Cell Biology Summary by Joana Costa Campos

MBBS COURSE
Subject: Cell Biology

Student: Joana Costa Campos
Teacher: XiangDong Wang
Chinese name: 乔安娜 (小乔)
Grade: 2021
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Homework Compilation

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INDEX
• Chapter 1 – Introduction to Cell Biology

§ Terms: Cell Theory, Cell Biology
1- Write down briefly the history of cell biology.
2- Why Molecular Biology is the essential base of Cell Biology?
3- What do you want to learn in the course of Cell Biology?
4- Why do you think that cell is life?
5- Please draw a picture to show the anatomy of a mammalian cell and indicate each part of the cell and its
function in the cell.
• Chapter 2 – Cell Membrane and Cross Membrane Transportation

§ Terms: amphipathic molecule, liquid crystal state, membrane asymmetry, unit membrane, fluid
mosaic model, lipid raft, passive transport, active transport, facilitated diffusion, symport,
cotransport, receptor mediated endocytosis, contact inhibition
1- Please describe the molecular components of cell membrane.
2- What are the characteristics of cell membrane?
3- What is unit membrane? Why this model is still be used in cell biology and other subjects?
4- What is fluid mosaic model? Why is this model popularly accepted?
5- How many kinds of passive transport? How many kinds of active transport? Please give examples!
6-What is receptor mediated endocytosis? Please explain the related mechanism for familial
hypercholesterolemina.
• Chapter 3 – Endomembrane System

§ Terms: endomembrane system, microsome, signal peptide, signal peptide recognition particle,
translocator, signal peptide hypothesis
Endoplasmic Reticulum
1- How many kinds of protein are synthesized, transported and modified in RER? please explain each step of
these process.
2- Please write down how many kinds of glycosylation, tell where they take place and what are the function of
glycosylation.
3- Explain the function of ER. What is the marker enzyme of ER?
Golgi Complex
1- What is the characteristics of Golgi Complex in morphology, what is the function of Golgi Complex?
2- Briefly explain types of protein glycosylation, and their characteristics and sites of formation.
3- How can Golgi Complex sort protein? Give an example.
4- what is the marker enzyme of Golgi Complex?

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Lysosome
§ Terms: Primary lysosome, Secondary lysosome, Tertiary lysosome
1- How many kinds of lysosomes according to enzyme activity?
2- How does lysosome form? What are functions of lysosomes?
3- How do lysosomes digest materials from outside the cell and inside the cells?
4.What are the marker enzymes of lysosome and peroxisome? What are the major differences
between the two organelles?
5- Why do call lysosome and peroxisome heterogenous organelles?
6- What are the functions of peroxisome? Compare the detoxification function of peroxisome and
smooth ER.
Vesicle Transport
§ Terms: Vesicle transport, COPII coated vesicle, COPI coated vesicle, genetic lysosome
diseases
1- How many kinds of major vesicles? what are the transports mediated by them, and what are the
orientations?
2- What are the significance of vesicle transport?
3- Explain the mechanism of vesicle transport has the proper direction.
4- What is the pathological mechanism of silicosis?
Endomembrane system and vesicle transportation
1- What is endomembrane system? Please list the members of organelles in endomembrane system.
2- Please list the proteins synthesized in attached ribosomes and free ribosomes!
3- Please describe the process of synthesis, modification, and transportation of secretion protein, membrane
protein and lysosomal protein.
4- How many kinds of coated vesicles? And what determines their orientations?
5-How can a vesicle dock successfully and exactly merge with target membrane organelles?
6- Why peroxisome is a special member of endomembrane system?
• Chapter 4 – Mitochondria
§ Terms: semiautonomous organelle, ATP Synthase Complex, TIM, TOM
1- Please describe the structure characteristics of mitochondria. How can the mitochondria make
ATP?
2- Please describe the characteristics of mitochondrial genome

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• Chapter 5 – Cytoskeleton
§ Terms: Cytoskeleton, Microtubule-organizing centers (MTOCs), Microtubule-Associated
proteins, intermediate filament, motor proteins
1.Please describe the structure characteristics of each member of cytoskeleton and describe how they
assembly.
2.Please describe the functions of each member of cytoskeleton in a cell.
• Chapter 6 – Cell Nucleus

§ Terms: Nuclear pore complex, nuclear lamina, nucleosome, centromere, telomere, nucleolus,
euchromatin, heterochromatin, nuclear matrix (nuclear skeleton)
1- How can the nucleolus form? What are the roles of nucleolus?
2- Is it passive or active transport via nuclear pore complex? Why?
3- Describe the structures from nucleosome?
4- Under Electron microscope, what can we observe in the nucleolus?
• Conclusion

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Chapter 1 – Introduction to Cell Biology
Important Terms
Cell theory: The Cell theory has created by three important Germany biologists, Matthias
Schleiden, who studied botany, the zoologist Theodore Schwann, and Rudolph Virchow, a
pathologist. They state that the cell is the structural unit of life, all organisms are made up of one
or more cells, and cells only arise from the division of pre-existing cells.
Cell Biology: Cell Biology is a subject to study cell structures (including cell membrane,
different organelles and other functional structures), functions, and behaviours (activities), such
as proliferation, differentiation, response, metabolism, movement, senescence, and cell death
(birth, aging, illness and dead). Cell biology study cells at three main types of levels, Molecular
biology level, Light Microscope and Electron Microscope level.

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2- Write down briefly the history of cell biology.
The discovery of the cell would not have been possible if not for advancements to the
microscope. The first optical compound microscope was created in late 16th century by
Zacharias Jensen. In 1665, cells were observed for the first time in life thanks to Robert Hook.
His microscope used three lenses and a stage light, which illuminated and enlarged the
specimens. These advancements allowed Hooke to see something wondrous when he placed
a piece of cork under the microscope. He gave the name “cells” like in the rooms in the old
dynasty.
After his discovery, scientists and biologists around the world started to get more interest
about this theme, and started to studding cell structures under light microscope. It was the
case of Leeuwenhoek, a simple Dutch man without any higher education but very smart and
curious about life. He made a best microscope and did very important discoveries in the history
of Biology. He observed a lot of cells such as bacteria, free-living and parasitic
microscopic protists, sperm cells, blood cells, microscopic nematodes and rotifers, and much
more.
As it was referred above, Matthias Schleiden and Theodore Schwann raised all the
organisms are composed of cells and cell is the physiological and functional unit of life. Later
on, Rodolph Virchow raised that cells can only come from the exiting cells. These three
scientists created the Cell Theory.
Curiosity moved many people to start searching more and more details in the cell and its
functions using the under light microscope, because know they know that cell is the basic unit
of life, and so a new branch of Biology was created, the Cytology. With the technology
development impacting this study, three events are important, namely, gene theory, tissue or
cell culture, differential centrifugation separation the components of the cell.
In 1931, two German scientists, Ernst Ruska and Max Knoll, found a way to achieve a
resolution greater than that of light, the Electron Microscope. With this invention, people
observed some structures undetected under light microscope and they also could get more
detailed information about cells and live.

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One of the biggest discoveries, which marked a milestone in the history of science, was
dated in 1953 when James Watson and Francis Crick found the DNA double helix structure,
and the genetic information code, modern molecular biology started, then cell biology was
established.
Cell biology is the base of bio-medical causes and it is a frontier subject. By
understanding how cells work in healthy and diseased states, cell biologists working in
animal, plant and medical science will be able to develop new vaccines, more effective
medicines, plants with improved qualities and through increased knowledge a better
understanding of how all living things live. Therefore, the translational medicine depends on
its notions and techniques.

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Historical Landmarks in Determining cell structure

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3- Why Molecular Biology is the essential base of Cell Biology
As we learned in our classes, Cell Biology is the study of the cell structures, functions and
activities. Molecular Biology a branch of biology which studies the molecular basis of biological
activity, dealing with the ultimate physicochemical organization of living matter and especially
with the molecular basis of inheritance and protein synthesis.
The reason why most molecular biologists focus on genes and proteins is because
proteins perform a huge diversity of functions within living cells and genes contain the
information required to make more proteins.
The study of molecular biology provides a solid notion base for Cell Biology to develop
because molecular biology not also plays an important role in understanding formations,
actions and regulations of various parts of cells, but also can be used to efficiently target new
drugs, vaccines, diagnose disease and understand the physiology of the cell and how living
things live.

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4- What do you want to learn in the course of Cell Biology.
My father always used to say “O saber não ocupa lugar” which literally means that “the
knowledge doesn’t take place (in the brain)”. Even knowing that I’ll not be a scientist or
biologist, since little girl that I have interest about cell biology contents. Besides that, I’m a
Traditional Chinese Medicine doctor and I know how important is it for us, doctors, to be able
to fully understand all the mechanisms behind healthy and illness states, to understand the
diseases, as well as the effect of drugs in our body, and so on. My father was the best doctor
that I ever met and the most acknowledgeable person that I knew, and he always emphasised
the important of cell biology in a medical practitioner’s live in order to perform better diagnoses
and consequent better treatments for our patients.
5- Why do you think that cell is life?

I think cell is live because all the organisms compose of cells and cells are the basic
structures of all living organisms. Cell is also the metabolic unit, all metabolic activity is based
on cells. And the ones which happen outside of the cell need the cells to provide enzymes.
The cell is the base for development, every individual comes from fertilized egg through
proliferation and differentiation they become to an individual. During this process, the genetic
information is passed from generation to generation, including genetic disease, so we can also
state that is cell is the bridge of inheritance.
Cell is the unique substance to duplicate. And virus, which is non cell structure of life,
depends on cells’ DNA to duplicate, and after infection can make use of the machineries of the
cell to produce their genetic material and protein and repack a new virus to infect other kind of
cells.

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6- Draw a picture to show the anatomy of a mammalian cell and
indicate each part of the cell and its function in the cell.
1- Collagen
2- Elastin 14- Cytoplasm
3- Proteoglycan complex 15- Golgi Complex
4- Fibronectin 16- Vacuole
5- Laminin 17- Cell
6- Integrin 18- Microfilaments
7- Actin filaments 19- Secretory vesicle
8- Peroxisome 20- Plasmatic membrane
9- Mitochondria 21- Smooth Endoplasmic Reticulum
10- Nucleus (the structure), Nuclear 22- Microtubules
Envelope (the purple layer) 23- Centrioles
11- Nuclear Pore 24- Chromatin
12- Rough Endoplasmic Reticulum (the 25- Nucleolus
structure), Ribosome (green spots) 26- Extracellular Matrix

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Brief functions explanation about the Cell Organelles
mentioned above
1- Collagen: is protein molecules made up of amino acids. It provides structural support to
the extracellular space of connective tissues. Due to its rigidity and resistance to stretching, it is
the perfect matrix for skin, tendons, bones, and ligaments.
2- Elastin: is a key extracellular matrix (ECM) protein that provides resilience and elasticity
to tissues and organs. Elastin is roughly 1000 times more flexible than collagens; thus, the main
function of elastin is the elasticity of tissues.
3- Proteoglycan complex: The major biological function of proteoglycans derives from the
physicochemical characteristics of the glycosaminoglycan component of the molecule,
which provides hydration and swelling pressure to the tissue enabling it to withstand
compressional forces. Example, hyaluronic acid.
4- Fibronectin: is an extracellular matrix (ECM) component that, through binding integrin

receptors of the cell surface, acts as a key player of the communication between the intra and
the extracellular environment, thus controlling cell behaviour.
5- Laminin: In both developing and intact tissues, laminins are incorporated into
basement membranes, which separate parenchymal cells from the connective tissue. Laminins
play important roles in tissue morphogenesis and homeostasis by regulating tissue
architecture, cell adhesion, migration and matrix-mediated signaling.
6- Integrin: function as transmembrane linkers (or “integrators”), mediating the

interactions between the cytoskeleton and the extracellular matrix that are required for cells to
grip the matrix.

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7- Actin filaments: are particularly abundant beneath the plasma membrane, where they
form a network that provides mechanical support, determines cell shape, and allows
movement of the cell surface, thereby enabling cells to migrate, engulf particles, and divide.
8- Peroxisome: are organelles that sequester diverse oxidative reactions and play
important roles in metabolism, reactive oxygen species detoxification, and signaling.
9- Mitochondria: are 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).
10- Nucleus (the structure), Nuclear Envelope (the purple layer): The nucleus controls and
regulates the activities of the cell (e.g., growth and metabolism) and carries the genes,
structures that contain the hereditary information. The nuclear envelope separates the contents
of the nucleus from the cytoplasm and provides the structural framework of the nucleus. The
nuclear membranes, acting as barriers that prevent the free passage of molecules between the
nucleus and the cytoplasm, maintain the nucleus as a distinct biochemical compartment.
11- Nuclear Pore: is a large complex of proteins that allows small molecules and ions to
freely pass, or diffuse, into or out of the nucleus. Nuclear pores also allow necessary proteins to
enter the nucleus from the cytoplasm if the proteins have special sequences that indicate they
belong in the nucleus.
12- Rough Endoplasmic Reticulum (the structure), Ribosome (green spots): The rough
endoplasmic reticulum is a membranous organelle that functions to produce proteins with the
help of ribosomes on the membrane surface. A ribosome functions as a micro-machine for
making proteins. Ribosomes are composed of special proteins and nucleic acids. The translation
of information and the linking of amino acids are at the heart of the protein production process.

