CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

 There are 118 different elements and

Lesson 1
have been organized into periodic table

Atoms & Molecules and

Elements

Definition & Function

Atoms
 Atoms are the basic building blocks from which
everything around us is built.
 The size of an atom depends on which element it is,
basically they are the different types of atoms. We
can identify which atom is it by counting its
protons.
 Made up of three types of tiny particles:
 Nuclear Symbols
 Box that represents different elements

 Protons - positively charged particles,  Also represent the number of electrons present in
the element
found in nucleus of an atom
 Neutrons - particles that contain no
charge, found in nucleus of an atom  A number of protons that determines
 Electrons - negatively charged particles, which element it is, the number of
found outside nucleus of an atom. neutrons can vary between the individual
atoms of an element as long as the
Ions number of protons remains the same it's
still the same element
 Particle, atom or molecule with a net electrical
charge.
 An atom became ion if the number of protons and
the number of electrons is no longer balance. Thus,
this atom became charge.
 Ions are formed when an atom loss or gain electron.

Elements

N.M. Nery
1
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

ISOTOPES Lesson 2

 Are different forms of the same element that

have the same number of protons but a different
number of neutrons.
 Only vary in the number of neutrons they have,
chemically they all react in basically the same Chemical Bonds
way.
 because they all have different numbers of Definition & Function
neutrons the different isotopes will have
different masses
 Any of the interactions that account for
 Relative Atomic Mass – average mass of all
the association of atoms into molecules,
the isotopes that make up a particular
ions, crystals, and other stable species
element.
that make up the familiar substances of
the everyday world.
 the electrostatic attractive forces
Molecules, Compounds, & Mixtures
between atoms strong enough for the
 Molecule atoms act as a single unit, this attraction
 a group of two or more atoms that are held is created by the transferring or sharing
together by chemical bonds. of electrons.
 Compound
 Are substances that contain two or more Chemical Bounding
different elements and that atoms are held
together by chemical bonds.  Process by which elements combine
 Elements involved are always found in the to form a compound.
same proportions in compound.
 Mixture
 Consists of two or more substances that are
not chemically combined together.
 No bonding or chemical reactions are
involved in creating a mixture. Therefore,
this can be separate using physical methods
like: filtration, crystallization or distillation

N.M. Nery
2
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

Lesson 3

2 Major Chemical Bounds  Covalent Bonds:

 Share electron to get fuller shell.
 form when two or more atoms share one
or more electrons.
 chemical bond that involves the sharing
of electron pairs between atoms. These
electron pairs are known as shared pairs
or bonding pairs, and the stable balance
of attractive and repulsive forces between
atoms.

EXAMPLE:

 Ionic Bonds:
 Transfer electrons to get fuller shell
 form when one atom gives one or more
electrons to another atom.
 ionic bond is an attraction between two
atoms due to one transferring an electron
(or several electrons) to the other.

EXAMPLE:

Organic Molecules:

Functional Groups, Monomers & Polymers

Organic molecule

N.M. Nery
3
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

 A molecule that forms the basic structures of all
living things.
 A complex molecule that is primarily made of
carbon atoms bonded with other elements
and/or other carbon atoms.
 There are four main kinds of organic molecules
that together build up the cells in our bodies.
is responsible for the characteristic
chemical reactions of that compound.
 Groups of atoms that has extremely
important role in compounds
functionality.
Role of Functional Groups

