SOẠN MIDTERM

Lecture 3: The Cell 1

1) Describe the structure and function of the components of the endomembrane system.
2) Briefly explain the role of mitochondria, chloroplasts, and peroxisomes.
3) Describe the functions of the cytoskeleton.
4) Compare the structure and functions of microtubules, microfilaments, and intermediate
filaments.
5) Describe four different intercellular junctions
Lecture 4: The Cell 2
1) Name the three stages of cellular respiration; for each, state the region of the eukaryotic cell
where it occurs and the products that result
2) Distinguish between fermentation and anaerobic respiration. Distinguish between obligate and
facultative anaerobes
3) Describe the similarities and differences between oxidative phosphorylation in mitochondria
and photophosphorylation in chloroplasts
4) Describe two important photosynthetic adaptations that minimize photorespiration.
5) Describe the role of apoptosis in normal development and degenerative disease in vertebrate
Lecture 5: Genetic 1
1) List the phases of the cell cycle; describe the sequence of events during each phase.
2) Distinguish between the following terms: somatic cell and gamete; autosome and sex
chromosomes; haploid and diploid.
3) Describe the events that characterize each phase of meiosis and three events that occur
during meiosis I but not mitosis.
4) Name and explain the three events that contribute to genetic variation in sexually
reproducing organisms
5) Explain how carrier recognition, fetal testing, and newborn screening can be used in genetic
screening and counseling.
Lecture 6: Genetic 2
1) Outline the process of DNA replication: what is required?
2) Describe replicating at the ends of eukaryotic chromosomal DNA. How telomerase
enzymes lengthen telomeres?
3) What is the difference between transcription and translation? Describe the events of
initiation, elongation, and termination of transcription and translation.
4) What is epigenetic Inheritance? Explain how histone acetylation affect chromatin structure
and the regulation of transcription.
5) Why is regulation of gene expression important? How can, for example, a cell in the retina
of your eye makes different proteins from a cell in your liver when both cells have exactly the
same DNA

SOLUTION
Lecture 3: The Cell 1
1. Describe the structure and function of the components of the endomembrane system.
#The endomembrane system include:
– Nuclear envelope – Lysosomes
– Endoplasmic reticulum – Vacuoles
– Golgi apparatus – Plasma membrane.
*Nuclear envelope:
- Structure:
+ The nuclear envelope is made up of two membranes: an inner and an outer membrane.
+ The nuclear envelope is a two-membrane structure. Both membranes are lipid bilayers
with proteins attached to them.
+ Four phospholipid series are also included.
- Function:
+ Nuclear pores are microscopic gaps in the nuclear envelope that have been identified. The
pores allow the content of the nucleus to flow in and out. It also serves as a link between the
outside and interior membranes.
+ During the interphase phase of cell division, the surface area of the nuclear envelope
expands and doubles the nuclear pores.
+ The nucleus is protected by a double membrane with many pores that assist limit the
crossing of macromolecules like proteins and RNA while allowing free passage of water,
ions, ATP, and tiny molecules. The cell's information flow is controlled by the membrane,
which is carried by macromolecules.

*Endoplasmic reticulum:
- Structure:
+ Cisternae are a network of tubules and sacs made up of membranous tubules.
+ Internal/cisternal space separated from cytosol in the ER lumen cavity.
+ Smooth and Rough ER are included.
- Function:
+ Its primary function is to support the cell's structure.
 + It also acts as a conduit for material (protein and lipids) to be transported from one region
of the cell to another.
+ Proteins and lipids are generated in the rough endoplasmic reticulum due to the presence of
the ribosome, which aids in the regeneration of cell membranes. Membrane biogenesis is the
name given to this process. (The term "biogenesis" refers to the production of a material by
living matter.)

* Golgi apparatus:
- Structure:
+ There appear to be a lot of flattened pouches near together. Cisternae is the name for this
flat-tube/pouch-like structure.
+ The Golgi apparatus cisternae are separated into three compartments: Cis face, Medial
(middle section of the cisternae), and Trans face.
+ The two sections The Cis Golgi network and the Trans Golgi network are the cis and trans
face's outer pouches, respectively. Both the trans Golgi network and the cis Golgi network play
key roles in the Golgi Apparatus.
- Function:
+ The secretory function of the Golgi apparatus is its primary function.
+ It creates secretory vesicles, which contain cellular secretions such as enzymes, proteins,
and cellulose, among other things.
+ The Golgi apparatus is also involved in cell wall, plasma membrane, and lysosome
production.

* Lysosomes:
- Structure:
+ Lysosomes are small, spherical sacs that are uniformly dispersed throughout the
cytoplasm.
+ A lysosome is a tiny vesicle containing strong enzymes that is surrounded by a single
membrane.
- Funtion:
+ Lysosomes, often known as digestive sacks, serve as an intercellular digestive system.
+ Lysosomes also degrade worn-out and poorly functioning cellular organelles to make room
for their replacement.

*Vacuoles:
- Structure:
+ The vacuole is a water-filled organelle with a membrane that holds inorganic ions and
organic molecules. The tonoplast, or vacuolar membrane, contains a variety of transporters. The
import and export of chemicals through the vacuolar membrane are controlled by these
transporters, which act as pumps or valves.
 Proton generator.
 Aquaporins are a type of protein that can be found in water.
 Transporters of ions.
- Function:
+ They keep the turgor pressure inside the cell constant by absorbing excess water and
dispersing it out.
+ Because of its acidic nature and the presence of digestive enzymes, the vacuole plays an
essential role in the digestion of a variety of substances.
+ Proteins, amino acids, lipids, and carbohydrates are stored in vacuoles in seeds and fruits.
Plants use these stored chemicals during the germination or growth of a new plant.
+ It also helps plant cells defend themselves by accumulating heavy metals like cadmium and
arsenic.
+ Autophagy is a process in which cellular components are digested and recycled, and
vacuoles are involved.

* Plasma membrane:
- Structure:
+ Lipids (phospholipids and cholesterol), proteins, and carbohydrates make up this
component.
- Function:
+ The plasma membrane's principal role is to protect the cell from its surroundings.
+ The plasma membrane also helps group cells together to form tissues by anchoring the
cytoskeleton to give the cell shape and adhering to the extracellular matrix and neighboring cells.
+ The cell potential is also maintained by the membrane.
+ To build plant and animal tissues, the cell membrane interacts with the cell membranes of
neighbouring cells.
+ Proteins and lipids make up the majority of the cell membrane. While lipids aid in the
flexibility of membranes, proteins monitor and regulate the chemical climate of the cell and aid
in the movement of molecules over the membrane.
+ Because the lipid bilayer is semi-permeable, only some chemicals can diffuse through it.

2. Briefly explain the role of mitochondria, chloroplasts, and peroxisomes.

+ Mitochondria create the energy that the cell requires to survive and function. Mitochondria
use a series of chemical events to convert glucose into adenosine triphosphate (ATP), an
energy molecule that is used to power a variety of cellular operations. Mitochondria store
 calcium for cell signaling, create heat, and are important in cell development and death in
addition to creating energy.
+ Plants and photosynthetic protists require chloroplasts for survival and growth. They're in
charge of photosynthesis, which is the process of converting light energy into sugar and other
organic compounds that plants and algae utilize as food. They also create amino acids and
lipid components that are required for the development of chloroplast membranes.
+ The main functions of peroxisomes are lipid metabolism and reactive oxygen species
processing. Peroxisomes also have the following functions:
 They are involved in a variety of oxidative reactions.
 They are involved in lipid metabolism as well as D-amino acid, polyamine, and bile acid
catabolism.
 Various enzymes, such as peroxidase and catalase, convert reactive oxygen species such
as peroxides generated during the process to water.
 Peroxisomes aid photosynthesis and seed germination in plants. They keep energy from
being lost during photosynthesis and carbon fixation.

3. Describe the functions of the cytoskeleton.

- The cytoskeleton serves a variety of purposes. It first determines the form of the cell. This
is particularly crucial in cells without cell walls, such as animal cells, which do not have a
thick outer layer to give them structure. It can also cause a cell to migrate. Microfilaments
and microtubules can disintegrate, reassemble, and contract, allowing cells to crawl and
migrate. Microtubules also assist cells move by forming structures such as cilia and flagella.
- The cytoskeleton not only structures the cell and keeps its organelles in place, but it also
helps organelles move around the cell. When a cell engulfs a molecule, for example,
microfilaments pull the vesicle carrying the ingested particles into the cell. Similarly, during cell
division, the cytoskeleton aids in the movement of chromosomes.
- The cytoskeleton can be compared to a building's frame. The cytoskeleton is the "frame"
of the cell, keeping things in place, providing support, and giving the cell a specific shape, much
like the frame of a building.

4. Compare the structure and functions of microtubules, microfilaments, and intermediate

filaments.

Microtubules Microfilaments Intermediate

Filament
Structure - Hollow tube, cylindrical made - Solid, made up of 2 - Hollow with 4-5
up of 13 protofilaments. intertwined strands of protofilaments coiled
- Largest (about 23nm). actin. into cables.
- Thinnest filaments - With fibers having a
(about 7 nanometers diameter near the
 thick). middle of the
spectrum.
Main - Cell reshaping. -In addition to actin, the - Serve primarily as a
functions - Directing organelle movement. protein myosin plays a scaffolding support
role in cellular structure and are
- Chromosome separation during
movement. involved in the
cell division.
formation of cell-to-
cell interactions.