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13- Lysosome: are membrane-bound organelles found in every eukaryotic cell. They are
widely known as terminal catabolic stations that rid cells of waste products and scavenge
metabolic building blocks that sustain essential biosynthetic reactions during starvation.
14- Cytoplasm: is the gel-like fluid inside the cell. It is the medium for chemical reaction. It
provides a platform upon which other organelles can operate within the cell. All of the functions
for cell expansion, growth and replication are carried out in the cytoplasm of a cell.
15- Golgi Complex: functions as a factory in which proteins received from the ER are
further processed and sorted for transport to their eventual destinations: lysosomes, the plasma
membrane, or secretion. In addition, as noted earlier, glycolipids and sphingomyelin are
synthesized within the Golgi.
16- Vacuole: is a membrane-bound cell organelle. In animal cells, vacuoles are generally
small and help sequester waste products. In plant cells, vacuoles help maintain water balance.
Sometimes a single vacuole can take up most of the interior space of the plant cell.
17- Cell: the unit base of life, provide structure for the body, take in nutrients from food,
convert those nutrients into energy, and carry out specialized functions. Cells also contain the
body's hereditary material and can make copies of themselves. Cells have many parts, each with
a different function.
18- Microfilaments: are the smallest filaments of the cytoskeleton. They have roles in cell
movement, muscle contraction, and cell division.
19- Secretory vesicle: play an important role in moving molecules outside of the cell,
through a process called exocytosis. They are crucial for healthy organ and tissue function. For
example, secretory vesicles in the stomach will transport protein-digesting enzymes to help
break down food.

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20- Plasmatic membrane: is found in all cells and separates the interior of the cell from
the outside environment. The cell membrane consists of a lipid bilayer that is semipermeable.
The cell membrane regulates the transport of materials entering and exiting the cell.
21- Smooth Endoplasmic Reticulum: functions in many metabolic processes.

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.
22- Microtubules: Microtubules, with intermediate filaments and microfilaments, are the
components of the cell skeleton which determinates the shape of a cell. Microtubules are
involved in different functions including the assembly of mitotic spindle, in dividing cells, or
axon extension, in neurons.
23- Centrioles: are paired barrel-shaped organelles located in the cytoplasm of animal
cells near the nuclear envelope. Centrioles play a role in organizing microtubules that serve as
the cell's skeletal system. They help determine the locations of the nucleus and other organelles
within the cell.
24- Chromatin: Chromatin fibers are coiled and condensed to form chromosomes.
Chromatin makes it possible for a number of cell processes to occur including DNA replication,
transcription, DNA repair, genetic recombination, and cell division.
25- Nucleolus: The primary function of the nucleolus consists in ribosomal RNA (rRNA)
transcription, rRNA processing and ribosome subunit assembly
26- Extracellular Matrix: it helps cells attach to, and communicate with, nearby cells, and
plays an important role in cell growth, cell movement, and other cell functions. The extracellular
matrix is also involved in repairing damaged tissue.

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Chapter 2 – Cell Membrane and Transmembrane
Transportation
Important Terms
Amphipathic molecule: an amphipathic molecule is a molecule that has both polar and
non-polar parts. Phospholipids, for example, have non-polar fatty acid “tails” and polar
phosphate “heads.” “Polarity” is an important property of molecules that determines how they
will interact with other molecules.
Liquid crystal state: are a state of matter which has properties between those of
conventional liquids and those of solid crystals. For instance, a liquid crystal may flow like a
liquid, but its molecules may be oriented in a crystal-like way.

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Membrane Asymmetry: the membrane is a bilayer of lipids. Proteins associate with lipids
in membrane in three forms, integrated protein, periphery protein and lipid linked proteins.
Both proteins and lipids have fluidity and asymmetry arrangement in the membrane.
The cell membrane tends to have different composition on one side of the
membrane than on the other side of the membrane. Additionally, the cell membrane's
phospholipids are distributed asymmetrically across the lipid bilayer, in a phenomenon called
membrane phospholipid asymmetry. The cell membrane is an asymmetric structure. That
means that the two sides of membrane are structurally and functionally different.
Unit Membrane: a lipoprotein membrane which encloses many cells and cell organelles
and is composed of two electron-dense layers enclosing a less dense layer. The limiting
membrane of cells and various organelles viewed formerly as a 3- layered structure with an
inner lipid layer and two outer protein layers and currently as a fluid phospholipid bilayer with
intercalating proteins.

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Fluid Mosaic Model: a model that describes the structure of cell membranes. In this
model, a flexible layer made of lipid molecules is interspersed with large protein molecules
that act as channels through which other molecules enter and leave the cell.
This model was raised by Singer and Nicolson in 1972. Bilayers of phospholipids
constitute the skeleton of membrane, proteins such as channels, receptors, transporters are
interspersed into the lipid skeleton.
The fluidity of the lipids provides the environment for confirmation changes of
membrane proteins. The membrane proteins like mosaic particles are embedded into the lipid
skeleton. The membrane proteins are able to do lateral motion and rotation.

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Lipid Raft: lipid raft is not a model but a special area in the membrane with special
functions. The surface of the membrane is not even, some area form bulge, that is lipid raft. To
be strict, it is a special area or structure in the membrane rather than a model. Its outer layer of
lipids contains more sphingomyelin cholesterol, GPI anchored protein, long and saturated fatty
chains, less fluidity. Also is lot of transmembrane proteins. The inner layer with some anchored
protein, enzymes. The structure provides a platform for some protein conformation changes.,
and these components are considered special components of liquid rafts. The plasma
membranes of cells contain combinations of glycosphingolipids, cholesterol and protein
receptors organized in glycolipoprotein lipid micro domains.
Passive Transport: transporter mediated transportation has two types, one is passive
transport, to transport materials from high concentration to low concentration, without using
energy. Passive transport including carrier protein mediated facilitated diffusion and ion
channel mediated ion transporting, carrier protein facilitated diffusion, channel protein
regulated ion transportation. Passive transport does not require energy input. An example of
passive transport is diffusion, the movement of molecules from an area of high concentration
to an area of low concentration. Carrier proteins and channel proteins are involved in
facilitated diffusion.

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Active Transport: is the movement of all types of molecules across a cell membrane
against its concentration gradient. Active transport uses cellular energy, unlike passive
transport, which does not use cellular energy. The ion pump, proton pump, ion driven co-
transportation are examples of Active transport.
Facilitated diffusion: It is the process of spontaneous passive transport (as opposed to

active transport) of molecules or ions across a biological membrane via specific
transmembrane integral proteins.
Passive transport including carrier protein mediated facilitated diffusion and ion channel
mediated ion transporting. Facilitated diffusion is a form of facilitated transport involving the
passive movement of molecules along their concentration gradient, guided by the presence of
another molecule (usually an integral membrane protein forming a pore or channel).

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Symport: The passenger and the driver are transported in the same direction. A
mechanism of transport across a membrane in which two different molecules move in the same
direction.
Often, one molecule can move up an electrochemical gradient because the movement of
the other molecule is more favourable.
Sodium and glucose symport takes place in the intestine, from the gut lumen to the insides
of the cells lining the gut.
Antiport is the coupled transport of two different molecules or ions through a membrane
in opposite directions by a common carrier mechanism. This mechanism is ATP dependent.
Uniport is the transport of molecule or ion across a membrane through facilitated
diffusion without coupling to the transport of another molecule or ion (as opposed
to symport and antiport)

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Cotransport: is a coupled transport A special kind of active transport, where two
molecules travel together. One is a driver (the ion) the other is a passenger. The driver diffuses
down its electrochemical gradient, but it cannot do so unless it has the passenger. ATP is not
directly involved, but it sets up the electrochemical gradient used to propel the driver.
Receptor mediated endocytosis: it is a process by which cells absorb metabolites,

hormones, proteins (and in some cases viruses) by the inward budding of the plasma
membrane. Only the receptor-specific substances can enter the cell through this process.
It provides an efficient pathway for taking up specific macromolecules from the
extracellular fluid. It also provides a selective concentrating mechanism that increases the
efficiency of internalization of particular ligands more than a Hundredfold without taking in a
correspondingly large volume of extracellular fluid.
Importing specific macromolecules (hormones) into the cell by the inward budding of
vesicles formed from coated pits (receptors).
The nerve impulse makes neuron cell release acetylcholine, the latter associates with
muscle membrane Receptor （ligand-gated sodium channel）, therefore, makes sodium
comes into the muscle cells, because voltage change, calcium channel in muscle cells open,
calcium moves in, which results in the calcium gated calcium release channel in ER
(sarcoplasmic reticulum) open, calcium is released from ER to cytosol, the muscle contracts.

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Post prandial blood lipids form low density lipoprotein （ LDL ） with some bad
cholesterol harmful to our cardiovascular system, esp. the artery. LDL will be cleared by
receptor mediated endocytosis.
Receptor mediated endocytosis it’s important because it provides an efficient pathway
for taking up specific macromolecules from the extracellular fluid. (specificity) It also provides
a selective concentrating mechanism that increases the efficiency of internalization of
particular ligands more than a hundredfold without taking in a correspondingly large volume
of extracellular fluid. (enrichment).

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Contact Inhibition: it is a regulatory mechanism that functions to keep cells growing into
a layer one cell thick (a monolayer). If a cell has plenty of available substrate space, it replicates
rapidly and moves freely. This process continues until the cells occupy the entire subtract. The
contact inhibition has an important role in cancer diseases. If the cells lose the contact
inhibition, they can growing more than normal, passing the limit of the subtract.

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1- Please describe the molecular components of cell membrane.
As we know, a cell membrane is composed of bilayer of phospholipids, and associated
with proteins. Lipids constitute the skeleton of the membrane and is the amphiphilic structure
membrane lipid. In it, we can find three types of lipids, the phospholipids, cholesterol and
glycolipids.
The phospholipids include, phosphoglycerates and sphingomyelin, and are basic
components consisting more than 50% of the lipid membrane. The cholesterol has the function
to stabilize membrane structure and modulate the fluidity of membrane. The glycolipid only
consists about 5% or less of the membrane ，located outer layer of membrane.
Proteins can be associate with lipids in membrane in three forms, integrated protein,
periphery protein and lipid linked proteins. Both proteins and lipids have fluidity and asymmetry
arrangement in the membrane. The cell membrane might associate with other cell structure to
form some specific structure. Such as, polysaccharide form the coat or glycocalyx of cell
membrane, cell membrane associate with cytoskeleton to form cilia or flagella, cell membrane
form Ruffle or lamellipodium. Thanks to the variety of membrane components, the membrane
proteins can be associated with the bilayer in various ways.
The principal components of the plasma membrane are lipids proteins, and carbohydrate
groups that are attached to some of the lipids and proteins. A phospholipid is a lipid made of
glycerol, two fatty acid tails, and a phosphate-linked head group.

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2- What are the characteristics of cell membrane?
As the membrane lipid bilayer is a two-dimensional fluid (Liquid crystal state), we can
considerer two important characteristics, Asymmetry and Fluidity
The Asymmetry includes the asymmetry distribution of lipids, proteins and sugar chains
in the cell membrane
The fluidity of the membrane it’s important to guarantee its biological functions. The
fluidity depends on the liquid-crystal state, on the different movements of the lipids that
composed the membrane, and also by the membrane proteins (which have different
movements like lateral diffusion and rotation).

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3- What is unit membrane? Why this model is still be used in cell biology
and other subjects?
After several experiments using the Electron microscope, Robertson proposed unit
membrane concept for biological membranes.
According to this concept, the biological membrane is a lipid bilayer of phospholipids.
As so, each single unit of phospholipid membrane which summation of them forms the bilayer
cell membrane is a unit membrane.
The phospholipid bilayer is composed by of two amphiphilic lipid molecules that each
molecule has two heads one is hydrophobic (lipoid tail) and the other one is hydrophilic
(phosphate polar head).
The external layer is a hydrophilic layer made of protein molecules of diameter 20A−25A.
The middle layer is a light hydrophobic layer made of phospholipids of diameter 25A−35A.
Each couple of two molecules are called a unit membrane.

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4- What is fluid mosaic model? Why this model is popularly accepted?
The fluid mosaic model was proposed by S.J. Singer and Garth L. Nicolson.
The fluid mosaic model describes the cell membrane as a tapestry of several types of
molecules (phospholipids, cholesterols, and proteins) that are constantly moving. This
movement helps the cell membrane maintain its role as a barrier between the inside and
outside of the cell environments.
In this model, a flexible layer made of lipid molecules is interspersed with large protein
molecules that act as channels through which other molecules enter and leave the cell.
The fluidity of the plasma membrane is affected by four conditions, the length of the fatty
acid tail, temperature, the amount of cholesterol present in that part of the layer, and degree of
saturation of fatty acid tails.
Therefore, we can understand that the cell membrane is flexible to be able to move,
however, there are some restrictions on the fluidity of the plasma membrane. The first one is
the lipid rafts, where lipid domains found on the external leaflet of the plasma membrane like
cholesterol, glycosphingolipids, glycosylphosphatidylinositol, that build a kind of blocks,
making that membrane area tighter and less fluid. The other is protein complexes made of
proteins and glycoproteins that are diffused within the plasma membrane. These help in the
transport of ions and metabolites, cell signalling, adhesion, and migration, but affects the
fluidity of the membrane.

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5- How many kinds of passive transport? How many kinds of active
transport? Please give examples!
Passive transport is a type of cellular transport in which substances such as ions and
molecules move down their respective concentration gradients. It means that the substance
tends to move from an area of higher concentration to an area of lower concentration.
Substances tend to move towards the region where they are few. Since their movement
is downhill or along their concentration gradient, the process does not require metabolic
energy (ATP) as opposed to active transport, another type of cellular transport that essentially
requires ATP to move substances against their concentration gradient. On this type of
transportation can be or not carrier by protein mediated.
Passive transport including carrier protein mediated, facilitated diffusion and ion channel
mediated ion transporting. The rate of passive transport depends on the permeability of the cell
membrane, which, in turn, depends on the organization and characteristics of the membrane
lipids and proteins.
The four main kinds of passive transport are simple diffusion, facilitated diffusion,
filtration, and osmosis.
Simple Diffusion is the movement of substances from a region of higher concentration to
lower concentration. The difference in the concentration of the two areas is termed as
concentration gradient and the process of diffusion continues until this gradient
neutralizes. Diffusion occurs in liquid and gases because their particles move randomly from
one place to another. It is an important process in living things required for different life
processes. The substances move in and out of the cells by simple diffusion.
Facilitated diffusion is the passive transportation of ions or molecules across the cell
membrane through specific transmembrane integral proteins. The molecules, which are large
and insoluble require a carrier substance for their transportation through the plasma
membrane. This process does not require any cellular or external energy. As an example of
facilitated diffusion, we have the process when glucose is absorbed into the cells by a Glucose
transporter (GLUT4), or also other ion channels and aquaporins.