Organic Chemistry Organic Chemistry Functional Groups

 The manner in which the functional
 Study of carbon compounds, nearly all of which
groups indulge in a chemical reaction can
also contain hydrogen atoms be further modified with the help of other
functional groups, and these groups can
4 main kinds of organic molecules: also be interconverted. Therefore, it can be
understood that functional groups are the
 Carbohydrates
moieties which exhibit their own distinct
 the main energy source for the human body. features and properties independent of the
 Monomers: molecule they are attached to.
 Monosaccharide
 Proteins Nomenclature of Common Functional
 Proteins may be structural, regulatory, contractile, Groups
or protective; they may serve in transport, The common functional groups, along with the
storage, or membranes; or they may be toxins or prefix and the suffix which must be used in their
enzymes. nomenclature are provided in this subsection.
 Monomers: Additionally, a brief description of the
 Amino Acids constitution of each of these groups is also
 Nucleic acids provided.
 Main information-carrying molecules of the cell,
Hydrocarbon
and, by directing the process of protein synthesis,
they determine the inherited characteristics of - formed from carbon and hydrogen
every living thing.
 Monomers: Alkanes
 Nucleotide - contain only carbon-carbon and carbon-hydrogen
 Lipids/ Fats
 provide cells with energy, store energy, and help
form cell membranes.
 Monomers:
single bonds
 Fatty acids
 Glycerol Alkenes
- contain a carbon-carbon double bond
Functional Groups

 Groups of atoms within a molecule that

have a consistent and specific behavior
 functional group is a specific group of
atoms or bonds within a compound that

N.M. Nery
4
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

Alkynes the aldehyde group may be written as –CH=O

- contain a carbon-carbon triple bond or as –CHO

Carboxylic Acids
- contain a “carboxylic acid” group – a
carbonyl (C=O) group bonded to a hydroxyl
group at the carbonyl carbon atom
Arenes - note that in condensed structural formulas,
- contain a benzene group the carboxylic acid group may be written as –
COOH

Carboxylic Amides
Alcohols (Amides)
- contain an –OH (“hydroxyl”) group bonded to a
- contain an “amide” group
tetrahedral carbon atom.

– a carboxylic acid (-COOH) group where the

-OH group is replaced with an amine

Carboxylic Esters (Esters)

- contain an “ester” group – a carboxylic acid
(-COOH) group where the H atom is replaced
with a carbon containing group.
Ethers
- contain an oxygen atom bonded to two carbon

Carboxylic Anhydrides (Anhydrides)

- contain an “anhydride”
group – an oxygen
atom bonded to two
C=O (“carbonyl”)
atom groups by single bonds. groups

Amines
- contain an “amino” group – a N atom bonded to
1, 2, or 3 carbon atom groups by single bonds.
Nitriles
- contain a “cyano” group (C≡N) bonded to a
Aldehydes and Ketones carbon atom group (i.e., at the carbon atom of
- contain a C=O (“carbonyl”) group the cyano group)
- note that in condensed structural formulas,

N.M. Nery
5
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY
Monomers
 Mono - means one
 A molecule of any of a class of compounds,
mostly organic, that can react with other
molecules to form very large molecules, or
polymers.
 As functional groups bond with carbon chains
they form simple molecules called monomers.
Polymers
 'Poly-' means many
 A polymer is a substance or material consisting
of very large molecules, or macromolecules,
composed of many repeating subunits. Due to
their broad spectrum of properties, both synthetic
and natural polymers play essential and
ubiquitous roles in everyday life.
 Monomers then bond together to form complex
molecules called polymers.
TO REMEMBER:
Carbohydrates are formed from
monosaccharides and produce
energy. Proteins are formed from amino acids
and build cellular structures. Lipids are formed
from glycerol and fatty acids to create fats.
And nucleic acids are formed from nucleotides
to create genetic material.
Lesson 4
Adenosine
triphosphate (ATP)
Definition & Molecules
 Adenosine triphosphate, or ATP for short, is the
energy currency of life. ATP is a high-energy
molecule found in every cell. Its job is to store
and supply the cell with needed energy.
 ATP is responsible for the energy needed to
perform muscle contractions, nerve impulses,
metabolism functions, and other various life-
sustaining functions. It supplies the energy for
chemical and mechanical reactions in every
cell.
 ATP is found in the cytoplasm of the cell. The
cytoplasm is the gel-type filler of the cell
where all of the organelles of the cell hang
out. This location makes sense because the
ATP needs to be near all of the cell parts so
that it can supply them with the energy they
need for chemical and mechanical reactions.
 ATP gets its energy by breaking down food. It
is created in the mitochondria, the powerhouse
factory organelle, during the process of
cellular respiration. The energy is obtained
from breaking down food
Energy Molecule
 Adenosine triphosphate is a high-energy
molecule. The main ingredients of this molecule
are carbon, hydrogen, nitrogen, oxygen, and
phosphorus. Its chemical formula is:
C10 H16 N5 O13 P3
N.M. Nery
6
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

Lesson 5

 There are three sections of the ATP molecule.