5. Describe four different intercellular junctions:

- Plasmodesmata (in plant cell):
+ Plant cells, which are surrounded by cell walls, are unable to communicate with one
another via large stretches of plasma membrane, as animal cells can. They do, however, have
plasmodesmata (singular, plasmodesma), which are specialized junctions where a hole is
punched in the cell wall to allow direct cytoplasmic exchange between two cells.
+ The plasma membrane that lines the plasmodesmata is continuous with the membranes
of the two cells. A thread of cytoplasm runs through each plasmodesma, containing an even
thinner thread of endoplasmic reticulum.
+ Passive diffusion allows molecules below a particular size (the size exclusion limit) to
travel freely through the plasmodesmal channel. The size exclusion limit varies between plants
and even within a plant's cell types. Although the process is poorly understood, plasmodesmata
may selectively dilate to allow the passage of particular big molecules, such as proteins.

- Gap functions:
+ Gap junctions in animal cells function similarly to plasmodesmata in plant cells: they
are channels between adjoining cells that allow ions, water, and other substances to pass through.
cubed. Gap junctions and plasmodesmata, on the other hand, are structurally distinct.
+ Gap junctions arise in vertebrates when a group of six membrane proteins called
connexins join together to form a long, donut-like structure called a connexon. A channel formed
between adjacent animal cells when the pores, or "doughnut holes," of connexons align. (Gap
junctions are also formed in invertebrates, but they employ a different group of proteins called
innexins).
+ Gap junctions are very crucial in cardiac muscle because the electrical signal to
contract spreads quickly between heart muscle cells when ions travel through them, allowing the
cells to contract simultaneously.

- Tight junctions:
 + Not all cell junctions result in cytoplasmic connections. Tight junctions, on the other
hand, provide a watertight closure between two adjacent animal cells.
+ At the point of a tight junction, multiple discrete groups of tight junction proteins called
claudins hold cells tightly against each other, each of which connects with a partner group on the
opposite cell membrane. The groups are separated into strands that form a branching network,
with more strands resulting in a more secure closure.
+ Tight connections prevent liquid from leaking between cells, allowing a layer of cells
(such as those lining an organ) to act as an impenetrable barrier. The bladder's epithelial cells, for
example, have tight connections that prevent urine from seeping into the extracellular area.

- Desmosomes:
+ Desmosomes, which behave like spot welds between adjacent epithelial cells, may be
seen in animal cells. A desmosome is a protein-protein combination. Some of these proteins span
the membrane, while others serve as anchors for the cell's junction.
+ Cadherins, which are specialized adhesion proteins, are located on both cell membranes
and interact in the gap between them to hold the membranes together. The cadherins adhere to
the cytoplasmic plaque (red in the figure at right), which connects to the intermediate filaments
and helps anchor the junction inside the cell.
+ Desmosomes bind nearby cells together, ensuring that cells in stretchy organs and
tissues like skin and heart muscle stay connected in a continuous sheet.

Lecture 4: The Cell 2

1) Name the three stages of cellular respiration; for each, state the region of the eukaryotic cell
where it occurs and the products that result.
- Cellular respiration is the breakdown and release of energy from food molecules such as
glucose by individual cells. The process is comparable to burning, however it does not produce
the same amount of light or heat as a campfire. This is due to the fact that cellular respiration
releases glucose's energy in modest increments. It converts the released energy into ATP
molecules, which are energy-carrying molecules that let cells power metabolic operations. Many
chemical processes occur during cellular respiration, but they can all be summarized using this
chemical equation:
C6H12O6+6O2⟶6CO2+6H2O+Energy
- When the energy released is chemical energy in the form of ATP (vs. thermal energy as heat).
The equation above demonstrates how glucose (C6H12O6) and oxygen (O2) combine to produce
carbon dioxide (CO2) and water (H2O) while also releasing energy. It is an aerobic process since
oxygen is necessary for cellular respiration.
- All living creatures' cells, including autotrophs and heterotrophs, engage in cellular respiration.
They all catabolize glucose to produce ATP. Glycolysis, pyruvate transformation, the Krebs
cycle (also known as the citric acid cycle), and oxidative phosphorylation are the three primary
phases of cellular respiration, with an intermediate stage.

Figure 1: The phases of cellular respiration are depicted below. Glycolysis is the

 A glucose molecule with six carbon atoms is broken into two three-carbon molecules in this
first stage. Pyruvate is the name for the three-carbon molecule. Acetyl CoA is formed when
pyruvate is oxidized. These two phases take place in the cell's cytoplasm. Acetyl CoA enters the
matrix of mitochondria, where it is completely oxidized into CO2 via the Krebs cycle. Finally,
during the oxidative phosphorylation process, the electrons taken from food go down the electron
transport chain in the mitochondrion's inner membrane. The electrons lose energy as they
proceed down the ETC and eventually to oxygen. This energy is used to phosphorylate AMP,
which results in the production of ATP.

- Three stages of cellular respiration:

*First stages: glycolysis
+ The first stage of cellular respiration is glycolysis. It takes place in the cell's cytoplasm.
"Glucose splitting" is the definition of glycolysis. This is precisely what occurs at this point.
Enzymes break down a molecule of glucose into two smaller pyruvate molecules. This activity,
which takes place in the cytosol of the cytoplasm, produces ATP.
+ The term "glycolysis" refers to the process of breaking glucose, which is exactly what
happens at this stage. Enzymes break down a molecule of glucose into two pyruvate molecules.
Glyceraldehyde 3-phosphate is formed from glucose (a molecule containing 3 carbons and a
phosphate group). This procedure necessitates the usage of two ATP molecules. The
glyceraldehyde 3-phosphates are then transformed to pyruvate (a 3-carbon molecule). This yields
two ATP and two NADH.
+ At the onset of glycolysis, energy is required to break the glucose molecule into two
pyruvate molecules. The second step of cellular respiration is reached by these two molecules.
Two molecules of ATP give the energy required to divide glucose. Energy is released during
glycolysis, and this energy is needed to generate four molecules of ATP. As a result, during
glycolysis, there is a net gain of two ATP molecules. Through a process known as reduction,
high-energy electrons are also transferred to energy-carrying molecules known as electron
carriers. NAD+ is the electron carrier in glycolysis. Two molecules of NADH are formed when
electrons are transferred to two molecules of NAD+. In stage III of cellular respiration, the
energy held in NADH is utilized to produce additional ATP. The following is what is created at
the end of glycolysis:
 2 NADH molecules.
 2 net ATP molecules.

*Second stages: Citric Acid Cycle:

+ It takes place in the matrix of the mitochondrion of eukaryotes. When acetyl-CoA interacts
with OAA, a four-carbon molecule, the Citric Acid Cycle begins. Citric acid, which has six
carbon atoms, is the result of this process. The Krebs cycle is sometimes known as the citric acid
cycle because of this. Citric acid undergoes a sequence of reactions that release energy when it is
formed. This energy is stored in ATP and electron carriers molecules. NAD+ and FAD are the
two forms of energy-carrying electron carriers in the Krebs cycle. During the Kreb Cycle,
electrons are transferred to FAD, resulting in the formation of a molecule of FADH2. As a
byproduct of these processes, carbon dioxide is produced. The Krebs cycle's final stage
regenerates OAA, the molecule that started it all. This molecule is required for the cycle's next
turn. Because glycolysis breaks glucose into two pyruvate molecules, two turns are required.
+ The original glucose molecule has been totally broken down after the second round through
the Citric Acid Cycle. Carbon dioxide is formed when all six of its carbon atoms mix with
oxygen. A total of 16 energy-carrier molecules have been used to store the energy from their
chemical bonds. These are the molecules:
 2 ATP  2 FADH2
 8 NADH  6 CO2 : 2 CO2

*Final stages: Oxidative phosphorylation:

 + Occurs within the mitochondrial inner membrane. The ultimate stage of aerobic cellular
respiration is oxidative phosphorylation. Electron transport chain and chemiosmosis are the two
substages of oxidative phosphorylation. Energy from NADH and FADH2, which are produced
during the preceding phases of cellular respiration, is used to build ATP in these steps.
+ In this stage, the other energy-storing molecules from glycolysis and the Krebs cycle are
used to make a lot more ATP molecules. In reality, up to 34 molecules of ATP are created during
this step. Because electron transport necessitates the presence of oxygen, this stage is also
aerobic. The oxygen reacts with the hydrogen in the energy-storing molecules to become
hydrogen. Another waste product is water as a result of this process.

2) Distinguish between fermentation and anaerobic respiration. Distinguish between obligate

and facultative anaerobes.
* Difference between:
Fermentation Anaerobic respiration
1 Induced by low oxygen concentrations. O2 is not required in the process.
2 Refers to any group of chemical reactions Refers to a type of cellular respiration
induced by microorganisms to convert that occurs in the absence of oxygen.
sugars into carbon dioxide and ethanol.
3 An extracellular process. An intracellular process.
4 Glycolysis does not follow citric acid Glycolysis follows citric acid cycle and
cycle and electron transport chain. electron transport chain.
5 Total ATP production is 4. Total ATP production is 38.
6 Enzymes extracted from the fermenting Enzymes extracted from the cells
cells can process the reaction in an cannot process the anaerobic
extracellular medium. respiration in an extracellular medium.

