cellular and molecular

Sheila Motahari
Lesson 1
 History of research
•1632–1723: Antonie van Leeuwenhoek taught himself to make lenses, constructed basic optical microscopes and
drew protozoa, such as Vorticella from rain water, and bacteria from his own mouth.

•1665: Robert Hooke discovered cells in cork, then in living plant tissue using an early compound microscope. He
coined the term cell (from Latin cella, meaning "small room"[1]) in his book Micrographia (1665).

•1839: Theodor Schwann and Matthias Jakob Schleiden elucidated the principle that plants and animals are made of
cells, concluding that cells are a common unit of structure and development, and thus founding the cell theory.

•1855: Rudolf Virchow stated that new cells come from pre-existing cells by cell division (omnis cellula ex cellula).

•1859: The belief that life forms can occur spontaneously (generatio spontanea) was contradicted by Louis
Pasteur (1822–1895) (although Francesco Redi had performed an experiment in 1668 that suggested the same
conclusion).

•1931: Ernst Ruska built the first transmission electron microscope (TEM) at the University of Berlin. By 1935, he had
built an EM with twice the resolution of a light microscope, revealing previously unresolvable organelles.

•1953: Based on Rosalind Franklin's work, Watson and Crick made their first announcement on the double
helix structure of DNA.
•1981: Lynn Margulis published Symbiosis in Cell Evolution detailing the endosymbiotic theory.
 Cell (biology)

The cell (from Latin cella, meaning "small room") is the basic structural, functional, and biological unit of all known
organisms.
Cells are the smallest units of life, and hence are often referred to as the "building blocks of life".
The study of cells is called cell biology, cellular biology, or cytology.
Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such
as proteins and nucleic acids.
Most plant and animal cells are only visible under a light microscope, with dimensions between 1 and
100 micrometres.
Electron microscopy gives a much higher resolution showing greatly detailed cell structure. Organisms can be
classified as unicellular (consisting of a single cell such as bacteria) or multicellular (including plants and animals).
Most unicellular organisms are classed as microorganisms.
The number of cells in plants and animals varies from species to species; it has been estimated that humans contain
somewhere around 40 trillion (4×1013) cells.
The human brain accounts for around 80 billion of these cells.
Cells were discovered by Robert Hooke in 1665, who named them for their resemblance to cells inhabited
by Christian monks in a monastery.
Cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are
composed of one or more cells, that cells are the fundamental unit of structure and function in all living organisms,
and that all cells come from pre-existing cells.
Cells emerged on Earth at least 3.5 billion years ago
A eukaryotic cell (left) and prokaryotic cell (right)
 Prokaryotic cells
Prokaryotes include bacteria and archaea, two of the three domains of life.
Prokaryotic cells were the first form of life on Earth, characterized by having vital biological processes including cell signaling.
They are simpler and smaller than eukaryotic cells, and lack a nucleus, and other membrane-bound organelles.
The DNA of a prokaryotic cell consists of a single circular chromosome that is in direct contact with the cytoplasm.
The nuclear region in the cytoplasm is called the nucleoid.
Most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 μm in diameter
Prokaryotes
 Prokaryotes are unicellular organisms that lack organelles or other internal membrane-bound structures
 They are found in both domains – Bacteria and Archaea
 Prokaryotic cells lack a defined nucleus, but have a region in the cell, termed the nucleoid, in which a
single chromosomal, circular, double-stranded DNA molecule is located.
 Archaeal membranes have replaced the fatty acids of bacterial membranes with isoprene; some
archaeal membranes are monolayer rather than bilayer.
 nucleoid: the irregularly-shaped region within a prokaryote cell where the genetic material is localized •
plasmid: a circle of double-stranded DNA that is separate from the chromosomes, which is found in
bacteria and protozoa
 osmotic pressure: the hydrostatic pressure exerted by a solution across a semipermeable membrane
from a pure solvent
 The Plasma Membrane :In archaeal cell membranes, isoprene (phytanyl) chains linked to glycerol
replace the fatty acids linked to glycerol in bacterial membranes.
 Some archaeal membranes are lipid monolayers instead of bilayers.
 Archaeal phospholipids
 differ from those found in Bacteria and Eukarya in two ways.
 • First, they have branched phytanyl(isoperene) sidechains instead of linear ones.
 • Second, an ether bond instead of an ester bond connects the lipid to the glycerol.
 • The compound ester possesses a carbon-carbonyl-oxygen bond, while the ether compound has a carbon-
oxygen-carbon bond.
Infolding of the p.m. of all gram + and gram – bacteria give rise two main types of structures :
• Mesosomes ( chondriods) :- an organelle of bacteria that appears as an invagination of the plasma
membrane and functions either in DNA replication and cell division or excretion of exoenzymes
• They are seen in Nitrosomonas(chemoautotrophic) and Rhodopseudomonas (photosynthetic pigment)
bacteria.
• Mesosome are also involved in cross-wall (septum) formation during the division of cell.
• Chromatophores :
• these are photosynthetic pigment-bearing membranous structure of photosynthetic bacteria.
• they vary in form as vesicles, tubes, bundled tubes, stacks or thylakoid ( as in cynobacteria)
• Rhodospirillum rubrum
Cell Wall
The primary function of the cell wall is to protect the cell from harsh conditions in the outside environment.
When present, there are notable similarities and differences among the cell walls of archaea, bacteria, and
eukaryotes.
The major component of bacterial cell walls is called peptidoglycan (or murein); it is only found in bacteria.
Structurally, peptidoglycan resembles a layer of meshwork or fabric (Figure 12). Each layer is composed of long
chains of alternating molecules of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). The structure of
the long chains has significant two-dimensional tensile strength due to the formation of peptide bridges that connect
NAG and NAM within each peptidoglycan layer. In gram-negative bacteria, tetrapeptide chains extending from each
NAM unit are directly cross-linked, whereas in gram-positive bacteria, these tetrapeptide chains are linked by
pentaglycine cross-bridges. Peptidoglycan subunits are made inside of the bacterial cell and then exported and
assembled in layers, giving the cell its shape.
Schematic representation of the peptidoglycan network structure Peptidoglycan Structure
Peptidoglycan (murein), an essential and specific component of the
bacterial cell envelope, forms a mesh-like layer outside the
cytoplasmic membrane, is responsible for rigidity and shape of
bacterial cells and protects them from osmotic disruption.
Indeed, any inhibition of its biosynthesis (mutation, antibiotic) or its
specific degradation (e.g. by lysozyme) during cell growth will result
in cell lysis.
Peptidoglycan also contributes to the maintenance of a defined cell
shape and serves as a scaffold for anchoring other cell envelope
components such as proteins and teichoic acids.
It is intimately involved in the processes of cell growth and cell
division.
It is a polymer that occurs in cell walls of both Gram-positive and
Gram-negative bacteria but has not been found in Archaea.
In Gram-positive bacteria it represents about 30-70% of the cell wall
aside from polysaccharides, teichoic or teichuronic acids.
It is only a minor component in Gram-negative cell walls that mainly
consist of lipopolysaccharides and lipoproteins. The investigation of
peptidoglycan structure exerts a vital roles in understanding immune
responses, the action of antibiotics and mechanisms of resistance,
phage susceptibility and serological behavior, and on bacteria
classification and identification.

