Cells

Definition of cell:

- A cell is the smallest unit that is capable of performing life functions.

- Examples of cells: Amoeba Proteus, plant stem, bacteria, red blood cell, nerve cell.

Types of cells:

- Prokaryotic: Bacteria, Archaea

- Eukaryotic: Protists (unicellular organisms) , fungi, plants, and animals.

Prokaryotic:

- Don’t have internal structures surrounded by membranes.

- Few internal structures.
- One - celled organisms, bacteria.
- Ring-shaped DNA
- They have cell wall, cell membrane, ribosomes, flagella, capsule, and nucleoid (DNA)

Eukaryotic:

- Contains organelles surrounded by membranes.

- Organelles can be said to have the same functions to a cell as organs have to an organism.
- Plant, animal, and fungi cells.

Cell parts:

Surrounding the cell:

Cell membrane:
- Outer membrane of the cell that controls movement in and out of the cell.
- Double layered.
- Compared to the skin of a human.

Cell wall:
- Most commonly found in plant cell, fungi, and bacteria.
- Support, protect and give consistency to the cells.

Inside the cell:

Nucleus:
- Direct cell activities like protein synthesis.
- Separated from cytoplasm by nuclear membrane.
- Surrounded and has its own membrane.
- Contains genetic material - DNA.

Nuclear membrane:
- Surrounds nucleus.
- Made of two layers of lipids.
- Openings allows materials to enter and leave nucleus.
- Has pores, holes.

Chromosomes:
- In nucleus.
- DNA wrapped around proteins (histones).
- Genetic information for the proteins in the organisms.

Nucleolus:
- Inside nucleus.
- Is the filler of the nucleus.
- Built up by proteins and nucleic acids.
- Function: forms new ribosomes.

Cytoplasm:
- Gel - like mixture.
- Is the filler of the cell.
- Surrounded by cell membrane.

Endoplasmic Reticulum:
- Moves materials around in the cell (logistic center).
- Smooth type: lacks ribosomes.
- Rough type: ribosomes embedded in surface.

Ribosomes:
- Each cell contains thousands of ribosomes.
- Produce proteins, cell factory of proteins which is important.
- Found on RER and floating throughout the cytoplasm.

Mitochondria:
- Produces energy through chemical reactions (cell respiration) – can be called the cell power
plant.
- (According to the endosymbiotic theory, a free-living prokaryote was assimilated by other cells
and evolved to mitochondria (1.5 billion years ago, the origin of eukaryotes)).
- Produce ATP.

Golgi apparatus:
- Protein “packaging plant”.
- Moves materials out of the cells (logistic export).
- Discovered by Camille Golgi in 1896, he received a Nobel prize for the discovery.

Lysosome:
- Digestive “waste plants” for proteins, fats, non-functioning organelles, and carbohydrates.
- Transport indigestive material to cell membrane for removal.
- Cell breaks down if lysosome explodes (contains harmful enzymes).
 Vacuoles:
- Membrane- bound sacs for storage and waste removal.
- Contains water solution.
- Helps plants maintain shapes.
- Most abundant in plants.
- Are huge and take the most place in the plant cell.

Chloroplast:
- Usually found in plant cells (algae and cyanobacteria).
- Contains green chlorophyll.
- Where photosynthesis takes place.

Examples of cells:

- Egg cells
- Sperm cells
- Red blood cells
- Nerve cells
- Stem cells

Stem cells:

- Cells that aren’t specialized and can differentiate into all types of cells.
- Found in embryos and in adults mainly in bone marrow.
- Morula - are totipotent stem cells, solid mass of blastomeres resulting from a number of
cleavages of a zygote, or fertilized egg. A morula is usually produced in those species the eggs of
which contain little yolk and, consequently, undergo complete cleavage.
- Blastula – pluripotent stem cells, produced during the development of an embryo by repeated
cleavage of a fertilized egg. The cells of the blastula form an epithelial (covering) layer, called the
blastoderm, enclosing a fluid-filled cavity, the blastocoel. Can’t develop into a completely new
organism.
- Adult stem cells are multipotent or unipotent.
- Blood stem cells: red blood cell, white blood cell and platelets.
- Stem cell will divide many times, and when it divides it can turn into a new stem cell or into a
specialized stem cell.
- Why do we have stem cells?
- To produce and replace dead or damaged cells.
- Stem cells are even used in medications. For example, the treatment of leukemia,
transplantation of the bone marrow from another human (stem cell) is used to treat leukemia.
Even there are some researches that say stem cells will be also used for Parkinson’s disease and
diabetes.
Embryonic stem cell:
- Embryonic stem cells are found in blastocyst.
- Cells inside = “inner cell mass” , outer layer of cells = “trophectoderm”  embryonic stem cells
taken from the inner cell mass  fluid from nutrients, culture in the lab to grow more cells.
 - These are pluripotent stem cells, meaning they can divide into more stem cells or can become
any type of cell in the body. This versatility allows embryonic stem cells  to be used to regenerate
or repair diseased tissue and organs.
Tissue stem cells:
- Tissue stem cells are found in bone marrow, skin, surface of the eye, brain, breast, intestines,
muscles, and testicles.
- Some tissues and organs within your body contain small caches of tissue-specific stem cells
whose job it is to replace cells from that tissue that are lost in normal day-to-day living or in
injury, such as those in your skin, blood, and the lining of your gut.
Stomatic stem cell:
- Somatic stem cells are responsible for tissue maintenance and repair throughout life. Studies on
blood, skin and intestinal epithelium have revealed that multiple types of stem cells with distinct
roles perform such regenerative functions.

- Mitochondria – Cells with many mitochondria typically undertake energy-consuming processes

(e.g., neurons, muscle cells).
- ER – Cells with extensive ER networks undertake secretory activities (e.g., plasma cells, exocrine
gland cells).
- Lysosomes – Cells rich in lysosomes tend to undertake digestive processes (e.g., phagocytes).
- Chloroplasts – Cells with chloroplasts undergo photosynthesis (e.g., plant leaf tissue but not root
tissue).
Organelles:

- Organelles are specialized sub-structures within a cell that serve a specific function
- Prokaryotic cells do not typically possess any membrane-bound organelles, whereas eukaryotic
cells possess several

Universal Organelles (prokaryote  and  eukaryote):

Ribosomes:  
Structure: Two subunits made of RNA and protein; larger in eukaryotes than prokaryotes.
Function:   Site of polypeptide synthesis (this process is called translation).

Cytoskeleton:
Structure:   A filamentous scaffolding within the cytoplasm (fluid portion of the cytoplasm is the cytosol).
Function:  Provides internal structure and mediates intracellular transport (less developed in
prokaryotes).
Plasma membrane:
Structure:  Phospholipid bilayer embedded with proteins (not an organelle per se, but a vital structure)
Function:  Semi-permeable and selective barrier surrounding the cell.

Eukaryotic Organelles (animal cell  and  plant cell):

Nucleus:
Structure: Double membrane structure with pores; contains an inner region called a nucleolus.
Function: Stores genetic material (DNA) as chromatin; nucleolus is site of ribosome assembly.

Endoplasmic Reticulum:
Structure:   A membrane network that may be bare (smooth ER) or studded with ribosomes (rough ER).
Function:  Transports materials between organelles (smooth ER = lipids; rough ER = proteins).

Golgi Apparatus:
Structure:  An assembly of vesicles and folded membranes located near the cell membrane
Function:   Involved in the sorting, storing, modification and export of secretory products

Mitochondrion:
Structure:  Double membrane structure, inner membrane highly folded into internal cristae.
Function:  Site of aerobic respiration (ATP production).
Peroxisome:
Structure:  Membranous sac containing a variety of catabolic enzymes.
Function:  Catalyzes breakdown of toxic substances (e.g., H 2O2) and other metabolites.

Centrosome:
Structure:  Microtubule organizing center (contains paired centrioles in animal cells but not plant cells)
Function:  Radiating microtubules form spindle fibers and contribute to cell division (mitosis / meiosis).

Plant Cells Only

Chloroplast:
Structure:  Double membrane structure with internal stacks of membranous discs (thylakoids).
Function:   Site of photosynthesis – manufactured organic molecules are stored in various plastids.

Vacuole (large and central):

Structure:  Fluid-filled internal cavity surrounded by a membrane (tonoplast).
Function:  Maintains hydrostatic pressure (animal cells may have small, temporary vacuoles).