* Difference between obligate and facultative anaerobes:

Obligate anaerobe Facultative anaerobe
Definition - In the lack of oxygen, an organism lives - An organism that can grow and
in an anaerobic environment. survive in both aerobic and
anaerobic conditions.
Presence of - Is killed. - Is not killed.
oxygen
Respiration - Anaerobic respiration or fermentation. - Aerobic respiration, anaerobic
respiration and fermentation.
 In a culture - At the bottom. - Mostly at the top, but it pervades
tube the culture medium.
Examples - Actinomyces, Bacteroides, Clostridium, - Staphylococcus spp,
Fusobacterium, Peptostreptococcus, Streptococcus spp, Escherichia coli,
Porphyromonas, Prevotella, Salmonella, Listeria,
Propionibacterium, and Veillonella. Corynebacterium and Shewanella
oneidensis.

3) Describe the similarities and differences between oxidative phosphorylation in mitochondria

and photophosphorylation in chloroplasts.
*Similarities:
- Photophosphorylation and oxidative phosphorylation (oxphos) are two methods that cells use to
produce ATP.
- Electrons are transmitted through a sequence of membrane proteins in both circumstances.
- Electrons provide energy for protons (H+) to be pumped to one side of the membrane.
- Protons go back through an enzyme (ATP-synthase) that converts them to ATP.

*Differences:
- When it occurs:
+ Oxphos is produced during the process of cellular respiration.
+ Photophosphorylation is a process that occurs during photosynthesis.
- Where it's found:
+ Oxphos is found inside mitochondria.
+ Photophosphorylation takes place within thylakoids (in chloroplasts)
- Source of energy:
+ Oxphos gets its energy from glucose.
+ Sunlight as a source of energy for photophosphorylation
- Acceptor of electrons:
+ The ultimate electron acceptor in oxphos is molecular oxygen.
+ NADP+ is the ultimate electron acceptor in photophosphorylation.

4) Describe two important photosynthetic adaptations that minimize photorespiration.

- The two most important photosynthetic adaptations that reduce photorespiration are C4 and
CAM plants. CO2 is initially added to a three-carbon molecule called PEP by an enzyme called
PEP carboxylase, which has a high affinity for CO2. The four-carbon chemical generated in the
leaf's mesophyll cells is delivered to bundle-sheath cells, which are tightly packed around the
veins. Rubisco breaks down the chemical to release CO2, which he then fixes into the Calvin
cycle.
- In CAM plants break down the molecules to release CO2 during daylight hours, allowing the
Calvin cycle to continue. Succulent plants' stomata close during the day to minimize water loss,
but open at night to absorb CO2 and convert it into a range of organic acids. Carbon fixation and
the Calvin cycle are not structurally separated in the CAM pathway.

Figure 2: C4 pathway (Robert Bear et al). Figure 3: CAM pathway (Robert Bear et al).

Explain the figures:

- In C4 pathway: CO2 formed an organic acid, which attracted vascular annulus cells. =>CO2
will be released, allowing them to take part in the Calvin cycle.
- In CAM pathway: CO2 fixation takes place only at night, and CO2 is released from the "store"
throughout the day and participates in the Calvin cycle.

5) Describe the role of apoptosis in normal development and degenerative disease in vertebrate.
*About the apoptosis:
 Figure 4: Apoptosis (Dr. Tobias, 2020 November 5).

- Apoptosis, sometimes known as "cellular suicide," is a type of programmed cell death. It differs
from necrosis, which occurs when cells die as a result of an injury.
- Apoptosis is a controlled process in which the contents of a cell are packaged into little
membrane packets for collection by immune cells.
- Apoptosis is a cell death process that removes cells during development, eliminates potentially
malignant and virus-infected cells, and keeps the body in balance.

*Apoptosis' role in proper development:

+ Maintain tissue homeostasis and multicellular organism function
+ Replace old cells with new ones.
+ Shape an organ by removing cells that aren't needed any longer.
+ Contributing to the formation process by generating new ideas
+ Apoptotic cells emit mitotic signals, which trigger compensatory growth.
*The role of apoptosis in vertebrate degenerative disease:
+ There is a natural imbalance between the synthesis and breakdown of articular cartilage
components.
+ Eventually, cartilage cells die owing to apoptosis (cell death) or the body's natural
aging process.
+ Chondrocytes die as a result of cell death (apoptosis). The bone is revealed when
cartilage is removed, and it becomes fibrous and hard.

Reference:
1)
Boundless.com CC BY-SA, ‘Glycolysis’. Available at:
https://courses.lumenlearning.com/boundless-biology/chapter/glycolysis/

4)
Robert Bear, David Rintoul, OpenStax CNX, ‘Photosynthetic pathways’.Available at:
https://www.khanacademy.org/science/biology/photosynthesis-in-plants/photorespiration--c3-c4-
cam-plants/a/c3-c4-and-cam-plants-agriculture

5)
Dr. Tobias Pusterla, ‘Apoptosis – what assay should I use’, (2020, November 05). Available at:
https://www.bmglabtech.com/apoptosis-what-assay-should-i-use/

Lecture 5: Genetic 1
1) List the phases of the cell cycle; describe the sequence of events during each phase.
- The cell cycle is a sequence of events including cell growth and division that results in the
formation of two new daughter cells. On their way to cell division, cells go through a series of
carefully controlled and regulated stages of growth, DNA replication, and division that result in
the formation of two identical (clone) cells. Interphase and mitotic phase are the two primary
phases of the cell cycle (Figure 1). The cell expands and DNA is duplicated during interphase.
During the mitotic phase, the cell divides, and the replicated DNA and cytoplasmic contents are
separated.
 Figure 1: Interphase and mitotic phases make up the cell cycle. The cell develops and the nuclear
DNA is duplicated during interphase. The mitotic phase comes after the interphase. The duplicated
chromosomes are separated and distributed into daughter nuclei during the mitotic phase. In most
cases, the cytoplasm is also divided, resulting in two daughter cells (Siyavila et al).

* Interphase:
- The longest phase of the cell cycle is interphase. The cell reaches its maximal size, performs
typical cellular tasks, replicates its DNA, and prepares for cell division during this phase. The G1,
G2, and S phases are the three sections of this stage.
+ G1 phase: Because there is little change evident at the microscopic level, the initial stage
of interphase is dubbed the G1 phase (first gap). The cell, on the other hand, is very active
biochemically during the G1 stage. The cell is assembling the components of chromosomal DNA
and accompanying proteins, as well as storing enough energy to finish the task of replicating
each chromosome in the nucleus.
+ S phase: Nuclear DNA remains in a semi-condensed chromatin structure throughout
interphase. DNA replication can occur in the S phase through mechanisms that result in the
creation of identical pairs of DNA molecules (sister chromatids) that are securely connected to
the centromeric region. During the S phase, the centrosome is duplicated. The mitotic spindle,
which orchestrates the movement of chromosomes during mitosis, will be formed by the two
centrosomes. The centrosomes of animal cells are coupled with a pair of rod-like items, the
centrioles, that are at right angles to each other at the center of each animal cell. Centrioles aid in
the organization of cell division. Other eukaryotic species, such as plants and most fungi, lack
centrioles in their centrosomes.
 + G2 phase: The cell refills its energy stores and synthesizes proteins required for
chromosomal manipulation during the G2 phase. To generate resources for the mitotic phase,
several cell organelles are duplicated, and the cytoskeleton is disassembled. During G2, there
may be increased cell proliferation. Before the cell may start the first stage of mitosis, the last
preparations for the mitotic phase must be completed.
+ But not all cells follow the traditional cell cycle pattern, in which a newly created
daughter cell experiences the preparatory phases of interphase before entering the mitotic phase.
The G0 phase is when cells are not actively preparing to divide. The cell is in a quiescent
(inactive) state, which occurs when the cell cycle is completed. Some cells reach G0 for a short
time before entering G1 in response to an external signal. Other cells, such as mature heart
muscle and nerve cells, that never or seldom divide, remain in G0 indefinitely.

*Mitotic phase: Mitosis and cytokinesis are strongly connected activities in the mitotic phase (M
phase). The chromosomes in the cell nucleus separate into two identical sets in two nuclei during
mitosis. The cytoplasm, organelles, and cell membrane then separate into two cells with about
equal shares of these biological components during cytokinesis. We'll now go through what
happens during M-phase, which contains the four main phases of mitosis (prophase, metaphase,
anaphase, and telophase) as well as the fifth cytokinesis phase:
 Prophase
 Prometaphase
 Metaphase
 Anaphase
 Telophase
By late telophase, cytokinesis is well started.
- Prophase: Prophase is the first stage of
Figure 2: Prophase in Animal cell (Siyavula et al).
mitosis, when chromosomes recruit
condensin and begin a condensation process
that will last until metaphase. During
prophase, cohesin is largely eliminated from
the arms of sister chromatids in most
species, permitting the resolution of
individual sister chromatids. However,
cohesin is preserved at the centromere, the
most constrained portion of the
chromosome. As the two pairs of centrioles
travel to opposing poles and microtubules
begin to polymerize from the duplicated
centrosomes during prophase, the spindle
begins to develop.
 Figure 3: Prophase in Plant cell (Siyavula et al).