Peptidoglycan is a heteropolymer that consists of glycan strands that are crosslinked by peptides.
The glycan backbone is composed of alternating units of N-acetylglucosamine and N-acetylmuramic acid linked by β-1,4-glycosidic bonds.
The peptide subunits usually contain four alternating L- and D-amino acids, and they are connected to the glycan stands via the lactyl groups of the N-
acetylmuramic acid residues.
Cross-linking of the glycan strands generally occurs between the carboxyl group of D-Ala at position 4 and the amino group of the diamino acid at position 3, either
directly or through a short peptide bridge.
Peptidoglycan is composed of polymers of alternating NAM and NAG subunits, which are cross-linked by peptide
bridges linking NAM subunits from various glycan chains. This provides the cell wall with tensile strength in two
dimensions.
 Since peptidoglycan is unique to bacteria, many antibiotic drugs are designed to interfere with peptidoglycan
synthesis, weakening the cell wall and making bacterial cells more susceptible to the effects of osmotic
pressure
 In addition, certain cells of the human immune system are able “recognize” bacterial pathogens by detecting
peptidoglycan on the surface of a bacterial cell;
 these cells then engulf and destroy the bacterial cell, using enzymes such as lysozyme, which breaks down
and digests the peptidoglycan in their cell walls .
 The Gram staining protocol is used to differentiate two common types of cell wall structures (Figure).
 Gram-positive cells have a cell wall consisting of many layers of peptidoglycan totaling 30–100 nm in
thickness. These peptidoglycan layers are commonly embedded with teichoic acids (TAs), carbohydrate
chains that extend through and beyond the peptidoglycan layer.
 Bacteria contain two common cell wall structural types.
Gram-positive cell walls are structurally simple, containing a thick layer of peptidoglycan with embedded
teichoic acid external to the plasma membrane.
Gram-negative cell walls are structurally more complex, containing three layers: the inner membrane, a thin
layer of peptidoglycan, and an outer membrane containing lipopolysaccharide.
TA is thought to stabilize peptidoglycan by increasing its rigidity.
TA also plays a role in the ability of pathogenic gram-positive bacteria such as Streptococcus to bind to certain
proteins on the surface of host cells, enhancing their ability to cause infection.
In addition to peptidoglycan and TAs, bacteria of the family Mycobacteriaceae have an external layer of
waxy mycolic acids in their cell wall,these bacteria are referred to as acid-fast, since acid-fast stains must be used
to penetrate the mycolic acid layer for purposes of microscopy