In the center is a sugar molecule called ribose.
Attached to one end of the ribose are rings of
carbon and nitrogen that form a base known as
adenine. At the other end of the ribose is a
group of three phosphates. The group of three
Cell Membrane
phosphates is the key to the energy in the
molecule.
 The three phosphate atoms are linked together Functional Groups, Monomers & Polymers
by phosphate bonds. The energy is actually Cell Membrane - a fluid, flexible barrier that covers
locked in these bonds. Enzymes will come a cell and it is a flexible barrier on the outside of a
along and tell these bonds to break. The cell that protects it.
phosphate group will actually break free of the
ATP molecule and release a lot of energy. Cell membrane serves three important
 The cell will use this energy to perform other functions for a cell:
reactions such as building proteins. When the
organism is resting, the reverse reaction takes 1. Protecting the cell
place, and the phosphate will re-attach itself to 2. Regulating the transportation of
the ribose base of the molecule. molecules and ions
3. Communicating with other cells

 The cell membrane also regulates cellular

Atp - Adp Cycle transport. The membrane can do so because it

is selectively permeable. That means it only
allows certain molecules to enter and exit a
cell

CELL SIGNALING

- In order to detect a signal (that is, to be a target

cell), a neighbor cell must have the right
receptor for that signal. When a signaling
molecule binds to its receptor, it alters the shape
or activity of the receptor, triggering a change
inside of the cell. Signaling
molecules are often called
ligands, a general term for
molecules that bind

N.M. Nery
7
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

specifically to other molecules (such as  Endocrine signaling - When cells need

receptors).
- The message carried by a ligand is often relayed
through a chain of chemical messengers inside
the cell. Ultimately, it leads to a change in the
cell, such as alteration in the activity of a gene
or even the induction of a whole process, such
as cell division.
- Cell membranes help cells communicate with
other cells through
 Intracellular signaling (within-cell) -
occurs within the cell itself
to transmit signals over long distances,
they often use the circulatory system as
a distribution network for the messages
they send. In long-distance endocrine
signaling, signals are produced by
specialized cells and released into the
bloodstream, which carries them to
target cells in distant parts of the body.
Signals that are produced in one part of
the body and travel through the
circulation to reach far-away targets are
known as hormones.

 Autocrine signaling - a cell signals to

itself, releasing a ligand that binds to
receptors on its own surface (or,
 Paracrine signaling - allows a cell to
depending on the type of signal, to
target another cell by a signal molecule
receptors inside of the cell). This may
that may diffuse between them. these
seem like an odd thing for a cell to do,
cells are still close but need not be
but autocrine signaling plays an
connected. The ligands in paracrine
important role in many processes. For
signaling tend to be rapidly reabsorbed
instance, autocrine signaling is
and rapidly degraded; the ligands are
important during development, helping
typically not traveling far as this is local
cells take on and reinforce their correct
signaling.
identities.
 Intercellular signaling (between-cells) - a
cell communicates with another cell.

 Signaling by direct contact - close

together cells that can allow ions or
other small molecules to pass and by
doing so, they don’t have to pass across

the plasma membrane.

N.M. Nery
8
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

 Synaptic signaling - One unique  phospholipids arrange themselves into a

example of paracrine signaling is
synaptic signaling, in which nerve cells
transmit signals. This process is named
for the synapse, the junction between
two nerve cells where signal
transmission occurs
phospholipid bilayer with the nonpolar
areas is in the middle, away from any
water.
 It also allows this area in between to be
separated from the outside and inside,
water can be found on the inside and
outside areas.