- Prometaphase: Prometaphase begins with the nuclear membrane being abruptly fragmented
into many small vesicles, which will later be divided between the future daughter cells. The
nuclear membrane must be broken down before the spindle can be assembled. The microtubules
of the growing spindle do not have access to the chromosomes until the nuclear membrane
breaks apart, because the centrosomes are positioned outside the nucleus in animal cells.
Prometaphase is a very active stage of the cell cycle. As they grow out of the centrosomes,
microtubules rapidly build and disintegrate, looking for attachment sites at chromosome
kinetochores, which are complex platelike structures that develop during prometaphase on one
face of each sister chromatid near its centromere. Microtubules emerging out of both poles of the
spindle pull and tug chromosomes in opposite directions during prometaphase, until the pole-
directed forces are finally balanced. Sister chromatids do not break apart during this tug-of-war
because the cohesin that remains at their centromeres keeps them together. Chromosomes are bi-
oriented near the conclusion of prometaphase, which means that the kinetochores on sister
chromatids are attached to opposing poles of the spindle by microtubules.
 Figure 4: Difference between Prometaphase and metaphase (Siyavula et al).

- Metaphase: During metaphase, chromosomes reach their most compressed form, when the
centromeres of all the cell's chromosomes line up at the spindle's equator. In cytogenetics,
metaphase is particularly valuable since chromosomes are most easily seen at this stage.
Furthermore, mitotic poisons like colchicine can be used to experimentally stop cells from
entering metaphase. During metaphase, video microscopy reveals that chromosomes temporarily
halt migrating. The appropriate assembly of the spindle is determined by a complicated
checkpoint mechanism, and only cells with properly assembled spindles enter anaphase.

Figure 5: Metaphase in animal cell (Siyavula et al). Figure 6: Metaphase in plant cell (Siyavula et al).
- Anaphase: The rapid separation of sister chromatids marks the transition of cells from
metaphase to anaphase. The protease separase rapidly degrades the cohesin molecules that
connect the sister chromatids, resulting in chromatid separation. During anaphase, there are two
types of movements. The kinetochore microtubules shorten and the chromosomes migrate
toward the spindle poles during the initial stage of anaphase. As the non-kinetochore
microtubules pass past each other during the second half of anaphase, the spindle poles separate.
Motor proteins that connect microtubules with opposite polarity and then "walk" toward the end
of the microtubules are hypothesized to catalyze these latter movements.

Figure 7: Anaphase in animal cell (Siyavula et al). Figure 8: Anaphase in plant cell (Siyavula et al).

- Telophase: The chromosomes reach the opposite poles during telophase, or "distance phase,"
and begin to decondense (unravel), relaxing into a chromatin shape. The mitotic spindles are
depolymerized into tubulin monomers, which are then used to put together the cytoskeletal
components for each daughter cell. Nucleosomes appear within the nuclear region, and nuclear
envelopes form surrounding the chromosomes.

Figure 9: Telophase in animal cell (Siyavula et al) Figure 10: Telophase in plant cell (Siyavula et al)

- Cytokinesis: Cytokinesis is the process through which the cytoplasm divides. Cytokinesis is the
process of the cytoplasm separating into two, not a stage of mitosis. The cell membrane of an
animal cell constricts. The cell is divided in two by this invagination or in-folding of the
cytoplasm. The cell plate divides the cytoplasm in half in a plant cell, forming a cross wall.
There are now two genetically identical daughter cells that are genetically similar to each
other and to the parent cell.

Figure 11: A ring of actin filaments forms

near the metaphase plate during
cytokinesis in animal cells. The ring
shrinks, creating a cleavage furrow that
splits the cell in half. Golgi vesicles
agglomerate near the old metaphase
plate in plant cells, generating a
phragmoplast. The vesicles of the
phragmoplast fuse to produce a cell plate
that grows from the center toward the
cell walls, and the membranes of the
vesicles fuse to form a plasma membrane
that divides the cell in half (HAW, 2017).

2) Distinguish between the following terms: somatic cell and gamete; autosome and sex
chromosomes; haploid and diploid.
*Difference between:
Somatic cell Gamete
Definition - Any type of biological cell that isn't - Gametes are mature male or
a reproductive cell is referred to as a female germ cells capable of
somatic cell. merging with additional germ
cells of the opposite sex to
generate a zygote.
Ploidy - The genome of somatic cells is - A haploid genome is found in
diploid. gametes.
Homologous - Homologous chromosomal pairs are - Individual chromosomes are
Pairs found in somatic cells. found in gametes.
Reproduction - Asexual reproduction is aided by - Sexual reproduction is aided by
somatic cells. gametes.
Male and - Both sexes have the same somatic - There are two types of gametes:
Female cells cells. male and female. Male gametes
are sperms, while female
gametes are called ova.
Production - Mitosis produces somatic cells - Meiosis a process that produces
during asexual reproduction. gametes during sexual
reproduction.
Number of - A single stem cell produces two - From a single germ cell, 4
Daughter cells identical daughter cells. daughter cells are formed.
per one division
 cycle
Differentiation - Mitosis differentiates cells into - Germ cell meiosis produces
numerous types of somatic cells, each cells that are directly utilized as
of which is specialized for a specific gametes.
role.
Formation of - Somatic cells have a role in the - The construction of structures
structures creation of body structures such as is not aided by gametes.
organs.
Found in - Somatic cells are distributed - Gametes can only be found in
throughout the body. reproductive organs.
Fusion during - During reproduction, somatic cells - During reproduction, gametes
Reproduction do not unite with other somatic cells. are fused with gametes of the
opposite sex.
Origin - Stem cells give rise to somatic cells. - Germ cells are the source of
gametes.
Mutations - Somatic cell mutations are not - Gamete mutations are passed
passed on to the progeny. As a result, on to their progeny. As a result,
they have no bearing on evolution. they contribute to the evolution
of the species.
Examples - Muscle cells, neuron cells, and blood - Sperms and ova.
cells.

*Difference between:
Autosomes Sex chromosomes
Definition - The characteristic Is determined by - Gender is determined by
autosomes are identical in both males chromosomes of the sexes.
and females. They differ in size, form, and
behavior between males and
females.
Labeling - Autosomes are assigned numbers - Are labeled with the letters
ranging from 1 to 22. XY, ZW, XO and ZO.
Availability - Autosomes make up the majority pf - Sex chromosomes make up a
chromosomes in a genome. small percentage of a genome’s
chromosomes.
Homogeneity - In human, the 22 pairs of autosomes - Female chromosomes (XX)
are homologous. are homologous
(homomorphic), whereas male
chromosomes (XY) are
 heterologous (non-
homologous).
Position of the - Because autosomes are - The centromere position
centromere homomorphic, the centromere differs between male and
position are identical. female chromosomes due to
heteromorphic sex
chromosomes. The centromere
in male and female
chromosomes is I the same
place.
Number of Genes - The number of genes on autosomes - The X chromosome has about
ranges from 200 to 2000. In humans, 300 genes, but the Y
the largest chromosome, chromosome chromosome has only a few
1, has roughly 2800 genes. genes due to its short size.
Genetic disorders - Mandelian inheritance is seen in - Sex-related diseases manifest
autosomal disorders. themselves in a variety of ways.
Inheritance that isn’t
Mendelian.

* Difference between
Haploid Diploid
Definition - A cell or creature that has paired or two - A cell or organism that
sets of chromosomes, one from each parent, contains only one copy of
is known as a diploid. each chromosome is called
haploid or monoploid.
Cell division - Mitotic cell division results in the - Meiotic cell division results
formation of these cells. in the formation of these
cells.
Number of - They have twice as many chromosomes as - They have half the number
chromosomes haploid cells because they have two sets of of chromosomes as diploid
chromosomes. cells since they have a single
set of chromosomes.
Type of cell - Diploid cells are commonly seen in the - Haploidy can be found in
somatic cells of many animals sex cells or gametes from a
variety of vertebrates.
Similarity - After mitosis, diploid cells are genetically - Due to crossing over,
with the plant identical to their parent cell. haploid cells following
cells meiosis are not genetically
identical to their parents.
 Alternation of - The sporophytic stage of the lifecycle is a - The gametophytic stage of
generation diploid stage. the lifecycle is the haploid
stage.
- In the life cycle of most bryophyte-like - In the life cycle of most
mosses, the diploid stage is less common bryophyte-like mosses, the
than the haploid stage. haploid stage predominates
over the diploid stage.
- In the life cycle of most
Pteridophyta, such as ferns,
- In the life cycle of Pteridophyta, such as the haploid stage is less
ferns, the diploid stage predominates over prominent than the diploid
the haploid stage. stage.
Type of egg - Fertilized eggs give rise to diploid - Unfertilized eggs give rise
creatures. to haploid creatures.
Number of - Human diploid cells have 46 - Human haploid cells have
chromosomes chromosomes. 23 chromosomes.
in humans
Importance - Diploid cells are necessary for organisms' - Sexual reproduction and
growth and development. genetic diversity rely on
haploid cells.
Organisms - Humans, frogs, fish, and most plants are - Male ants, bees, and wasps
examples of diploid creatures. are examples of haploid
creatures.