(A) Some gram-positive bacteria, including members of the Mycobacteriaceae, produce waxy mycolic acids
found exterior to their structurally-distinct peptidoglycan. (b) The acid-fast staining protocol detects the presence
of cell walls that are rich in mycolic acid. Acid-fast cells are stained red by carbolfuschin
Gram-negative cells have a much thinner layer of peptidoglycan
(no more than about 4 nm thick) than gram-positive cells, and the overall
structure of their cell envelope is more complex.
In gram-negative cells, a gel-like matrix occupies the periplasmic
space between the cell wall and the plasma membrane, and there is a
second lipid bilayer called the outer membrane, which is external to the
peptidoglycan layer (Figure).
This outer membrane is attached to the peptidoglycan by murein lipoprotein.
The outer leaflet of the outer membrane contains the
molecule lipopolysaccharide (LPS), which functions as an endotoxin in
infections involving gram-negative bacteria, contributing to symptoms such as
fever, hemorrhaging, and septic shock.
Each LPS molecule is composed of Lipid A, a core polysaccharide, and an O
side chain that is composed of sugar-like molecules that comprise the
external face of the LPS (Figure).
The composition of the O side chain varies between different species and
strains of bacteria. Parts of the O side chain called antigens can be detected
using serological or immunological tests to identify specific pathogenic strains
like Escherichia coli O157:H7, a deadly strain of bacteria that causes bloody
diarrhea and kidney failure.

The outer membrane of a gram-negative bacterial cell contains lipopolysaccharide (LPS), a toxin composed of Lipid A
embedded in the outer membrane, a core polysaccharide, and the O side chain.
Archaeal cell wall structure differs from that of bacteria in several significant ways.
First, archaeal cell walls do not contain peptidoglycan; instead, they contain a similar polymer called
pseudopeptidoglycan (pseudomurein) in which NAM is replaced with a different subunit.
Other archaea may have a layer of glycoproteins or polysaccharides that serves as the cell wall instead of
pseudopeptidoglycan.
Last, as is the case with some bacterial species, there are a few archaea that appear to lack cell walls entirely.
Phage/virus receptor locations in Gram-positive Bacteria, Gram-negative Bacteria, and two types of Archaea. Cell wall and
membrane structures are depicted for select classic groups of Bacteria and Archaea (i.e. mesophilic Archaea noted for colonizing
humans). Known phage/virus receptor sites are indicated by stars. Note that most of the components to which bacterial phages
attach (peptidoglycans, lipopolysaccharides, lipoteichoic acid, and fatty acid D-glycerol ester phospholipids) are absent in
Archaea. Although both Bacteria and Archaea possess membrane proteins and pili, they are not highly conserved between these
Domains of life.
Glycocalyces and S-Layers
Although most prokaryotic cells have cell walls, some may have additional cell envelope structures exterior to the
cell wall, such as glycocalyces and S-layers. A glycocalyx is a sugar coat, of which there are two important types:
capsules and slime layers. A capsule is an organized layer located outside of the cell wall and usually composed of
polysaccharides or proteins (Figure). A slime layer is a less tightly organized layer that is only loosely attached to
the cell wall and can be more easily washed off. Slime layers may be composed of polysaccharides, glycoproteins,
or glycolipids.
Glycocalyces allows cells to adhere to surfaces, aiding in the formation of biofilms (colonies of microbes that form in
layers on surfaces). In nature, most microbes live in mixed communities within biofilms, partly because the biofilm
affords them some level of protection. Biofilms generally hold water like a sponge, preventing desiccation. They also
protect cells from predation and hinder the action of antibiotics and disinfectants. All of these properties are
advantageous to the microbes living in a biofilm, but they present challenges in a clinical setting, where the goal is
often to eliminate microbes.

(a) Capsules are a type of glycocalyx

composed of an organized layer of
polysaccharides. (b) A capsule stain
of Pseudomonas aeruginosa, a
bacterial pathogen capable of causing
many different types of infections in
humans.
The ability to produce a capsule can contribute to a microbe’s pathogenicity (ability to cause disease) because the
capsule can make it more difficult for phagocytic cells (such as white blood cells) to engulf and kill the
microorganism.
Streptococcus pneumoniae, for example, produces a capsule that is well known to aid in this bacterium’s
pathogenicity.
capsules are difficult to stain for microscopy; negative staining techniques are typically used.
An S-layer is another type of cell envelope structure; it is composed of a mixture of structural proteins and
glycoproteins.
In bacteria, S-layers are found outside the cell wall, but in some archaea, the S-layer serves as the cell wall.
The exact function of S-layers is not entirely understood, and they are difficult to study; but available evidence
suggests that they may play a variety of functions in different prokaryotic cells, such as helping the cell withstand
osmotic pressure and, for certain pathogens, interacting with the host immune system.
A prokaryotic cell has three regions:
1-Enclosing the cell is the cell envelope – generally consisting of a plasma membrane covered by a cell
wall which, for some bacteria, may be further covered by a third layer called a capsule. Though most
prokaryotes have both a cell membrane and a cell wall, there are exceptions such as Mycoplasma (bacteria)
and Thermoplasma (archaea) which only possess the cell membrane layer. The envelope gives rigidity to the
cell and separates the interior of the cell from its environment, serving as a protective filter. The cell wall
consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also
prevents the cell from expanding and bursting (cytolysis) from osmotic pressure due to
a hypotonic environment. Some eukaryotic cells (plant cells and fungal cells) also have a cell wall.