In animal cells: Is storage of nutrients and water

Cell Wall:
Structure:   External outer covering made of cellulose (not an organelle per se, but a vital structure).
Function:  Provides support and mechanical strength; prevents excess water uptake.
Animal Cells Only

Lysosome:
Structure:  Membranous sacs filled with hydrolytic enzymes.
Function:  Breakdown / hydrolysis of macromolecules (presence in plant cells is subject to debate).

Eukaryote structure:

Animal cell:

- Nucleus – shown as double membrane structure with pores.

- Mitochondria – double membrane with inner one folded into cristae; no larger than half the
nucleus in size.
- Golgi apparatus – shown as a series of enclosed sacs (cisternae) with vesicles leading to and
from.
- Endoplasmic reticulum – interconnected membranes shown as bare (smooth ER) and studded
(rough ER).
- Ribosomes – labelled as 80S.
- Cytosol – internal fluid labelled as cytosol (‘cytoplasm' is all internal contents minus the nucleus).
- Nucleus, chloroplasts, and mitochondria have their own DNA, genetics materials.

Plant cell:
 - Vacuole – large and occupying majority of central space (surrounded by tonoplast).
- Chloroplasts – double membrane with internal stacks of membrane discs (only present in
photosynthetic tissue).
- Cell wall – labelled as being composed of cellulose, thicker than cell membrane.
- Shape – brick-like shape with rounded corners.

Prokaryote structure:

Prokaryotic cell:

- Pili – shown as single lines.

- Flagella – shown as thicker and significantly longer lines than the pili.
- Ribosomes – labelled as 70S.
- Cell wall – labelled as being composed of peptidoglycan, thicker than cell membrane.
- Shape – appropriate for bacteria chosen (e.g., E. coli is a rod-shaped bacillus).
- Size – appropriate dimensions (e.g., length of cell twice the width).

Real cell:

Free ribosomes: produce proteins needed in the cell

 - On the chromosomes we have something called telomeres. Telomeres form the ends of human
chromosomes. Telomeres shorten with each round of cell division and this mechanism limits
proliferation of human cells to a finite number of cell divisions by inducing replicative
senescence, differentiation, or apoptosis.

The cell membrane

- Phospholipids: contains three different parts, the phosphate group, glycerol which is an alcohol,
and, on the glycerol, there are two fatty acids attached.
- Amphipathic – a molecule with both hydrophilic and hydrophobic properties.
- All phospholipids have a polar hydrophilic head group and nonpolar hydrophobic hydrocarbon
tails. Glycerophospholipids are characterized by their glycerol backbone. Long carbon chains
connected to the first and second carbon of glycerol provide the hydrophobic part of the
molecule. The phosphate and additional head group structure provide the hydrophilic portion of
the molecule. In sphingomyelin the backbone is sphingosine. A long-chain fatty acid provides the
second hydrophobic tail. Note that both phosphatidylcholine and sphingomyelin have a choline-
containing polar head group.

The hydrophobic effect drives rearrangement of lipids, including the formation of bilayers. The driving
force of the hydrophobic effect is the tendency of water molecules to maximize their hydrogen bonding
between the oxygen and hydrogen atoms. Phospholipids placed in water would potentially disrupt the
hydrogen bonding of water clusters. This causes the phospholipids to bury their nonpolar tails by
forming micelles, bilayers, or monolayers.
What happens to fat if you put in water?

“It doesn’t solve, it forms droplets of fat in water. It is due to that fat it’s not solvent in water because its
hydrophobic, it doesn’t like water. “

- The phosphate head or group is hydrophilic, likes water.

Cell membrane structure:

The proteins in the membrane have different functions, for example:

- Hormone binding sites (hormone receptors), for example the insulin receptor.
- Link cell or groups of cells together to form organs. (Cell adhesion).
- Cell-to-cell communication, for example receptors for neurotransmitters at synapses.
- Channels for passive transport to allow hydrophilic particles to pass the membrane.
- Pumps for active transport which use ATP to move particles across the membrane.

Phospholipid bilayer:
- All phospholipids have a polar hydrophilic head group and nonpolar hydrophobic hydrocarbon
tails. Glycerophospholipids are characterized by their glycerol backbone. Long carbon chains
connected to the first and second carbon of glycerol provide the hydrophobic part of the
molecule. The phosphate and additional head group structure provide the hydrophilic portion of
the molecule. In sphingomyelin the backbone is sphingosine. A long-chain fatty acid provides the
second hydrophobic tail. Note that both phosphatidylcholine and sphingomyelin have a choline-
containing polar head group.

