Ch 2: Take a tour inside the cell

Diversity of cells

  • Eukarya – Plants, animals, fungi, and protists
  • Bacteria – Single-celled microorganisms
  • Archaea – Single-celled microorganisms

The four eukaryotic kingdoms are fungi, protists, Animalia, and Plantae. Kingdom Plantae includes plants that manufacture their own food. Kingdom Animalia is for animals that ingest and digest food from external sources rather than making their own. Kingdom fungi are decomposers who decompose organic wastes to obtain nutrients. Kingdom protists are for all other organisms which do not fit in either of the other three kingdoms.

Two main classes of cells:

  • Eukaryotic cells – These have a central nucleus, cell membrane, the cells are complex, membrane-bound organelles, and much larger
  • Prokaryotic cells – These have no central nucleus, rather, genetic information is located within the nucleoid, no membrane-bound organelles, the cell is simple and much smaller than a eukaryotic cell.

Prokaryotic cells include archaea and bacteria and lack a central nucleus and other membrane-bound organelles. Eukaryotes include plant and animal cells that have a nucleus and membrane-bound organelles. The mitochondria and chloroplast were free-living and were engulfed by prokaryotic cells. This is explained by the endosymbiotic theory.

Differences between eukaryotic and prokaryotic cell

  1. Eukaryotic cells are larger than the prokaryotic cells.
  2. Eukaryotic cells are more complex than prokaryotic cells.
  3. Eukaryotic cells have a true nucleus while prokaryotic cells do not.
  4. Eukaryotic cells have specialized structures in the cytoplasm called organelles and are membrane-bound, while the prokaryotic cell has no membrane-bound organelles.
  5. Not all eukaryotic cells have a cell wall, while all prokaryotic cells have a cell wall.
Common grounds for all cells
  • All cells have a cytoplasm
  • All cells have a genetic material
  • All cells make proteins for their functions

Customs: Plasma membrane

  • This restricts the movement of substances in and out of the cell
  • It is made up of two lipid layers (bilayer), with hydrophobic and hydrophilic ends

The plasma membrane is made up of two layers of phospholipids with many proteins embedded in it. The role of the plasma membrane is to regulate entry and exit of molecules through osmosis, and diffusion among other transport processes. Proteins present in the cell membrane act as receptors, enzymes, structural components, and pumps. The cell membrane is described as being amphipathic because it contains hydrophilic heads as well as the hydrophobic tails. The phosphate end is the polar side and the fatty-acid tails are the non-polar.

  • Phospholipids – Have polar and non-polar ends
  • Proteins – Both integral and peripheral
  • Sterols – Embedded in the plasma membrane and which controls its fluidity
  • Carbohydrates – Acting as receptors and junctions

Within the cell membrane, glycoproteins are used for recognition and acting as receptors and antigens. Glycolipids are attached to the phospholipids together with sugar molecules. Cholesterol helps maintain the fluidity of the cell by preventing its melting in high temperatures and freezing in low temperatures.

Other cellular components

  • The cytoplasm – Fluid-like interior of the cell where organelles found floating
  • DNA-containing region – Maybe a central nucleus or another region of the cell (nucleoid)


  • The site for protein synthesis made up of ribosomal RNA and proteins.
  • Each ribosome has large ribosomal subunits and small ribosomal subunits. Prokaryotic ribosomes are smaller than eukaryotic ribosomes.
  • There are the membrane-bound ribosomes, those found on the surface of rough endoplasmic reticulum and the free ribosomes in the cytoplasm

Ribosomes are the site for protein synthesis and are the most numerous organelles in the cell. They can be found floating freely in the cytoplasm or embedded on the rough endoplasmic reticulum. If the protein is to be used within the cell, it is produced by the free-floating ribosomes, and if the protein is to be used outside the cell, it is produced by the ribosomes attached to the rough endoplasmic reticulum.

The endoplasmic reticulum

The endoplasmic reticulum is an extensive network of membranes composed of both rough and smooth regions. It forms the internal transport system of the cell and helps modify proteins and synthesis of lipids. Rough endoplasmic reticulum has no ribosomes, synthesizes lipids, steroid sex hormones, and helps in detoxification of drugs by adding hydroxyl groups to make them soluble and be flushed out of the body. Rough endoplasmic reticulum has embedded ribosomes and is involved in the synthesis of proteins.