Structure of a typical prokaryotic cell

2-Inside the cell is the cytoplasmic region that contains the genome (DNA), ribosomes and various sorts of
inclusions. The genetic material is freely found in the cytoplasm. Prokaryotes can carry extrachromosomal
DNA elements called plasmids, which are usually circular. Linear bacterial plasmids have been identified in several
species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes
Lyme disease.Though not forming a nucleus, the DNA is condensed in a nucleoid. Plasmids encode additional
genes, such as antibiotic resistance genes.

3-On the outside, flagella and pili project from the cell's surface. These are structures (not present in all prokaryotes)
made of proteins that facilitate movement and communication between cells.
Eukaryotic cells

Plants, animals, fungi, slime moulds, protozoa, and algae are all eukaryotic.
These cells are about fifteen times wider than a typical prokaryote and can be as much as a thousand times greater
in volume.
The main distinguishing feature of eukaryotes as compared to prokaryotes is compartmentalization: the presence of
membrane-bound organelles (compartments) in which specific activities take place.
Most important among these is a cell nucleus,
an organelle that houses the cell's DNA.
This nucleus gives the eukaryote its name, which means "true kernel (nucleus)".
Other differences include:
•The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls
may or may not be present.
•The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated
with histone proteins.
• All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane.
•Some eukaryotic organelles such as mitochondria also contain some DNA.
•Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in
chemosensation, mechanosensation, and thermosensation. Each cilium may thus be "viewed as a sensory
cellular antennae that coordinates a large number of cellular signaling pathways, sometimes coupling the signaling
to ciliary motility or alternatively to cell division and differentiation."
•Motile eukaryotes can move using motile cilia or flagella.
•Motile cells are absent in conifers and flowering plants.
• Eukaryotic flagella are more complex than those of prokaryotes.
The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules.
There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is
an important component of the cell and performs a wide array of functions.
Combined, these molecules make up the majority of a cell’s mass.
Biological macromolecules are organic, meaning that they contain carbon.
In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements.

1-Carbohydrates
2-lipids
3-Proteins
4-nucleic acids
 Carbohydrates

Carbohydrates are macromolecules with which most consumers are somewhat familiar.
To lose weight, some individuals adhere to “low-carb” diets.
Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to compete at
a high level.
Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates.
Carbohydrates provide energy to the body, particularly through glucose, a simple sugar.
Carbohydrates also have other important functions in humans, animals, and plants.
Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule.
the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules.
Carbohydrates are classified into three subtypes:
monosaccharides, disaccharides, and polysaccharides.
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple
sugars, the most common of which is glucose.
In monosaccharides, the number of carbon atoms usually ranges from
three to six.
Most monosaccharide names end with the suffix -ose.
Depending on the number of carbon atoms in the sugar, they may be
known as trioses (three carbon atoms), pentoses (five carbon atoms), and
hexoses (six carbon atoms).
Monosaccharides may exist as a linear chain or as ring-shaped
molecules; in aqueous solutions, they are usually found in the ring form.
The chemical formula for glucose is C6H12O6.
In most living species, glucose is an important source of energy.
During cellular respiration, energy is released from glucose, and that
energy is used to help make adenosine triphosphate (ATP).
Plants synthesize glucose using carbon dioxide and water by the process
of photosynthesis, and the glucose, in turn, is used for the energy
requirements of the plant.
The excess synthesized glucose is often stored as starch that is broken
down by other organisms that feed on plants.
Galactose (part of lactose, or milk sugar) and fructose (found in fruit)
are other common monosaccharides. Although glucose, galactose, and
fructose all have the same chemical formula (C6H12O6), they differ
structurally and chemically (and are known as isomers) because of
differing arrangements of atoms in the carbon chain.
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction
(a reaction in which the removal of a water molecule occurs).
During this process, the hydroxyl group (–OH) of one monosaccharide combines with a
hydrogen atom of another monosaccharide, releasing a molecule of water (H2O) and forming
a covalent bond between atoms in the two sugar molecules.
Common disaccharides include lactose, maltose, and sucrose.
Lactose is a disaccharide consisting of the monomers glucose and galactose.
It is found naturally in milk.
Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two
glucose molecules.
The most common disaccharide is sucrose, or table sugar, which is composed of the
monomers glucose and fructose.
A long chain of monosaccharides linked by covalent bonds is known as
a polysaccharide (poly- = “many”).
The chain may be branched or unbranched, and it may contain different types of
monosaccharides.
Polysaccharides may be very large molecules. Starch, glycogen, cellulose, and chitin are
examples of polysaccharides.
 Polysaccharides
Polysaccharides are very large, high molecular weight biological molecules that
are almost pure carbohydrate.
They are constructed by animals and plants from simpler, monosaccharide
molecules, by joining together large numbers of the simpler molecules using
glycosidic bonds (-O-).
In some of the largest polysaccarhide structures there can be 10,000 individual
units joined together.
There is a large diversity of polysaccharide form; they can differ in the type of
sugar, the connections between the sugars and the complexity of the overall
molecule.
Sometimes known as glycans, there are three common and principal types of
polysaccharide, cellulose, starch and glycogen, all made by joining together
molecules of glucose in different ways.
Starch is the stored form of sugars in plants and is made up of amylose and amylopectin (both polymers of
glucose).
Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including
roots and seeds. The starch that is consumed by animals is broken down into smaller molecules, such as glucose.
The cells can then absorb the glucose.