Fluid mosaic model:

- Fluid: pliable/easy moved

- Mosaic: made of many different molecules (lipids, proteins, carbohydrates)
- Contains: protein channel (transport protein), globular protein, glycoprotein, carbohydrate,
cholesterol, glycolipid, peripheral protein, integral protein, filaments of cytoskeleton, surface
protein, alpha-helix protein.

- Integral protein: proteins that cross both layers of the phospholipid bilayer.
- Peripheral proteins: proteins that are only on the top half or the bottom half of the phospholipid
bilayer.
- The principle of the fluid mosaic model of biological membranes as proposed by Singer and
Nicolson. In this model, globular integral membrane proteins are freely mobile within a sea of
phospholipids and cholesterol.
Double membrane:
Prophase: Prophase is the first phase of mitosis, the process that separates the duplicated genetic
material carried in the nucleus of a parent cell into two identical daughter cells. During prophase, the
complex of DNA and proteins contained in the nucleus, known as chromatin, condenses. The chromatin
coils and becomes increasingly compact, resulting in the formation of visible chromosomes.
Chromosomes are made of a single piece of DNA that is highly organized. The replicated chromosomes
have an X shape and are called sister chromatids. The sister chromatids are pairs of identical copies of
DNA joined at a point called the centromere. Then, a structure called the mitotic spindle begins to form.
The mitotic spindle is made of long proteins called microtubules that begin forming at opposite ends of
the cell. The spindle will be responsible for separating the sister chromatids into two cells. Prophase is
followed by the second phase of mitosis, known as prometaphase.

- Nuclear membrane breaking up.

- Chromosomes are supercoiled, DNA is packed tight.
- Centrosomes start to produce microtubules. (fibers)

Metaphase: Metaphase is the third phase of mitosis, the process that separates duplicated genetic
material carried in the nucleus of a parent cell into two identical daughter cells. During metaphase, the
cell's chromosomes align themselves in the middle of the cell through a type of cellular "tug of war." The
chromosomes, which have been replicated and remain joined at a central point called the centromere,
are called sister chromatids.
Prior to metaphase, protein formations called kinetochores formed around the centromere. Long protein
filaments called kinetochore microtubules extended from poles on either end of the cell and attached to
the kinetochores. During metaphase, the kinetochore microtubules pull the sister chromatids back and
forth until they align along the equator of the cell, called the equatorial plane. There is an important
checkpoint in the middle of mitosis, called the metaphase checkpoint, during which the cell ensures that
it is ready to divide. Once the cell has established that all of the chromosomes are properly aligned and
that the kinetochores are correctly attached, the cell enters the fourth phase of mitosis, known as
anaphase.

- Chromosomes are lined up at the equator of the cell.

- Microtubules attach the centromere.
Anaphase: Anaphase is the fourth phase of mitosis, the process that separates the duplicated genetic
material carried in the nucleus of a parent cell into two identical daughter cells. Before anaphase begins,
the replicated chromosomes, called sister chromatids, are aligned at along the equator of the cell on the
equatorial plane. The sister chromatids are pairs of identical copies of DNA joined at a point called the
centromere. During anaphase, each pair of chromosomes is separated into two identical, independent
chromosomes. The chromosomes are separated by a structure called the mitotic spindle. The mitotic
spindle is made of many long proteins called microtubules, which are attached to a chromosome at one
end and to the pole of a cell at the other end. The sister chromatids are separated simultaneously at
their centromeres. The separated chromosomes are then pulled by the spindle to opposite poles of the
cell.

- Microtubules getting shorter pulling the chromosomes to each pole. (Sister chromatids are
separated.)

Telophase: Telophase is the fifth and final phase of mitosis, the process that separates the duplicated
genetic material carried in the nucleus of a parent cell into two identical daughter cells. Telophase begins
once the replicated, paired chromosomes have been separated and pulled to opposite sides, or poles, of
the cell. During telophase, a nuclear membrane forms around each set of chromosomes to separate the
nuclear DNA from the cytoplasm. The chromosomes begin to uncoil, which makes them diffuse and less
compact. Along with telophase, the cell undergoes a process called cytokinesis that divides the
cytoplasm of the parental cell into two daughter cells.