3) Describe the events that characterize each phase of meiosis and three events that occur
during meiosis I but not mitosis.
- Meiosis: Meiosis is an essential phase in sexual reproduction because it involves the nuclear
division of diploid cells into haploid cells. Meiosis is divided into two parts, each of which goes
through the same steps as mitosis (prophase, prometaphase, metaphase, anaphase, telophase).
* Meiosis I:
+ Prophase I: Chromosomes condense and become visible inside the nucleus during
prophase I. Homologous chromosomes migrate closer together as the nuclear sheath breaks
down. A lattice of proteins connecting homologous chromosomes originates at certain sites and
spreads to cover the whole length of the chromosomes. Synapsis is the close pairing of
homologous chromosomes. Genes on the chromatids of homologous chromosomes are aligned
with each other in synapsis. In a process known as crossing over, the synaptonemal complex
facilitates the exchange of chromosomal segments between non-sister homologous chromatids.
The initial source of genetic diversity created by meiosis is crossover events. A single crossover
event between homologous non-sister chromatids causes chromosomes to exchange DNA. The
synaptonemal complex breaks down after crossover, and the cohesin link between homologous
pairs is also broken. The pairs are only held together at the chiasmata at the end of prophase I,
and they are called tetrads because the four sister chromatids of each pair of homologous
chromosomes are now visible.
+ Prometephase I: The development of the spindle fiber apparatus, in which spindle fiber
microtubules bind to the kinetochore proteins at the centromeres, is the most important process
in prometaphase I. Centrosomes at the cell's opposite poles produce microtubules. At the
kinetochores, the microtubules migrate toward the cell's center and bind to one of the two
merged homologous chromosomes. Each tetrad is connected to microtubules from both poles at
the conclusion of prometaphase I, with one homologous chromosome facing each pole.
Furthermore, the nuclear membrane has completely degraded.
+ Metaphase I: Tetrads travel to the metaphase plate during metaphase I, with kinetochores
facing opposing poles. The homologous pairs align themselves at the equator at random. The
second process that imparts variety into gametes or spores is this occurrence. The tetrads are
arranged differently in each cell that goes through meiosis. The number of variants in a set is
determined by the number of chromosomes in the set. At the metaphase plate, there are two
options for orientation. As a result, the maximum number of alignments is 2n, where n is the
number of chromosomes per set. Given these two methods, it's exceedingly unlikely that any two
meiosis-derived haploid cells will have the identical genetic makeup.
+ Anaphase I: The microtubules pull the linked chromosomes apart during anaphase I. At
the centromere, the sister chromatids are still closely bonded together. In anaphase I, the
microtubules connected to the fused kinetochores force the homologous chromosomes apart,
breaking the chiasmata.
+ Telophase I: The split chromosomes arrive at opposite poles in telophase I. In some
organisms, during telophase I, the chromosomes decondense and nuclear envelopes form around
the chromatids.
- Cytokinesis: The physical separation of the cytoplasmic components into two daughter cells,
known as cytokinesis, occurs without the nuclei reforming. Cytokinesis divides the contents of
cells in nearly all animal species and some fungi via a cleavage furrow (constriction of the actin
ring that leads to cytoplasmic division). Golgi vesicles fusing at the metaphase plate create a cell
plate in plants during cell cytokinesis. The creation of cell walls that separate the two daughter
cells will be aided by this cell plate.
 The first meiotic division produces two haploid cells as a result. The cells are haploid because
each pair of homologous chromosomes has just one copy at each pole. As a result, only one
complete pair of chromosomes is present. Even while each homolog has just one chromosomal
set, it nonetheless has two sister chromatids.

*Meiosis II:
+ Prophase II: The chromosomes condense again after decondensing in telophase I. Nuclear
envelopes split into vesicles if they form. New spindles are produced as the centrosomes that
were replicated during interphase I migrate away from each other toward opposite poles.
 + Prometaphase II: The spindle is fully formed and the nuclear envelopes have been totally
broken down. Each sister chromatid has its own kinetochore, which connects to microtubules
from opposing poles.
+ Metaphase II: At the cell's equator, the sister chromatids are maximally condensed and
aligned.
+ Anaphase II: Kinetochore microtubules pull the sister chromatids apart and push them
toward opposite poles. The cell is elongated by non-kinetochore microtubules.
+ Telophase II: Chromosomes decondense, the nuclear membrane recovers, and the cell
divides (cytokinesis) into four haploid daughter cells.
 The sister chromatids within the two daughter cells split during meiosis II, resulting in the
formation of four additional haploid gametes.

*Three events that occur during meiosis I but not mitosis is:
- The homologous chromosomal pairs get connected and joined together with the synaptonemal
complex during meiosis I. Chiasmata form, and homologous chromosomes crossover, forming
tetrads along the metaphase plate, with kinetochore fibers from opposite spindle poles linked to
each kinetochore of a homolog in a tetrad. Only in meiosis I do all of these things happen.
- The ploidy level is lowered from two to one when the tetrad is broken apart and the
homologous chromosomes shift to opposite poles. Meiosis I is known as a decrease division
because of this. During mitosis, the ploidy level does not decrease.
- On the metaphase plate, divided kinetochores attached to kinetochore fibers from opposite
poles line up with duplicated chromosomes (just one set, as the homologous pairs have now been
separated into two different cells). The kinetochores divide during anaphase II and mitotic
anaphase, and sister chromatids, now known as chromosomes, are dragged to opposite poles. In
contrast to the daughter cells produced by meiosis, the two daughter cells of mitosis are identical.
They are distinct because each chromosome has at least one crossing. Meiosis II is not a
reduction division because, while the resultant cells have fewer copies of the genome, they still
have one set of chromosomes, just as they had at the end of meiosis I. As a result, equatorial
division is the name given to Meiosis II.

4) Name and explain the three events that contribute to genetic variation in sexually reproducing
organisms:
*The following are the three major sources of genetic variation resulting from sexual
reproduction:
 Crossing the border (in prophase I)
 Chromosomes in a random order (in metaphase I)
 Mixture of gametes from different parents at random.
- Crossing over:
+ During prophase I, the exchange of DNA segments between homologous chromosomes is
known as crossing over.
 + At locations termed chiasmata, genetic material is exchanged between non-sister
chromatids.
+ All four chromatids that make up the bivalent will be genetically distinct as a result of
this recombination.
+ Recombinants are chromosomes that contain DNA from both homologous
chromosomes.
+ Recombinant chromosomal offspring will have unique gene combinations not found in
either parent.
- Random Orientation:
+ The orientation of homologous chromosomes towards opposing poles is arbitrary when
they line up in metaphase I.
+ When bivalents separate in anaphase I, each bivalent's orientation is determined
independently, which means that different combinations of maternal and paternal chromosomes
can be inherited.
 The total number of possible combinations in gametes is 2n, where n is the number of
haploid chromosomes.
 Humans have 46 chromosomes (n = 23), allowing them to produce 8,388,608 distinct
gametes (223).
 If gamete crossover happens, the number of possible gamete pairings grows exponentially.
- Random Fertilization:
+ The creation of a diploid zygote is the consequence of the fusing of two haploid gametes.
 This zygote can then divide and differentiate into a growing embryo through
mitosis.
+ Because meiosis produces genetically separate gametes, random egg and sperm
fertilization will always produce diverse zygotes.
 After fertilization, identical twins are created by the complete division of the
zygote into two distinct cell masses.

5) Explain how carrier recognition, fetal testing, and newborn screening can be used in genetic
screening and counseling.
*Carrier recognition: Carrier screening is a term used to describe genetic testing performed on a
person who does not have any overt phenotype for a genetic condition but has one variant allele
within a gene(s) associated with a diagnosis but does not have any overt phenotype for a genetic
disorder. Every pregnant woman should be given information regarding carrier screening.
Carrier screening and counseling should preferably be done prior to pregnancy so that couples
can learn about their reproductive risk and consider the widest range of reproductive options
possible. Any or all screenings can be declined by a patient. When a person is discovered to be a
carrier for a genetic illness, his or her family members are at risk of inheriting the same mutation.
The patient should be encouraged to tell his or her family members about the risk and carrier
screening options. If a person is discovered to be a carrier for a disease, the patient's reproductive
partner should be offered testing so that they can get educated genetic counseling regarding the
possibilities for pregnancy. Hereditary counseling should be delivered if both partners are
carriers of a genetic disorder.
- Two major avenues:
+ Pedigrees: It show how a certain genetic trait has been passed down through the
generations then used to predict future.
+ Blood test and DNA probes: Unexpressed recessive genes can be detected using blood
tests and DNA probes.
- Such testing can detect Sickling, Tay-Sachs, and cystic fibrosis genes.
Figure 1: DNA probes
2D structured DNA probes
are depicted
schematically. (A) stem-
loop structured DNA
probe with ferrocene (Fe)
as signal molecule; (B)
stem-loop structured DNA
probe with enzyme-based
signal amplification. (C)
stem-loop structured DNA
probe with fluorescent
molecule for signal
production; (D) aptamer
nano-flares with
fluorescent reporters
Fluorescent, DNA (F-DNA)
sensor (Du et al.87)
 Figure 2: Pedigree Chart

- This analysis aids in the

identification of genotypes,
phenotypes, and the prediction of
how a trait will be passed down in
the future.

