it is the
L-isomer.
Chirality
Optical activity
A levorotatory (–) substance rotates polarized
light to the left. [E.g., lglucose; (-)-glucose]
A dextrorotatory (+) substance rotates
polarized light to the right. [E.g., d-glucose;
(+)-glucose]
Molecules which rotate the plane of of
polarized light are optically active.
Most biologically important molecules are
chiral, and hence are optically active. Often,
living systems contain only one of all of the
possible stereochemical forms of a
compound. In some cases, one form of a
molecule is beneficial, and the enantiomer is a
poison (e.g., thalidomide).
Stereochemistry matters!
Monosaccharides
The monosaccharides are the simplest of
the carbohydrates, since they contain
only one polyhydroxy aldehyde or ketone
unit.
Monosaccharides are classified according
to the number of carbon atoms they
contain:
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 Chemical properties of monosaccharides

The presence of an aldehyde is indicated by

the prefix aldo- and a ketone by the prefix
keto-.

Physical Properties of Monosaccharides

Most monosaccharides have a sweet taste
(fructose is sweetest; Oxidation of Monosaccharides
73% sweeter than sucrose).
They are solids at room temperature.
Aldehydes and ketones that have an OH
They are extremely soluble in water:
group on the carbon next to the carbonyl
Despite their high molecular weights,
group react with a basic solution of Cu2+
the presence of large numbers of OH
(Benedict’s reagent) to form a red-orange
groups make the monosaccharides
precipitate of copper(I) oxide (Cu2O).
much more water soluble than most
molecules of similar MW. Sugars that undergo this reaction are
called reducing sugars. (All of the
Glucose can dissolve in minute
monosaccharides are reducing sugars.)
amounts of water to make a syrup (1
g/ 1 ml H2O).
Physical Properties of Monosaccharides
The relative sweetness of sugars (sucrose =
1.00)

Why hemiacetals are important?

Hemiacetals and acetals are important
functional groups because they appear in
sugars. ... First, an acid catalyst must be used
because alcohol is a weak nucleophile; and
second, the water produced with the acetal
must be removed from the reaction by a

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process such as a molecular sieves or a Dean- Disaccharides
Stark trap.

Formation of Phosphate esters

Phosphate esters can form at the 6-carbon of
aldohexoses and aldoketoses.

Phosphate esters of monosaccharides are

found in the sugarphosphate backbone of
DNA and RNA, in ATP, and as intermediates in
the metabolism of carbohydrates in the body

Oligosaccharides

Glycoside Formation
Hemiacetals yield acetals upon treatment
with an alcohol and an acid catalyst

treatment of monosaccharide hemiacetals

with an alcohol and acid catalyst yields an Polysaccharides
acetal, called a glycoside

Important monosaccharides

Polysaccharides contain hundreds or

thousands of carbohydrate units.

Polysaccharides are not reducing sugars,

since the anomeric carbons are connected
through glycosidic linkages.

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We will consider three kinds of
polysaccharides, all of which are polymers of
glucose: starch, glycogen, and cellulose.
Starch
Amylopectin consists of long chains of glucose
(up to 105 molecules)
connected by α(1→4) glycosidic linkages, with
α(1→6) branches every 24 to 30 glucose units
along the chain.

80%-90% of the starch in plants is in this form

Glycogen

Starch is a polymer consisting of D-glucose

units.

Starches (and other glucose polymers) are

usually insoluble in water because of the high
molecular weight, but they can form thick
colloidal suspensions with water.
There are two forms of starch:
amylose
amylopectin
Glycogen, also known as animal starch, is
structurally similar to amylopecon, containing
both α(1→4) glycosidic linkages and α(1→6)
branch points.
Glycogen is even more highly branched,
however, with branches occuring every 8 to
12 glucose units.

Glycogen is abundant in the liver and

muscles; on hydrolysis it forms glucose, which
maintains normal blood sugar level and
provides energy

Cellulose
Amylose consists of long, unbranched chains
of glucose (from 1000 to 2000 molecules)
connected by α(1→4) glycosidic linkages.

10%-20% of the starch in plants is in this

form.

Amylose forms helices (coils) which can trap

molecules of iodine,forming a characteristic
deep blue-purple color. (Iodine is often used
as a test for the presence of starch.