Cell membrane Components and

Structure

 Phospholipids
 A thin polar membrane made of two layers
  Cholesterol
of lipid molecules. These membranes are  If temperatures drop, the cholesterol function as
a kind of spacer between these phospholipids,
flat sheets that form a continuous barrier
keeping them from becoming too packed.
 Or vice versa, the cholesterol can actually
function to connect phospholipids to keep them
from being too fluid in warm temperatures.
 Proteins
 ferrying nutrients across the plasma
membrane, receiving chemical signals
around all cells.  from outside the cell, translating
 Phospholipids are amphiphilic this means chemical signals into intracellular
its both polar and nonpolar action, and sometimes anchoring the
 Hydrophilic - Polar head of the cell in a particular location
phospholipid  Peripheral protein - like the name
 Hydrophobic - nonpolar tails  suggests, tend to be on the peripheral area
of the membrane. So, while they tend to be
Outside H2O

Inside H2O
N.M. Nery
9
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY
on exterior areas of the membrane, they
generally are not going to go through the
membrane. Have an assortment of
functions such as acting as enzymes to
speed up reactions or attaching to the
cytoskeleton structures to help with cell
shape.
 Integral protein - with their potential to
go through the membrane, are frequently
involved in all kinds of transporting
methods for all kinds of materials.
 Carbohydrates
 receptors for viruses and other pathogens to
FU
NCTION:
 Cell Recognition - Helps on recognition of cell in
other cells.
 Adhesion - Carbohydrate molecules hold the cells
together with each other or it help cell to bind to
other tissue.
 Cell-cell signaling - Help to signal the other cell in
order to bring other cell towards itself or signal
other cell to go to a certain area of the body.
 Cell-pathogen interaction - Pathogen bind
themselves to the carbohydrates of the cells to
infect the cells Blood groups are determined by cell
surface carbohydrates of erythrocytes, and they
also have the ability to trigger immunological
responses.
 carbohydrate determines that person's blood type
 TYPES:
 Proteoglycans - consist of long polysaccharide
chains linked covalently to a protein core, are
found mainly outside the cell as part of the
extracellular matrix. provides hydration and
swelling pressure to the tissue enabling it to
withstand compressional forces.
 Glycoproteins - hydrophilic nature allows them to
function in the aqueous environment, where they
act in cell-cell recognition and binding of other
molecules. Cell surface glycoproteins are also
important for cross-linking cells and proteins (e.g.,
collagen) to add strength and stability to a tissue.
 Glycolipids - to maintain stability of the
membrane and to facilitate cell–cell interactions.
Glycolipids can also act as receptors for viruses
and other pathogens to enter cells.
 Glycosphingolipids - involved in the
regulation of cell growth, differentiation,
and neoplastic transformation through
participation in cell–cell communication,
and possible interaction with receptors and
signaling systems.
 Glycoglycerolipids - to maintain stability
of the membrane and to facilitate cell–cell
interactions. Glycolipids can also act as
enter cells.
 Glycosylphosphatidylinositol - anchor the
protein to the cell membrane
.
The Fluid Mosaic Model
With all these different components, it can be hard to
visualize how components of a cell fit together. To help
meet this challenge, scientists have developed the fluid
mosaic model, a picture scientist use to represent the
structure of a cell membrane. The fluid mosaic model
shows how the phospholipids, proteins, carbohydrates, and
cholesterol join together to create a cell membrane. A
mosaic is a type of art in which small pieces of glass are
arranged to make a larger picture. The same is true for a
N.M. Nery
10
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

cell membrane. Although the individual components throughare mitosis, allow passive and active transport, produce
Lesson 6
small, they form a remarkable barrier when put together.energy, create metabolic reactions and aid in reproduction.

2 Kinds of Cells
Eukaryotic Cell
 Are organisms that all fit in this last domain can
may be protists, plants, animals, or fungi.
 They can be unicellular or they can be
multicellular, which means they can be made up
of many cells.
 "eukaryote" typically refers to the organism itself
and when describing its cells, those are
eukaryotic cells.
 Some of Eukaryotic Cell don’t have cell wall
(i.e., animal cell).
 Do have nucleus (DNA in nucleus)
 Prokaryotic Cell
Are organisms that can be bacteria and
archaea.
They have no membrane-bound
organelles.
Unicellular which means they are single-
celled organisms.