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Looking at the transporter channel, GLUT4, we can notice its incredibly important in
diabetes. GLUT4 is a glucose transporter found in fat and skeletal muscle. Insulin triggers GLUT4
to insert into the membranes of these cells so that glucose can be taken in from the blood. Since
this is a passive mechanism, the amount of sugar entering our cells is proportional to how much
sugar we consume, up to the point that all our channels are being used (saturation). In type II
diabetes mellitus, cells do not respond as well to the presence of insulin, and so do not insert
GLUT4 into their membranes. This can lead to soaring blood glucose levels which can cause
heart disease, stroke, and kidney failure.
The cell membrane is permeable only to a few molecules that are smaller in size and non-
polar. Therefore, facilitated diffusion with the help of transmembrane proteins is important.
Filtration is the process of separating solids from liquids and gases. The selective
absorption of nutrients in the body is an example of filtration. This process does not require any
energy and takes place along the concentration gradient. The kidneys are an example of a
biological filter. The blood is filtered by the glomerulus and the necessary molecules are
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reabsorbed. In the process of filtration, the cell membrane permits only those substances which
are soluble and could easily pass through its pores.
In the process of osmosis, water and other molecules pass through a selectively
permeable membrane in order to balance the concentration of other substances.
Osmosis is affected by the concentration gradient and temperature. The greater the
concentration gradient, the faster is the rate of osmosis. Also, the rate of osmosis increases with
the increase in temperature.
There is a theory of conflict about the process of osmosis. Few biologists suggest that
osmosis is an active transport and not passive transport.
Summarising, Simple and facilitated diffusions refer to the net movement of molecules
from higher to lower concentrations. Osmosis refers to the diffusion of a solvent (usually water
molecules) through a semipermeable membrane from lower to higher solute concentrations.
Filtration is the movement of water and solute molecules across the cell membrane driven by
hydrostatic pressure that is generated by the cardiovascular system.
Besides the examples that I gave above, this ones are more simple to understand the
passive transportation:
o Ethanol enters our body and hits the bloodstream. This happens because the ethanol
molecules undergo simple diffusion and pass through the cell membrane without any
external energy.
o Reabsorption of nutrients by the intestines by separating them from the solid waste and
transporting the nutrients through the intestinal membrane into the bloodstream.
o When a raisin is soaked in water the water moves inside the raisin by the process of
osmosis and it swells.
But sometimes our body needs to move molecules against their gradient. In this case, we
have the active transportation, which transport materials from low concentration to high
concentration, by using biological energy (ATP). In another words, Active transport is the
movement of all types of molecules across a cell membrane against its concentration gradient.
Active transport uses cellular energy, unlike passive transport, which does not use cellular
energy.

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We can divide the active transport in two main groups, primary or secondary active
transport. The Primary (direct) active transport involves the direct use of metabolic energy
(example of ATP hydrolysis) to mediate transport, and the secondary (indirect) active transport
involves coupling the molecule with another moving along an electrochemical gradient.
The definitions of Antiport, Symport and cotransport were given anteriorly on the terms
designations part, and so, I will skip that explanation.
There are 3 main types of active transport include different kind ion pumps and two bulk
mechanisms (vesicle transport), exocytosis and endocytosis.
For the ion pumps, the Ion pump hydrolyze ATP for active transport including P-class ion
pump, V-class proton pump, F-class proton pump, ABC transport. However, there is a very
classic example, the sodium-potassium pump, which moves both types of ions against the
concentration gradient.
Basically, the way one of these sodium-potassium pumps work is that 3 sodium ions from
inside the cell bind to a carrier protein in the cell membrane. Then, an ATP molecule is broken
down by an enzyme called sodium-potassium-ATPase, releasing energy and causing the
protein to change shape, pushing the sodium ions out of the cell.

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Then, 2 potassium ions from outside the cell bind to the protein and it changes shape
again, depositing the potassium into the cell.
Other example, this time for secondary transportation is the Calcium pumps when a
muscle contracts. The nerve impulse makes neuron cell release acetylcholine, the latter
associates with muscle membrane Receptor (ligand-gated sodium channel), therefore, makes
sodium comes into the muscle cells, Because voltage change, calcium channel in muscle cells
open, calcium moves in, which results in the calcium gated calcium release channel in ER
(sarcoplasmic reticulum) open, calcium is released from ER to cytosol, the muscle contracts.
Exocytosis is when a transport vesicle inside the cell fuses with the cell membrane and
then whatever is inside the transport vesicle can be released out into the extracellular
fluid. There is three types of endocytosis, phagocytosis, pinocytosis, and receptor-mediated
endocytosis.

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Phagocytosis is the process by which a cell uses its plasma membrane to engulf a large
particle. A good example of this in the human body is when a white blood cell such as a
neutrophil or a macrophage engulfs a bacterium. The WBC surrounds the bacterium and forms
a vesicle called a phagosome to hold it inside. Then, a lysosome merges with the phagosome
and lends a hand by destroying the bacterium with enzymes. The waste material is released via
exocytosis.
Pinocytosis is when the plasma membrane pinches inwards to form a vesicle around
extracellular fluid containing useful molecules. This process may not be as flashy as
phagocytosis, but it occurs in all of the body’s cells, not just in specialized ones like
macrophages and neutrophils.
Receptor-mediated endocytosis is similar in that part of the plasma membrane forms a
vesicle around the molecules being taken in by the cell. However, these molecules bind to
receptors on the outside of the membrane first, and the vesicle that forms is surrounded by a
special protein called clathrin. The endothelial cells lining the blood vessels take in LDL (low-
density lipoproteins) in this way.

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This table below can give a general view about the types of transportation that I explained
in this question.

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6- What is receptor mediated endocytosis? Please explain the related
mechanism for familial hypercholesterolemia.
Receptor-mediated endocytosis (that I explained above in terms definitions) is a form of
endocytosis in which receptor proteins on the cell surface are used to capture a specific target
molecule. The receptors, which are transmembrane proteins, cluster in regions of the plasma
membrane known as coated pits. This name comes from a layer of proteins, called coat proteins,
that are found on the cytoplasmic side of the pit. Clathrins are the most best studies coat
proteins.
When the receptors bind to their specific target molecule, endocytosis is triggered, and
the receptors and their attached molecules are taken into the cell in a vesicle. The coat proteins
participate in this process by giving the vesicle its rounded shape and helping it bud off from
the membrane. Receptor-mediated endocytosis allows cells to take up large amounts of
molecules that are relatively rare (present in low concentrations) in the extracellular fluid.

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Although receptor-mediated endocytosis is intended to bring useful substances and into
the cell (like hormones for example) by the inward budding of vesicles formed from coated pits
(receptors). Therefore, the importance of receptor mediated endocytosis is because it provides
an efficient pathway for taking up specific macromolecules from the extracellular fluid.
(specificity). It also provides a selective concentrating mechanism that increases the efficiency
of internalization of particular ligands more than a hundredfold without taking in a
correspondingly large volume of extracellular fluid (enrichment).

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Familial hypercholesterolemia
In a normal person, the form of cholesterol called low-density lipoprotein or LDL ("bad"
cholesterol) is removed from the blood by receptor-mediated endocytosis. In people who have
familial hypercholesterolemia, there is an abnormality of membrane receptor, in the LDL
receptors, which make them don't work right or may be missing entirely. People with this
condition can have life-threateningly high levels of cholesterol in their blood because their cells
cannot remove LDL particles from the bloodstream.
A monolayer of phospholipid and unesterified cholesterol forms the surface membrane,
and fatty acid esters of cholesterol make up the hydrophobic core. One copy of the hydrophobic
Apo-B protein is embedded in the membrane. This protein mediates binding of LDL particles to
specific cell-surface receptors. During receptor-mediated endocytosis various extracellular
nutritional and regulatory molecules bind to plasma membrane receptors and rapidly enter
target cells. The LDL is delivered to lysosomes where it is degraded and its cholesterol is
released for use in the synthesis of membranes, steroid hormones and bile acids.

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Chapter 3 – Endomembrane Systems
Important Terms
Endomembrane system: the structure and functions of the endoplasmic reticulum, Golgi
complex, endosomes, lysosomes, and vacuoles. All these parts form an endomembrane system
which the individual components function is part of a coordinated unit (Mitochondria and
chloroplasts are not part of this interconnected system). The endomembrane systems work
together to synthetise, modify, package and transport lipids and proteins.
Microsome: A heterogeneous collection of vesicles formed from the endomembrane

system (primarily the endoplasmic reticulum and Golgi complex) after homogenization.

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Signal peptide: (sometimes referred to as signal sequence, targeting signal, localization
signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short
peptide (normally 16-30 amino acids long) present at the N terminus of the majority of newly
synthesized endomembrane proteins, including ER, Golgi complex retention proteins, secretion
protein, lysosomal proteins and plasma membrane proteins.
Signal peptide recognition particle: signal-recognition particle (SRP): Ribonucleoprotein

particle that binds an ER signal sequence on a partially synthesized polypeptide chain and
directs the polypeptide and its attached ribosome to the endoplasmic reticulum.

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Translocator: Membrane-bound protein that mediates the transport of another protein
across a membrane.
Signal peptide hypothesis: The signal hypothesis proposes that proteins destined for
secretion, which involves the movement of the protein across a biological membrane, are
originally manufactured with an initial sequence of amino acids that may or may not present in
the mature protein.
The site of synthesis of a protein is determined by the sequence of amino acids in the N-
terminal portion of the polypeptide, which is the first part to emerge from the ribosome during
protein synthesis (Sabatini & Dobberstein, 1970).
1. Secretory proteins contain a signal sequence at their N- terminus that directs the
emerging polypeptide and ribosome to the ER membrane.
2. The polypeptide moves into the cisternal space of the ER through a protein lined,
aqueous channel in the ER membrane. It was proposed that the polypeptide moves through the
membrane as it is being synthesized, that is, co-translationally.
A hypothesis to explain how ribosomes become attached to membranes within cells in
order to deliver the appropriate proteins to cell organelles, such as mitochondria and
chloroplasts, or transport proteins outside the cell membrane. It proposes that the leading end
of the nascent polypeptide chain consists of a signal peptide. This sticks out from the ribosome
and is recognized by a ribonucleoprotein particle called a signal recognition particle (SRP).
When the complex of ribosome and SRP encounters a membrane, the SRP binds to a docking
protein (signal recognition particle receptor) on the membrane surface. Synthesis of the
polypeptide, which has hitherto been stalled, now resumes, and the polypeptide (or fully formed
protein) passes into the membrane, where the signal peptide is removed by a signal peptidase
enzyme. Once translation is completed, the ribosome dissociates and is freed from the
membrane. It is thought that the signal sequence tags the protein for insertion at particular sites,
by interacting with membrane-bound glycoproteins (signal sequence receptors). If the signal
sequence is not the correct one, the ribosome is released before delivering its protein. The
hypothesis, which was formulated in the early 1970s by workers including Gunter Blobel and
César Milstein, is now widely accepted.

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ENDOPLASMATIC RETICLE
1- How many kinds of proteins are synthesized, transported and modified
in RER? Please explain each step of these process.
Approximately one-third of the proteins encoded by a mammalian genome are
synthesized on ribosomes attached to the cytosolic surface of the RER membranes and released
into the ER lumen in a process called co-translational translocation.
These include (a) secreted proteins, (b) integral membrane proteins, and (c)soluble
proteins that reside within compartments of the endomembrane system, including the ER, Golgi
complex, lysosomes, endosomes, vesicles and plant vacuoles.
Other polypeptides are synthesized on “free” ribosomes, it means on ribosomes that are
not attached to the RER and are subsequently released into the cytosol. This class includes (a)
proteins destined to remain in the cytosol (such as the enzymes of glycolysis and the proteins
of the cytoskeleton), (b) peripheral proteins of the cytosolic surface of membranes (such as
spectrins and ankyrins that are only weakly associated with the plasma membrane’ s cytosolic
surface), (c) proteins that are transported to the nucleus , and (d) proteins to be incorporated
into peroxisomes, chloroplasts, and mitochondria. Proteins in the latter two groups are
synthesized to completion in the cytosol and then imported post translationally into the
appropriate organelle across its boundary membrane(s).
A schematic model of the synthesis of a secretory protein (or a lysosomal enzyme) on a
membrane-bound ribosome of the RER:
STEP 1: Synthesis of the polypeptide begins on a free ribosome. As the signal sequence
(shown in red) emerges from the ribosome, it binds to the SRP.
STEP 2: SRP stops further translation until the SRP-ribosome-nascent chain complex can
make contact with the ER membrane. The SRP-ribosome complex then collides with and binds
to an SRP receptor (SR) situated within the ER membrane.
STEP 3: Attachment of this complex to the SRP receptor is followed by release of the SRP
and the association of the ribosome with a translocon of the ER membrane.
STEP 4: These latter events are accompanied by the reciprocal hydrolyis of GTP molecules
(not shown) bound to both the SRP and its receptor. In the model depicted molecules (not

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shown) bound to both the SRP and its receptor. In the model depicted here, the signal peptide
then binds to the interior of the translocon, displacing the plug from the channel and allowing
the remainder of the polypeptide to translocate through the membrane cotranslationally.
After the nascent polypeptide passes into the lumen of the ER, the signal peptide is cleaved
by a membrane protein (the signal peptidase, not shown), and the protein undergoes folding
with the aid of ER chaperones, such as BiP. Studies suggest that translocons are organized into
groups of two or four units rather than singly as shown here. (b) Cross-sectional view of the
translocon channel from the side based on the X-ray crystal structure of an archaebacterial
translocon. The hourglass shape of the aqueous channel and its helical plug are evident. The
ring of hydrophobic side chains (green) situated at the narrowest site within the channel is also
shown. (c) Representation of a ribosome-translocon complex in the act of synthesis and
translocation of a nascent protein based on cryo-EM. The exit channel within the ribosome is
seen to be aligned with the conducting channel within the translocon. PCC, protein conducting
channel; NC, nascent chain; P-tRNA, peptidyl-t-RNA; 40S and 60S, ribosomal subunits.