- The cell starts to divide.

- Nuclear membrane is reformed.
- Chromosomes uncoiled, means to break down.
- Microtubules break down.
- After telophase the rest of the cell divides in a process called cytokinesis. And the result is two
genetically identical cells.

The most important molecules in the body:

- Fatty acids : Fatty acids are the building blocks of the fat in our bodies and in the food we eat.
During digestion, the body breaks down fats into fatty acids, which can then be absorbed into
the blood. Fatty acid molecules are usually joined together in groups of three, forming a
molecule called a triglyceride. We can find fatty acids in adipose tissue (body fat).

- Saturated fatty acids: Saturated fatty acids (SFA) contain no double bond; this type of fat can be
synthesized by the body and its major dietary source is food from animal sources, such as full-fat
dairy products, red meat, and poultry. Moreover, there are numerous types of SFA according to
length of their chain (contains 4–16 carbon atoms).

- Unsaturated fatty acids: Unsaturated fatty acid carbon chains contain one or more double bonds
with a terminal carboxylic group (–COOH), unlike saturated fatty acids, which contain no double
 bonds. These fatty acids are subdivided into two groups depending on the number of double
bonds.

- Glucose: Glucose, C₆H₁₂O₆ , is the main type of sugar in the blood and is the major source of
energy for the body's cells. Glucose comes from the foods we eat, or the body can make it from
other substances. Glucose is carried to the cells through the bloodstream. Several hormones,
including insulin, control glucose levels in the blood.

- Amino acids: Amino acids are small molecules that are the building blocks of proteins. Proteins
serve as structural support inside the cell, and they perform many vital chemical reactions. Each
protein is a molecule made up of different combinations of 20 types of smaller, simpler amino
acids. Protein molecules are long chains of amino acids that are folded into a three-dimensional
shape. Chemically, an amino acid is a molecule that has a carboxylic acid group and an amine
group that are each attached to a carbon atom called a carbon.
- R-group determine which amino acid it is and there are 20 different amino acids in our body.
Biological molecules:

All biological molecules fall into one of four categories:

- Carbohydrates
- Lipids
- Proteins
- Nucleic acids

Carbohydrates:

- Contain C,H,O
- Many hydroxyls group
- Often end in -ose
- Primary source of energy for cells
- All sugars are carbohydrates

Monosaccharide:

- Simple sugars with the formula Cx(H2O)X

- The monomer of larger carbohydrates
- Soluble in water (due to many polar -OH groups)
- Immediate energy source for cell respiration
- For example:
- glucose C6H12O6
- fructose C6H12O6
Disaccharide:

- Result from two monosaccharides bonding together in a condensation reaction.

- Soluble in water (due to many polar -OH groups)

- For example:
- Maltose (glucose + glucose)
- Sucrose (glucose + fructose)
Polysaccharide:
- Chains of 100-100’s monosaccharides (usually glucose) bonded together 
- Function as energy storage or cell structure
- Starch (amylose) in plants
- Glycogen in animals
- Cellulose in plant cell wall
Lipid:
- Contain C, H, O
- Mostly hydrocarbons (∴ nonpolar & hydrophobic)
Triglyceride:
- 3 fatty acids bonded to a glycerol 
- Energy storage in animals and some plants
- Examples:
o Fats (solid at room temp)
o Oils (liquid at room temp)

Phospholipid:

- Phosphate group and two fatty acids bonded to a glycerol

- They can form lipid bilayers because of their amphiphilic characteristic.
- Example:  cell membrane phospholipid
Steroids/Sterols:

- Four fused rings of carbon atoms with functional group(s) attached

- Examples:
o cholesterol (cell membrane fluidity)
o testosterone (hormone)
o progesterone (hormone)

Protein:

- Contain C, H, O and N
- Polymers of many amino acids bonding together in a condensation reaction 
- MANY cellular functions

o contraction

o transport

o immune defense

o enzyme’s structure 
Polypeptide:

- A long chain of amino acids that folds up to become the functional protein
- Examples:
o insulin (hormone)
o helicase (enzyme)
o keratin (structure)