The Cell
 Cells are the
Structure, basic building
Function And majorblocks
types of all living things. Cells
also contain the body's hereditary material and can make
copies of themselves. Cells provide six main functions.
They provide structure and support, facilitate growth
Don’t have nucleus (free floating DNA)
the word "prokaryote" is typically used to
refer to the organism. When you are
describing its cell, you are describing a
prokaryotic cell.
All prokaryotic cell has cell wall.

N.M. Nery
11
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY
11 major types of Cells
 Stem Cell - unique in that they originate as
unspecialized cells and have the ability to
develop into specialized cells that can be used
to build specific organs or tissues. Stem cells
can divide and replicate many times in order to
replenish and repair tissue.
 Bone Cell - connective tissue that compromise
a major component of the skeletal system.
Bones are made up of a matrix of collagen and
calcium phosphate minerals.
 Osteoclasts - are large cells that decompose
bone for resorption and assimilation while
they heal.
 Osteoblasts - regulate bone mineralization
and produce osteoid, an organic substance
of the bone matrix, which mineralizes to
form bone.
 Osteocytes - aid in the formation of bone
and help maintain calcium balance.
(Osteoblasts mature to form osteocytes).
 Blood Cells - from transporting oxygen
throughout the body to fighting infection,
blood cell activity is vital to life. Blood cells
are produced by bone marrow.
 Red blood cells - determine blood type
and are responsible for transporting
oxygen.
 White blood cells - are immune system
cells that destroy pathogens and provide
immunity.
N.M. Nery
12
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

 Platelets - help clot blood to prevent
excessive blood loss due to broken or
by a layer of connective tissue (dermis) and an
underlying subcutaneous layer. It protects
internal structures of the body from damage,
prevents dehydration, acts as a barrier against
germs, stores fat, and produces vitamins and
hormones.

damaged blood vessels.

 Muscle cells - enables all bodily movement
 Skeletal muscle tissue - attaches to bones
to facilitates voluntary movement. These
muscle cells are covered by connective
tissue, which protects and supports
muscle fiber bundles.
 Cardiac muscle cells - form involuntary  Fat Cells- also called adipocytes, are a major
muscle, or muscle that doesn't require cell component of adipose tissue. Adipocytes
conscious effort to operate, found in the contain droplets of stored fat (triglycerides)
heart. These cells aid in heart contraction that can be used for energy. When fat is stored,
and are joined to one another by its cells become round and swollen. produce
intercalated discs that allow for heartbeat hormones that influence sex hormone
synchronization. metabolism, blood pressure regulation, insulin
 Smooth muscle tissue - is involuntary sensitivity, fat storage and use, blood clotting,
muscle that lines body cavities and forms and cell signaling.
the walls of many organs such as
kidneys, intestines, blood vessels, and
lung airways.

 Skin Cells- The skin is composed of a layer of

epithelial tissue (epidermis) that is supported

N.M. Nery
13
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

 Nerve Cells- neurons are the most basic

unit of the nervous system. Nerves send
signals between the brain, spinal cord, and

 Sex cells- gametes are reproductive cells

created in male and female gonads that
bring new life into existence. Male sex cells
or sperm are motile and have long, tail-like
projections called flagella. Female sex cells
or ova are non-motile and relatively large in
comparison to male gametes. In sexual
other body organs via nerve impulses.

 Endothelial Cells - form the inner lining of

the cardiovascular system and lymphatic
system structures. They make up the inner
layer of blood vessels, lymphatic vessels,
and organs including the brain, lungs, skin,
and heart. Endothelial cells are responsible
for angiogenesis or the creation of new
blood vessels. They also regulate the
movement of macromolecules, gases, and
fluid between the blood and surrounding
tissues as well as help manage blood
reproduction, sex cells unite during
pressure.
fertilization to form a new individual. While
other body cells replicate by mitosis,
gametes reproduce by meiosis.