Starch, a word that comes from old English and means to stiffen, is also a polysaccharide made in plants. It is
primarily an energy storage molecule, or fuel, for the plant and for its seeds.
If the starch molecules are gently broken down by acid hydrolysis, the disaccharide maltose is produced,
indicating that the glucose molecules in starch are also joined together by linking the C1 carbon of one sugar to
the C4 carbon of the next sugar in the sequence. However, in this case, the glucose molecules are joined using
alpha-glycosidic bonds.
However, these molecules are not straight or totally linear. At intervals along the starch molecule there are
branches produced by another kind of glycosidic link between the C1 carbon on one sugar and the C6 carbon on
the next sugar.
When stored starch granules are removed from plants and placed in water they swell and release two types of
material; amylose and amylopectin

Glycogen is the storage form of glucose in humans and other vertebrates, and is made up of monomers of glucose.
Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle
cells. Whenever glucose levels decrease, glycogen is broken down to release glucose.
Cellulose is one of the most abundant natural biopolymers. The cell walls of plants are mostly made of
cellulose, which provides structural support to the cell. Wood and paper are mostly cellulosic in nature.
Cellulose is made up of glucose monomers that are linked by bonds between particular carbon atoms in the
glucose molecule. The carbon atom number 1 (C1) in one sugar is linked to the fourth carbon atom (C4) of the
next sugar in an extended array. Tiny forces called hydrogen bonds hold the glucose molecules together, and
the chains in close proximity. Although each hydrogen bond is very, very weak, when thousands or millions of
them form between two cellulose molecules the result is a very stable, very strong complex that has
enormous strength.

chitin :Carbohydrates serve other functions in different animals. Arthropods, such as insects, spiders, and crabs,
have an outer skeleton, called the exoskeleton, which protects their internal body parts. This exoskeleton is made of
the biological macromolecule chitin, which is a nitrogenous carbohydrate. It is made of repeating units of a
modified sugar containing nitrogen.

Thus, through differences in molecular structure, carbohydrates are able to serve the very
different functions of energy storage (starch and glycogen) and structural support and
protection (cellulose and chitin).
Every other glucose monomer in cellulose is flipped over and packed tightly as extended long
chains.
This gives cellulose its rigidity and high tensile strength:which is so important to plant cells.
Cellulose passing through our digestive system is called dietary fiber.
While the glucose-glucose bonds in cellulose cannot be broken down by human digestive
enzymes, herbivores such as cows, buffalos, and horses are able to digest grass that is rich in
cellulose and use it as a food source.
In these animals, certain species of bacteria reside in the rumen (part of the digestive system
of herbivores) and secrete the enzyme cellulase.
The appendix also contains bacteria that break down cellulose, giving it an important role in
the digestive systems of ruminants.
Cellulases can break down cellulose into glucose monomers that can be used as an energy
source by the animal.
Structure and function of cellulose and starch in plants and glycogen in humans AND Use of molecular
visualisation software to compare cellulose, starch and glycogen
 Lipids
 include a diverse group of compounds that are united by a common feature.
 Lipids are hydrophobic (“water-fearing”), or insoluble in water, because they are nonpolar
molecules.
 This is because they are hydrocarbons that include only nonpolar carbon-carbon or carbon-
hydrogen bonds.
 Lipids perform many different functions in a cell. Cells store energy for long-term use in the
form of lipids called fats.
 Lipids also provide insulation from the environment for plants and animals.
 For example, they help keep aquatic birds and mammals dry because of their water-repelling
nature.
 Lipids are also the building blocks of many hormones and are an important constituent of the
plasma membrane.
 Lipids include fats, oils, waxes, phospholipids, and steroids.
A fat molecule, such as a triglyceride, consists of two main components: glycerol and fatty acids.
Glycerol is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups.
Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty
acid.”
The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18
carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the
glycerol molecule with a covalent bond.