- It is possible to investigate the

pattern of inheritance from parents
to offspring. It also aids in the
identification of recessive and
dominant characteristics.

- In a pedigree analysis, symbols are

used to indicate males, females,
people with certain conditions,
people who have had children
together, and so on.

*Fetal testing:
- Amniocentesis: at 14-16 weeks, the amniotic fluid is removed.
+ Amniocentesis is used early in pregnancy to diagnose chromosomal and other fetal
problems such as:
+ Edwards' syndrome (Trisomy 21) .
+ Down syndrome (Trisomy 21) + Patau syndrome (Trisomy 13) (Trisomy 18).
+ Aneuploidies of the chromosomes of the male and female.
+ Neural tube defects (diseases affecting the development of the brain and spinal column)
– alpha-fetoprotein levels cause anencephaly (a baby born with an undeveloped brain and an
incomplete skull) and spina bifida/split spine (a birth condition in which the spine and
membranes surrounding the spinal cord do not close completely during early development).
+ Metabolic illnesses that are uncommon.
 Figure 3: Amniocentesis (Anindita Das, page 3)

- Chronic villus sampling (CVS): at 8-10 weeks, a little amount of tissue is suctioned from the
placenta  Know result in 24h.

Figure 4:
Chorionic Villus
Sampling

- Examination of
fetal
chromosomes,

- Performed via
ultrasound:
abdominal or
vaginal.

- High risk of
miscarriage (Y
Học Tổng Hợp,
2018)
- Ultrasound: non-invasive technique for revealing structure.

- Fetoscopy: uterine fiberscope (using in serious situation).

* Newborn screening: Every newborn gets screened for a range of diseases that aren't detected at
birth. Doctors can check for rare genetic, hormone-related, and metabolic abnormalities that can
cause major health problems with a simple blood test. Doctors can diagnose babies immediately
and begin therapy as soon as possible thanks to newborn screening.
- The following tests are included in newborn screening:
+ Metabolic disorders.
+ Hormone problems.
+ Hemoglobin problems.
+ Other problems.
- Done by: the baby's heel is pricked and a little blood sample is collected. This occurs before the
newborn leaves the hospital, usually within the first two days of his or her life. If your baby was
not born in a hospital, talk to your doctor about newborn screening. After the first 24 hours of
life, a blood sample should be collected. However, some babies are tested within the first 24
hours because moms and newborns are occasionally discharged within one day. If this occurs,
doctors advise waiting 1 to 2 weeks before taking another sample. In some states, all neonates
are subjected to two tests.
Reference:
1)
Siyavula et al, ‘Siyavula’s open Life Sciences Grade 10 textbook, chapter 3’. Available at:
https://intl.siyavula.com/read/science/grade-10-lifesciences/cell-division/03-cell-division-02

HAW, ‘Cytokinesis – Definition of Cytokinesis in Animal & Plant Cells’. Biology Dictionary, 28
Apr. 2017. Available at:
https://www.differencebetween.com/difference-between-plant-and-vs-animal-cytokinesis/

5)
L.T.T.Ha, ‘ Các phương pháp chẩn đoán thai dị tật bẩm sinh’. (2018, July 2). Available at:
https://yhoctonghop.vn/cac-phuong-phap-chan-doan-thai-di-tat-bam-sinh-yhth

Anindita Das, ‘ Amniocentesis’. Available at:

http://www.rnlkwc.ac.in/pdf/studymaterial/zoology/Sem%20VI%20Amniocentesis.pdf

Lecture 6: Genetic 2
1) Outline the process of DNA replication: what is required?
*Outline the process of DNA replication:
Step 1: Replication Fork Formation
- The double-stranded molecule must be "unzipped" into two single strands before it can be
duplicated. Adenine (A), thymine (T), cytosine (C), and guanine (G) are the four nucleotides that
form pairings between the two strands of DNA. Adenine can only bind to thymine, while
cytosine can only attach to guanine. These connections between base pairs must be broken in
order to unwind DNA. DNA helicase is the enzyme responsible for this. The replication fork is
formed when a DNA helicase breaks the hydrogen bonds between base pairs, separating the
strands into a Y shape. This location will serve as the starting point for replication.
- Both strands of DNA are directed, with a 5' and 3' end. The side group to which the DNA
backbone is connected is indicated by this notation. A phosphate (P) group is coupled to the 5'
end, whereas a hydroxyl (OH) group is attached to the 3' end. Because replication only moves in
the 5' to 3' direction, this directionality is critical. The replication fork, on the other hand, is bi-
directional; one strand is directed 3' to 5' (leading strand), while the other is orientated 5' to 3'
(following strand) (lagging strand). To account for the directional difference, the two sides are
replicated using two distinct methods.

Step 2: Primer Binding

- The leading strand is the most straightforward to duplicate. A tiny piece of RNA called a
primer attaches to the 3' end of the strand after the DNA strands have been split. The primer
always binds and serves as the replication's starting point. DNA primase is the enzyme that
creates primers.

Step 3: Elongation
- DNA polymerases are the enzymes responsible for elongation, which is the process of
producing a new strand. In bacteria and human cells, there are five main types of DNA
polymerases. Polymerase III is the principal replication enzyme in bacteria like E. coli, while
polymerase I, II, IV, and V are responsible for error checking and repair. During replication,
DNA polymerase III attaches to the strand at the primer site and begins adding new base pairs
that are complementary to the strand. Polymerases alpha, delta, and epsilon are the major
polymerases involved in DNA replication in eukaryotic cells. The newly generated strand is
continuous because replication happens in the 5' to 3' direction on the leading strand.
- Multiple primers bind to the lagging strand to start replication. The primers are barely a few
bases apart. Between the primers, DNA polymerase adds Okazaki fragments, which are little bits
of DNA. Because the freshly produced fragments are disconnected, the replication process is
discontinuous.

Step 4: Termination
- Exonuclease eliminates all RNA primers from the original strands once both the continuous and
discontinuous strands have been produced. After that, the primers are replaced with the proper
bases. Another exonuclease checks, removes, and replaces any flaws in the freshly produced
DNA. Okazaki fragments are joined together by another enzyme called DNA ligase to produce a
single strand. Because DNA polymerase can only add nucleotides in the 5′ to 3′ direction, the
ends of linear DNA pose a challenge. Telomeres are DNA sequences that are repeated at the
ends of parent strands.
- Telomeres operate as protective caps at the ends of chromosomes, preventing them from
merging with neighboring chromosomes. Telomerase is a type of DNA polymerase that
catalyzes the synthesis of telomere sequences at the ends of DNA. The parent strand and its
complementary DNA strand coil into the well-known double helix shape once completed. At the
end of replication, two DNA molecules are produced, each with one strand from the parent
molecule and one new strand.

Figure 5: Mechanism of DNA Synthesis (Dr. Maho et al, 2019 Feb 26)

*Requirement of DNA replication: To initiate and propagate DNA synthesis, four fundamental
components are required. Substrates, templates, primers, and enzymes are the four components.
- Substrates:
+ For DNA synthesis, four deoxyribonucleotide triphosphates (dNTPs) are required (the sole
difference between deoxyribonucleotides and ribonucleotides is that deoxyribonucleotides do not
have an OH group at position 2' on the ribose ring). dATP, dGTP, dTTP, and dCTP are the four
types. The deoxynucleotide monophosphate is integrated into the new DNA strand after the high
energy phosphate bond between the a and b phosphates is severed.
+ NTPs (ribonucleoside triphosphates) are also needed to start and maintain DNA synthesis.
NTPs are utilized to make RNA primers, while ATP is used as an energy source for some of the
enzymes that start and keep DNA synthesis going at the replication fork.
- Template:
+ Base pairing with the template strand of the DNA selects the nucleotide that will be
integrated into the developing DNA chain. The DNA strand that is transcribed into a
complimentary strand of DNA is referred to as the template.
- Primer:
+ DNA polymerase, the enzyme that makes DNA, can only add nucleotides to a strand or
primer of DNA or RNA that is base matched with the template.
- The following enzymes are involved in the replication of eukaryotic DNA:
+ DNA helicase - as it proceeds along the DNA, it unwinds and splits double-stranded DNA.
By breaking hydrogen bonds between nucleotide pairs in DNA, it generates the replication fork.
+ DNA primase is an RNA polymerase that produces RNA primers. Primers are small RNA
molecules that serve as templates for DNA replication to begin.
+ DNA polymerases - add nucleotides to the leading and lagging DNA strands to make new
DNA molecules.
+ Topoisomerase, also known as DNA Gyrase, unwinds and rewinds DNA strands to
prevent tangles and supercoiled DNA.
+ DNA ligase - binds DNA fragments together by establishing phosphodiester connections
between nucleotides.
+ Exonucleases - remove nucleotide bases from the end of a DNA chain.
- Other factors Required for DNA Sythesis:
+ Topoisomerase: eliminates the positive supercoils that arise when the helicase unwinds the
fork.
+ Origin-binding Protein: attaches to the origin DNA and partially denatures it while
interacting with another enzyme termed helicase.