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To summarise:
Process of protein secretion and secretion:
o Ribosomes assemble proteins from polypeptides entering rough ER
o Proteins move through the rough ER, where they are further modified
o Transport vesicles containing the proteins are pinched off form the rough ER
o Transport vesicles fuse with the membrane of the Golgi complex and the
proteins are released to the inside
o Within the Golgi complex the proteins are further processed and stored
o Vesicles containing the finished proteins are pinched off from the Golgi
complex
o Vesicles travel to the cell membrane, fuse with the cell membrane, and
release the proteins to the outside.
Process of protein synthesis in Rough Endoplasmatic Reticle:

o mRNA – ribosome complex is directed to rough ER by a signal-recognition
particle (SRP)
o SRP is released and polypeptide grows into cisternae
o The protein is released into the cisternae and sugar groups are added
o The protein folds into a three-dimensional conformation
o The protein is enclosed in a transport vesicle and moves toward the Golgi
apparatus

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2- Please write down how many glycosylation, tell where they take place
and what are the function of glycosylation.
Glycosylation is a critical function of the biosynthetic-secretory pathway in the
endoplasmic reticulum (ER) and Golgi apparatus. Approximately half of all proteins typically
expressed in a cell undergo this modification, which entails the covalent addition of sugar
moieties to specific amino acids. Most soluble and membrane-bound proteins expressed in the
endoplasmic reticulum are glycosylated to some extent, including secreted proteins, surface
receptors and ligands, and organelle-resident proteins. Additionally, some proteins that are
trafficked from the Golgi to the cytoplasm are also glycosylated. Lipids and proteoglycans can
also be glycosylated, significantly increasing the number of substrates for this type of
modification.
The reactions by which sugar groups are added to proteins and lipids. The addition of
carbohydrate, or glycosylation, is the most complex of the modification of proteins.
o Golgi Complex provide the sites for protein and lipid modification
o Glycoprotein glycosylation
o Glycolipid glycosylation
o Protein glycosylation :
• N-linked glycosylation :primarily formed in RER, modified there,
further modified in Golgi Complex
• O-linked glycosylation: formed in Golgi complex
Sugar is linked with Ser, Thrat OH, the first sugar is galactose or N—acetylgalactosamine
The sugar chain of glycolipid is added in Golgi complex:

o Enzymes for modification are integrated proteins or
transmembrane proteins
o Compartment of enzymes distribution
o Enzyme activity lies in inner membrane Surface
o Remove or add some sugar unit

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3- Explain the function of ER. What is the marker enzyme of ER?
The endoplasmic reticulum (ER) comprises a network of membranes that penetrates
much of the cytoplasm. The ER probably evolved from invaginations of the plasma membrane
Enclosed within the ER is an extensive space, or lumen, that is separated from the surrounding
cytosol by the ER membrane.
As will be evident in the following discussion, the composition of the luminal (or cisternal)
space inside the ER membranes is quite different from that of the surrounding cytosolic space.
Like other subcellular organelles, the ER is a highly dynamic structure undergoing continual
turnover and reorganization.
The endoplasmic reticulum is divided into two sub compartments, the rough endoplasmic
reticulum (RER) and the smooth endoplasmic reticulum (SER).
The rough ER is defined by the presence of ribosomes bound to its cytosolic surface,
whereas the smooth ER lacks associated ribosomes. The RER is typically composed of a network
of flattened sacs (cisternae), where each layer is connected to its neighbours by helicoidal
membranes. The main functions of rough ER are harbour ribosomes for vesicular transported
proteins, and protein folding and disulphide linkage formation in RER by the help of chaperone
protein, proteins will suffer a process of maturation and selection, is the site for endomembrane
synthesis, primary modification and transportation (protein glycosylation and protein
transportation).
The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no
ribosomes on its cytoplasmic surface.
Functions of smooth ER include Lipids synthesis and transportation (phospholipids,
cholesterol, fat, steroid hormones, glycolipids, etc), it is involved in glycogen metabolism,
detoxification, phospholipid translocation, reserve for Calcium (important for muscular
contraction), and helps bile synthesis and secretion.
The marker enzyme for ER is glucose-6-phosphatase.
GOLGY COMPLEX
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1- What is the characteristics of Golgi Complex in morphology, what is the
function of Golgi Complex?
The Golgi complex, also known as a Golgi apparatus, is a cell organelle that helps process
and package proteins and lipid molecules, especially proteins destined to be exported from the
cell. Named after its discoverer, Camillo Golgi, the Golgi body appears as a series of stacked
membranes.
The Golgi apparatus is a series of stacked membranes that are located within the
cytoplasm (gel-like fluid held in the cell membrane) in all eukaryotic cells (complex cells). We
can divide the membrane system into three parts, cis Golgi network, Golgi stack (composed by
three cisternas, cis, medial and trans), and trans Golgi network. It can typically be found
adjacent to the nucleus and rough endoplasmic reticulum. Its chemical components are 40%
lipids, 60% proteins. We can also find many kind of enzymes (glycosyltransferase, which is the
marker enzyme, phospholipase , oxidoreductase) and sugar chains (increasing from the cis to
trans part of the complex).
The Golgi Complex has several functions:
o A transition station for endomembrane protein transportation
o Golgi Complex provide the sites for protein and lipid modification (glycoprotein
glycosylation, glycolipid glycosylation, protein glycosylation)
o the place for Glycolipid formation and modification (the sugar chain of glycolipid is
added in Golgi complex)
o A place for protein hydrolysis or cutting (maturation)
o Protein sorting (the process of lysosomal enzyme protein formation, the
membrane proteins are also from ER and Golgi)
o an important site for membrane lipid transportation and renewing

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2- Briefly explain types of protein glycosylation, and their characteristics
and sites of formation.
Golgi Complex provide the sites for protein and lipid modification:
• Glycoprotein glycosylation
• Glycolipid glycosylation
• Protein glycosylation:
o N-linked glycosylation: primarily formed in RER, modified there,
further modified in Golgi Complex,
o O-linked glycosylation:
• formed in Golgi complex
• Sugar is linked with Ser,Thrat OH，the first sugar is galactose
or N— acetylgalactosamine
In Golgi complex the N-linked glycosylation initially occurs in the cis Golgi part, to after
passing through all the parts of this complex. The O-glycosylation occurs post-translationally
on serine and threonine side chains in the Golgi apparatus.

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3- How can Golgi Complex sort protein? Give an example.
In the final stage of transport through the Golgi apparatus, modified proteins and lipids
are sorted in the trans Golgi network and are packaged into vesicles at the trans face. These
vesicles then deliver the molecules to their target destinations, such as lysosomes or the cell
membrane.
Some molecules, including certain soluble proteins and secretory proteins, are carried in
vesicles to the cell membrane for exocytosis (release into the extracellular environment). The
exocytosis of secretory proteins may be regulated, whereby a ligand must bind to a receptor to
trigger vesicle fusion and protein secretion. In addition, within the vesicles are proteases that
cut many secretory proteins at specific amino acid positions. This often results in activation of
the secretory protein, an example being the conversion of inactive proinsulin to active insulin
by removing a series of amino acids.
Some secretory proteins will cease to be transported if their carbohydrate groups are
modified incorrectly or are not permitted to form. In some cases the carbohydrate groups are
necessary for the stability or activity of the protein or for targeting the molecule for a specific
destination.
Lysosomal enzymes are transported from the TGN in clathrincoated vesicles (which are
the third and last type of coated vesicles to be discussed). The structure of clathrin-coated
vesicles is in connection with endocytosis, a process that is better understood than budding at
the TGN. It will suffice at this point to note that the coats of these vesicles contain:
• an outer lattice composed of the protein clathrin, which forms a structural
scaffold
• an inner shell composed of protein adaptors, which covers the surface of
the vesicle membrane that faces the cytosol.
Lysosomal enzymes are recognized by an enzyme in the cis cisternae that transfers a
phosphorylated N -acetylglucosamine from a nucleotide sugar donor to one or more mannose
residues of N -linked oligosaccharides. The glucosamine moiety is then removed in a second
step by a second enzyme, leaving mannose 6-phosphate residues as part of the oligosaccharide
chain.
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Schematic diagram showing the pathways followed by a lysosomal enzyme (black) from
its site of synthesis in the ER to its delivery to a lysosome. The mannose residues of the
lysosomal enzyme are phosphorylated in the Golgi cisternae and then selectively incorporated
into a clathrincoated vesicle at the TGN.
The mannose 6-phosphate receptors are thought to have a dual role, they interact
specifically with the lysosomal enzymes on the luminal side of the vesicle, and they interact
specifically with adaptors on the cytosolic surface of the vesicle. The mannose 6-phosphate
receptors separate from the enzymes and are returned to the Golgi complex. The lysosomal
enzymes are delivered to an endosome and eventually to a lysosome. Mannose 6-phosphate
receptors are also present in the plasma membrane, where they capture lysosomal enzymes
that are secreted into the extracellular space and return the enzymes to a pathway that directs
them to a lysosome.
4- What is the marker enzyme of Golgi Complex?

The mark enzyme for Golgi complex is Glycosyltransferase.

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LYSOSOMES AND PEROXISOMES
Important terms
Primary Lysosome: are small vesicles directly from Golgi Complex. They are
homogeneous, dense, membrane-bound organelles packed with acid hydrolases capable of
breaking down polymers of all types. The low pH required for hydrolase activity (below pH 5) is
maintained by a membrane ATP-dependent hydrogen ion pump, and so the enzymes in this
stage have no activity. A major function of lysosomes is to breakdown or digest material
entering from the extracellular environment.
Secondary Lysosome: are formed as primary lysosome merges with autophagosome or

heterophagosome. It means that, after primary lysosomes have fused with endosomes and are
in the process of digestion, they are called secondary lysosomes. Secondary lysosomes are
easily identified when they are large and heterogeneous. Because the digestion process is
active, the enzymes in this stage are also fully activated too.
Tertiary Lysosome: are those lysosomes in which only indigestible food materials have
been left, so is a state of post enzymatic digestion. In this stage the enzyme activity is almost
exhausted. The primary role of lysosome is to process the “garbage” inside the cell for recycle.
Intracellular digestion results in complete breakdown of the phagocytosed material or
indigestible residues that persist in the form of residual bodies. Residual bodies sometimes
consist of tightly packed membranes (indicated by arrows), reflecting the difficulty lysosomal
enzymes have with lipid digestion. The residual body in this micrograph is the end result
of autophagy rather than phagocytosis. The swirls of lipid are the remains of the organelle
membranes. All cells use lysosomes for the removal of cellular components as they undergo
routine turnover. Because lysosome is able to clean heterophogosome, it also has the function
to protect the cell. Besides, lysosome involves thyroid hormone formation and development
during acrosomal reaction.

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This table describe the principal differences between primary and secondary lysosomes:
1- How many kinds of lysosomes according to enzyme activity?

According to the type of enzymatic activity, we can consider the following types of
lysosomes:
o Primary lysosome: is a newly formed from Golgi Complex, with no enzyme
activity
o Secondary lysosome: primary lysosome merge with phagosomes or
autophagosome to make the secondary lysosome and trigger the proton
pump, pH will drop to 5.0 and the enzymes will be active at this kind of
lysosome
o Tertiary lysosome: the enzymes are used up, no enzyme activity, so it is also
named as post-lysosome, telolysosome or residual body

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2- How those lysosome form ? What are functions of lysosomes?
As it was mentioned before, we can understand that different lysosomes are formed by
different processes and also have different functions.
Primary lysosomes are formed initially on the ER, where the lysosomal enzyme is
synthesized and carbohydrate added. After this process, it’ll be transferred by the Golgi
complex, where the mannose is phosphorylated. In the Trans Golgi network Mannose 6-
phosphate binds to receptor. The PH is lowered, enzyme dissociated from receptor. Finally, the
Phosphate group is removed and primary lysosome is formed.
Secondary lysosomes are the vesicles formed with the fusion of primary lysosomes to
the endosomes. Here, endosomes, including phagosomes and pinosomes, contain materials
to be digested. Generally, phagosomes either contain food particles or pathogens. On the other
hand, pinosomes contain extracellular materials.
The Tertiary lysosome, as I explained detailly in the terms definition’s section, are a state
of post enzymatic digestion, in other ways, are the trash bin of the cell system, which contains
the residual bodies that are produced from the digestive process.
The lysosome functions, in general, are
o It is a recycle bin for resource reusing and environment cleaning, it protects
the cell
o Involving in hormone formation
o Special functions in development
§ Help to getting rid of extra or old or used tissue of cells (Bone
remodeling, Mammal uterus cycle, human menstruation)
§ Fertilization (acrosome reaction)

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3- How do lysosomes digest materials from outside the cell and inside
the cells?
The residues from the metabolic processes digested by lysosomes can came from
outside or inside of the cell. According to that, the digestive process varies. Outside
residues are digested by endocytosis, and inside residues by autophagia.
4- What are the marker enzymes of lysosome and peroxisome? What

are the major differences between the two organelles?
The marker enzymes for these two organelles are, Acidic phosphatase for lysosome and
Catalase for peroxisome.
Peroxisomes is an organelle specialized for caring out oxidative reaction. Peroxisomes are
small, membrane-enclosed organelles that contain enzymes involved in a variety of metabolic
reactions, including several aspects of energy metabolism.
They are recognized in many species by the presence of a central crystalline core of urate
oxidase, as seen in the peroxisomes from rat liver and rat brain. In humans, this crystalline core
is not present since urate, a product of purine breakdown, is excreted directly rather than, as in
other species, degraded prior to excretion. Therefore, transmission electron micrographs do not
distinguish between lysosomes and peroxisomes in human tissue. Both are present as
membrane-bound organelles packed with electron-dense enzymes. Histochemistry clearly
demonstrates, however, that lysosomal and peroxisomal enzyme content are different.