Lipids include fats, such as

triglycerides, which are made
up of fatty acids and glycerol,
phospholipids, and steroids.
During this covalent bond formation, three water molecules are released.
The three fatty acids in the fat may be similar or dissimilar.
These fats are also called triglycerides because they have three fatty acids. Some fatty acids have common
names that specify their origin.
For example, palmitic acid, a saturated fatty acid, is derived from the palm tree.
Arachidic acid is derived from Arachis hypogaea, the scientific name for peanuts.
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between
neighboring carbons in the hydrocarbon chain, the fatty acid is saturated.
Saturated fatty acids : are saturated with hydrogen; in other words, the number of hydrogen atoms attached
to the carbon skeleton is maximized.
unsaturated fatty acid :When the hydrocarbon chain contains a double bond, the fatty acid is
an unsaturated fatty acid.
Most unsaturated fats are liquid at room temperature and are called oils.
If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if
there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).
Saturated fats tend to get packed tightly and are solid at room temperature.
Animal fats with stearic acid and palmitic acid contained in meat, and the fat with butyric acid contained in
butter, are examples of saturated fats.
Mammals store fats in specialized cells called adipocytes, where globules of fat occupy most of the cell.
In plants, fat or oil is stored in seeds and is used as a source of energy during embryonic development.
Saturated fatty acids are fatty
acids with no double bonds and
unsaturated fatty acids are fatty acid
with one or more double bonds.
This is the biggest difference between a
saturated and unsaturated fatty acid
Unsaturated fats or oils are usually of plant origin and contain
unsaturated fatty acids.
The double bond causes a bend or a “kink” that prevents the fatty
acids from packing tightly, keeping them liquid at room temperature.
Olive oil, corn oil, canola oil, and cod liver oil are examples of
unsaturated fats.
Unsaturated fats help to improve blood cholesterol levels, whereas
saturated fats contribute to plaque formation in the arteries, which
increases the risk of a heart attack.
In the food industry, oils are artificially hydrogenated to make them
semi-solid, leading to less spoilage and increased shelf life.
Simply speaking, hydrogen gas is bubbled through oils to solidify
them.
During this hydrogenation process, double bonds of the cis-
conformation in the hydrocarbon chain may be converted to double
bonds in the trans-conformation.
This forms a trans-fat from a cis-fat.
The orientation of the double bonds affects the chemical properties of
the fat.
Essential fatty acids
 are fatty acids that are required but not synthesized by the human body.
 Consequently, they must be supplemented through the diet.
 Omega-3 fatty acids fall into this category and are one of only two known essential fatty
acids for humans (the other being omega-6 fatty acids).
 They are a type of polyunsaturated fat and are called omega-3 fatty acids because the third
carbon from the end of the fatty acid participates in a double bond.
 Salmon, trout, and tuna are good sources of omega-3 fatty acids.
 Omega-3 fatty acids are important in brain function and normal growth and development.
They may also prevent heart disease and reduce the risk of cancer.
 Like carbohydrates, fats have received a lot of bad publicity.
 It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain.
 However, fats do have important functions. Fats serve as long-term energy storage.
 They also provide insulation for the body.
 Therefore, “healthy” unsaturated fats in moderate amounts should be consumed on a
regular basis.
Phospholipids
are the major constituent of the plasma membrane.
Like fats, they are composed of fatty acid chains attached to a glycerol or similar backbone.
Instead of three fatty acids attached, however, there are two fatty acids and the third carbon of the glycerol
backbone is bound to a phosphate group. The phosphate group is modified by the addition of an alcohol.A
phospholipid has both hydrophobic and hydrophilic regions.
The fatty acid chains are hydrophobic and exclude themselves from water, whereas the phosphate is hydrophilic
and interacts with water.
Cells are surrounded by a membrane, which has a bilayer of phospholipids.
The fatty acids of phospholipids face inside, away from water, whereas the phosphate group can face either the
outside environment or the inside of the cell, which are both aqueous.

•Phospholipids consist of a glycerol molecule, two fatty acids, and a phosphate group that is modified by an
alcohol.
•The phosphate group is the negatively-charged polar head, which is hydrophilic.
•The fatty acid chains are the uncharged, nonpolar tails, which are hydrophobic.
•Since the tails are hydrophobic, they face the inside, away from the water and meet in the inner region of the
membrane.
•Since the heads are hydrophilic, they face outward and are attracted to the intracellular and extracellular fluid.
•If phospholipids are placed in water, they form into micelles, which are lipid molecules that arrange themselves in
a spherical form in aqueous solutions.
Phospholipid Molecule
 A phospholipid is a molecule with two fatty acids
and a modified phosphate group attached to a
glycerol backbone.
 The phosphate may be modified by the addition
of charged or polar chemical groups.
 Two chemical groups that may modify the
phosphate, choline and serine, are shown here.
 Both choline and serine attach to the phosphate
group at the position labeled R via the hydroxyl
group indicated in green.

Phospholipid Bilayer
 The phospholipid bilayer consists of two
adjacent sheets of phospholipids, arranged
tail to tail.
 The hydrophobic tails associate with one
another, forming the interior of the
membrane.
 The polar heads contact the fluid inside and
outside of the cell
Structure of a Phospholipid Molecule
 A phospholipid is an amphipathic molecule which means it has both a hydrophobic and a hydrophilic
component.
 A single phospholipid molecule has a phosphate group on one end, called the “head,” and two side-
by-side chains of fatty acids that make up the lipid “tails. ”
 The phosphate group is negatively charged, making the head polar and hydrophilic, or “water
loving.”
 The phosphate heads are thus attracted to the water molecules in their environment.
 The lipid tails, on the other hand, are uncharged, nonpolar, and hydrophobic, or “water fearing.” A
hydrophobic molecule repels and is repelled by water.
 Some lipid tails consist of saturated fatty acids and some contain unsaturated fatty acids.
 This combination adds to the fluidity of the tails that are constantly in motion.