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Because of the β-linkages, cellulose has a
different overall shape from
amylose, forming extended straight chains
which hydrogen bond to each other, resulting
in a very rigid structure.
Cellulose is an important structural
polysaccharide, and is the single most
abundant organic compound on earth. It is
the material in plant cell walls that provides
strength and rigidity; wood is 50% cellulose.
Most animals lack the enzymes needed to
digest cellulose, although it does provide
needed roughage (dietary fiber) to stimulate
contraction of the intestines and thus help
pass food along through the digestive system.
Some animals, such as cows, sheep, and
horses, can process cellulose through the use
of colonies of bacteria in the digestive system
which are capable of breaking cellulose down
to glucose; ruminants use a series of
stomachs to allow cellulose a
longer time to digest. Some other animals
such as rabbits reprocess digested food to
allow more time for the breakdown of
cellulose to occur.
Cellulose is also important industrially, from
its presence in wood, paper, cotton,
cellophane, rayon, linen, nitrocellulose
(guncotton), photographic films (cellulose
acetate), etc.
LIPIDS
Lipids are biological molecules that are
insoluble in water but soluble in nonpolar
solvents.
Lipids have a wider spectrum of compositions
and structures because they are defined in
terms of their physical properties (water
solubility).
Lipids are the waxy, greasy, or oily
compounds found in plants and animals.
wax coating that protects plants
used as energy storage
structural components (cell membranes)
insulation against cold
Lipids are divided into:
aponifiable lipids
contain esters, which can undergo
saponification (hydrolysis under basic
conditions) (waxes, triglycerides,
phosphoglycerides, sphingolipids)
Nonsaponifiablelipids
do not contain ester groups, and
cannot be saponified (steroids,
prostaglandins)
Saponifiable lipids can also be divided into
groups:
Simple lipids
contain two types of components (a
fatty acid and an alcohol)
Complex lipids
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 contain more than two components insoluble lipids in the blood, and in the actions
(fatty acids, an alcohol, and other of soaps.
components)

Fatty lipids
Fatty acids are long-chain carboxylic acids:

Characteristics of Fatty Acids

They are usually have straight chains (no

branches) that are about 10 to 20 carbon
atoms in length.

They usually have an even number of carbon

Properties of Fatty acids
atoms (counting the carboxyl carbon).

The carbon chains may be saturated (all single

The long, nonpolar hydrocarbon tails of fatty
bonds) or unsaturated (containing double
acids are responsible for most of the fatty or
bonds). Other than the carboxyl group and
oily characteristics of lipids.
the double bonds, there are usually no other
The carboxyl (COOH) group is hydrophilic functional groups.
under basic conditions, such as physiological
Shorter fatty acids usually have lower melting
pH (7.4):
points than longer ones (stearic acid [18C] =
700C, palmitic acid [16C] = 630C).

Saturated v. Unsaturated fatty acid

Micelles

In aqueous solutions, fatty acids associate

with each other in spherical clusters called
micelles, in which the hydrocarbon tails tangle
each other up through dispersion forces,
leaving a “shell” of polar carboxylate ions
The cis-double bonds in unsaturated fatty
facing outwards, in contact with the water. –
acids put an inflexible “kink” in the carbon
Micelles are important in the transport of
chain, preventing the molecules from packing
together as tightly as saturated fatty acids do.

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For example, stearic acid (saturated), oleic
acid (one double bond), and linoleic acid (two
double bonds) all have 18 carbons in the
chain, but their melting points are drastically
different:
Essential fatty acids
Most of the fatty acids we need can be
synthesized in the body. Two fatty acids,
linoleic acid and linolenic acid, both
polyunsaturated fatty acids with 18-carbon
chains, cannot be synthesized in the body and
must be obtained from the diet. These are
essential fatty acids. Both are found in plant
and fish oils. In the body, they are used to
produce hormonelike substances that
regulate blood pressure, blood clotting, blood
lipid levels, the immune response, and
inflammatory reactions.
Fats and Oils
Animal fats and vegetable oils are esters
composed of three molecules of a fatty acid
connected to a glycerol molecule, producing a
structure called a triglyceride or a
triacylglycerol:
The fatty acids in a triglyceride molecule are
usually not all the same; natural triglycerides
are often mixtures of many different
triglyceride molecules.
Fats are triglycerides that are solids at room
temp.
usually derived from animals
mostly saturated fatty acids
Oils are triglycerides that are liquids at room
temp.
usually derived from plants or fish
mostly unsaturated fatty acids
Chemical properties of fats and oils
Triglycerides can be broken apart
with water and an acid catalyst
(hydrolysis), or by digestive
enzymes called lipases:
Saponification
In saponification reactions,
triglycerides react with strong
bases (NaOH or KOH) to form the
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carboxylate salts of the fatty acids, called Waxes are insoluble in water, and not as
soaps. easily hydrolyzed as fats and oils. They often
occur in nature as protective coatings on
Soaps feathers, fur, skin, leaves, and fruits.
NaOH produces a “hard” soap, commonly
Sebum, secreted by the sebaceous glands of
found in bar soaps; KOH produces a “soft”
the skin, contains waxes that help to keep skin
soap, such as those in shaving creams and
soft and prevent dehydration.
liquid soaps.
Waxes are used commercially to make
These salts combine two solubility
cosmetics, candles, ointments, and protective
characteristics:
polishes.
a long, nonpolar, water-insoluble
Phosphoglycerides
(hydrophobic) hydrocarbon “tail.”
Phosphoglyceridesare complex lipids that are
–a charged, water-soluble
major components of cell membranes.
(hydrophilic) “head.”
Phosphoglyceridesand related compounds are
In water, the “tails” become
also called phospholipids.
tangled, leaving the charged
heads sticking out into the Aminoalcoholsin Phosphoglycerides
solution, forming a structure
called a micelle.
Hydrogenation

The most abundant phosphoglyceridescontain

the alcohols choline, ethanolamine, or serine
attached to the phosphate group.
In hydrogenation reactions, alkenes are
converted into alkanes with hydrogen gas (H2 Lecithins
) 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
Phosphoglyceridesthat contains the
trans isomers (trans fats).
aminoalcoholcholine are called lecithins:
Waxes
The fatty acids at the first and second
Waxes are simple lipids contain a fatty acid
positions are variable, so there are a number
joined to a long-chain (12-32 carbons) alcohol.
of different possible lecithins.