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Their differences between lysosomes and peroxisomes are summarised in the following
table.

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5- Why do call lysosome and peroxisome heterogeneous organelles?
Those organelles, Lysosomes and Peroxisomes, are considered heterogeneous because
the can diverse in size and contents.
6- What are the functions of peroxisome? Compare the detoxification

function of peroxisome and smooth ER.
Detoxification refers to a physiological process in which a harmful or toxic substance is
converted into a less harmful or harmless substance. The liver is mainly responsible for
detoxification in the human body.
Detoxification in the Peroxisome and other functions:
1）. Detoxification
Largely exists in animal hepatocytes and kidney cells
There are two major enzymes for detoxification:
FAD dependent oxidase to produce hydrogen peroxide （H2O2）
RH2+O2 → R +H2O2
catalase：to make H2O2 form water
R′H2+H2O2→R′+2H2O
2) Regulation of oxygen concentration
3) Metabolism of molecules with nitrogen
Detoxification in Smooth ER:

The Smooth Endoplasmic Reticulum in hepatocytes has a lot of cytb5, cytP450，NADPH-
cytochrome reductase, NADH –cytb5 reductase et al, the electron transfer enzyme system. The
substrates will be oxidized or modified with OH, therefore, toxicity will be lost and will be moved
out of our cells and bodies easily.

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Summarizing, Peroxisomes and Endoplasmic reticulum (smooth) are toxic detoxifying
organelles found in the cells.
The smooth endoplasmic reticulum (SER) has numerous enzymes that degrade inorganic
substances such as drugs and alcohol. The SER transforms the harmful substances into water
and soluble products that are removed through excretion. For this reason, numerous SER is
found in liver cells where toxic substances are detoxified.
Peroxisomes also contain numerous enzymes for detoxifying toxic substances and
hydrogen peroxide. The enzymes convert toxic hydrogen peroxide into a water molecule.
Alcohol and other toxic substances are detoxified by enzymes that catalyze hydrogen transfer
from these substances to oxygen through oxidation. As a result of the oxidation, toxic
substances are detoxified. So, peroxisomes neutralizing the free radicals, which cause cellular
damage and death. Peroxisomes also have an important role in the lipid mechanism, breaking
down the fatty acids and amino acids by oxidative reactions.

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VESICLE TRANSPORTATION
Important terms
Vesicle Transport: is a very important cellular activity, responsible for molecular traffic
between a variety of specific membrane-enclosed compartments. For that, a vesicle, a unit
membrane which enclosed organelles for transportation, is used. The selectivity of such transport
is therefore key to maintaining the functional organization of the cell. For example,
lysosomal enzymes must be transported specifically from the Golgi apparatus to lysosomes, not to
the plasma membrane or to the ER. Some of the signals that target proteins to specific organelles,
such as lysosomes, were discussed earlier in this chapter. These proteins are transported within
vesicles, so the specificity of transport is based on the selective packaging of the intended cargo into
vesicles that recognize and fuse only with the appropriate target membrane. Because of the central
importance of vesicular transport to the organization of eukaryotic cells, understanding the
molecular mechanisms that control vesicle packaging, budding, and fusion is a major area of
research in cell biology. There are two ways for protein transport inside the cell, one is directed
by signal sequence or targeting sequence, specially for transport of proteins from free
ribosomes (naked individual transport, limited to short distance transport) the other is vesicle
transport (enclosed collective transport, for both long and short distance transport). The specific
structure of coated vesicle determines the orientation of vesicle transport. Vesicle transport is a
precise process under multi-step control. The specific recognition between vesicle with v-
SNARE and target membrane with t-SNARE guarantee the accuracy of cargo unloading. Vesicle
transport is the base for the transport and exchange of protein and lipid.

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The characteristic of the transport are:
o 1. normal transporting ways among endomembrane system parts such as
:ER→Golgi；Golgi→lysosome；secretion particle →extracelluar part.
o 2. target organelles have specific membrane marker.
o 3. vesicle transporting move along microtubules, motion power is from motor
proteins.
The formation of vesicles is dependent on coat proteins that will, under proper conditions,
self-assemble into spherical cages. When associated with transmembrane proteins, they can
pull the attached membrane along into a spherical shape also. The major types of coat proteins
used in vesicle formation are COPII, COPI, and Clathrin.
COPII coated vesicles: a type of coated vesicle which is formed in Endoplasmic Reticulum
that generally move from ER to Golgi Complex.
COPI coated vesicles: a type of coated vesicle which are used between parts of the Golgi
apparatus as well as to form vesicles going from the Golgi back to the ER, in order to sending
back the escape retention proteins to ER.
Clathrin coated vesicles: a type of coated vesicle that can be formed in the trans Golgi
network of Golgi complex and also formed from the plasma membrane for endocytosis.

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Genetic Lysosome disease: are inherited metabolic diseases that are characterized by an
abnormal build-up of various toxic materials in the body’s cells as a result of enzyme
deficiencies. In our classes, we study two exemples:
o Tay-Sachs disease: is a rare, neurodegenerative disorder in which deficiency of an
enzyme (hexosaminidase A) results in excessive accumulation of certain fats (lipids) known as
gangliosides in the brain and nerve cells. This abnormal accumulation of gangliosides leads to
progressive dysfunction of the central nervous system. When one of these lysosomal enzymes
(such as hexosaminidase A) is missing or ineffective, glycosphingolipids start to build up in the
lysosome. If there is too much accumulation of these materials in the lysosome, the cells in the
nervous system degenerate and die, triggering an inflammatory response that amplifies
damage in surrounding tissue.
§ N- acetyl β glucosidase A → GM2 accumulation → loss sight, num,

paralysis

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1- How many kinds of major vesicles? What are the transports mediated by
them, and what are the orientations?
The five main type of vesicles are transport vesicles, lysosomes, peroxisomes, extracellular
vesicles, and secretory vesicles. The transport vesicles that we have been study can be first
divided them according to their coat, coated vesicles and non-coated vesicles (naked vesicles).
The coated vesicles are divided into three kinds: COPII, COPI and Clathrin coated vesicles).
Several distinct classes of coated vesicles have been identified. They are distinguished by
the proteins that make up their coat, the places of formation, their appearance in the electron
microscope, and their role in cell trafficking, and chemicals transported by them.
In this lecture, we focus on the three best studied coated vesicles that we know, and which
I mentioned above. They are mediated by endocytosis and exocytosis, contains GTP binders to
form their coat, each of them have specific adaptor protein, and they have a selected orientation.
1. COPII-coated vesicles move materials from the ER “forward” to the ERGIC and Golgi
complex (COP is an acronym for coat proteins.)
2. COPI-coated vesicles move materials in a retrograde direction (1) from the ERGIC and
Golgi stack “backward” toward the ER and (2) from trans Golgi cisternae “backward” to cis Golgi
cisternae. Additional roles for COPI vesicles have been debated.
3. Clathrin-coated vesicles move materials from the TGN to endosomes, lysosomes, and
plant vacuoles. They also move materials from the plasma membrane to cytoplasmic
compartments along the endocytic pathway. They have also been implicated in trafficking from
endosomes and lysosomes.
The table below summarize the types of coated vesicles, their components and adaptor
proteins and GTPs, and also their Orientations.

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2- What are the significance of vesicle transport?
Vesicle transport is very important for cell’s correct functions and life. Starting point that
the vesicle transport is a basic way for intercellular materials exchange. Proteins and membrane
lipids are transported by vesicles. Therefore, we can verify that the membrane lipid
transportation depends on this process. But, for proteins transportation is a little bit more
complex because the wrong “delivery” of proteins in our body can cause severe disease. That’s
the reason why this process is assured and dependent on signal peptide, to in order to mark the
target sequency, and the vesicle is an enclosed transportation.
In the same order, transportation is highly ordered and strictly controlled logistic
transportation, to assure the right orientation of the transportation. The targeted proteins for
transportation is selected and controlled. This one is a closed vehicle transportation. As an
example we have the role of the chaperones in proteins maturation.
The vesicle transportation is also important due the fact that there is a specific recognition
and induced fusion guarantees the unloading properly. Related to the membrane proteins
recognition, to the V-SNARE and T-SNARE process (the words SNARE means soluble N-ethyl
maleimide-sensitive factor attachment protein receptors). v-SNARE and t-SNARE recognition is
essential for vesicle docking and fusion or unloading

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3- Explain the mechanism of vesicle transport has the proper direction.
A lot of people think that the vesicle transportation inside of the cell is messy and in a
random direction until get to the target. But they are completely wrong. The vesicle transport
mechanism is very well organized thanks to an important structure in side of the cells, the
cytoskeleton. Is like the vesicle is the cargo and the motor proteins the delivery guy that will
deliverer it.
These proteins bind to vesicles and organelles and use energy from ATP to move them
along the microtubule or microfilament network. Two families of motor proteins,
the kinesins and dyneins, move vesicles along microtubules, and members of
the myosin family move them along microfilaments. The myosin family is also important in cell
movement.
The direction of movement of vesicles along the cytoskeleton is absolutely dependent on
the polarity of the microfilaments and microtubules. Some motor proteins move from the minus
end to the plus end and others in the opposite direction.
Besides that, we cannot forget the importance of the V-SNARE and T-SNARE in the delivery
role. As it was mention before, the SNARE system acts like a target-receptor, which guide the
specific vesicles to the proper direction, to connect the correspondent receptor.

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4- What is the pathological mechanism of silicosis?
Silicosis is a long-term lung disease caused by inhaling large amounts of crystalline silica
dust, usually over many years. Silica is a substance naturally found in certain types of stone,
rock, sand and clay. Working with these materials can create a very fine dust that can be easily
inhaled.
Whit the inhalation of crystalline silica, the alveolar macrophages will detect the silica’s
receptors and will binding them by endocytosis. The negative charge of this component (SiO2)
will create damage to the lysosomes membrane, and generating cell necrosis. This will further
affect other cells, and an inflammatory process results. Therefore, fibers will be formed and also
the lose function for those cells.
Poly-2-vinylpyridine-N-oxide (PVNO,P-204) Is used as a treatment, in order to bind the
SiO2 and protect the lysosomal membrane.

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ENDOMEMBRANE SYSTEM AND VESICLE TRANSPORTATION
1- What is endomembrane system? Please list the members of organelles

in endomembrane system.
The Endomembrane System is a group of membranes and organelles in eukaryotic cells
that works together to modify, package, and transport lipids and proteins.
In other words, the Endomembrane System is the intracellular membrane organelles with
unit membrane structure.
The organelles that are part of that system includes nuclear membrane, endoplasmic
reticulum (smooth and rough), Golgi complex, Lysosomes, Peroxisomes and all kinds of vesicles
(like vacuoles, for example). As it was referred above, this system guarantees the post protein
synthesis modification and protein transport in a series of membrane composed vesicles, in a
sequential order, in different functionally specified space, in a highly secured way and in an
efficient way.

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2- Please list the proteins synthesized in attached ribosomes and free
ribosomes!
The free Ribosomes can synthetize enzyme proteins and membrane proteins of
peroxisome protein, majority of mitochondrial proteins, cytosol and nucleus proteins. In
general, free Ribosomes synthesize proteins that remain in the cell, such as hemoglobin in red
blood cells or contractile proteins in muscle cells. Polyribosomes attached to the endoplasmic
reticulum synthesize proteins for export from the cell (example, digestive enzymes) and for
placement within the plasma membrane (example, ion channel proteins).
In the attached ribosomes the proteins synthetized are membranes proteins, secretion
proteins, retention proteins, and lysosome enzyme proteins and membrane proteins.
Attached ribosomes produce proteins which are exported from the cell to the outside.
These proteins include digestive enzymes, polypeptide hormones, cell surface receptors, cell
signaling molecules, etc. These proteins are secreted from the cell using secretory vesicles.
The table below describes the main difference in this two types of Ribosomes.

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3- Please describe the process of synthesis, modification, and
transportation of secretion protein, membrane protein and lysosomal protein.
A common pool of ribosomes synthesizes the proteins that stay in the cytosol and those
that are transported into the ER. The ER signal sequence on a newly formed polypeptide chain
binds to SRP, which directs the translating ribosome to the ER membrane. The mRNA molecule
remains permanently bound to the ER as part of a polyribosome, while the ribosomes that move
along it are recycled; at the end of each round of protein synthesis, the ribosomal subunits are
released and rejoin the common pool in the cytosol. A thin section electron micrograph of
polyribosomes attached to the ER membrane. The plane of section in some places cuts through
the ER roughly parallel to the membrane, giving a face-on view of the rosette like pattern of the
polyribosomes.
There are two important sequences for transmembrane proteins the start-transfer
sequence (equivalent to signal peptide of secretion protein) and the stop-transfer sequence. The
star-transfer sequence leads the new synthesized peptide into the lumen of RER via
translocator.
During the peptide move into the translocator, when the stop-transfer sequence reaches
the translocator, it will stop moving. The translocator moves away, the stop transfer sequence
becomes the transmembrane sequence.

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4- How many kinds of coated vesicles? And what determines their
orientations?
They are three types of coated vesicles, according to our cell biology’s classes. mediated
by endocytosis and exocytosis, contains GTP binders to form their coat, each of them have
specific adaptor protein, which can selected their orientation (V-SNARE and T-SNARE).
1. COPII-coated vesicles move materials from the ER “forward” to the ERGIC and Golgi
complex (COP is an acronym for coat proteins.)
2. COPI-coated vesicles move materials in a retrograde direction (1) from the ERGIC and
Golgi stack “backward” toward the ER and (2) from trans Golgi cisternae “backward” to cis Golgi
cisternae. Additional roles for COPI vesicles have been debated.
3. Clathrin-coated vesicles move materials from the TGN to endosomes, lysosomes, and
plant vacuoles. They also move materials from the plasma membrane to cytoplasmic
compartments along the endocytic pathway. They have also been implicated in trafficking from
endosomes and lysosomes.
The table below summarize the types of coated vesicles, their components and adaptor
proteins and GTPs, and also their Orientations.