Phospholipids and Biological Membranes

 The cell membrane consists of two adjacent layers of
phospholipids, which form a bilayer.
 The fatty acid tails of phospholipids face inside, away from
water, whereas the phosphate heads face the outward
aqueous side.
 Since the heads face outward, one layer is exposed to the
interior of the cell and one layer is exposed to the exterior.
 As the phosphate groups are polar and hydrophilic, they
are attracted to water in the intracellular fluid.
Steroids and Waxes
 Unlike the phospholipids and fats discussed earlier, steroids have a ring structure.
 Although they do not resemble other lipids, they are grouped with them because they are
also hydrophobic.
 All steroids have four, linked carbon rings and several of them, like cholesterol, have a
short tail.
 Cholesterol is a steroid.
 Cholesterol is mainly synthesized in the liver and is the precursor of many steroid
hormones, such as testosterone and estradiol.
 It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which
help in the breakdown of fats and their subsequent absorption by cells. Although
cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of
the body.
 It is a key component of the plasma membranes of animal cells.
 Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid.
 Examples of animal waxes include beeswax and lanolin.
 Plants also have waxes, such as the coating on their leaves, that helps prevent them from
drying out.
Cholesterol
 is another steroid. It is incorporated into cell membranes to make the cell more rigid and form a protective barrier to
keep out harmful substances that try to enter the cell.
 Because cell membranes are nonpolar in the interior (due to the hydrophobic tails), other nonpolar molecules can
pass through them.
 Cholesterol is nonpolar, so it passes through easily, providing the membrane with a solid structure.
 This is also one reason cholesterol can be so dangerous.
 If there is too much cholesterol in the blood, it won't dissolve and can build up, blocking arteries and veins.
 Lowering levels of cholesterol can help reduce the risk of heart-related conditions and diseases.
Proteins
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of
all macromolecules.
Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they
may be toxins or enzymes.
Each cell in a living system may contain thousands of different proteins, each with a unique function.
Their structures, like their functions, vary greatly.
They are all, however, polymers of amino acids, arranged in a linear sequence.
The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long
chains, and the amino acids can be in any order.
For example, proteins can function as enzymes or hormones.
Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins.
Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts.
Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds. An example of an enzyme is
salivary amylase, which breaks down amylose, a component of starch.
Hormones are chemical signaling molecules, usually proteins or steroids, secreted by an endocrine gland or group of
endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism,
and reproduction. For example, insulin is a protein hormone that maintains blood glucose levels.
 Proteins have different shapes and molecular weights;
 some proteins are globular in shape whereas others are fibrous in nature.
 For example, hemoglobin is a globular protein, but collagen, found in our
skin, is a fibrous protein.
 Protein shape is critical to its function.
 Changes in temperature, pH, and exposure to chemicals may lead to
permanent changes in the shape of the protein, leading to a loss of
function or denaturation
 All proteins are made up of different arrangements of the same 20 kinds of
amino acids.
Amino acids are made up of a central carbon
bonded to :
an amino group (–NH2),
a carboxyl group (–COOH),
a hydrogen atom.
The central carbon’s fourth bond varies among the
different amino acids, as seen in these examples of
alanine, valine, lysine, and aspartic acid.
The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is,
whether it is acidic, basic, polar, or nonpolar).

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function.
Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed
by a dehydration reaction.
The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water
molecule.
The resulting bond is the peptide bond.
The products formed by such a linkage are called polypeptides.
While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a
polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined
together, have a distinct shape, and have a unique function.

Because of the structure of the amino acids, a polypeptide chain has directionality, meaning that it has two ends
that are chemically distinct from one another. At one end, the polypeptide has a free amino group, and this end is
called the amino terminus (or N-terminus). The other end, which has a free carboxyl group, is known as the carboxyl
terminus (or C-terminus). The N-terminus is on the left and the C-terminus is on the right for the very short
polypeptide shown above.
 The properties of the side chain determine an amino acid’s chemical behavior (that is, whether it is considered acidic,
basic, polar, or nonpolar). For example, amino acids such as valine and leucine are nonpolar and hydrophobic, while
amino acids like serine and glutamine have hydrophilic side chains and are polar. Some amino acids, such as lysine
and arginine, have side chains that are positively charged at physiological pH and are considered basic amino acids.
(Histidine is sometimes put in this group too, although it is mostly deprotonated at physiological pH.) Aspartate and
glutamate, on the other hand, are negatively charged at physiological pH and are considered acidic.