Eukaryotic cells

  • Cell walls – mechanical strength, not present in animal cells
  • Chloroplast – Needed for photosynthesis, and not present in animal cells
  • Large central vacuoles – Needed for storage of nutrients, not present in animal cells
  • Centrioles –  Needed for cell division, not present in plants
  • This contains the genetic material (DNA) in the form of chromosomes or chromatic.
  • There are the nucleoli within the nucleus – This is where ribosomal subunits are located and which directs the synthesis of large and small ribosomal subunits
  • Surrounded by the nuclear envelope

The endomembrane system

  • This is the post office of the cell
  • The endomembrane system consists of rough endoplasmic reticulum which synthesizes proteins, smooth endoplasmic reticulum that synthesizes lipids.
  • Golgi apparatus is a stack of flattened membrane sacs that package substances, peroxisomes which helps break down lipids such as fatty acid and other molecules, and vesicles that carry molecules around the cell.

All structures of the endomembrane system are Nuclear envelope, plasma membrane, endoplasmic reticulum, lysosomes, vacuoles, and reticulum. The function of the endomembrane system is to synthesize proteins and transport them within and without the cell. Metabolism and movement of lipids and lastly, detoxifying poisons, and drugs.

The mitochondria as the fireplace

  • The cell uses mitochondria to make energy through a process called cellular respiration
  • The space between the two membranes of mitochondria is called intermembrane space
  • The matrix is the inside of the matrix

Mitochondria are called the powerhouse of the cell because it produces most ATP molecules in cellular respiration. Both TCA cycle and Oxidative phosphorylation occurs inside the mitochondria. The number of mitochondria in a cell depends on the type of cell and amount of energy needed by the cell. For instance, the muscle cell needs a large amount of energy and hence more mitochondria than in a cell whose purpose is to transmit nerve impulse only. Mitochondria have two membranes: the outer membrane which covers the organelle and the inner membrane which is folded to form cristae that increase the surface area for cellular respiration.


  • Plant cells and other photosynthetic cells use light to make glucose that is the main source of energy
  • Thylakoid is fluid-filled space which has chlorophyll to trap light energy

Fluid-filled space inside the chloroplast is called the stroma, and the stacks of membranes in the stroma form what is known as grana. The stroma contains enzymes that control the process of carbon fixation. Light reactions of photosynthesis provide energy, NADPH, and ATP for light-independent reactions. The general function of the chloroplast is to absorb and convert light energy into sugar molecules that produce ATP and NADPH.


  • Microfilaments – Made of the protein actin, helps cells contract, allow cells to crawl and helps in animal cell division
  • Microtubules – Made up of protein tubulin, mostly found in cilia and flagella and helps in vesicle movement within the cell
  • Intermediate filaments – composed of various proteins and reinforces other proteins.
  • Cilia and flagella – Cilia are shorter and more numerous. Cilia beat to move materials and fluid along surfaces.

Cytoskeleton refers to the network of fibers made of protein, which supports the cell and anchors the organelles within the cytoplasm. The three types of cytoskeleton are actin filaments, microtubules, and intermediate filaments. The microtubules are composed of a and b tubulin protein subunits which separate the chromosomes during cell division. The intermediate filaments have overlapping tetramers of protein. Out of the three types, the microtubules are the largest. The four components required so as to move material along the microtubules are a vesicle, motor protein to provide energy-driven motion, microtubules, and the connector molecule.

The cell wall

  • Made up of cellulose and for woody plants, lignin
  • Fungal cells have chitin
  • The bacterial cell wall has peptidoglycan among other components

The three functions of the cell wall are protecting the internal contents of the cell, acting as the skeleton, and regulating the growth of cells. The cell wall is made up of cellulose and pelcin, forming a thick, stiff, and rigid inner primary and secondary wall.

Prokaryotic cells

  • Smaller than eukaryotic cells
  • Capsule – helps bacteria cells avoid capture by cells of the human immune system and helps attach to surfaces and other cells.
  • Pili and fimbriae are used for attachment on surfaces
  • Bacteria flagella help the bacterial cell to move around

A prokaryote is defined as a single-celled organism that lacks membrane-bound organelles and whose DNA is found freely floating in the cytoplasm. The oldest prokaryote was formed around 3.5 billion years ago. All prokaryotes have a 70S ribosome, cytoplasm, cell membrane, and peptidoglycan cell wall.

Revision Summary and Tests

What are the two different types of cells?
eukaryotic (more complex, with nucleus and membrane bound organelles), prokaryotic (simpler, smaller and without nucleus)

Plasma membrane
-All cells contain it
-is a selective barrier. in small things, non polar, not charged
-cell increases in size, volume grows more proportionately than are (plasma) hence why cells split before getting too large

Why do organisms generally have many cells, not smaller cells?
-cells increase, volume grows way more than area, so cell splits before it gets too large

What is the fluid inside a cell?
Cytosol, cytoplasm

What are chromosomes?
Carry genes in form of DNA

What are ribosomes
organelle that makes proteins

What are some differences between prokaryotic and eukaryotic cells?
1) location of DNA – prokaryotes dont have
2) other membrane bound organelles – prokaryotes dont
3) complexity – eukaryotes more complex
4) size – eukaryotes tend to be larger
5) Presence of flagella/fimbriae – prokaryotes have, eukaryotes dont

Prokaryotes have:
fimbrae – movement on the surface of some
nucleoid – region where cell’s DNA is, but not enclosed
ribosomes – make proteins
plasma membrane
cell wall/capsule
flagella – for movement

What is the nucleoid?
In prokaryotes, it is where the cell’s DNA is stored, but it is NOT an enclosed organelle.