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5- How can a vesicle dock successfully and exactly merge with target
membrane organelles?
A vesicle can dock successfully and exactly merge with target membrane organelles due
the SNARE complex.
SNAREs, (soluble N-ethyl maleimide-sensitive factor attachment protein receptors) can be
divided into two categories: vesicle or v-SNAREs, which are incorporated into the membranes
of transport vesicles during budding, and target or t-SNAREs, which are associated with nerve
terminal membranes. This recognition system is essential for vesicle docking and fusion or
unloading.
Therefore, the V-SNARE on the vesicle membrane will dock will the T-SNARE of the
membrane. Once they connected, the cargo is delivered to the membrane. Normally this process
is mediates exocytosis but can also mediate the fusion of vesicles with membrane-bound
compartments (such as a lysosome).

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6- Why Peroxisome is a special member of endomembrane system?
Peroxisomes are considered a special member of the endomembrane system because
their protein synthesis is dependent on free ribosomes in the cytosol instead of attached
ribosomes in rough ER. The transport of these proteins requires a specific peptide sequence or
signal. The roles of peroxisome lie in detoxification and oxygen balance.

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Chapter 4 – Mitochondria
Important Terms
Semiautonomous Organelle: Chloroplast and mitochondria are called semi-autonomous
organelles because they have their own genetic material (DNA) and are capable of synthesizing
proteins required for their functioning. Semi- autonomous organelles are those organelles
which can survive on their own.
Mitochondria encode their own mRNA, ribosomes, tRNAs and proteins.
However, most of the proteins in mitochondria are encoded by nuclear DNA, synthesized
in cytosol. Because the growth and proliferation of mitochondria were controlled by both
nuclear genome and it’s own genome mitochondria are called semiautonomous organelle.
The protein synthesis for mitochondria encoded peptides is inhibited by antibiotics, Such
as erythromycin, tetracycline, choramphinicol. While the synthesis of protein encoded by
nucleus is inhibited by cycloheximide. Therefore, doctors needs to pay attention to antibiotic
dose when using antibiotics.
ATP Synthase Complex: ATP synthase is a protein that catalyses the formation of the
energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP)
and inorganic phosphate (Pi). It is classified under ligases as it changes ADP by the formation
of P-O bond (phosphodiester bond). The formation of ATP from ADP and Pi is energetically
unfavourable and would normally proceed in the reverse direction. In order to drive this
reaction forward, ATP synthase couples ATP synthesis during cellular respiration to an
electrochemical gradient created by the difference in proton (H+) concentration across the
inner mitochondrial membrane in eukaryotes or the plasma membrane in bacteria. During
photosynthesis in plants, ATP is synthesized by ATP synthase using a proton gradient created
in the thylakoid lumen through the thylakoid membrane and into the chloroplast stroma.

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An F-ATPase consists of two main subunits, FO and F1, which has a rotational motor
mechanism allowing for ATP production. ATP synthase is a molecular machine. ATP synthase is
an enzyme that creates the energy storage molecule adenosine triphosphate. This complex then
evolved greater efficiency and eventually developed into today's intricate ATP synthases.
TIM/TOM complex: is a protein complex in cellular biochemistry which translocate

proteins produced from nuclear DNA through the mitochondrial membrane for use in oxidative
phosphorylation. In enzymology, the complex is described as an mitochondrial protein-
transporting ATPase ,or more systematically ATP phosphohydrolase (mitochondrial protein-
importing), as the TIM part requires ATP hydrolysis to work.
Only 13 proteins necessary for a mitochondrion are actually coded in mitochondrial DNA.
The vast majority of proteins destined for the mitochondria are encoded in the nucleus and
synthesized in the cytoplasm. These are tagged by an N-terminal signal sequence. Following
transport through the cytosol from the nucleus, the signal sequence is recognized by a receptor
protein in the translocase of the outer membrane (TOM) complex. The signal sequence and
adjacent portions of the polypeptide chain are inserted in the TOM complex, then begin

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interaction with a translocase of the inner membrane (TIM) complex, which are hypothesized
to be transiently linked at sites of close contact between the two membranes. The signal
sequence is then translocated into the matrix in a process that requires an electrochemical
hydrogen ion gradient across the inner membrane. Mitochondrial Hsp70 binds to regions of the
polypeptide chain and maintains it in an unfolded state as it moves into the matrix.
The ATPase domain is essential during the interactions of the proteins Hsp70 and subunit
Tim44.Without the presence of ATPase, carboxy-terminal segment is not able to bind to protein
of Tim44.As mtHsp70 transmits the nucleotide state of the ATPase domain with alpha-helices A
and B, Tim44 interacts with the peptide binding domain to coordinate the protein bind.
Under Electron Microscope, people observed the contact sites between inner and outer
membranes, which is named as translocation contact site. Experiments confirmed that it is the
site for protein enter and leave mitochondria.
The contact site in inner membrane, is named as Tim, While the contact site in outer
membrane is called Tom.

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1- Please describe the structure characteristics of mitochondria. How can
the mitochondria make ATP?
Mitochondria are often referred to as the powerhouses of the cell. They help turn the
energy we take from food into energy that the cell can use. But, there is more to mitochondria
than energy production. Mitochondria are also involved in other tasks, such as signalling
between cells and cell death, otherwise known as apoptosis.
Present in nearly all types of human cell, mitochondria are vital to our survival. They
generate the majority of our adenosine triphosphate (ATP), the energy currency of the cell.
Mitochondria are small, often between 0.75 and 3 micrometres and are not visible under
the microscope unless they are stained. They have two membranes, an inner and outer
membrane, with an intermembrane space between them.
The outer membrane contains proteins known as porins, which allow movement of ions
into and out of the mitochondrion. Enzymes involved in the elongation of fatty acids and the
oxidation of adrenaline can also be found on the outer membrane. It also contains many
complexes of integral membrane proteins that form channels through which a variety of
molecules and ions move in and out of the mitochondrion. We called them porins. The portion
of lipids and proteins in the outer membrane is Lipid/protein=1/1
The inner membrane is richly endowed with cardiolipin, a phospholipid that possesses
four, rather than the usual two, fatty acyl chains. The presence of this phospholipid in high
concentration makes the inner membrane nearly impermeable to ions, electrons, and protons.
This membrane contains a variety of enzymes. It contains ATP synthase which generates
ATP in the matrix, and transport proteins that regulate the movement of metabolites into and
out of the matrix. The inner membrane is arranged into cristae in order to increase the surface
area available for energy production via oxidative phosphorylation. The portion of lipids and
proteins in the inner membrane is Lipid/protein=1/4
Between those two membranes, there is two spaces, the matrix and the intermembrane
space, which play a critical role in the transport of protons across mitochondrial membranes
during oxidative phosphorylation.

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Matrix contains the enzymes of the Krebs (TCA) and fatty acid cycles, alongside DNA,
RNA, ribosomes and calcium granules.
The intermembrane space is essential for the ATP production. It stores the energy in form
of protons (H+) given by NADH and FADH2. These protons will be the key to transform the ADP
into ATP, in the APT synthase complex.
Another structure that we can obviously notice is the presence of cristae. These cristae are
the folds of the inner membrane. They increase the surface area of the membrane, therefore
increasing the space available for chemical reactions.
These folds greatly increase the surface area available to house the machinery needed for
aerobic respiration. It increases both the surface and space between the two membranes.
In mitochondria we need to consider two important steps, the Citric Acid Cycle and the
Oxidative Phosphorylation but to master the ATP production we should start from the early
beginning.
The APT production, also named cellular respiration process, starts outside of the
mitochondria, in the cytosol. The glycolysis is the process where the simple sugar is broken
down to for Pyruvate.

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Pyruvate enters in the mitochondria, and it’s transformed into Acetyl CoA. Besides
glycolysis, the fatty acids can also be transformed into Acetyl CoA and be used to produce
energy, but the amount of ATP produced is less. The Acetyl CoA will be modify in the Citric Acid
Cycle, also named by the Krebs cycle.
This cycle is complex but summarising, the molecules that enter and circulate through the
citric acid cycle are made mostly of carbon atoms. To understand how the citric acid cycle
works, we need to follow how the carbon atoms are rearranged through the cycle. Molecules,
called electron shuttles, accept the energy released by stepwise rearrangements and the
subtraction of carbons in the form of electrons. Electron shuttles are small organic molecules,
such as NAD+ and FAD that transport high energy electrons to where they need to be by gaining
electrons (through “reduction”) and losing electrons (through “oxidation”).

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The Final products of this cycle included three molecules of NADH and one of FADH2.
These two products are transported to the electrons transport chain, where will lose their
protons to the intermembrane space. This process will increase the protons (H+) concentration
on the intermembrane space. Consequently, to control the protons concentration, the APT
synthase complex will be activated and catalyze the synthesis of ATP from ADP and phosphate,
driven by a flux of protons across a gradient generated by electron transfer from the proton
chemically positive to the negative side.
During these two processes 36 ATP molecules are produced. So, all together there are 38
molecules of ATP produced in aerobic respiration plus 2 ATP are formed outside the
mitochondria.

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2- Please describe the characteristics of mitochondrial genome.
Different from the other organelles, mitochondria have their own set of DNA. But,
mitochondrial genome is different from the nuclear genome. The main characteristic of
mitochondrial genome are:
o The mtDNA structure is very tight (No intron)
o There is no histones combine with mtDNA
o mtDNA is asymmetric
o Codons are not rigidly paired with anticodons, some codons means different sense
o Two replication origins
o Two promoters with poly-cistronic style

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Chapter 5 – Cytoskeleton
Important Terms
Cytoskeleton: In a cell, the nucleus is always located in the middle of a cell, and
mitochondria spread in different area. From the point of view of physics, it is impossible because
of gravity. The reason that all the organelles in a cell have their location instead of sit in the
bottom of the cell is that the cell has cytoskeleton.
The cytoskeleton is a complex, dynamic network of interlinking protein filaments present
in the cytoplasm of all cells, including bacteria and archaea. It extends from the cell nucleus to
the cell membrane and is composed of similar proteins in the various organisms. In eukaryotes,
it is composed of three main components, microfilaments, intermediate filaments and
microtubules, and these are all capable of rapid growth or disassembly dependent on the cell's
requirements.
In a cell, fiber proteins form a protein network to support the cell or to keep the shape of
the cell or provide facilities for cell movement. This protein network is called cytoskeleton. It’s
made up of three primary protein filaments, Microtubules, Microfilaments, and Intermediate
filaments.

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Microtubule-organizing centers (MTOCs): is a structure found in eukaryotic cells from
which microtubules emerge. MTOCs have two main functions: the organization of eukaryotic
flagella and cilia and the organization of the mitotic and meiotic spindle apparatus, which
separate the chromosomes during cell division. The MTOC is a major site of microtubule
nucleation and can be visualized in cells by immunohistochemical detection of γ-tubulin. The
morphological characteristics of MTOCs vary between the different phyla and kingdoms.
In animals, the two most important types of MTOCs are:
1) the basal bodies associated with cilia and flagella and
2) the centrosome associated with spindle formation.
Under normal physiological conditions, the assembly of microtubule always starts in a

specific core or location, these kinds of core locations are called microtubule organizing centers
(MTOC), usually locate around centrosome or the base of cilium. All the microtubule organizing
center have γ tubulin ring complex (γ-TuRC) that is capable of initiating microtubule growth.
γ-TuRC provides an initiation site for α tubulin/β tubulin heterodimer assembly, the minus
end. The microtubule organizing center is the major player for microtubule nucleation.

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Microtubule-Associated proteins: In addition to tubulin heterodimers, microtubules also
possess microtubule-associated proteins (MAPs). MAPs are defined as a group of proteins that
bind microtubules. MAPs typically have one domain that attaches to the side of a microtubule
and another domain that extends outwards as a filament from the microtubule’s surface.
MAPs functions include to speeds up polymerization, facilitate assembly, stabilizes the
microtubules, and assist in the intracellular movement of organelles and vesicles.
Recent advances in structural biology provide new insights into the molecular modes of
MAP–microtubule interactions, thus beginning to explain the specific structural roles of MAPs.
MAPs can serve as linkers to other cellular cytoskeletal elements, organelles, and
membranes, thus playing versatile roles in the control of cell function. It controls the activity of
other microtubule-interacting proteins, such as severing enzymes and molecular motors.
Emerging evidence suggests that MAP–microtubule interactions are controlled by post-
translational modifications of both MAPs and microtubules. MAPs can form dense, long-lived
islands on microtubule surfaces, and can also undergo phase separation.

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Microtubule-associated proteins (MAPs) were initially discovered as proteins that bind to
and stabilize microtubules. Today, an ever-growing number of MAPs reveals a more complex
picture of these proteins as organizers of the microtubule cytoskeleton that have a large variety
of functions. MAPs enable microtubules to participate in a plethora of cellular processes such
as the assembly of mitotic and meiotic spindles, neuronal development, and the formation of
the ciliary axoneme. Although some subgroups of MAPs have been exhaustively characterized,
a strikingly large number of MAPs remain barely characterized other than their interactions with
microtubules. We provide a comprehensive view on the currently known MAPs in mammals.
We discuss their molecular mechanisms and functions, as well as their physiological role and
links to pathologies.
Regarding to the microtubules formation, MAPs bind to the tubulin subunits that make up
microtubules to regulate their stability. A large variety of MAPs have been identified in many
different cell types, and they have been found to carry out a wide range of functions. These
include both stabilizing and destabilizing microtubules, guiding microtubules towards specific
cellular locations, cross-linking microtubules and mediating the interactions of microtubules
with other proteins in the cell.
Within the cell, MAPs bind directly to the tubulin dimers of microtubules. This binding can
occur with either polymerized or depolymerized tubulin, and in most cases leads to the
stabilization of microtubule structure, further encouraging polymerization. Usually, it is the C-
terminal domain of the MAP that interacts with tubulin, while the N-terminal domain can bind
with cellular vesicles, intermediate filaments or other microtubules. MAP-microtubule binding
is regulated through MAP phosphorylation. This is accomplished through the function of the
microtubule-affinity-regulating-kinase (MARK) protein. Phosphorylation of the MAP by the
MARK causes the MAP to detach from any bound microtubules. This detachment is usually
associated with a destabilization of the microtubule causing it to fall apart. In this way the
stabilization of microtubules by MAPs is regulated within the cell through phosphorylation.