A few other amino acids have R groups with special properties, and these will prove to be important when we
look at protein structure:
•Proline has an R group that’s linked back to its own amino group, forming a ring structure. This makes it an
exception to the typical structure of an amino acid, since it no longer has the standard NH_33​start subscript,
3, end subscript^++start superscript, plus, end superscript amino group. If you think that ring structure looks a
little awkward, you’re right: proline often causes bends or kinks in amino acid chains.
•Cysteine contains a thiol (-SH) group and can form covalent bonds with other cysteines. We'll see why this is
important to protein structure and function in the article on orders of protein structure
Finally, there are a few other “non-canonical” amino acids that are found in proteins only under certain
conditions.
Peptide bonds
Each protein in your cells consists of one or more polypeptide chains. Each of these polypeptide chains is made
up of amino acids, linked together in a specific order. A polypeptide is kind of like a long word that is "spelled out"
in amino acid letters^44start superscript, 4, end superscript. The chemical properties and order of the amino acids
are key in determining the structure and function of the polypeptide, and the protein it's part of. But how are amino
acids actually linked together in chains?
The amino acids of a polypeptide are attached to their neighbors by covalent bonds known as a peptide bonds.
Each bond forms in a dehydration synthesis (condensation) reaction. During protein synthesis(Opens in a new
window), the carboxyl group of the amino acid at the end of the growing polypeptide chain chain reacts with the
amino group of an incoming amino acid, releasing a molecule of water. The resulting bond between amino acids
is a peptide bond
 Protein Structure
the shape of a protein is critical to its function.
To understand how the protein gets its final shape or conformation, we need to understand the four levels of
protein structure:
primary, secondary, tertiary, and quaternary.
The unique sequence and number of amino acids in a polypeptide chain is its primary structure.
The unique sequence for every protein is ultimately determined by the gene that encodes the protein.
Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain,
causing a change in protein structure and function.
In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution, causing a change in both the
structure and function of the protein.
What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta
chains that each consist of about 150 amino acids.
The molecule, therefore, has about 600 amino acids.
The structural difference between a normal hemoglobin molecule and a sickle cell molecule:that dramatically
decreases life expectancy in the affected individuals—is a single amino acid of the 600.
Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells
assume a crescent or “sickle” shape, which clogs arteries.
This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and
abdominal pain for those who have this disease.
Protein structure levels: Primary, Secondary, Tertiary, and Quaternary.
From Amino acid to Alpha helix, Beta sheet, peptide, and protein molecule
 Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the
secondary structure of the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet
structures.
 Both structures are held in shape by hydrogen bonds.
 In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid
chain.
 In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the
polypeptide chain.
 The R groups are attached to the carbons, and extend above and below the folds of the pleat.
 The pleated segments align parallel to each other, and hydrogen bonds form between the same pairs of atoms
on each of the aligned amino acids.
 The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins.

 The unique three-dimensional structure of a polypeptide is known as its tertiary structure.

 This structure is caused by chemical interactions between various amino acids and regions of the polypeptide.
 Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein.
 There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that
involved in the secondary structure.
 When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the
protein, whereas the hydrophilic R groups lay on the outside.
 The former types of interactions are also known as hydrophobic interactions.
In nature, some proteins are formed from several polypeptides,
also known as subunits, and the interaction of these subunits
forms the quaternary structure.
Weak interactions between the subunits help to stabilize the
overall structure.
For example, hemoglobin is a combination of four polypeptide
subunits.

The four levels of protein structure can be observed in these illustrations

 Each protein has its own unique sequence and shape held together by chemical
interactions.
 If the protein is subject to changes in temperature, pH, or exposure to chemicals, the
protein structure may change, losing its shape in what is known as denaturation as
discussed earlier.
 Denaturation is often reversible because the primary structure is preserved if the
denaturing agent is removed, allowing the protein to resume its function. Sometimes
denaturation is irreversible, leading to a loss of function.
 One example of protein denaturation can be seen when an egg is fried or boiled.
 The albumin protein in the liquid egg white is denatured when placed in a hot pan,
changing from a clear substance to an opaque white substance.
 Not all proteins are denatured at high temperatures; for instance, bacteria that survive in
hot springs have proteins that are adapted to function at those temperatures.
 Nucleic Acids

Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions
for the functioning of the cell.
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic
material found in all living organisms, ranging from single-celled bacteria to multicellular mammals.
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but
instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein
synthesis and its regulation.
DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a
polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon)
sugar, and a phosphate group . Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a
phosphate group.
 DNA Double-Helical Structure
DNA has a double-helical structure. It is composed of two strands, or polymers, of
nucleotides. The strands are formed with bonds between phosphate and sugar groups of
adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen
bonds, and the strands coil about each other along their length, hence the “double helix”
description, which means a double spiral.

The alternating sugar and phosphate groups lie on the outside of each
strand, forming the backbone of the DNA.
The nitrogenous bases are stacked in the interior, like the steps of a
staircase, and these bases pair; the pairs are bound to each other by
hydrogen bonds.
The bases pair in such a way that the distance between the backbones
of the two strands is the same all along the molecule.
The rule is that nucleotide A pairs with nucleotide T, and G with C

Chemical structure of DNA, with colored label identifying the four bases as well as the phosphate and deoxyribose components
of the backbone.