What are some differences bw an animal and a plant cell?
Animal – has centriole, lysosomes, ECM
Plant – has central vacuole, chloroplasts, amyloplast (starch grain), cell wall, chlorophyll, photosynthesizes

Cell Membrane is also known as
Plasma membrane

What are membranes made of usually?
A double layer of phospholipids, as well as other lipids (like cholesterol) and proteins

What is the primary purpose of a cell membrane?
To control movement in and out of the cell, define cell from outside space

The nucleus
-part of the endomembrane system
-contains most of genes
-has double membrane itself
-has pores that allow mRNA in and out of the nucleus
-pore complex lines each pore and regulates entrance and exit of proteins

Structure of the nucleus

DNA is loacted in
chromosomes, made up of a material called chromatin (proteins and DNA)

what is the nucleolus?
Nucleolus produces ribosomes

-make proteins
-both in prokaryotic and eukaryotic

Notice that there is a space b/w small subunit and large subunit. This is where the ribosome pieces together a protein.

Transport vesicles
Transport vesicles budd off ER and other endomembrane organelles. It fuses with their membrane.
-walks along tracks of microtubules (think kinesin feet)

What is the golgi Apparatus
A stack of flattened sacks

What happens in the golgi?
-packing, sorting, modification of phospholipids, proteins
-many polsyaccharides are made here
-storage of lysosome enzymes

membranous sac of digestive enzymes
-mergers with food vacuoles at eats them!

-water balance,
-waste storage
-food storage

What is the central vacuole in a plant cell?
In plants, holds food, water, waste, starch
-also helps to hold up the cell (it’s HUGE)
solution inside vacuole is sap and not cytosol

What are the organelles in the endomembrane system? What organelles are membrane bound?
endoplasmic reticulum
Central Vacuole

What are the two types of ER?
-made of rough ER – protein synthesis and storage, smooth er – lipid synthesis

What do rough ER do?
-Rough ER has ribosomes attached
-these ribosomes are where protein syntehsis takes place
-transport vesicles bud from rough ER

What do smooth ER do?
-outer surface lacks ribosomes – smooth
-synthesices lipids

structure of ER

What are chloroplasts
only in plant cells, source of photosynthesis

What is the structure of a chlorplast?
outside is outer membrane
inner membrane
In the stroma (flui), there are stacks of thylakoids

Structure of a chlorplast

Mitochondria’s function
site of metabolic activity, creates ATP
extracts energy from food

Structure of mitochondria
outside layer smooth
inbetween is intermembrane space
inside membrane layer folded into layers of cristae

Structure of a mitochondria

network of fibers extending through cytoplasm for support and movement
Motor proteins interact with cytoskeleton for cell motility – flagellum and cilia

What are the two types of cytoskeleton fibers we learned about?
1) microtubules

Main functions: cell motility, maintenance of cell shape, chorosome movements in cell division (division spindle forms here), organelle movements
Structure-hollow tubes made from proteins

Cilia and flagella are made out of which cytoskeleton type?

What is the difference between cilia and flagella
Cilia – usualy has many, but shorter and they beat like oars. Can also be used for senseing what’s going on ouside cell
Flagella, one or a few, longer, undulating motion that generates movement

What is the structure of microtubules?
They grow by adding subunits (protwins). they are HOLLOW
they are organized in centrosomes

What are centrioles?
used for cell division in animal cells, grows out of centrosomes. Division spindle grows out of the centrioles.

Which is the thickest cytoskeleton type?

Main functions: maintenance of cell shape, changes in cell shape, muscle contraction, cell motility, cell division (cleavage formation), muscle contraction, cytoplasmic streaming
Structure-globular protein actin.