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Intermediate filaments: are cytoskeletal structural components found in the cells of
vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an
invertebrate, the cephalochordate Branchiostoma.
Intermediate filaments are composed of a family of related proteins sharing common
structural and sequence features. Initially designated 'intermediate' because their average
diameter (10 nm) is between those of narrower microfilaments (actin) and wider myosin
filaments found in muscle cells, the diameter of intermediate filaments is now commonly
compared to actin microfilaments (7 nm) and microtubules (25 nm). Animal intermediate
filaments are subcategorized into six types based on similarities in amino acid sequence and
protein structure. Most types are cytoplasmic, but one type, Type V is a nuclear laminae. Unlike
microtubules, IF distribution in cells show no good correlation with the distribution of either
mitochondria or endoplasmic reticulum.
Most of the monomers of intermediate filament are filamentous including the ammonia
head, the carboxyl tail and the middle α -helix area. A pair of adjacent monomers align in
parallel and the α-helix area of the two monomers form a dimer helix. A pair of the dimer helix
forms a tail to head tetramer. This tetramer is a basic unit of intermediate filament. A lot of
tetramers line up to form one longer intermediate protofilament. Eight protofilaments wrap up
to form an intermediate filament. Intermediate filaments lack polarity.
Intermediate filaments tend to be more resistant to chemical disruption than other types
of cytoskeletal elements and more difficult to solubilize.
Unlike microfilaments and microtubules, IFs are a chemically heterogeneous group of
structures that, in humans, are encoded by at least 50 different genes. The polypeptide subunits
of IFs can be divided into six major classes based on their tissue distribution. Most of these
polypeptides have a similar arrangement of domains (alpha helix region) that allows them to
form similar looking filaments. Namely, the structural similarities among intermediate
filaments.

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Motor Proteins: are a class of molecular motors that can move along the cytoplasm of
animal cells. Motor proteins, such as myosins and kinesins, move along cytoskeletal filaments
via a force-dependent mechanism that is driven by the hydrolysis of ATP molecules. Nucleotide
hydrolysis and controlled inorganic phosphate release by motor proteins causes restructuring
of core domains that control the association of the motor protein with the filaments, other
proteins, and the fresh supply of nucleotides.
Motor proteins propel themselves along the cytoskeleton using a mechanochemical
cycle of filament binding, conformational change, filament release, conformation reversal, and
filament rebinding. In most cases, the conformational changes on the motor protein prevents
subsequent nucleotide binding and/or hydrolysis until the prior round of hydrolysis and
release is complete.
Controlled hydrolysis of nucleotides and inorganic phosphate release by motor proteins
can generate mechanical forces that can be used for:
o Translocating the motor proteins themselves along the filaments
o Stabilizing and/or moving the filaments (i.e., contractile stress fibers) & escorting
cargo that is attached to the motor protein (e.g., vesicles, organelles, other proteins) to
specific regions in the cell
o Transport of substances in a particular direction, or polarity, along the filaments.
This directionality is achieved by specific conformational changes that allow movement
in only one direction.

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Motor proteins utilizing the cytoskeleton for movement fall into two categories based on
their substrate: microfilaments or microtubules. Actin motors such as myosin move along
microfilaments through interaction with actin, and microtubule motors such as dynein and
kinesin move along microtubules through interaction with tubulin.
There are two basic types of microtubule motors, plus-end motors and minus-end motors,
depending on the direction in which they "walk" along the microtubule cables within the cell.
The best prominent example of a motor protein is the muscle protein myosin which
"motors" the contraction of muscle fibers in animals. Motor proteins are the driving force behind
most active transport of proteins and vesicles in the cytoplasm. Kinesins and cytoplasmic
dyneins play essential roles in intracellular transport such as axonal transport and in the
formation of the spindle apparatus and the separation of the chromosomes during mitosis and
meiosis. Axonemal dynein, found in cilia and flagella, is crucial to cell motility, for example in
spermatozoa, and fluid transport, for example in trachea.

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1- Please describe the structure characteristics of each member of
cytoskeleton and describe how they assembly.
The eukaryotic cytoskeleton is a network of three long filament systems, made from the
repetitive assembly and disassembly of dynamic protein components. The primary filament
systems comprising the cytoskeleton are microtubules, Microfilaments, and intermediate
filaments. It creates an internal architecture to give a cell its shape through elaborate linkage to
itself, the plasma membrane, and internal organelles.
The cytoskeleton structure is modified by adhesion to neighbouring cells or to
the extracellular matrix (ECM). The strength and the type of these adhesions are pivotal for
regulating the assembly/disassembly of the cytoskeleton components. This dynamic property
enables cellular movement, which is governed by forces (both internal and external). This
information is sensed by mechanosensors and disseminated via the cytoskeleton leading to
chemical signalling and response.
Although subunits of all three filament systems are present throughout the cell,
differences in the subunit structures and the attractive forces between them impart each system
with variable stabilities and distinct mechanical properties. These characteristics explain their
distribution in particular structures and/or regions of the cell. Numerous cytoskeletal-
associated proteins also help to regulate the spatial and temporal distribution of the
cytoskeleton. The organization and assembly of one filament system is influenced by the others
in a coordinated fashion for most cellular functions.

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Microtubules
Microtubules are hollow cylinders that are approximately 25nm in diameter and vary in
length from 200 nm to 25 μm, and its wall thickness is around 5nm. They are formed by the
lateral association of between 12 and 17 protofilaments into a regular helical lattice. Each
protofilament consists of repeating units of polymerized alpha (α) and beta (β) tubulin
monomers, all pointed in the same direction. Multiple contacts within the microtubule, between
both tubulin subunits and the protofilaments, impart rigidity.
Microtubule assembly involves three steps: protofilaments form from αβ-tubulin subunits;
protofilaments associate to form the wall of the microtubule; and addition of more subunits to
the ends of the protofilaments elongates the microtubule.
Structure of microtubules is composed by dimers of α- and β-tubulin that polymerize to
form microtubules, which are composed of 13 protofilaments assembled around a hollow core.
Tubulin dimers can depolymerize as well as polymerize, and microtubules can undergo rapid
cycles of assembly and disassembly.

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Microfilaments
Microfilaments are composed of globular subunits of the protein actin filaments. Actin
filaments can create a number of linear bundles, two-dimensional networks, and three-
dimensional gels, and actin binding proteins can influence the specific structure the filaments
will form.
Monomers of the protein actin polymerize to form long, thin fibers. They are approximately
8 nm in diameter and the thinnest of the cytoskeletal filaments. In the presence of ATP, actin
monomers polymerize to form a stiff filament composed of two strands of actin molecules
wound around each other in a double helix. Because each actin subunit has polarity and all the
subunits of an actin filament are pointed in the same direction, the entire microfilament has
polarity.
Actin molecules present in the cells of many different vertebrate and invertebrate species
are very similar to each other in their amino acid sequence, attesting to their highly conserved
nature. Depending on their isoelectric point. There are three classes of actin: α actin of muscle,
and β actin and γ actin of non-muscle cells.
The filaments also possess a faster growing plus end and a slower growing minus end.
When the actin filament reaches its desired length, members of a family of small proteins,
capping proteins, attach to the plus end, terminating the lengthening of the filament. The
process of shorting of actin filaments is regulated in the presence of ATP, ADP, and Calcium.
To assembly, each microfilament, which is made up of two helical, interlaced strands of
subunits. Much like microtubules, actin filaments are polarized. Electron micrographs have
provided evidence of their fast-growing barbed-ends and their slow-growing pointed-end.

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Generally, actin filament polymerization occurs over three phases: A nucleation phase, an
elongation phase and a steady state phase.
During the nucleation phase the formation of a stable “actin nucleus” occurs. This is
usually comprised of three actin monomers in complex. In the elongation phase monomers are
rapidly added to the filament at the (+ve) or barbed end and this is often facilitated by additional
elongation factors such as formin. For this process to occur, the (+) end of the filament must be
exposed, and this means removal of capping protein.
Microtubules (tubulin) or bundles of microfilaments (actin) are thought to cause
movement, in some instances, by disassembly or assembly of subunits. Possible examples are
the pulling of a chromosome toward a pole in mitosis (anaphase) or the deformation of a cell
membrane to change the shape of a cell.

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Intermediate filaments
Intermediate filaments are a primary component of the cytoskeleton, although they are not
found in all eukaryotes, and are absent in fungi and plants. These filaments, which extend
throughout the cytoplasm and inner nuclear membrane are composed from a large family of
proteins that can be broadly grouped into five classes:
o Type I and II: Keratins
o Type III: Desmin, vimentin
o Type IV: Neurofilaments
o Type V: Lamins
The primary function of intermediate filaments is to create cell cohesion and prevent the
acute fracture of epithelial cell sheets under tension. This is made possible by extensive
interactions between the constituent protofilaments of an intermediate filament, which
enhance its resistance to compression, twisting, stretching and bending forces. These
properties also allow intermediate filaments to help stabilize the extended axons of nerve cells,
as well as line the inner face of the nuclear envelope where they help harness and protect the
cell’s DNA.
General, it as a diameter of approximately 10 nm, which is intermediate between that of
microtubules and microfilaments. It has no polar. It is comparatively tough, not easily be
depolymerized. Sometimes, some special members, phosphorylation will make it
depolymerized, such as lamina in nucleus.

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Most of the monomers of intermediate filament are filamentous including the ammonia
head, the carboxyl tail and the middle α -helix area. A pair of adjacent monomers align in
parallel and the α-helix area of the two monomer form a dimer helix. A pair of the dimer helix
forms a tail to head tetramer. This tetramer is a basic unit of intermediate filament. A lot of
tetramers line up to form one longer intermediate protofilament. 8 protofilaments wrap up to
form an intermediate filament. Intermediate filaments lack polarity.
Intermediate filaments tend to be more resistant to chemical disruption than other types
of cytoskeletal elements and more difficult to solubilize. The characteristics of intermediate
filament: It has no polar. It is comparatively tough, not easily be depolymerized. Sometimes,
some special members, phosphorylation will make it depolymerized, such as lamina in nucleus.
Unlike microfilaments and microtubules, IFs are a chemically heterogeneous group of
structures that, in humans, are encoded by at least 50 different genes. The polypeptide subunits
of IFs can be divided into six major classes based on their tissue distribution. Most of these
polypeptides have a similar arrangement of domains (alpha helix region) that allows them to
form similar looking filaments. Namely, the structural similarities among intermediate
filaments.

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2. Please describe the functions of each member of cytoskeleton in a cell.
Functions of Microtubule
1. Microtubules as structural supports and organizers.
2. The distribution of microtubules in a cell helps determine the shape of that cell. In
plant cells, microtubules play an indirect role in maintaining cell shape through
their influence on the formation of the cell wall. Microtubules are also thought to
play a role in maintaining the internal organization of cells.
3. To form mitosis spindle and centriole for CS separation and cell division.
4. To form cilia (flagellum) for special movement.
5. To work as tracks for vesicle transportation.
Functions of Microfilaments
Form a band just beneath the plasma membrane that:
1. To provides mechanical strength to the cell cell-cell connection: anchored junction
anchors the centrosomes at opposite poles of the cell during mitosis
2. Cell movement
3. muscle movement: interact with myosin ("thick") filaments in skeletal muscle fibers
to provide the force of muscular contraction
Functions of intermediate filaments

The major function of intermediate filaments is to provide structural support for the cell.
Their great tensile strength is important in protecting cells from stresses and strains. Some other
functions of intermediate filaments:
1. provide mechanical strength to the long axons found in some neurons
2. cell-cell junction, anchored junctions (desmosomes, hemidesmosomes）
3. provide the net to hold the organelles.

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Chapter 6 – Endomembrane Systems
Important Terms
Nuclear Pore Complex: NPCs (Nuclear pore complexes) are indispensable for cell function
and are at the center of several human diseases. NPCs is a two units membranes’ structure that
provide access to the nucleus and regulate the transport of proteins(DNA polymerase, RNA
polymerase and other proteins), subunit of ribosome, and RNA (mRNA and tRNA) across the
nuclear envelope. Also assists in organizing the chromatin. They are aqueous channels
generated from a complex network of evolutionarily conserved proteins known as
nucleoporins.
The structure of the NPC a cylindrical ring-like structure lined with nucleoporins capable
of binding to transport factors governs its transport function. This rings are composed by:
o I Cytoplasmic ring
o II nuclear ring
o III Spoke
1. column subunit
2. luminal subunit
3. annular subunit
o IV Central plug

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Nuclear Lamina: is a structure near the inner nuclear membrane and the peripheral
chromatin. It is composed of lamins, which are also present in the nuclear interior, and lamins
associated proteins.
The nuclear lamina is a dense (~30 to 100 nm thick) fibrillar network inside the nucleus of
a eukaryotic cell. It is composed of intermediate filaments and membrane associated proteins.
The Nuclear lamina it has the following functions:
o providing mechanical support
o the nuclear lamina regulates important cellular events such as DNA replication and
cell division.
o Additionally, it participates in chromatin organization and it anchors the nuclear
pore complexes embedded in the nuclear envelope.