 Pancreatic Cells- functions as both an

exocrine and endocrine organ, meaning that
it discharges hormones both through ducts

N.M. Nery
14
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY
and directly into other organs. Pancreatic
cells are important for regulating blood
glucose concentration levels as well as for
the digestion of proteins, carbohydrates, and
fats.
 Cancer Cells- work to destroy the body.
Cancer results from the development of
abnormal cell properties that cause cells to
divide uncontrollably and spread to other
locations. Cancer cell development can
originate from mutations stemming from
exposure to chemicals, radiation, and
ultraviolet light. Cancer can also have
genetic origins such as chromosome
replication errors and cancer-causing
viruses of the DNA.
Structured and function
Plasma membrane or Cell membrane
 is a selectively permeable. This selectivity is a
type of protection and helps keep the harmful
riffraff out.
 a biological membrane that separates the interior
of all cells from the outside environment. The cell
membrane consists of a lipid bilayer, including
cholesterols that sit between phospholipids to
maintain their fluidity at various temperatures.
 To gain permission to enter the cell, you need to
meet with the border patrol, which are protein
molecules that are stationed along the fatty
bilayers of the plasma membrane.
Nucleus
 The control center of the cell that contains DNA.
DNA is the abbreviation of deoxyribonucleic
acid, which is the genetic material that contains
the instructions for building the body.
 It serves to maintain the integrity of the cell by
facilitating transcription and replication
processes. It's the largest organelle inside the cell
taking up about a tenth of the entire cell volume.
N.M. Nery
15
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY
 Cytoplasm
 is the gel-like substance inside the plasma
membrane. This is where much of the cell's
activity take place, and it contains the
metabolic machines or organs of the cell,
called organelles.
 is composed of water, salts, and various
organic molecules. Some intracellular
organelles, such the nucleus and
mitochondria, are enclosed by membranes
that separate them from the cytoplasm.
 The cytoplasm is responsible for holding
the components of the cell and protects
them from damage. It stores the molecules
required for cellular processes and is also
responsible for giving the cell its shape.
 Organelles
 Mitochondria - membrane-bound cell organelles
(mitochondrion, singular) that generate most of the
chemical energy needed to power the cell's
biochemical reactions. Chemical energy produced
by the mitochondria is stored in a small molecule
called adenosine triphosphate (ATP)
 Rough endoplasmic reticulum or rough ER -
This is an extensive organelle composed of greatly
convoluted but flattish sealed sacs, which are
contiguous with the nuclear membrane. It is called
'rough' endoplasmic reticulum because it is studded
on its outer surface (the surface in contact with the
cytosol) with ribosomes. The endoplasmic
reticulum can either be smooth or rough, and in
general its function is to produce proteins for the
rest of the cell to function.
 Ribosomes - are minute particles consisting
of RNA and associated proteins that function
to synthesize proteins. Proteins are needed
for many cellular functions such as repairing
damage or directing chemical processes.
Ribosomes can be found floating within the
cytoplasm or attached to the endoplasmic
reticulum.
N.M. Nery
16
 CHAPTER 2 - CHEMICAL AND CELLULAR BIOLOGY

 Smooth endoplasmic reticulum or

smooth ER - make cellular products like
hormones and lipids. The smooth ER also
acts as a detoxification center. It
synthesizes lipids, phospholipids as in
plasma membranes, and steroids. Cells that
secrete these products, such as cells of the
testes, ovaries, and skin oil glands, have an
excess of smooth endoplasmic reticulum.

 Difference between rough endoplasmic

reticulum and smooth ER - difference
between RER and SER is the presence of
ribosomes. When ribosomes attach to the
surface of an ER, it gives a characteristic
rough appearance; hence it is called Rough
ER. On the other hand, a smooth ER does

not have ribosomes on its surface. It

possesses ribosomes attached to its
membrane.

N.M. Nery
17