Plant cell walls
-made from microfibrils of cellulose
-primary cell wall (young plant cell, thin and flexible)
-middle lamella (b/w primary walls of adjacent cells, have pectins)
-secondary cell – matures and stops growing, plant cell strengthens its walls

Final Template for Test Reminder

small molecules
water, inorganic ions, small organic molecules

what is the most abundant small molecule

proteins, polysaccharides, nucleic acids; only only be synthesized; synthesis involves lining monomers to form polymers

tips of cells that are most diverse, genetic material is circular, chromosomes not contain with nucleus but exist within the nucleic, cell membranes surrounded by outer cell wall, and are single cellular; two domains Bacteria and archaea

types of cells that have genetic material in the form of linear chromosomes with tightly associated proteins called histones; chromosomes contained within the nucleus, plasma membrane may or may not be surrounded by cell wall (animal vs. plant), single cellular or multicellular

plasma membrane
phospholipid bilayer; some bacteria have inner and outer membrane, some only one membrane

cell wall
complex of proteins and polysaccharides; surrounds plasma membrane, periplasmic space exists between cell wall and outer, protects cell and helps maintain its shape

central region containing DNA

invagination of plasma membrane; functions in synthesis of DNA, protein secretion

plasma membrane
phospholipid bilayer; contains integral proteins and peripheral proteins; lipid molecules and proteins move laterally (fluid mosaic model); hydrophilic head, hydrophobic tail = amphipathic; membrane function separates cells from the environment ; membrane proteins have many functions

__ regulates the chemical reactions within the cell

__ control uptake of molecules when in the plasma membrane

Transport proteins
_ care carriers, channels, and pumps that get molecules across membrane into cell

cell wall
only in plants; structure- located outside of the plasma membrane, made of later of cellulose microfibrils; cell wall produced as cell matures; function- connects plant cells into tissue; regulates growth and shape of cell; allows transfer of materials from one cell to another through plasmodesmata

long chains of glucose molecules hydrogen bonded together forming bundles embedded in networks of other polysaccharides

plasma membrane lined channel though cell wall that connects cytosol of adjacent cells

management; structure- sounded by 2 concentric membranes that make up the nuclear envelope; membranes are fused tougher at distant areas which create small nuclear pores; contains nucleolus, and chromatin, and a network of fibrous proteins called lamins; function- carries hereditary information which is passed from one cell to its daughter cell; regulates activities occurring in the cell

along inner membrane surface that maintains the shape and binds to dNA

endoplasmic reticulum
structure- formed by membrane continuous with outer nuclear membrane; consists of networks of interconnecting flattering sacs tubes and channels; two general form , RER and SER.

Rough ER
has ribosomal site where amino acids polymerize to form proteins; function- synthesizes plasma membrane, organieels, and secretes proteins (chymotrypsin)

Smooth ER
no ribosomes, and is continuous with the RER- function: synthesizes fatty acids and phospholipids in liver, and detoxifies hydrophobic pesticides and carcinogens

structure- composed of fat membrane bound sacs arranges in stack surrounded by tubules and vesicles with 3 regions: cis, medial, trans function- enzymes modify secretory and membrane proteins differently going from cis, medial to trans. vesicles that leave the golgi apparatus can becomes a lysosome or fuse to the cell membrane and be secreted

structure- consists of membranous vesicles formed from the golgi complex; vesicles contain acid hydrolases low pH maintained by H+ pumps and Cl- channels in lysosomal membrane function- degrades materials taken into cell by phagocytosis and obsolete components of cell; enzymes degrade polymers into monomeric subunits; problems with the function of the enzymes can cause disease

structure- consists of membrane bound vesicle that contains oxidases and catalase function- oxidases use molecular oxygen to oxidize organic molecules which produces hydrogen peroxide; catalase degrades hydrogen peroxide to toyed water and oxygen; primarily fatty acids oxidized to yield acetyl groups which are used in cholesterol synthesis; degrades toxic molecules in liver and kidney cells defective enzyme function can cause disease

what enzyme degrades hydrogen peroxide to yield water and oxygen

structure- oval shaped and surrounded by a double membrane; inner membrane folds inward creating a series of shelves surrounding inner region function- ATP production through Krebs cycle and electron transport

specific to plants; structure- consists of compartments within the cytoplasm surrounded by single membrane; as plant cells mature, the vacuoles within the cell use to fuse to form one large fluid filled vacuole; maintains an acidic pH due to the H+ pumps and Cl- channels function: stores water, ions, and nuctrienes; enzymes and acid degrade substrates, osmotic influx of water produces turgor pressure

structure- component surrounded by a double membrane, inner membrane moms a network of flattened sac that contain photosynthetic pigments, chlorophyll function- chlorophyll pigments and other photosynthetic pigments capture energy from the sun and transform it to chemical energy and stored in glucose

structure- network of filamentous proteins within the cytoplasm with 3 classes function- regulates position of organelles within the cell; provides routes for transport of vesicles; plays a role in cell division and cell movement

actin filaments- threadlike proteins hat form bundles, important in muscle cells

intermediate filaments
fibrous proteins found in cells that receive a lot of stress such as cells of the skin

long, hollow tubules important in mitosis, movement of cilia and flagella

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