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Nucleosome: is a section of DNA that is wrapped around a core of proteins. In other words,
nucleosome is the unit of chromatin.
Inside the nucleus, DNA forms a complex with proteins called chromatin, which allows
the DNA to be condensed into a smaller volume. When the chromatin is extended and viewed
under a microscope, the structure resembles beads on a string.
Our genetic materials are DNAs, which are so delicate and easier to be broken. In fact, our
genetic materials are kept integrity, because DNAs are associated with histone proteins to form
nucleosomes, many nucleosomes form chromatin. Everybody knows the term chromosome,
esp. during mitotic division.
Each nucleosome is made up of an octamer of proteins, duplicates of each of four types
of histones (H2A, H2B,H3 and H4). Besides ,there is a H1 protein to fix the structure.
The nucleosome is also wrapped with one and 3/4 turns (about 150 base pairs) of the DNA
molecule, which continues as linker DNA extending to the next “bead”. The spacing between
each nucleosome is about 200 base pairs.

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Centromere: is the specialized DNA sequence of a chromosome that links a pair of sister
chromatids (a dyad).During mitosis, spindle fibers attach to the centromere via the kinetochore.
Centromeres were first thought to be genetic loci that direct the behaviour of chromosomes.
The physical role of the centromere is to act as the site of assembly of the kinetochores, a
highly complex multiprotein structure that is responsible for the actual events of chromosome
segregation . binding microtubules and signalling to the cell cycle machinery when all
chromosomes have adopted correct attachments to the spindle, so that it is safe for cell division
to proceed to completion and for cells to enter anaphase.
Telomere: is a region of repetitive nucleotide sequences associated with specialized

proteins at the ends of linear chromosomes. Although there are different architectures,
telomeres, in a broad sense, are a widespread genetic feature most commonly found in
eukaryotes. In most, if not all, species possessing them, they protect the terminal regions of
chromosomal DNA from progressive degradation and ensure the integrity of linear
chromosomes by preventing DNA repair systems from mistaking the very ends of the DNA
strand for a double strand break.

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Nucleolus: In the nucleus, there is one or two condensed area, which is called nucleolus.
The nucleolus is usually visible as a dark, round spot in the nucleus. The nucleolus is the
site of ribosomal RNA synthesis and ribosome assembly, which is observed only during
interphase because it dissipates during cell division. Once assembled, ribosomes are
transported to the cell cytoplasm, where they serve as the sites for protein synthesis.
The nucleolus is made up of proteins and RNA. It is the site of rRNA (ribosomal ribonucleic
acid) synthesis
There are Four distinct areas of the nucleolus:
o Fibrillar center(FC): containing rRNA chromatin ，which composes the nucleolus
center.
o Dense fibrillar component(DFC): containing nucleolar RNAs being transcribed;
o Granular component(GC): in which maturing ribosomal subunits are assembled;
o The nucleolar matrix: a network of fibers that participates in nucleolar
organization.
Therefore, to summarise its functions, the nucleolus is the site of ribosomal RNA synthesis
and ribosome assembly. As rDNA being transcripted into rRNA, Ribosomal proteins are imported
from the cytoplasm and conjugated with ribosomal RNA to form the ribosomal subunits which
then pass through the nuclear pore complex into the cytoplasm before being assembled into
fully active ribosomes.

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Euchromatin and Heterochromatin: In a nucleus, the chromatin is not always the same;
some area is condensed, while most parts of chromatin is relaxed. The status of chromatin
determines its transcription activity.
Depending on its transcriptional activity, chromatin may be condensed as
heterochromatin or extended as euchromatin.
Heterochromatin are a tightly packed form of DNA in the nucleus. They are so compactly
organized that they are inaccessible to the protein involved in gene expression. Even the
crossing over cannot take place. It is visible under light microscope, which located mostly at the
periphery of the nucleus but also forms irregular clumps throughout the nucleus. It is
condensed inactive form which means it is not active in RNA synthesis.
Heterochromatin can be divided into two types:
o Facultative Heterochromatin: In some types of cells or in certain
developmental phases, some euchromatin becomes condensed, losing their
transcriptional function and turns into heterochromatin. It is a way to close gene
activity. For example: X Chromosome
o Constitutive Heterochromatin: Except for replication, this type of
heterochromatin is always in a condensed inactive form during the whole cell cycle.
Euchromatin is defined as the area of the chromosome which is rich in gene concentration
and actively participates in the transcription process. It is scattered throughout the nucleus and
not visible under light microscope, which is the active form of chromatin where the genetic
material of the DNA molecules is being transcribed into RNA.
These are loosely packed form of chromatin. These are active during transcription. It
contains 90% of the entire human genome. Housekeeping genes are one of the forms of
euchromatin.

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The following table describe the important differences between Euchromatin and
Heterochromatin:
Sex Chromatin is the number of chromosomes in somatic cells is specific for the species
and is called the Genome, the total genetic makeup. In humans the genome is made up of 46
chromosomes representing 23 homologous pairs of chromosomes. Of the 23 pairs 22 are called
autosomes, whereas the remaining pair that determines gender is the sex chromosomes.
Barr Body: microscopic study of interphase nuclei of cells from female displays a very
tightly coiled clump of chromatin, the sex chromatin (Barr Body), the inactive counterpart of the
two X Chromosomes. It is a facultative heterochromatin, which is one of the two X
chromosomes becoming condensed randomly in female cells.

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Nuclear matrix (nuclear skeleton): is the network of fibers in the nucleus as cytoskeleton
is to the cell although nuclear matrix is more dynamic. Thus, similar to cytoskeleton, the nuclear
matrix largely provides mechanical support.
The nuclear matrix consists of the insoluble structural framework of the nucleus, which
includes the pore complex, an internal ribonucleoprotein network, and residual nucleolus.
Beside the structures mentioned above, it also includes the nuclear lamina, which is the
dense fibrous network juxtaposes the nuclear envelope and continuous outside to
the endoplasmic reticulum.
There are two major components of the nuclear lamina:
o Intermediate filaments, particularly lamins
o Nuclear lamin-associated membrane proteins.
The nuclear matrix is suggested to generally have the following components: the residual
elements of the nuclear envelope, i.e. the pore complex-lamina, the residual nucleoli, and a
granular and fibrous matrix structure extending throughout the nucleus.
The pore complex-lamina is the residual framework that is left when the nuclear envelope
is treated with buffers (such as those containing non-ionic detergents, nucleases, etc.). As for
the residual nucleoli, it pertains to the residual structure (nucleolar matrix) following extraction
procedures. Different proteins are apparently associated with the nuclear matrix. Proteins
referred to as SARs (Scaffold Associated Regions) are said to play a role in chromatin
organization. They provide attachment sites for the DNA loops during the interphase. There were
also reports of the existence of actin in the nucleus. The actin in the nucleus is implicated in RNA
transcription and metabolism.

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The nuclear matrix provides structural support to the nucleus, maintaining the overall
shape and size of the nucleus. Since it includes the nuclear lamina, the nuclear matrix is, thus,
associated with the organizing of the genetic information since the nuclear lamina, in particular,
is involved in DNA replication and cell division. The nuclear lamina also aids in the chromatin
organization as well as in anchoring the nuclear pore complexes in the nuclear envelope. The
association of the matrix with proteins such as SARs led to its implication in different nuclear
events, such as chromosomal organization, gene localization, and regulation of DNA
transcription and replication.

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1-How can the nucleolus form? What are the roles of nucleolus?
The nucleolus is the most prominent structure in a cell nucleus. It’s a nuclear compartment
which contains highly dense chromatin and number of associated proteins. It is the site of
ribosomal RNA (rRNA) transcription, pre-rRNA processing and ribosome subunit assembly. All
of these material passes through the nuclear pores to reach the cytoplasm. In the cytoplasm,
the ribosomes and the tRNA will conjugate in order to synthetize proteins. The nucleolus is a
dynamic structure that assembles around the clusters of rRNA gene repeats during late
telophase, persists throughout interphase and then disassembles as cells enter mitosis.
During interphase, several nucleoli may join together to form a larger one. In general, cells
having intense protein synthesis show larger nucleoli. It is also larger in large cells and in
growing cells. However, in some cells, like sperm, the nucleolus is not visible. The nucleolus
disappears during mitosis, allowing chromatin to be packaged into chromosomes. Although the
nucleolus is not always visible, and disappears in some cell cycle phases, a cell without
nucleolus is regarded as dead or is dying.
The nucleolus disappears during the mitotic prophase, allowing the reorganization of
chromatin to make up the chromosomes. Both, nucleolar chromatin and proteins are distributed
and packaged in different chromosomes. During telophase, nucleolar chromatin
decondensates and gather nucleolar proteins to form new nucleoli. For a nucleolus to be
formed, besides gathering chromatin and proteins, nucleolar activity must be initiated:
transcription and splicing of pre-45S ribosomal RNA, and ribosomal subunits assembly.

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2- Is it passive or active transport via nuclear pore complex? Why?
The Nuclear Pore Complex provides two types of nucleocytoplasmic transport: passive
diffusion of small molecules and active chaperon-mediated translocation of large molecules.
Some small molecules such as sugars, amino acids, nucleotide, nucleoside can be
transported through free diffusion. Large molecules or complex via active transportation.
For example, the karyophilic proteins.
karyophilic proteins are synthesized in cytosol by free ribosomes, will be transported into
nucleus, which are called karyophilic proteins. these proteins include histones, DNA
polymerase, RNA polymerase et al.
Nucleoplasmin is a karyophilic protein, associates H 2 A H, 2 B and assists nucleosome
assembly. karyophilic protein enters nucleus needs a special sequence, namely, nuclear
localization sequences (NLS) or nuclear localization signal (NLS, usually, contains 4-8 amino
acid residue, including Lys, Arg, Pro. the protein with NLS will associate with its receptor
(importin). the protein enters the nucleus and NLS will not be cleave off.

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3- Describe the structures from nucleosome.
A nucleosome is the basic repeating subunit of chromatin packaged inside the cell’s
nucleus. In humans, about six feet of DNA must be packaged into a nucleus with a diameter less
than a human hair, and nucleosomes play a key role in that process. A single nucleosome
consists of about 150 base pairs of DNA sequence wrapped (one and ¾ turns) around a core of
histone proteins. In forming a chromosome, the nucleosomes repeatedly fold in on themselves
to tighten and condense the packaged DNA. The spacing between each nucleosome is about
200 base pairs.
The nucleosomes are structural building blocks of the packing of DNA within a
chromosome. The packing problem of how to fit a very, very long stretch of DNA, which is about
a yard of DNA, inside a very small cell, which is about a hundredth of a millimeter in diameter,
has fascinated scientists for a long time. And it turns out how the cell does this--now--
remember that each cell in the body has this problem--is that it coils and super coils the DNA in
a multitude of complex ways. The fundamental building block of that coiling are nucleosomes,
which are blocks of essentially little spheres of histone proteins around which the DNA is
wrapped, and they look literally like beads on a string, except the beads have the DNA wrapped
around them instead of having the DNA go through them, as in the case of a bead on a string.
In more detail, we can say that each nucleosome is made up of an octamer of proteins,
duplicates of each of four types of histones (H2A, H2B,H3 and H4). Besides ,there is a H1 protein
to fix the structure.

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4- Under Electron microscope, what can we observe in the nucleolus?
The nucleolus is usually visible as a dark, round spot in the nucleus. The Picture above
represents the image that can be seeing by observe a nucleolus under electron microscope.
From here, we can notice three distinct nucleolar regions that can be distinguished
morphologically. The bulk of the nucleolus consists of a granular component (gc), which
contains ribosomal subunits in various stages of assembly.
Embedded within the granular regions are fibrillar centers (fc) that are surrounded by a
denser fibrillar component (dfc).
The inset shows a schematic drawing of these parts of the nucleolus. According to one
model, the fc contains the DNA that codes for ribosomal RNA, and the dfc contains the nascent
pre-rRNA transcripts and associated proteins. According to this model, transcription of the pre-
rRNA precursor takes place at the border between the fc and dfc.
Summarizing, under electron microscope we can observe:
o Fibrillar center (FC): containing rRNA chromatin ， which composes the
nucleolus center
o Dense fibrillar component (DFC): containing nucleolar RNAs being transcribed
o Granular component (GC): in which maturing ribosomal subunits are assembled
o The nucleolar matrix: a network of fibers that participates in nucleolar
organization

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Conclusion
The cell is the unit of live and for a doctor is very important to have knowledge about cell
functions, structures and behaviours to understand better the physiological and pathological
mechanism that life is made.
With this homework I could reach a good knowledge level about cell biology, its story, cell
components, functions, even the functions of each organelle.

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Grade: 2021

Cell Biology Summary by Joana Costa Campos

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MBBS COURSE

Subject: Cell Biology

Student: Joana Costa Campos

• Chapter 1 – Introduction to Cell Biology

• Chapter 2 – Cell Membrane and Cross Membrane Transportation

• Chapter 3 – Endomembrane System

Student: Joana Costa Campos

Student: Joana Costa Campos

• Chapter 6 – Cell Nucleus

Student: Joana Costa Campos

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Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

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5- Why do you think that cell is life?

Student: Joana Costa Campos

3- Proteoglycan complex 15- Golgi Complex

4- Fibronectin 16- Vacuole

5- Laminin 17- Cell

6- Integrin 18- Microfilaments

7- Actin filaments 19- Secretory vesicle

8- Peroxisome 20- Plasmatic membrane

9- Mitochondria 21- Smooth Endoplasmic Reticulum

10- Nucleus (the structure), Nuclear 22- Microtubules

Envelope (the purple layer) 23- Centrioles

11- Nuclear Pore 24- Chromatin

12- Rough Endoplasmic Reticulum (the 25- Nucleolus

structure), Ribosome (green spots) 26- Extracellular Matrix

4- Fibronectin: is an extracellular matrix (ECM) component that, through binding integrin

6- Integrin: function as transmembrane linkers (or “integrators”), mediating the

Student: Joana Costa Campos

9- Mitochondria: are membrane-bound cell organelles (mitochondrion, singular)

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Student: Joana Costa Campos

21- Smooth Endoplasmic Reticulum: functions in many metabolic processes.

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Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Facilitated diffusion: It is the process of spontaneous passive transport (as opposed to

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Student: Joana Costa Campos

Receptor mediated endocytosis: it is a process by which cells absorb metabolites,

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Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos

Student: Joana Costa Campos