2) Describe replicating at the ends of eukaryotic chromosomal DNA. How telomerase enzymes
lengthen telomeres?
* Replicating at the ends of eukaryotic chromosomal DNA:
- Replication in eukaryotes begins at numerous replication sources. Prokaryotes have a
mechanism that is very similar to this. To begin synthesis, a primer is required, which is then
expanded by DNA polymerase as it adds nucleotides one by one to the developing chain. The
leading strand is continually generated, whereas the lagging strand is synthesized in Okazaki
fragments, which are brief segments of DNA. The RNA primers are replaced by DNA
nucleotides, and DNA ligase joins the Okazaki fragments into one continuous strand. The ends
of chromosomes are problematic because the primer RNA at the 5' ends of the DNA cannot be
replaced with DNA, causing the chromosome to shrink. By duplicating the RNA template and
extending one strand of the chromosome, telomerase, an enzyme with an inherent RNA template,
extends the ends. Using the usual replication enzymes, DNA polymerase can then fill in the
complementary DNA strand. The ends of the chromosomes are so safeguarded.
 Figure 6: Mechanism of terminal region shortening during linear DNA replication (Zlir’a at el, 2012)
*
Telomerase enzymes lengthen telomeres:
- About of telomeres:
+ The tips of eukaryotic chromosomes include unique DNA "caps" called telomeres that
prevent gene loss as chromosomal ends wear down. Telomeres are made up of hundreds or
thousands of repeats of the same short DNA sequence, which varies by organism but in humans
and other mammals is 5'-TTAGGG-3'.
+ Because telomeres feature single-stranded overhangs that "look like" damaged DNA, they
must be shielded from a cell's DNA repair processes. The chromosome's overhang at the lagging
strand end is caused by imperfect end replication. Enzymes that break away part of the DNA
create the overhang at the leading strand end of the chromosome.
 + The single-stranded overhangs in some species (including humans) attach to
complementary repeats in surrounding double-stranded DNA, leading the telomere ends to form
protective loops. Telomere ends are also protected by proteins linked with them, which prevent
them from starting DNA repair processes.
+ The repeats that make up a telomere are slowly eaten away over many division cycles,
providing a buffer that protects the genes located within the core chromosome sections.
Telomere shortening has been linked to cell aging, and the steady loss of telomeres could explain
why cells can only divide so many times.
- About the telomerase enzyme:
+ Telomere shortening can be reversed in some cells by producing telomerase, an enzyme
that stretches chromosome telomeres. Telomerase is an RNA-dependent DNA polymerase,
which means it uses RNA as a template to create DNA.
- The way how to telomerase enzymes lengthen telomeres:
+ The enzyme attaches to a unique RNA molecule with a sequence that matches the
telomeric repeat. It uses this complementary RNA as a template to lengthen (add nucleotides to)
the overhanging strand of the telomere DNA. When the overhang is long enough, the standard
DNA replication machinery (that is, an RNA primer and DNA polymerase) can make a matching
strand, resulting in double-stranded DNA.
+ Because the primer isn't always positioned exactly at the chromosome's end and can't be
replaced with DNA, an overhang will remain. However, the telomere's overall length will be
longer.
+ Telomerase isn't found in most somatic cells (body cells), but it is found in germ cells
(cells that generate sperm and eggs) and some adult stem cells. These are cell types that must
divide frequently or, in the case of germ cells, give rise to a new organism with its telomeric
"clock" reset.
+ Telomeres are shortened in many cancer cells, and telomerase is active in these cells.
Excessive division (and consequently the growth of the cancerous tumor) could be slowed if
telomerase could be controlled by medications as part of cancer therapy.
Figure 7: The figure an illustration of how telomerase gradually lengthens telomeric DNA (Fatma Uzbas, CC BY-SA 3.0).

3) What is the difference between transcription and translation? Describe the events of
initiation, elongation, and termination of transcription and translation.
* Difference between transcription and translation:
Transcription Translation
Components - DNA, RNA polymerase core - mRNA, small and large
enzyme, σ subunit ribosomal subunits, initiation
factors, elongation factors, tRNA
 Template - DNA - mRNA
End of Product - RNA - Protein
Location - Nucleus/cytoplasm - Endoplasmic
(eukaryotes/prokaryotes) reticulum/cytoplasm
Controlling factor - RNA polymerase - Ribosomes
Action - The DNA template strand - The ribosome complex
reacts with RNA polymerase. interacts with the strand of
mRNA.

* Outline of initiation, elongation, and termination of transcription and translation:

- Transcription:
+ Overview:
 The initial stage in gene expression is transcription. The DNA sequence of a gene
gets transcribed into RNA during this process.
 The DNA double helix must unravel near the gene being transcribed before
transcription can begin. A transcription bubble is an area of opened-up DNA.
 One of the two exposed DNA strands is used as a template in transcription; this
strand is known as the template strand. The RNA product is complementary to the
template strand and is almost identical to the nontemplate (or coding) strand of
DNA. However, there is one significant difference: all T nucleotides in newly
synthesized RNA are substituted with U nucleotides.
+ Transcription initiation:

Figure 8: Initiation of transcription (OpenStax College, Biology, CC BY 4.0).

  To start transcribing a gene, RNA polymerase binds to the promoter region of the gene's
DNA. The promoter basically instructs the polymerase where to "sit down" on the DNA
and start transcribing.
 Each gene (or group of genes transcribed together in bacteria) has its own promoter.
DNA sequences in a promoter allow RNA polymerase or its helper proteins to connect to
the DNA. The polymerase can begin transcription after the transcription bubble has
formed.

Figure 9: Promoters in bacteria (OpenStax College, Biology, CC BY 4.0).

Figure 10: Promoters in Humans (OpenStax College, Biology, CC BY 4.0).

+ Elongation:
 The following step of transcription, elongation, can begin once RNA polymerase is in
place at the promoter. Elongation is the process through which the RNA strand lengthens
due to the insertion of additional nucleotides.
 RNA polymerase "walks" along one strand of DNA, known as the template strand, in the
3' to 5' direction during elongation. RNA polymerase adds a complementary (matching)
RNA nucleotide to the 3' end of the RNA strand for each nucleotide in the template.
 Figure 11: The elongation of transcription (OpenStax College, Biology, CC BY 4.0).

 The non-template, or coding, strand of DNA is almost identical to the RNA transcript.
However, RNA strands use the base uracil (U) instead of thymine (T), and the sugar in
the nucleotide is somewhat different. In the RNA transcript, each T of the coding strand
is replaced by a U, as seen in the diagram above.
+ Transcription termination:
 RNA polymerase will continue to transcribe until it receives instructions to halt.
Termination occurs when the polymerase transcribes a terminator sequence of DNA, and
it is the last step in the transcription process.
 Termination in bacteria:
 In bacteria, there are two types of termination strategies: Rho-dependent
and Rho-independent.
 The RNA contains a binding site for a protein termed Rho factor in Rho-
dependent termination. Rho factor attaches to this region and begins
"climbing" the transcript in the direction of RNA polymerase.
 Rho pulls the RNA transcript and the template DNA strand apart when it
catches up with the polymerase at the transcription bubble, releasing the
RNA molecule and putting an end to transcription. The transcription stop
point, which is situated later in DNA, enables RNA polymerase to pause,
allowing Rho to catch up.
  The hairpin is followed by a stretch of U nucleotides in the RNA that
correspond to A nucleotides in the template DNA in a terminator. Only a
weak contact exists between the corresponding U-A region of the RNA
transcript and the template DNA. The combination of this plus the stalled
polymerase creates enough instability for the enzyme to come off and
release the new RNA transcript.

Figure 12: Termination of bacteria (OpenStax College,Biology, CC BY 4.0)

 Termination in eukaryotes (like human):

 Transcription termination occurs differently in eukaryotes like humans,
depending on the type of gene involved. We'll look at how protein-coding
genes are terminated in this section.
 When a polyadenylation signal emerges in the RNA transcript, termination
begins. This is a nucleotide sequence that indicates the end of an RNA
transcript. An enzyme recognizes the polyadenylation signal and cuts the
RNA transcript nearby, freeing it from RNA polymerase.
 Surprisingly, RNA polymerase continues to transcribe after the transcript
has been released, often producing another 500-2000 nucleotides of RNA.
It eventually separates from the DNA through mechanisms that are still
unknown. The excess RNA is rarely translated and appears to be a
wasteful transcription byproduct.
- Translation:
+ Overview: Decoding a messenger RNA (mRNA) and utilizing its information to produce a
polypeptide, or chain of amino acids, is the process of translation. A polypeptide is essentially a
protein for most purposes (with the technical difference being that some large proteins are made
up of several polypeptide chains).
+ Initiation:
 We'll need a few key components to get started with translation. These are some of them:
  A ribosome is a type of cell that contains ribosome (which comes in two pieces, large
and small)
 An mRNA that contains the instructions for the protein we'll create.
 The first amino acid in the protein, nearly invariably methionine, is carried by an
"initiator" tRNA (Met)
 These puzzle pieces must fit together perfectly during initiation. They constitute the
initiation complex, which is the molecular configuration required to begin producing a
new protein.