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Because lecithinscontain negatively charged
oxygen atoms in the phosphate group and
positively charged nitrogen atoms in the
quaternary ammonium salt group, that end of
the molecule is highly hydrophilic, while the
rest of the molecule is hydrophobic.
This allows lecithin to act as an emulsifying
agent:
forms an important structural
component of cell membranes.
forms micelles which play a role in the
transport of lipids in the blood
stream.
Commercially, lecithin extracted from
soybeans is used as an emulsifying
agent in margarine and candies to
provide a smooth texture.
Cephalins
Phosphoglyceridesthat contains the
aminoalcoholsethanolamine or serine are
called cephalins:
Cephalins are found in most cell membranes,
and are particularly abundant in brain tissue.
They are also found in blood platelets, and
play a role in bloodclotting.
Sphingolipids
Sphingolipids are complex lipids that contain
sphingosine instead of glycerol.
Glycolipids
Glycolipids are sphingolipids that contain
carbohydrates (usually monosaccharides).
They are also referred to as cerebrosides
because of their abundance in brain tissue.
Biological membranes
Most cell membranes contain about 60%
lipids and 40% proteins:
phosphoglycerides(e.g., lecithin and
cephalin) sphingomyelin
cholesterol
The fluid-mosaic model of the cell pictures the
cell membrane as being composed of a lipid
bilayer, in which the nonpolar tails of lipids
point towards the “interior” of the bilayer,
leaving the polar, hydrophilic portions
pointing outwards.
Biological membranes
When the membrane is broken, the repulsion
between the nonpolar portion and water
causes the membrane to re-form.
Cell membranes also contain unsaturated
fatty acid chains that increase the flexibility or
fluidity of the membrane.
Some of the proteins in the membrane “float”
in the lipid bilayer like icebergs, while others
extend through the bilayer.
The lipid molecules are free to move laterally
within the bilayer like dancers on a crowded
dance floor.
Fluid mosaic model
The fluid mosaic model of membrane
structure proposes that lipids of the bilayer
are in constant motion, gliding from one part
of their bilayer to another at high speed.
Steroids
Steroids are classified as lipids because they
are soluble in nonpolar solvents, but they are
nonsaponifiablebecause the components are
not held together by ester linkages.
The basic steroid structure contains four
fused rings:
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 Cholesterol
Cholesterol is the most abundant steroid in
the body. It is an essential component of cell
membranes, and is a precursor for other
steroids, such as the bile salts, sex hormones,
vitamin D, and the adrenocorticoid hormones.
Adrenocorticoid hormones
Mineralocorticoids regulate ion concentration
(mainly Na+ ). Aldosterone influcesthe
absorption of Na+ and Clin kidney tubules,
thus regulating the retention of water in the
body

There is apparently a correlation between Sex hormones

high levels of cholesterol in the blood and Sex hormones produced in the testes and
atherosclerosis. ovaries regulate the production of sperm and
eggs and aid in the development of secondary
Bile Salts
sex characteristics.
Bile is a yellowish brown or green fluid
produced in the liver and stored in the gall Prostaglandins
bladder. Prostaglandins are cyclic compounds
synthesized from arachidonic acid. Like
Bile salts act like soaps and other emulsifiers:
hormones, they are involved in a host of body
they contain both polar and nonpolar regions,
processes, including reproduction, blood
helping to break fats in foods into smaller
clotting, inflammation, and fever. (Aspirin
pieces, allowing them to be hydrolyzed more
works by inhibiting prostaglandin production,
easily.
alleviating inflammation and fever. NSAIDs
Gallstones has the similar mechanism)
Bile salts also emulsify cholesterol in the bile,
so it can be removed in the small intestine. If
cholesterol levels are too high or the levels of
bile salts is too low, the cholesterol
precipitates and forms gallstones.

Gallstones can block the duct that allows bile

to be secreted into the duodenum. Fats are
no longer digested properly, and bile
pigments absorbed into the blood causes the
skin to become yellow and the stool to
become gray.

Adrenocorticoid hormones
Hormones are chemicals released by cells or
glands in one part of the body that send out
messages that affect cells in other parts of the
body. Many hormones are based on steroids.

The adrenocorticoid hormones are produced

in the adrenal glands (located on the top of
the kidney).

Glucocorticoids such as cortisol affect the

metabolism of carbohydrates. Cortisol and its
derivatives, cortisone and prednisolone
(synthetic) are powerful anti-inflammatory
drugs used to treat arthritis and asthma.

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