 Translation initiation in human’s

cells (and other eukaryotes' cells)
begins with the methionine-carrying
tRNA attaching to the small
ribosomal subunit. They recognize
the 5' GTP cap on the mRNA's 5' end
and attach to it (added during
processing in the nucleus). Then they
"walk" in the 3' direction along the
mRNA, halting when they reach the
start codon (often, but not always,
the first AUG).

 In the case of bacteria, things are a little different. The small ribosomal subunit does not
begin at the 5' end of the mRNA and proceed to the 3' end in this case. Instead, it binds to
specific mRNA sequences directly. Shine-Dalgarno sequences appear shortly before start
codons and "call attention" to them to the ribosome.
 + Elongation:
 Our first methionine-carrying tRNA is found in the P site, which is in the middle
of the ribosome. In another slot, known as the A site, a new codon is exposed next
to it. The following tRNA, whose anticodon is a perfect (complementary) match
for the exposed codon, will "land" at the A site.
 We've got two amino acids and a (very little) polypeptide now! The N-terminus of
the polypeptide is formed by methionine, whereas the C-terminus is formed by
the other amino acid, and we may want a polypeptide with more than two amino
acids. The mRNA is pulled through the ribosome by exactly one codon after the
peptide bond is created. The initial, empty tRNA can now drift out via the E
("exit") site because of this shift. It also reveals a new codon in the A site,
allowing the cycle to continue.
+ Termination:
 Polypeptides, like all good things, must come to an end at some point.
Termination is the final step in the translation process. When a stop codon (UAA,
UAG, or UGA) in the mRNA enters the A site, it causes termination.
 Stop codons are detected by release factors, which are proteins that fit nicely into
the P site (but aren't tRNAs). The enzyme that typically makes peptide bonds is
messed up by release factors, which cause it to add a water molecule to the last
amino acid in the chain. The chain is separated from the tRNA in this step, and
the newly formed protein is released.
 "Equipment" is a reusable term. After the small and large ribosomal subunits have
separated from each other and from the mRNA, each element can (and generally
does) participate in another round of translation.

4) What is epigenetic Inheritance? Explain how histone acetylation affect chromatin structure
and the regulation of transcription.
* Epigenetic Inheritance:
 Figure 1: Epigenetic inheritance that is
passed down via generations.
Environmental triggers that impact
pregnant female humans (F0) can affect
"directly" not only the first new
generation (F1), but also the germ cells
that constitute the second generation,
according to the traditional definition
of transgenerational epigenetic
inheritance (F2). As a result, only
alterations in F3 may be attributed to
"pure" epigenetic inheritance. The male
germline, on the other hand, can only
be altered for one generation, allowing
epigenetic inheritance to be observed
as early as F2. (Skinner et al, 2017).

- Many scientists have postulated and even proved in recent years that specific experiences
during an individual's life influence the development of his progeny, even at a distance. Some
events appear to alter genomic expression, influencing:
+ How the organism reacts to a changing environment (i.e., increased ontogenetic flexibility
—direct or synchronous effect)
+ How his descendants will improve their chances of surviving in a certain environment—
that is, how information about the environment will be passed to offspring (i.e., more
phylogenetic flexibility—indirect and both synchronous and asynchronous effects).

* Histone acetylation affects chromatin structure and the regulation of transcription:

- Histone tails are essential for gene transcription and expression. Because a large section of the
histone tail is not linked to DNA, it might be used as a binding site for transcription factors,
enzymes, and other proteins. Using cluster analysis, we discovered that the H4, H3, H2A, and
H2B histone tails have a single dominant DNA binding configuration, whereas H3-H2B have
numerous binding configurations with equal probability. The attractive contact between the
positively charged lysine and arginine residues and the negatively charged phosphate groups, and
hence the consequent charge neutralization, is the most important stabilizing factor for those
binding configurations. The results of molecular dynamics simulations in explicit solvent using
both implicit and explicit models match our findings.
 Figure 2:
- (-COCH3) are attached
to the lysine in the
histone tails.
- When lysine is
acetylated, their
positive charges are
neutral
→The histone tails no
longer bind to
neighboring
nucleosomes.
 Activation of
transcription. Group 5
(2021, slide45).

5) Why is regulation of gene expression important? How can, for example, a cell in the retina of
your eye makes different proteins from a cell in your liver when both cells have exactly the same
DNA.
* Regulation of gene expression:
- Definition of gene expression:
+ Gene expression is the process of using a gene to produce a protein. It covers the processes
of DNA transcription and mRNA translation in the protein synthesis. It could potentially
comprise further protein processing following synthesis.
+ Gene expression is regulated to ensure that the right proteins are produced at the right time
and in the right place. From the start of the transcription phase of protein synthesis to the
processing of a protein after synthesis, regulation can occur at any moment in the expression of a
gene. This topic focuses on the regulation of transcription, which is one of the most difficult
aspects of gene regulation in eukaryotic organisms.
 A cell contains the entire genome of an organism– ALL the DNA.
 Gene expression can be regulated:
o During transcription (transcriptional control).
o During translation (translational control).
o After translation (post-translational control).
 Regulation allows an organism to selectively transcribe (and then translate) only the
genes it needs to.
 Genes expressed depend on
+ The type of cell.
 + The particular needs of the cell at that time.
 Important to the development of an organisms, 1 single cell → 1 same cell in adults.
 Helps cells → specialized cells through differentiation.
 Transcription factors and repressors regulates different sets of genes.
- Gene regulation in Prokaryotes:
+ Prokaryotes organize their genome into operons.
+ Operon = a group of related genes.
• One promoter sequence at the very beginning.
• All the genes will be transcribed together (in one long strand of RNA).
- Example in bacteria:
+ Related genes in bacteria are frequently found in a cluster on the chromosome, where
they are produced as a single unit from a single promoter (RNA polymerase binding site). An
operon is a group of genes under the control of a single promoter. Operons are widespread in
bacteria but uncommon in eukaryotes like humans.
+ Genes that function in the same process are usually found in an operon. For example,
the lac operon comprises genes that encode proteins involved in the uptake and metabolism of
lactose, a substance that has been researched extensively. Operons allow the cell to express
multiple genes whose products are required at the same time.
+ However, operons do not contain all bacterial genes. In bacteria, some genes are
transcribed separately. Each of these independently transcribed genes has its own promoter and
regulatory DNA sequences. That is, the characteristics outlined below for operons also apply to
genes not found in operons in bacteria.
 Figure 3: Gene regulation in bacteria. (Kovach et al, 2014)

*A cell in the retina of your eye makes different proteins from a cell in your liver when both
cells have exactly the same DNA because: due to gene regulation makes cells different.
- Gene regulation is the process by which a cell determines which of the numerous genes in its
genome are "turned on" (expressed). Despite the fact that practically all of your body's cells have
the same DNA, gene regulation allows each cell type to have a unique collection of activated
genes. Your numerous cell types have diverse sets of proteins as a result of these different gene
expression patterns, making each cell type uniquely specialized to fulfill its task.
- One of the liver's functions, for example, is to eliminate poisonous compounds from the
bloodstream, such as alcohol. To accomplish this, liver cells express genes that code for alcohol
dehydrogenase subunits (pieces). This enzyme converts ethanol to a non-toxic compound.
Because neurons in the brain do not remove poisons from the body, these genes are kept inactive,
or "shut off." Similarly, because liver cells do not communicate signals via neurotransmitters,
neurotransmitter genes are turned off.
 Figure 1. Different cells have different genes “turned on”. (Alcohol et al, 2016)

- Many other genes change in their expression between liver cells and neurons (or any two cell
types in a multicellular organism like yourself).
 To sum up:
+ In a given cell type, specific cells have specific function → not occur Transcription and
Translation.
+ At any given time, only a subset → proteins. 
+ Gene regulation → different set of active genes → various cell types →uniquely
specialized cell.

Reference:
1)
Dr. Maho Yokoyama, Ph.D. ‘Mechanism of DNA synthesis’. (2019, February 26). Available at:
Mechanism of DNA Synthesis (news-medical.net)

2)
OpenStax College, Biology, CC BY 4.0. ‘DNA replication in eukaryotes ‘. Available at:
Telomeres and telomerase (article) | Khan Academy

3)
Albert Team, (2020 July 23). ‘Translation vs. Transcription: Similarities and Differences’ .
Available at:
https://www.albert.io/blog/translation-vs-transcription-similarities-differences/

OpenStax College, Biology, CC BY 4.0. Available at:

https://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-
dna-into-rna/a/stages-of-transcription

4)
Tyler J. Stevenson, (2018, September 28). Epigenetic Inheritance: Concepts, Mechanisms and
Perspectives. Available at:
Epigenetic Inheritance: Concepts, Mechanisms and Perspectives (nih.gov)

5)
Kovach, T. K. (2014, February 26). Jacob-Monod: The lac operon. In Gene control. Retrieved
from https://www.khanacademy.org/test-prep/mcat/biomolecules/gene-control/v/jacob-monod-
the-lac-operon(Opens in a new window).

Lumen Regulation of Gene Expression | Biology for Majors I

https://courses.lumenlearning.com/suny-wmopen-biology1/chapter/regulation-of-gene-
expression/